@unpublished{10013, abstract = {We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient-flow calibration in the sense of the recent work of Fischer et al. [arXiv:2003.05478] for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions.}, author = {Hensel, Sebastian and Laux, Tim}, booktitle = {arXiv}, title = {{Weak-strong uniqueness for the mean curvature flow of double bubbles}}, doi = {10.48550/arXiv.2108.01733}, year = {2021}, } @article{9928, abstract = {There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits.}, author = {Peruzzo, Matilda and Hassani, Farid and Szep, Gregory and Trioni, Andrea and Redchenko, Elena and Zemlicka, Martin and Fink, Johannes M}, issn = {2691-3399}, journal = {PRX Quantum}, keywords = {quantum physics, mesoscale and nanoscale physics}, number = {4}, pages = {040341}, publisher = {American Physical Society}, title = {{Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction}}, doi = {10.1103/PRXQuantum.2.040341}, volume = {2}, year = {2021}, } @phdthesis{10030, abstract = {This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning non-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.}, author = {Portinale, Lorenzo}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Discrete-to-continuum limits of transport problems and gradient flows in the space of measures}}, doi = {10.15479/at:ista:10030}, year = {2021}, } @phdthesis{9920, abstract = {This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.}, author = {Peruzzo, Matilda}, isbn = {978-3-99078-013-8}, issn = {2663-337X}, keywords = {quantum computing, superinductor, quantum metrology}, pages = {149}, publisher = {Institute of Science and Technology Austria}, title = {{Geometric superinductors and their applications in circuit quantum electrodynamics}}, doi = {10.15479/at:ista:9920}, year = {2021}, } @inproceedings{10432, abstract = {One key element behind the recent progress of machine learning has been the ability to train machine learning models in large-scale distributed shared-memory and message-passing environments. Most of these models are trained employing variants of stochastic gradient descent (SGD) based optimization, but most methods involve some type of consistency relaxation relative to sequential SGD, to mitigate its large communication or synchronization costs at scale. In this paper, we introduce a general consistency condition covering communication-reduced and asynchronous distributed SGD implementations. Our framework, called elastic consistency, decouples the system-specific aspects of the implementation from the SGD convergence requirements, giving a general way to obtain convergence bounds for a wide variety of distributed SGD methods used in practice. Elastic consistency can be used to re-derive or improve several previous convergence bounds in message-passing and shared-memory settings, but also to analyze new models and distribution schemes. As a direct application, we propose and analyze a new synchronization-avoiding scheduling scheme for distributed SGD, and show that it can be used to efficiently train deep convolutional models for image classification.}, author = {Nadiradze, Giorgi and Markov, Ilia and Chatterjee, Bapi and Kungurtsev, Vyacheslav and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence}, location = {Virtual}, number = {10}, pages = {9037--9045}, title = {{Elastic consistency: A practical consistency model for distributed stochastic gradient descent}}, volume = {35}, year = {2021}, } @inproceedings{10041, abstract = {Yao’s garbling scheme is one of the most fundamental cryptographic constructions. Lindell and Pinkas (Journal of Cryptograhy 2009) gave a formal proof of security in the selective setting where the adversary chooses the challenge inputs before seeing the garbled circuit assuming secure symmetric-key encryption (and hence one-way functions). This was followed by results, both positive and negative, concerning its security in the, stronger, adaptive setting. Applebaum et al. (Crypto 2013) showed that it cannot satisfy adaptive security as is, due to a simple incompressibility argument. Jafargholi and Wichs (TCC 2017) considered a natural adaptation of Yao’s scheme (where the output mapping is sent in the online phase, together with the garbled input) that circumvents this negative result, and proved that it is adaptively secure, at least for shallow circuits. In particular, they showed that for the class of circuits of depth δ , the loss in security is at most exponential in δ . The above results all concern the simulation-based notion of security. In this work, we show that the upper bound of Jafargholi and Wichs is basically optimal in a strong sense. As our main result, we show that there exists a family of Boolean circuits, one for each depth δ∈N , such that any black-box reduction proving the adaptive indistinguishability of the natural adaptation of Yao’s scheme from any symmetric-key encryption has to lose a factor that is exponential in δ√ . Since indistinguishability is a weaker notion than simulation, our bound also applies to adaptive simulation. To establish our results, we build on the recent approach of Kamath et al. (Eprint 2021), which uses pebbling lower bounds in conjunction with oracle separations to prove fine-grained lower bounds on loss in cryptographic security.}, author = {Kamath Hosdurg, Chethan and Klein, Karen and Pietrzak, Krzysztof Z and Wichs, Daniel}, booktitle = {41st Annual International Cryptology Conference, Part II }, isbn = {978-3-030-84244-4}, issn = {1611-3349}, location = {Virtual}, pages = {486--515}, publisher = {Springer Nature}, title = {{Limits on the Adaptive Security of Yao’s Garbling}}, doi = {10.1007/978-3-030-84245-1_17}, volume = {12826}, year = {2021}, } @inproceedings{10049, abstract = {While messaging systems with strong security guarantees are widely used in practice, designing a protocol that scales efficiently to large groups and enjoys similar security guarantees remains largely open. The two existing proposals to date are ART (Cohn-Gordon et al., CCS18) and TreeKEM (IETF, The Messaging Layer Security Protocol, draft). TreeKEM is the currently considered candidate by the IETF MLS working group, but dynamic group operations (i.e. adding and removing users) can cause efficiency issues. In this paper we formalize and analyze a variant of TreeKEM which we term Tainted TreeKEM (TTKEM for short). The basic idea underlying TTKEM was suggested by Millican (MLS mailing list, February 2018). This version is more efficient than TreeKEM for some natural distributions of group operations, we quantify this through simulations.Our second contribution is two security proofs for TTKEM which establish post compromise and forward secrecy even against adaptive attackers. The security loss (to the underlying PKE) in the Random Oracle Model is a polynomial factor, and a quasipolynomial one in the Standard Model. Our proofs can be adapted to TreeKEM as well. Before our work no security proof for any TreeKEM-like protocol establishing tight security against an adversary who can adaptively choose the sequence of operations was known. We also are the first to prove (or even formalize) active security where the server can arbitrarily deviate from the protocol specification. Proving fully active security – where also the users can arbitrarily deviate – remains open.}, author = {Klein, Karen and Pascual Perez, Guillermo and Walter, Michael and Kamath Hosdurg, Chethan and Capretto, Margarita and Cueto Noval, Miguel and Markov, Ilia and Yeo, Michelle X and Alwen, Joel F and Pietrzak, Krzysztof Z}, booktitle = {2021 IEEE Symposium on Security and Privacy }, location = {San Francisco, CA, United States}, pages = {268--284}, publisher = {IEEE}, title = {{Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement}}, doi = {10.1109/sp40001.2021.00035}, year = {2021}, } @inproceedings{10044, abstract = {We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a S^O(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(d w log(S)), d being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.}, author = {Kamath Hosdurg, Chethan and Klein, Karen and Pietrzak, Krzysztof Z}, booktitle = {19th Theory of Cryptography Conference 2021}, location = {Raleigh, NC, United States}, publisher = {International Association for Cryptologic Research}, title = {{On treewidth, separators and Yao's garbling}}, year = {2021}, } @phdthesis{10422, abstract = {Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.}, author = {Piankov, Anton}, issn = {2791-4585}, publisher = {Institute of Science and Technology Austria}, title = {{Towards designer materials using customizable particle shape}}, doi = {10.15479/at:ista:10422}, year = {2021}, } @unpublished{10803, abstract = {Given the abundance of applications of ranking in recent years, addressing fairness concerns around automated ranking systems becomes necessary for increasing the trust among end-users. Previous work on fair ranking has mostly focused on application-specific fairness notions, often tailored to online advertising, and it rarely considers learning as part of the process. In this work, we show how to transfer numerous fairness notions from binary classification to a learning to rank setting. Our formalism allows us to design methods for incorporating fairness objectives with provable generalization guarantees. An extensive experimental evaluation shows that our method can improve ranking fairness substantially with no or only little loss of model quality.}, author = {Konstantinov, Nikola H and Lampert, Christoph}, booktitle = {arXiv}, title = {{Fairness through regularization for learning to rank}}, doi = {10.48550/arXiv.2102.05996}, year = {2021}, } @unpublished{10762, abstract = {Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a new variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of non-additive systems very well. In particular, we observe substantial improvement over the standard coherent state estimates in the most challenging intermediate coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications.}, author = {Rzadkowski, Wojciech and Lemeshko, Mikhail and Mentink, Johan H.}, booktitle = {arXiv}, pages = {2105.15193}, title = {{Artificial neural network states for non-additive systems}}, doi = {10.48550/arXiv.2105.15193}, year = {2021}, } @phdthesis{9418, abstract = {Deep learning is best known for its empirical success across a wide range of applications spanning computer vision, natural language processing and speech. Of equal significance, though perhaps less known, are its ramifications for learning theory: deep networks have been observed to perform surprisingly well in the high-capacity regime, aka the overfitting or underspecified regime. Classically, this regime on the far right of the bias-variance curve is associated with poor generalisation; however, recent experiments with deep networks challenge this view. This thesis is devoted to investigating various aspects of underspecification in deep learning. First, we argue that deep learning models are underspecified on two levels: a) any given training dataset can be fit by many different functions, and b) any given function can be expressed by many different parameter configurations. We refer to the second kind of underspecification as parameterisation redundancy and we precisely characterise its extent. Second, we characterise the implicit criteria (the inductive bias) that guide learning in the underspecified regime. Specifically, we consider a nonlinear but tractable classification setting, and show that given the choice, neural networks learn classifiers with a large margin. Third, we consider learning scenarios where the inductive bias is not by itself sufficient to deal with underspecification. We then study different ways of ‘tightening the specification’: i) In the setting of representation learning with variational autoencoders, we propose a hand- crafted regulariser based on mutual information. ii) In the setting of binary classification, we consider soft-label (real-valued) supervision. We derive a generalisation bound for linear networks supervised in this way and verify that soft labels facilitate fast learning. Finally, we explore an application of soft-label supervision to the training of multi-exit models.}, author = {Bui Thi Mai, Phuong}, issn = {2663-337X}, pages = {125}, publisher = {Institute of Science and Technology Austria}, title = {{Underspecification in deep learning}}, doi = {10.15479/AT:ISTA:9418}, year = {2021}, } @inproceedings{14177, abstract = {The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during training or by post-hoc correcting a pre-trained model with a small number of labels.}, author = {Träuble, Frederik and Creager, Elliot and Kilbertus, Niki and Locatello, Francesco and Dittadi, Andrea and Goyal, Anirudh and Schölkopf, Bernhard and Bauer, Stefan}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, location = {Virtual}, pages = {10401--10412}, publisher = {ML Research Press}, title = {{On disentangled representations learned from correlated data}}, volume = {139}, year = {2021}, } @inproceedings{14176, abstract = {Intensive care units (ICU) are increasingly looking towards machine learning for methods to provide online monitoring of critically ill patients. In machine learning, online monitoring is often formulated as a supervised learning problem. Recently, contrastive learning approaches have demonstrated promising improvements over competitive supervised benchmarks. These methods rely on well-understood data augmentation techniques developed for image data which do not apply to online monitoring. In this work, we overcome this limitation by supplementing time-series data augmentation techniques with a novel contrastive learning objective which we call neighborhood contrastive learning (NCL). Our objective explicitly groups together contiguous time segments from each patient while maintaining state-specific information. Our experiments demonstrate a marked improvement over existing work applying contrastive methods to medical time-series.}, author = {Yèche, Hugo and Dresdner, Gideon and Locatello, Francesco and Hüser, Matthias and Rätsch, Gunnar}, booktitle = {Proceedings of 38th International Conference on Machine Learning}, location = {Virtual}, pages = {11964--11974}, publisher = {ML Research Press}, title = {{Neighborhood contrastive learning applied to online patient monitoring}}, volume = {139}, year = {2021}, } @inproceedings{14182, abstract = {When machine learning systems meet real world applications, accuracy is only one of several requirements. In this paper, we assay a complementary perspective originating from the increasing availability of pre-trained and regularly improving state-of-the-art models. While new improved models develop at a fast pace, downstream tasks vary more slowly or stay constant. Assume that we have a large unlabelled data set for which we want to maintain accurate predictions. Whenever a new and presumably better ML models becomes available, we encounter two problems: (i) given a limited budget, which data points should be re-evaluated using the new model?; and (ii) if the new predictions differ from the current ones, should we update? Problem (i) is about compute cost, which matters for very large data sets and models. Problem (ii) is about maintaining consistency of the predictions, which can be highly relevant for downstream applications; our demand is to avoid negative flips, i.e., changing correct to incorrect predictions. In this paper, we formalize the Prediction Update Problem and present an efficient probabilistic approach as answer to the above questions. In extensive experiments on standard classification benchmark data sets, we show that our method outperforms alternative strategies along key metrics for backward-compatible prediction updates.}, author = {Träuble, Frederik and Kügelgen, Julius von and Kleindessner, Matthäus and Locatello, Francesco and Schölkopf, Bernhard and Gehler, Peter}, booktitle = {35th Conference on Neural Information Processing Systems}, isbn = {9781713845393}, location = {Virtual}, pages = {116--128}, title = {{Backward-compatible prediction updates: A probabilistic approach}}, volume = {34}, year = {2021}, } @inproceedings{14181, abstract = {Variational Inference makes a trade-off between the capacity of the variational family and the tractability of finding an approximate posterior distribution. Instead, Boosting Variational Inference allows practitioners to obtain increasingly good posterior approximations by spending more compute. The main obstacle to widespread adoption of Boosting Variational Inference is the amount of resources necessary to improve over a strong Variational Inference baseline. In our work, we trace this limitation back to the global curvature of the KL-divergence. We characterize how the global curvature impacts time and memory consumption, address the problem with the notion of local curvature, and provide a novel approximate backtracking algorithm for estimating local curvature. We give new theoretical convergence rates for our algorithms and provide experimental validation on synthetic and real-world datasets.}, author = {Dresdner, Gideon and Shekhar, Saurav and Pedregosa, Fabian and Locatello, Francesco and Rätsch, Gunnar}, booktitle = {Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence}, location = {Montreal, Canada}, pages = {2337--2343}, publisher = {International Joint Conferences on Artificial Intelligence}, title = {{Boosting variational inference with locally adaptive step-sizes}}, doi = {10.24963/ijcai.2021/322}, year = {2021}, } @inproceedings{14179, abstract = {Self-supervised representation learning has shown remarkable success in a number of domains. A common practice is to perform data augmentation via hand-crafted transformations intended to leave the semantics of the data invariant. We seek to understand the empirical success of this approach from a theoretical perspective. We formulate the augmentation process as a latent variable model by postulating a partition of the latent representation into a content component, which is assumed invariant to augmentation, and a style component, which is allowed to change. Unlike prior work on disentanglement and independent component analysis, we allow for both nontrivial statistical and causal dependencies in the latent space. We study the identifiability of the latent representation based on pairs of views of the observations and prove sufficient conditions that allow us to identify the invariant content partition up to an invertible mapping in both generative and discriminative settings. We find numerical simulations with dependent latent variables are consistent with our theory. Lastly, we introduce Causal3DIdent, a dataset of high-dimensional, visually complex images with rich causal dependencies, which we use to study the effect of data augmentations performed in practice.}, author = {Kügelgen, Julius von and Sharma, Yash and Gresele, Luigi and Brendel, Wieland and Schölkopf, Bernhard and Besserve, Michel and Locatello, Francesco}, booktitle = {Advances in Neural Information Processing Systems}, isbn = {9781713845393}, location = {Virtual}, pages = {16451--16467}, title = {{Self-supervised learning with data augmentations provably isolates content from style}}, volume = {34}, year = {2021}, } @inproceedings{14180, abstract = {Modern neural network architectures can leverage large amounts of data to generalize well within the training distribution. However, they are less capable of systematic generalization to data drawn from unseen but related distributions, a feat that is hypothesized to require compositional reasoning and reuse of knowledge. In this work, we present Neural Interpreters, an architecture that factorizes inference in a self-attention network as a system of modules, which we call \emph{functions}. Inputs to the model are routed through a sequence of functions in a way that is end-to-end learned. The proposed architecture can flexibly compose computation along width and depth, and lends itself well to capacity extension after training. To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct settings: image classification and visual abstract reasoning on Raven Progressive Matrices. In the former, we show that Neural Interpreters perform on par with the vision transformer using fewer parameters, while being transferrable to a new task in a sample efficient manner. In the latter, we find that Neural Interpreters are competitive with respect to the state-of-the-art in terms of systematic generalization. }, author = {Rahaman, Nasim and Gondal, Muhammad Waleed and Joshi, Shruti and Gehler, Peter and Bengio, Yoshua and Locatello, Francesco and Schölkopf, Bernhard}, booktitle = {Advances in Neural Information Processing Systems}, isbn = {9781713845393}, location = {Virtual}, pages = {10985--10998}, title = {{Dynamic inference with neural interpreters}}, volume = {34}, year = {2021}, } @article{14117, abstract = {The two fields of machine learning and graphical causality arose and are developed separately. However, there is, now, cross-pollination and increasing interest in both fields to benefit from the advances of the other. In this article, we review fundamental concepts of causal inference and relate them to crucial open problems of machine learning, including transfer and generalization, thereby assaying how causality can contribute to modern machine learning research. This also applies in the opposite direction: we note that most work in causality starts from the premise that the causal variables are given. A central problem for AI and causality is, thus, causal representation learning, that is, the discovery of high-level causal variables from low-level observations. Finally, we delineate some implications of causality for machine learning and propose key research areas at the intersection of both communities.}, author = {Scholkopf, Bernhard and Locatello, Francesco and Bauer, Stefan and Ke, Nan Rosemary and Kalchbrenner, Nal and Goyal, Anirudh and Bengio, Yoshua}, issn = {1558-2256}, journal = {Proceedings of the IEEE}, keywords = {Electrical and Electronic Engineering}, number = {5}, pages = {612--634}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Toward causal representation learning}}, doi = {10.1109/jproc.2021.3058954}, volume = {109}, year = {2021}, } @inproceedings{14178, abstract = {Learning meaningful representations that disentangle the underlying structure of the data generating process is considered to be of key importance in machine learning. While disentangled representations were found to be useful for diverse tasks such as abstract reasoning and fair classification, their scalability and real-world impact remain questionable. We introduce a new high-resolution dataset with 1M simulated images and over 1,800 annotated real-world images of the same setup. In contrast to previous work, this new dataset exhibits correlations, a complex underlying structure, and allows to evaluate transfer to unseen simulated and real-world settings where the encoder i) remains in distribution or ii) is out of distribution. We propose new architectures in order to scale disentangled representation learning to realistic high-resolution settings and conduct a large-scale empirical study of disentangled representations on this dataset. We observe that disentanglement is a good predictor for out-of-distribution (OOD) task performance.}, author = {Dittadi, Andrea and Träuble, Frederik and Locatello, Francesco and Wüthrich, Manuel and Agrawal, Vaibhav and Winther, Ole and Bauer, Stefan and Schölkopf, Bernhard}, booktitle = {The Ninth International Conference on Learning Representations}, location = {Virtual}, title = {{On the transfer of disentangled representations in realistic settings}}, year = {2021}, } @unpublished{14221, abstract = {The world is structured in countless ways. It may be prudent to enforce corresponding structural properties to a learning algorithm's solution, such as incorporating prior beliefs, natural constraints, or causal structures. Doing so may translate to faster, more accurate, and more flexible models, which may directly relate to real-world impact. In this dissertation, we consider two different research areas that concern structuring a learning algorithm's solution: when the structure is known and when it has to be discovered.}, author = {Locatello, Francesco}, booktitle = {arXiv}, title = {{Enforcing and discovering structure in machine learning}}, doi = {10.48550/arXiv.2111.13693}, year = {2021}, } @unpublished{14278, abstract = {The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely, integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of almost every ellipse that preserves integrability near the boundary, is itself an ellipse. We apply this result to study local spectral rigidity of ellipses using the connection between the wave trace of the Laplacian and the dynamics near the boundary and establish rigidity for almost all of them.}, author = {Koval, Illya}, booktitle = {arXiv}, title = {{Local strong Birkhoff conjecture and local spectral rigidity of almost every ellipse}}, doi = {10.48550/ARXIV.2111.12171}, year = {2021}, } @phdthesis{10199, abstract = {The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness.}, author = {Toman, Viktor}, issn = {2663-337X}, keywords = {concurrency, verification, model checking}, pages = {166}, publisher = {Institute of Science and Technology Austria}, title = {{Improved verification techniques for concurrent systems}}, doi = {10.15479/at:ista:10199}, year = {2021}, } @article{8429, abstract = {We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.}, author = {Patxot, Marion and Trejo Banos, Daniel and Kousathanas, Athanasios and Orliac, Etienne J and Ojavee, Sven E and Moser, Gerhard and Sidorenko, Julia and Kutalik, Zoltan and Magi, Reedik and Visscher, Peter M and Ronnegard, Lars and Robinson, Matthew Richard}, issn = {2041-1723}, journal = {Nature Communications}, number = {1}, publisher = {Springer Nature}, title = {{Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits}}, doi = {10.1038/s41467-021-27258-9}, volume = {12}, year = {2021}, } @inproceedings{10854, abstract = {Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic CONGEST model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labelled graph under batch changes. We investigate, when a batch of alpha edge label changes arrive, - how much time as a function of alpha we need to update an existing solution, and - how much information the nodes have to keep in local memory between batches in order to update the solution quickly. Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. The diverse time complexity of our model spans from constant time, through time polynomial in alpha, and to alpha time, which we show to be enough for any task.}, author = {Foerster, Klaus-Tycho and Korhonen, Janne and Paz, Ami and Rybicki, Joel and Schmid, Stefan}, booktitle = {Abstract Proceedings of the 2021 ACM SIGMETRICS / International Conference on Measurement and Modeling of Computer Systems}, isbn = {9781450380720}, location = {Virtual, Online}, pages = {71--72}, publisher = {Association for Computing Machinery}, title = {{Input-dynamic distributed algorithms for communication networks}}, doi = {10.1145/3410220.3453923}, year = {2021}, } @article{10855, abstract = {Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs change, can an existing solution be updated efficiently, in a dynamic and distributed manner? To address this question, we define the batch dynamic \congest model in which we are given a bandwidth-limited communication network and a dynamic edge labelling defines the problem input. The task is to maintain a solution to a graph problem on the labeled graph under batch changes. We investigate, when a batch of α edge label changes arrive, \beginitemize \item how much time as a function of α we need to update an existing solution, and \item how much information the nodes have to keep in local memory between batches in order to update the solution quickly. \enditemize Our work lays the foundations for the theory of input-dynamic distributed network algorithms. We give a general picture of the complexity landscape in this model, design both universal algorithms and algorithms for concrete problems, and present a general framework for lower bounds. In particular, we derive non-trivial upper bounds for two selected, contrasting problems: maintaining a minimum spanning tree and detecting cliques.}, author = {Foerster, Klaus-Tycho and Korhonen, Janne and Paz, Ami and Rybicki, Joel and Schmid, Stefan}, issn = {2476-1249}, journal = {Proceedings of the ACM on Measurement and Analysis of Computing Systems}, keywords = {Computer Networks and Communications, Hardware and Architecture, Safety, Risk, Reliability and Quality, Computer Science (miscellaneous)}, number = {1}, pages = {1--33}, publisher = {Association for Computing Machinery}, title = {{Input-dynamic distributed algorithms for communication networks}}, doi = {10.1145/3447384}, volume = {5}, year = {2021}, } @article{9293, abstract = {We consider planning problems for graphs, Markov Decision Processes (MDPs), and games on graphs in an explicit state space. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems with k different target sets: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in a given sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds, based on the boolean matrix multiplication (BMM) conjecture and strong exponential time hypothesis (SETH), establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs, and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) problem-separation results showing that for MDPs the coverage problem is harder than the sequential target problem.}, author = {Chatterjee, Krishnendu and Dvořák, Wolfgang and Henzinger, Monika H and Svozil, Alexander}, issn = {0004-3702}, journal = {Artificial Intelligence}, number = {8}, publisher = {Elsevier}, title = {{Algorithms and conditional lower bounds for planning problems}}, doi = {10.1016/j.artint.2021.103499}, volume = {297}, year = {2021}, } @misc{13063, abstract = {We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.}, author = {Robinson, Matthew Richard}, publisher = {Dryad}, title = {{Probabilistic inference of the genetic architecture of functional enrichment of complex traits}}, doi = {10.5061/dryad.sqv9s4n51}, year = {2021}, } @article{9304, abstract = {The high processing cost, poor mechanical properties and moderate performance of Bi2Te3–based alloys used in thermoelectric devices limit the cost-effectiveness of this energy conversion technology. Towards solving these current challenges, in the present work, we detail a low temperature solution-based approach to produce Bi2Te3-Cu2-xTe nanocomposites with improved thermoelectric performance. Our approach consists in combining proper ratios of colloidal nanoparticles and to consolidate the resulting mixture into nanocomposites using a hot press. The transport properties of the nanocomposites are characterized and compared with those of pure Bi2Te3 nanomaterials obtained following the same procedure. In contrast with most previous works, the presence of Cu2-xTe nanodomains does not result in a significant reduction of the lattice thermal conductivity of the reference Bi2Te3 nanomaterial, which is already very low. However, the introduction of Cu2-xTe yields a nearly threefold increase of the power factor associated to a simultaneous increase of the Seebeck coefficient and electrical conductivity at temperatures above 400 K. Taking into account the band alignment of the two materials, we rationalize this increase by considering that Cu2-xTe nanostructures, with a relatively low electron affinity, are able to inject electrons into Bi2Te3, enhancing in this way its electrical conductivity. The simultaneous increase of the Seebeck coefficient is related to the energy filtering of charge carriers at energy barriers within Bi2Te3 domains associated with the accumulation of electrons in regions nearby a Cu2-xTe/Bi2Te3 heterojunction. Overall, with the incorporation of a proper amount of Cu2-xTe nanoparticles, we demonstrate a 250% improvement of the thermoelectric figure of merit of Bi2Te3.}, author = {Zhang, Yu and Xing, Congcong and Liu, Yu and Li, Mengyao and Xiao, Ke and Guardia, Pablo and Lee, Seungho and Han, Xu and Moghaddam, Ahmad and Roa, Joan J and Arbiol, Jordi and Ibáñez, Maria and Pan, Kai and Prato, Mirko and Xie, Ying and Cabot, Andreu}, issn = {1385-8947}, journal = {Chemical Engineering Journal}, number = {8}, publisher = {Elsevier}, title = {{Influence of copper telluride nanodomains on the transport properties of n-type bismuth telluride}}, doi = {10.1016/j.cej.2021.129374}, volume = {418}, year = {2021}, } @article{9793, abstract = {Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology.}, author = {Baldwin, Katherine T. and Tan, Christabel X. and Strader, Samuel T. and Jiang, Changyu and Savage, Justin T. and Elorza-Vidal, Xabier and Contreras, Ximena and Rülicke, Thomas and Hippenmeyer, Simon and Estévez, Raúl and Ji, Ru-Rong and Eroglu, Cagla}, issn = {1097-4199}, journal = {Neuron}, number = {15}, pages = {2427--2442.e10}, publisher = {Elsevier}, title = {{HepaCAM controls astrocyte self-organization and coupling}}, doi = {10.1016/j.neuron.2021.05.025}, volume = {109}, year = {2021}, } @article{9305, abstract = {Copper chalcogenides are outstanding thermoelectric materials for applications in the medium-high temperature range. Among different chalcogenides, while Cu2−xSe is characterized by higher thermoelectric figures of merit, Cu2−xS provides advantages in terms of low cost and element abundance. In the present work, we investigate the effect of different dopants to enhance the Cu2−xS performance and also its thermal stability. Among the tested options, Pb-doped Cu2−xS shows the highest improvement in stability against sulfur volatilization. Additionally, Pb incorporation allows tuning charge carrier concentration, which enables a significant improvement of the power factor. We demonstrate here that the introduction of an optimal additive amount of just 0.3% results in a threefold increase of the power factor in the middle-temperature range (500–800 K) and a record dimensionless thermoelectric figure of merit above 2 at 880 K.}, author = {Zhang, Yu and Xing, Congcong and Liu, Yu and Spadaro, Maria Chiara and Wang, Xiang and Li, Mengyao and Xiao, Ke and Zhang, Ting and Guardia, Pablo and Lim, Khak Ho and Moghaddam, Ahmad Ostovari and Llorca, Jordi and Arbiol, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {2211-2855}, journal = {Nano Energy}, number = {7}, publisher = {Elsevier}, title = {{Doping-mediated stabilization of copper vacancies to promote thermoelectric properties of Cu2-xS}}, doi = {10.1016/j.nanoen.2021.105991}, volume = {85}, year = {2021}, } @article{9212, abstract = {Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors.}, author = {Cavallari, Nicola and Artner, Christina and Benková, Eva}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, number = {7}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Auxin-regulated lateral root organogenesis}}, doi = {10.1101/cshperspect.a039941}, volume = {13}, year = {2021}, } @article{9953, abstract = {Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress.}, author = {Picard, Katherine and Bisht, Kanchan and Poggini, Silvia and Garofalo, Stefano and Golia, Maria Teresa and Basilico, Bernadette and Abdallah, Fatima and Ciano Albanese, Naomi and Amrein, Irmgard and Vernoux, Nathalie and Sharma, Kaushik and Hui, Chin Wai and C. Savage, Julie and Limatola, Cristina and Ragozzino, Davide and Maggi, Laura and Branchi, Igor and Tremblay, Marie Ève}, issn = {0889-1591}, journal = {Brain, Behavior, and Immunity}, pages = {423--439}, publisher = {Elsevier}, title = {{Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice}}, doi = {10.1016/j.bbi.2021.07.022}, volume = {97}, year = {2021}, } @article{10327, abstract = {Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated.}, author = {Li, Mengyao and Liu, Yu and Zhang, Yu and Han, Xu and Xiao, Ke and Nabahat, Mehran and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {1944-8252}, journal = {ACS Applied Materials and Interfaces}, keywords = {CuxS, PbS, energy conversion, nanocomposite, nanoparticle, solution synthesis, thermoelectric}, number = {43}, pages = {51373–51382}, publisher = {American Chemical Society }, title = {{PbS–Pb–CuxS composites for thermoelectric application}}, doi = {10.1021/acsami.1c15609}, volume = {13}, year = {2021}, } @article{9235, abstract = {Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies.}, author = {Li, Mengyao and Liu, Yu and Zhang, Yu and Han, Xu and Zhang, Ting and Zuo, Yong and Xie, Chenyang and Xiao, Ke and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Liu, Junfeng and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Engineering, General Physics and Astronomy, General Materials Science}, number = {3}, pages = {4967–4978}, publisher = {American Chemical Society }, title = {{Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide}}, doi = {10.1021/acsnano.0c09866}, volume = {15}, year = {2021}, } @article{10204, abstract = {Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.}, author = {Osang, Georg F and Edelsbrunner, Herbert and Saadatfar, Mohammad}, issn = {1744-6848}, journal = {Soft Matter}, number = {40}, pages = {9107--9115}, publisher = {Royal Society of Chemistry }, title = {{Topological signatures and stability of hexagonal close packing and Barlow stackings}}, doi = {10.1039/d1sm00774b}, volume = {17}, year = {2021}, } @inproceedings{9605, abstract = {Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. }, author = {Corbet, René and Kerber, Michael and Lesnick, Michael and Osang, Georg F}, booktitle = {Leibniz International Proceedings in Informatics}, isbn = {9783959771849}, issn = {18688969}, location = {Online}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Computing the multicover bifiltration}}, doi = {10.4230/LIPIcs.SoCG.2021.27}, volume = {189}, year = {2021}, } @inproceedings{9441, abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. }, author = {Boissonnat, Jean-Daniel and Kachanovich, Siargey and Wintraecken, Mathijs}, booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)}, isbn = {978-3-95977-184-9}, issn = {1868-8969}, location = {Virtual}, pages = {17:1--17:16}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations}}, doi = {10.4230/LIPIcs.SoCG.2021.17}, volume = {189}, year = {2021}, } @article{9393, abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, issn = {1572-8102}, journal = {Formal Methods in System Design}, pages = {401--428}, publisher = {Springer}, title = {{Faster algorithms for quantitative verification in bounded treewidth graphs}}, doi = {10.1007/s10703-021-00373-5}, volume = {57}, year = {2021}, } @article{10365, abstract = {The early development of many organisms involves the folding of cell monolayers, but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic causes and effects of local curvature remain unclear. Here we study epithelial cell monolayers on corrugated hydrogels engineered into wavy patterns, examining how concave and convex curvatures affect cellular and nuclear shape. We find that substrate curvature affects monolayer thickness, which is larger in valleys than crests. We show that this feature generically arises in a vertex model, leading to the hypothesis that cells may sense curvature by modifying the thickness of the tissue. We find that local curvature also affects nuclear morphology and positioning, which we explain by extending the vertex model to take into account membrane–nucleus interactions, encoding thickness modulation in changes to nuclear deformation and position. We propose that curvature governs the spatial distribution of yes-associated proteins via nuclear shape and density changes. We show that curvature also induces significant variations in lamins, chromatin condensation and cell proliferation rate in folded epithelial tissues. Together, this work identifies active cell mechanics and nuclear mechanoadaptation as the key players of the mechanistic regulation of epithelia to substrate curvature.}, author = {Luciano, Marine and Xue, Shi-lei and De Vos, Winnok H. and Redondo-Morata, Lorena and Surin, Mathieu and Lafont, Frank and Hannezo, Edouard B and Gabriele, Sylvain}, issn = {1745-2481}, journal = {Nature Physics}, number = {12}, pages = {1382–1390}, publisher = {Springer Nature}, title = {{Cell monolayers sense curvature by exploiting active mechanics and nuclear mechanoadaptation}}, doi = {10.1038/s41567-021-01374-1}, volume = {17}, year = {2021}, } @article{9298, abstract = {In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. }, author = {Klionsky, Daniel J. and Abdel-Aziz, Amal Kamal and Abdelfatah, Sara and Abdellatif, Mahmoud and Abdoli, Asghar and Abel, Steffen and Abeliovich, Hagai and Abildgaard, Marie H. and Abudu, Yakubu Princely and Acevedo-Arozena, Abraham and Adamopoulos, Iannis E. and Adeli, Khosrow and Adolph, Timon E. and Adornetto, Annagrazia and Aflaki, Elma and Agam, Galila and Agarwal, Anupam and Aggarwal, Bharat B. and Agnello, Maria and Agostinis, Patrizia and Agrewala, Javed N. and Agrotis, Alexander and Aguilar, Patricia V. and Ahmad, S. Tariq and Ahmed, Zubair M. and Ahumada-Castro, Ulises and Aits, Sonja and Aizawa, Shu and Akkoc, Yunus and Akoumianaki, Tonia and Akpinar, Hafize Aysin and Al-Abd, Ahmed M. and Al-Akra, Lina and Al-Gharaibeh, Abeer and Alaoui-Jamali, Moulay A. and Alberti, Simon and Alcocer-Gómez, Elísabet and Alessandri, Cristiano and Ali, Muhammad and Alim Al-Bari, M. Abdul and Aliwaini, Saeb and Alizadeh, Javad and Almacellas, Eugènia and Almasan, Alexandru and Alonso, Alicia and Alonso, Guillermo D. and Altan-Bonnet, Nihal and Altieri, Dario C. and Álvarez, Élida M.C. and Alves, Sara and Alves Da Costa, Cristine and Alzaharna, Mazen M. and Amadio, Marialaura and Amantini, Consuelo and Amaral, Cristina and Ambrosio, Susanna and Amer, Amal O. and Ammanathan, Veena and An, Zhenyi and Andersen, Stig U. and Andrabi, Shaida A. and Andrade-Silva, Magaiver and Andres, Allen M. and Angelini, Sabrina and Ann, David and Anozie, Uche C. and Ansari, Mohammad Y. and Antas, Pedro and Antebi, Adam and Antón, Zuriñe and Anwar, Tahira and Apetoh, Lionel and Apostolova, Nadezda and Araki, Toshiyuki and Araki, Yasuhiro and Arasaki, Kohei and Araújo, Wagner L. and Araya, Jun and Arden, Catherine and Arévalo, Maria Angeles and Arguelles, Sandro and Arias, Esperanza and Arikkath, Jyothi and Arimoto, Hirokazu and Ariosa, Aileen R. and Armstrong-James, Darius and Arnauné-Pelloquin, Laetitia and Aroca, Angeles and Arroyo, Daniela S. and Arsov, Ivica and Artero, Rubén and Asaro, Dalia Maria Lucia and Aschner, Michael and Ashrafizadeh, Milad and Ashur-Fabian, Osnat and Atanasov, Atanas G. and Au, Alicia K. and Auberger, Patrick and Auner, Holger W. and Aurelian, Laure and Autelli, Riccardo and Avagliano, Laura and Ávalos, Yenniffer and Aveic, Sanja and Aveleira, Célia Alexandra and Avin-Wittenberg, Tamar and Aydin, Yucel and Ayton, Scott and Ayyadevara, Srinivas and Azzopardi, Maria and Baba, Misuzu and Backer, Jonathan M. and Backues, Steven K. and Bae, Dong Hun and Bae, Ok Nam and Bae, Soo Han and Baehrecke, Eric H. and Baek, Ahruem and Baek, Seung Hoon and Baek, Sung Hee and Bagetta, Giacinto and Bagniewska-Zadworna, Agnieszka and Bai, Hua and Bai, Jie and Bai, Xiyuan and Bai, Yidong and Bairagi, Nandadulal and Baksi, Shounak and Balbi, Teresa and Baldari, Cosima T. and Balduini, Walter and Ballabio, Andrea and Ballester, Maria and Balazadeh, Salma and Balzan, Rena and Bandopadhyay, Rina and Banerjee, Sreeparna and Banerjee, Sulagna and Bánréti, Ágnes and Bao, Yan and Baptista, Mauricio S. and Baracca, Alessandra and Barbati, Cristiana and Bargiela, Ariadna and Barilà, Daniela and Barlow, Peter G. and Barmada, Sami J. and Barreiro, Esther and Barreto, George E. and Bartek, Jiri and Bartel, Bonnie and Bartolome, Alberto and Barve, Gaurav R. and Basagoudanavar, Suresh H. and Bassham, Diane C. and Bast, Robert C. and Basu, Alakananda and Batoko, Henri and Batten, Isabella and Baulieu, Etienne E. and Baumgarner, Bradley L. and Bayry, Jagadeesh and Beale, Rupert and Beau, Isabelle and Beaumatin, Florian and Bechara, Luiz R.G. and Beck, George R. and Beers, Michael F. and Begun, Jakob and Behrends, Christian and Behrens, Georg M.N. and Bei, Roberto and Bejarano, Eloy and Bel, Shai and Behl, Christian and Belaid, Amine and Belgareh-Touzé, Naïma and Bellarosa, Cristina and Belleudi, Francesca and Belló Pérez, Melissa and Bello-Morales, Raquel and Beltran, Jackeline Soares De Oliveira and Beltran, Sebastián and Benbrook, Doris Mangiaracina and Bendorius, Mykolas and Benitez, Bruno A. and Benito-Cuesta, Irene and Bensalem, Julien and Berchtold, Martin W. and Berezowska, Sabina and Bergamaschi, Daniele and Bergami, Matteo and Bergmann, Andreas and Berliocchi, Laura and Berlioz-Torrent, Clarisse and Bernard, Amélie and Berthoux, Lionel and Besirli, Cagri G. and Besteiro, Sebastien and Betin, Virginie M. and Beyaert, Rudi and Bezbradica, Jelena S. and Bhaskar, Kiran and Bhatia-Kissova, Ingrid and Bhattacharya, Resham and Bhattacharya, Sujoy and Bhattacharyya, Shalmoli and Bhuiyan, Md Shenuarin and Bhutia, Sujit Kumar and Bi, Lanrong and Bi, Xiaolin and Biden, Trevor J. and Bijian, Krikor and Billes, Viktor A. and Binart, Nadine and Bincoletto, Claudia and Birgisdottir, Asa B. and Bjorkoy, Geir and Blanco, Gonzalo and Blas-Garcia, Ana and Blasiak, Janusz and Blomgran, Robert and Blomgren, Klas and Blum, Janice S. and Boada-Romero, Emilio and Boban, Mirta and Boesze-Battaglia, Kathleen and Boeuf, Philippe and Boland, Barry and Bomont, Pascale and Bonaldo, Paolo and Bonam, Srinivasa Reddy and Bonfili, Laura and Bonifacino, Juan S. and Boone, Brian A. and Bootman, Martin D. and Bordi, Matteo and Borner, Christoph and Bornhauser, Beat C. and Borthakur, Gautam and Bosch, Jürgen and Bose, Santanu and Botana, Luis M. and Botas, Juan and Boulanger, Chantal M. and Boulton, Michael E. and Bourdenx, Mathieu and Bourgeois, Benjamin and Bourke, Nollaig M. and Bousquet, Guilhem and Boya, Patricia and Bozhkov, Peter V. and Bozi, Luiz H.M. and Bozkurt, Tolga O. and Brackney, Doug E. and Brandts, Christian H. and Braun, Ralf J. and Braus, Gerhard H. and Bravo-Sagua, Roberto and Bravo-San Pedro, José M. and Brest, Patrick and Bringer, Marie Agnès and Briones-Herrera, Alfredo and Broaddus, V. Courtney and Brodersen, Peter and Brodsky, Jeffrey L. and Brody, Steven L. and Bronson, Paola G. and Bronstein, Jeff M. and Brown, Carolyn N. and Brown, Rhoderick E. and Brum, Patricia C. and Brumell, John H. and Brunetti-Pierri, Nicola and Bruno, Daniele and Bryson-Richardson, Robert J. and Bucci, Cecilia and Buchrieser, Carmen and Bueno, Marta and Buitrago-Molina, Laura Elisa and Buraschi, Simone and Buch, Shilpa and Buchan, J. Ross and Buckingham, Erin M. and Budak, Hikmet and Budini, Mauricio and Bultynck, Geert and Burada, Florin and Burgoyne, Joseph R. and Burón, M. Isabel and Bustos, Victor and Büttner, Sabrina and Butturini, Elena and Byrd, Aaron and Cabas, Isabel and Cabrera-Benitez, Sandra and Cadwell, Ken and Cai, Jingjing and Cai, Lu and Cai, Qian and Cairó, Montserrat and Calbet, Jose A. and Caldwell, Guy A. and Caldwell, Kim A. and Call, Jarrod A. and Calvani, Riccardo and Calvo, Ana C. and Calvo-Rubio Barrera, Miguel and Camara, Niels O.S. and Camonis, Jacques H. and Camougrand, Nadine and Campanella, Michelangelo and Campbell, Edward M. and Campbell-Valois, François Xavier and Campello, Silvia and Campesi, Ilaria and Campos, Juliane C. and Camuzard, Olivier and Cancino, Jorge and Candido De Almeida, Danilo and Canesi, Laura and Caniggia, Isabella and Canonico, Barbara and Cantí, Carles and Cao, Bin and Caraglia, Michele and Caramés, Beatriz and Carchman, Evie H. and Cardenal-Muñoz, Elena and Cardenas, Cesar and Cardenas, Luis and Cardoso, Sandra M. and Carew, Jennifer S. and Carle, Georges F. and Carleton, Gillian and Carloni, Silvia and Carmona-Gutierrez, Didac and Carneiro, Leticia A. and Carnevali, Oliana and Carosi, Julian M. and Carra, Serena and Carrier, Alice and Carrier, Lucie and Carroll, Bernadette and Carter, A. Brent and Carvalho, Andreia Neves and Casanova, Magali and Casas, Caty and Casas, Josefina and Cassioli, Chiara and Castillo, Eliseo F. and Castillo, Karen and Castillo-Lluva, Sonia and Castoldi, Francesca and Castori, Marco and Castro, Ariel F. and Castro-Caldas, Margarida and Castro-Hernandez, Javier and Castro-Obregon, Susana and Catz, Sergio D. and Cavadas, Claudia and Cavaliere, Federica and Cavallini, Gabriella and Cavinato, Maria and Cayuela, Maria L. and Cebollada Rica, Paula and Cecarini, Valentina and Cecconi, Francesco and Cechowska-Pasko, Marzanna and Cenci, Simone and Ceperuelo-Mallafré, Victòria and Cerqueira, João J. and Cerutti, Janete M. and Cervia, Davide and Cetintas, Vildan Bozok and Cetrullo, Silvia and Chae, Han Jung and Chagin, Andrei S. and Chai, Chee Yin and Chakrabarti, Gopal and Chakrabarti, Oishee and Chakraborty, Tapas and Chakraborty, Trinad and Chami, Mounia and Chamilos, Georgios and Chan, David W. and Chan, Edmond Y.W. and Chan, Edward D. and Chan, H. Y.Edwin and Chan, Helen H. and Chan, Hung and Chan, Matthew T.V. and Chan, Yau Sang and Chandra, Partha K. and Chang, Chih Peng and Chang, Chunmei and Chang, Hao Chun and Chang, Kai and Chao, Jie and Chapman, Tracey and Charlet-Berguerand, Nicolas and Chatterjee, Samrat and Chaube, Shail K. and Chaudhary, Anu and Chauhan, Santosh and Chaum, Edward and Checler, Frédéric and Cheetham, Michael E. and Chen, Chang Shi and Chen, Guang Chao and Chen, Jian Fu and Chen, Liam L. and Chen, Leilei and Chen, Lin and Chen, Mingliang and Chen, Mu Kuan and Chen, Ning and Chen, Quan and Chen, Ruey Hwa and Chen, Shi and Chen, Wei and Chen, Weiqiang and Chen, Xin Ming and Chen, Xiong Wen and Chen, Xu and Chen, Yan and Chen, Ye Guang and Chen, Yingyu and Chen, Yongqiang and Chen, Yu Jen and Chen, Yue Qin and Chen, Zhefan Stephen and Chen, Zhi and Chen, Zhi Hua and Chen, Zhijian J. and Chen, Zhixiang and Cheng, Hanhua and Cheng, Jun and Cheng, Shi Yuan and Cheng, Wei and Cheng, Xiaodong and Cheng, Xiu Tang and Cheng, Yiyun and Cheng, Zhiyong and Chen, Zhong and Cheong, Heesun and Cheong, Jit Kong and Chernyak, Boris V. and Cherry, Sara and Cheung, Chi Fai Randy and Cheung, Chun Hei Antonio and Cheung, King Ho and Chevet, Eric and Chi, Richard J. and Chiang, Alan Kwok Shing and Chiaradonna, Ferdinando and Chiarelli, Roberto and Chiariello, Mario and Chica, Nathalia and Chiocca, Susanna and Chiong, Mario and Chiou, Shih Hwa and Chiramel, Abhilash I. and Chiurchiù, Valerio and Cho, Dong Hyung and Choe, Seong Kyu and Choi, Augustine M.K. and Choi, Mary E. and Choudhury, Kamalika Roy and Chow, Norman S. and Chu, Charleen T. and Chua, Jason P. and Chua, John Jia En and Chung, Hyewon and Chung, Kin Pan and Chung, Seockhoon and Chung, So Hyang and Chung, Yuen Li and Cianfanelli, Valentina and Ciechomska, Iwona A. and Cifuentes, Mariana and Cinque, Laura and Cirak, Sebahattin and Cirone, Mara and Clague, Michael J. and Clarke, Robert and Clementi, Emilio and Coccia, Eliana M. and Codogno, Patrice and Cohen, Ehud and Cohen, Mickael M. and Colasanti, Tania and Colasuonno, Fiorella and Colbert, Robert A. and Colell, Anna and Čolić, Miodrag and Coll, Nuria S. and Collins, Mark O. and Colombo, María I. and Colón-Ramos, Daniel A. and Combaret, Lydie and Comincini, Sergio and Cominetti, Márcia R. and Consiglio, Antonella and Conte, Andrea and Conti, Fabrizio and Contu, Viorica Raluca and Cookson, Mark R. and Coombs, Kevin M. and Coppens, Isabelle and Corasaniti, Maria Tiziana and Corkery, Dale P. and Cordes, Nils and Cortese, Katia and Costa, Maria Do Carmo and Costantino, Sarah and Costelli, Paola and Coto-Montes, Ana and Crack, Peter J. and Crespo, Jose L. and Criollo, Alfredo and Crippa, Valeria and Cristofani, Riccardo and Csizmadia, Tamas and Cuadrado, Antonio and Cui, Bing and Cui, Jun and Cui, Yixian and Cui, Yong and Culetto, Emmanuel and Cumino, Andrea C. and Cybulsky, Andrey V. and Czaja, Mark J. and Czuczwar, Stanislaw J. and D’Adamo, Stefania and D’Amelio, Marcello and D’Arcangelo, Daniela and D’Lugos, Andrew C. and D’Orazi, Gabriella and Da Silva, James A. and Dafsari, Hormos Salimi and Dagda, Ruben K. and Dagdas, Yasin and Daglia, Maria and Dai, Xiaoxia and Dai, Yun and Dai, Yuyuan and Dal Col, Jessica and Dalhaimer, Paul and Dalla Valle, Luisa and Dallenga, Tobias and Dalmasso, Guillaume and Damme, Markus and Dando, Ilaria and Dantuma, Nico P. and Darling, April L. and Das, Hiranmoy and Dasarathy, Srinivasan and Dasari, Santosh K. and Dash, Srikanta and Daumke, Oliver and Dauphinee, Adrian N. and Davies, Jeffrey S. and Dávila, Valeria A. and Davis, Roger J. and Davis, Tanja and Dayalan Naidu, Sharadha and De Amicis, Francesca and De Bosscher, Karolien and De Felice, Francesca and De Franceschi, Lucia and De Leonibus, Chiara and De Mattos Barbosa, Mayara G. and De Meyer, Guido R.Y. and De Milito, Angelo and De Nunzio, Cosimo and De Palma, Clara and De Santi, Mauro and De Virgilio, Claudio and De Zio, Daniela and Debnath, Jayanta and Debosch, Brian J. and Decuypere, Jean Paul and Deehan, Mark A. and Deflorian, Gianluca and Degregori, James and Dehay, Benjamin and Del Rio, Gabriel and Delaney, Joe R. and Delbridge, Lea M.D. and Delorme-Axford, Elizabeth and Delpino, M. Victoria and Demarchi, Francesca and Dembitz, Vilma and Demers, Nicholas D. and Deng, Hongbin and Deng, Zhiqiang and Dengjel, Joern and Dent, Paul and Denton, Donna and Depamphilis, Melvin L. and Der, Channing J. and Deretic, Vojo and Descoteaux, Albert and Devis, Laura and Devkota, Sushil and Devuyst, Olivier and Dewson, Grant and Dharmasivam, Mahendiran and Dhiman, Rohan and Di Bernardo, Diego and Di Cristina, Manlio and Di Domenico, Fabio and Di Fazio, Pietro and Di Fonzo, Alessio and Di Guardo, Giovanni and Di Guglielmo, Gianni M. and Di Leo, Luca and Di Malta, Chiara and Di Nardo, Alessia and Di Rienzo, Martina and Di Sano, Federica and Diallinas, George and Diao, Jiajie and Diaz-Araya, Guillermo and Díaz-Laviada, Inés and Dickinson, Jared M. and Diederich, Marc and Dieudé, Mélanie and Dikic, Ivan and Ding, Shiping and Ding, Wen Xing and Dini, Luciana and Dinić, Jelena and Dinic, Miroslav and Dinkova-Kostova, Albena T. and Dionne, Marc S. and Distler, Jörg H.W. and Diwan, Abhinav and Dixon, Ian M.C. and Djavaheri-Mergny, Mojgan and Dobrinski, Ina and Dobrovinskaya, Oxana and Dobrowolski, Radek and Dobson, Renwick C.J. and Đokić, Jelena and Dokmeci Emre, Serap and Donadelli, Massimo and Dong, Bo and Dong, Xiaonan and Dong, Zhiwu and Dorn, Gerald W. and Dotsch, Volker and Dou, Huan and Dou, Juan and Dowaidar, Moataz and Dridi, Sami and Drucker, Liat and Du, Ailian and Du, Caigan and Du, Guangwei and Du, Hai Ning and Du, Li Lin and Du Toit, André and Duan, Shao Bin and Duan, Xiaoqiong and Duarte, Sónia P. and Dubrovska, Anna and Dunlop, Elaine A. and Dupont, Nicolas and Durán, Raúl V. and Dwarakanath, Bilikere S. and Dyshlovoy, Sergey A. and Ebrahimi-Fakhari, Darius and Eckhart, Leopold and Edelstein, Charles L. and Efferth, Thomas and Eftekharpour, Eftekhar and Eichinger, Ludwig and Eid, Nabil and Eisenberg, Tobias and Eissa, N. Tony and Eissa, Sanaa and Ejarque, Miriam and El Andaloussi, Abdeljabar and El-Hage, Nazira and El-Naggar, Shahenda and Eleuteri, Anna Maria and El-Shafey, Eman S. and Elgendy, Mohamed and Eliopoulos, Aristides G. and Elizalde, María M. and Elks, Philip M. and Elsasser, Hans Peter and Elsherbiny, Eslam S. and Emerling, Brooke M. and Emre, N. C.Tolga and Eng, Christina H. and Engedal, Nikolai and Engelbrecht, Anna Mart and Engelsen, Agnete S.T. and Enserink, Jorrit M. and Escalante, Ricardo and Esclatine, Audrey and Escobar-Henriques, Mafalda and Eskelinen, Eeva Liisa and Espert, Lucile and Eusebio, Makandjou Ola and Fabrias, Gemma and Fabrizi, Cinzia and Facchiano, Antonio and Facchiano, Francesco and Fadeel, Bengt and Fader, Claudio and Faesen, Alex C. and Fairlie, W. Douglas and Falcó, Alberto and Falkenburger, Bjorn H. and Fan, Daping and Fan, Jie and Fan, Yanbo and Fang, Evandro F. and Fang, Yanshan and Fang, Yognqi and Fanto, Manolis and Farfel-Becker, Tamar and Faure, Mathias and Fazeli, Gholamreza and Fedele, Anthony O. and Feldman, Arthur M. and Feng, Du and Feng, Jiachun and Feng, Lifeng and Feng, Yibin and Feng, Yuchen and Feng, Wei and Fenz Araujo, Thais and Ferguson, Thomas A. and Fernández, Álvaro F. and Fernandez-Checa, Jose C. and Fernández-Veledo, Sonia and Fernie, Alisdair R. and Ferrante, Anthony W. and Ferraresi, Alessandra and Ferrari, Merari F. and Ferreira, Julio C.B. and Ferro-Novick, Susan and Figueras, Antonio and Filadi, Riccardo and Filigheddu, Nicoletta and Filippi-Chiela, Eduardo and Filomeni, Giuseppe and Fimia, Gian Maria and Fineschi, Vittorio and Finetti, Francesca and Finkbeiner, Steven and Fisher, Edward A. and Fisher, Paul B. and Flamigni, Flavio and Fliesler, Steven J. and Flo, Trude H. and Florance, Ida and Florey, Oliver and Florio, Tullio and Fodor, Erika and Follo, Carlo and Fon, Edward A. and Forlino, Antonella and Fornai, Francesco and Fortini, Paola and Fracassi, Anna and Fraldi, Alessandro and Franco, Brunella and Franco, Rodrigo and Franconi, Flavia and Frankel, Lisa B. and Friedman, Scott L. and Fröhlich, Leopold F. and Frühbeck, Gema and Fuentes, Jose M. and Fujiki, Yukio and Fujita, Naonobu and Fujiwara, Yuuki and Fukuda, Mitsunori and Fulda, Simone and Furic, Luc and Furuya, Norihiko and Fusco, Carmela and Gack, Michaela U. and Gaffke, Lidia and Galadari, Sehamuddin and Galasso, Alessia and Galindo, Maria F. and Gallolu Kankanamalage, Sachith and Galluzzi, Lorenzo and Galy, Vincent and Gammoh, Noor and Gan, Boyi and Ganley, Ian G. and Gao, Feng and Gao, Hui and Gao, Minghui and Gao, Ping and Gao, Shou Jiang and Gao, Wentao and Gao, Xiaobo and Garcera, Ana and Garcia, Maria Noé and Garcia, Verónica E. and García-Del Portillo, Francisco and Garcia-Escudero, Vega and Garcia-Garcia, Aracely and Garcia-Macia, Marina and García-Moreno, Diana and Garcia-Ruiz, Carmen and García-Sanz, Patricia and Garg, Abhishek D. and Gargini, Ricardo and Garofalo, Tina and Garry, Robert F. and Gassen, Nils C. and Gatica, Damian and Ge, Liang and Ge, Wanzhong and Geiss-Friedlander, Ruth and Gelfi, Cecilia and Genschik, Pascal and Gentle, Ian E. and Gerbino, Valeria and Gerhardt, Christoph and Germain, Kyla and Germain, Marc and Gewirtz, David A. and Ghasemipour Afshar, Elham and Ghavami, Saeid and Ghigo, Alessandra and Ghosh, Manosij and Giamas, Georgios and Giampietri, Claudia and Giatromanolaki, Alexandra and Gibson, Gary E. and Gibson, Spencer B. and Ginet, Vanessa and Giniger, Edward and Giorgi, Carlotta and Girao, Henrique and Girardin, Stephen E. and Giridharan, Mridhula and Giuliano, Sandy and Giulivi, Cecilia and Giuriato, Sylvie and Giustiniani, Julien and Gluschko, Alexander and Goder, Veit and Goginashvili, Alexander and Golab, Jakub and Goldstone, David C. and Golebiewska, Anna and Gomes, Luciana R. and Gomez, Rodrigo and Gómez-Sánchez, Rubén and Gomez-Puerto, Maria Catalina and Gomez-Sintes, Raquel and Gong, Qingqiu and Goni, Felix M. and González-Gallego, Javier and Gonzalez-Hernandez, Tomas and Gonzalez-Polo, Rosa A. and Gonzalez-Reyes, Jose A. and González-Rodríguez, Patricia and Goping, Ing Swie and Gorbatyuk, Marina S. and Gorbunov, Nikolai V. and Görgülü, Kıvanç and Gorojod, Roxana M. and Gorski, Sharon M. and Goruppi, Sandro and Gotor, Cecilia and Gottlieb, Roberta A. and Gozes, Illana and Gozuacik, Devrim and Graef, Martin and Gräler, Markus H. and Granatiero, Veronica and Grasso, Daniel and Gray, Joshua P. and Green, Douglas R. and Greenhough, Alexander and Gregory, Stephen L. and Griffin, Edward F. and Grinstaff, Mark W. and Gros, Frederic and Grose, Charles and Gross, Angelina S. and Gruber, Florian and Grumati, Paolo and Grune, Tilman and Gu, Xueyan and Guan, Jun Lin and Guardia, Carlos M. and Guda, Kishore and Guerra, Flora and Guerri, Consuelo and Guha, Prasun and Guillén, Carlos and Gujar, Shashi and Gukovskaya, Anna and Gukovsky, Ilya and Gunst, Jan and Günther, Andreas and Guntur, Anyonya R. and Guo, Chuanyong and Guo, Chun and Guo, Hongqing and Guo, Lian Wang and Guo, Ming and Gupta, Pawan and Gupta, Shashi Kumar and Gupta, Swapnil and Gupta, Veer Bala and Gupta, Vivek and Gustafsson, Asa B. and Gutterman, David D. and H.B, Ranjitha and Haapasalo, Annakaisa and Haber, James E. and Hać, Aleksandra and Hadano, Shinji and Hafrén, Anders J. and Haidar, Mansour and Hall, Belinda S. and Halldén, Gunnel and Hamacher-Brady, Anne and Hamann, Andrea and Hamasaki, Maho and Han, Weidong and Hansen, Malene and Hanson, Phyllis I. . and Hao, Zijian and Harada, Masaru and Harhaji-Trajkovic, Ljubica and Hariharan, Nirmala and Haroon, Nigil and Harris, James and Hasegawa, Takafumi and Hasima Nagoor, Noor and Haspel, Jeffrey A. and Haucke, Volker and Hawkins, Wayne D. and Hay, Bruce A. and Haynes, Cole M. and Hayrabedyan, Soren B. and Hays, Thomas S. and He, Congcong and He, Qin and He, Rong Rong and He, You Wen and He, Yu Ying and Heakal, Yasser and Heberle, Alexander M. and Hejtmancik, J. Fielding and Helgason, Gudmundur Vignir and Henkel, Vanessa and Herb, Marc and Hergovich, Alexander and Herman-Antosiewicz, Anna and Hernández, Agustín and Hernandez, Carlos and Hernandez-Diaz, Sergio and Hernandez-Gea, Virginia and Herpin, Amaury and Herreros, Judit and Hervás, Javier H. and Hesselson, Daniel and Hetz, Claudio and Heussler, Volker T. and Higuchi, Yujiro and Hilfiker, Sabine and Hill, Joseph A. and Hlavacek, William S. and Ho, Emmanuel A. and Ho, Idy H.T. and Ho, Philip Wing Lok and Ho, Shu Leong and Ho, Wan Yun and Hobbs, G. Aaron and Hochstrasser, Mark and Hoet, Peter H.M. and Hofius, Daniel and Hofman, Paul and Höhn, Annika and Holmberg, Carina I. and Hombrebueno, Jose R. and Yi-Ren Hong, Chang Won Hong and Hooper, Lora V. and Hoppe, Thorsten and Horos, Rastislav and Hoshida, Yujin and Hsin, I. Lun and Hsu, Hsin Yun and Hu, Bing and Hu, Dong and Hu, Li Fang and Hu, Ming Chang and Hu, Ronggui and Hu, Wei and Hu, Yu Chen and Hu, Zhuo Wei and Hua, Fang and Hua, Jinlian and Hua, Yingqi and Huan, Chongmin and Huang, Canhua and Huang, Chuanshu and Huang, Chuanxin and Huang, Chunling and Huang, Haishan and Huang, Kun and Huang, Michael L.H. and Huang, Rui and Huang, Shan and Huang, Tianzhi and Huang, Xing and Huang, Yuxiang Jack and Huber, Tobias B. and Hubert, Virginie and Hubner, Christian A. and Hughes, Stephanie M. and Hughes, William E. and Humbert, Magali and Hummer, Gerhard and Hurley, James H. and Hussain, Sabah and Hussain, Salik and Hussey, Patrick J. and Hutabarat, Martina and Hwang, Hui Yun and Hwang, Seungmin and Ieni, Antonio and Ikeda, Fumiyo and Imagawa, Yusuke and Imai, Yuzuru and Imbriano, Carol and Imoto, Masaya and Inman, Denise M. and Inoki, Ken and Iovanna, Juan and Iozzo, Renato V. and Ippolito, Giuseppe and Irazoqui, Javier E. and Iribarren, Pablo and Ishaq, 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Hongchuan and Jin, Li and Jin, Luqi and Jin, Meiyan and Jin, Si and Jo, Eun Kyeong and Joffre, Carine and Johansen, Terje and Johnson, Gail V.W. and Johnston, Simon A. and Jokitalo, Eija and Jolly, Mohit Kumar and Joosten, Leo A.B. and Jordan, Joaquin and Joseph, Bertrand and Ju, Dianwen and Ju, Jeong Sun and Ju, Jingfang and Juárez, Esmeralda and Judith, Delphine and Juhász, Gábor and Jun, Youngsoo and Jung, Chang Hwa and Jung, Sung Chul and Jung, Yong Keun and Jungbluth, Heinz and Jungverdorben, Johannes and Just, Steffen and Kaarniranta, Kai and Kaasik, Allen and Kabuta, Tomohiro and Kaganovich, Daniel and Kahana, Alon and Kain, Renate and Kajimura, Shinjo and Kalamvoki, Maria and Kalia, Manjula and Kalinowski, Danuta S. and Kaludercic, Nina and Kalvari, Ioanna and Kaminska, Joanna and Kaminskyy, Vitaliy O. and Kanamori, Hiromitsu and Kanasaki, Keizo and Kang, Chanhee and Kang, Rui and Kang, Sang Sun and Kaniyappan, Senthilvelrajan and Kanki, Tomotake and Kanneganti, Thirumala Devi and Kanthasamy, Anumantha G. and Kanthasamy, Arthi and Kantorow, Marc and Kapuy, Orsolya and Karamouzis, Michalis V. and Karim, Md Razaul and Karmakar, Parimal and Katare, Rajesh G. and Kato, Masaru and Kaufmann, Stefan H.E. and Kauppinen, Anu and Kaushal, Gur P. and Kaushik, Susmita and Kawasaki, Kiyoshi and Kazan, Kemal and Ke, Po Yuan and Keating, Damien J. and Keber, Ursula and Kehrl, John H. and Keller, Kate E. and Keller, Christian W. and Kemper, Jongsook Kim and Kenific, Candia M. and Kepp, Oliver and Kermorgant, Stephanie and Kern, Andreas and Ketteler, Robin and Keulers, Tom G. and Khalfin, Boris and Khalil, Hany and Khambu, Bilon and Khan, Shahid Y. and Khandelwal, Vinoth Kumar Megraj and Khandia, Rekha and Kho, Widuri and Khobrekar, Noopur V. and Khuansuwan, Sataree and Khundadze, Mukhran and Killackey, Samuel A. and Kim, Dasol and Kim, Deok Ryong and Kim, Do Hyung and Kim, Dong Eun and Kim, Eun Young and Kim, Eun Kyoung and Kim, Hak Rim and Kim, Hee Sik and Hyung-Ryong Kim, Unknown and Kim, Jeong Hun and Kim, Jin Kyung and Kim, Jin Hoi and Kim, Joungmok and Kim, Ju Hwan and Kim, Keun Il and Kim, Peter K. and Kim, Seong Jun and Kimball, Scot R. and Kimchi, Adi and Kimmelman, Alec C. and Kimura, Tomonori and King, Matthew A. and Kinghorn, Kerri J. and Kinsey, Conan G. and Kirkin, Vladimir and Kirshenbaum, Lorrie A. and Kiselev, Sergey L. and Kishi, Shuji and Kitamoto, Katsuhiko and Kitaoka, Yasushi and Kitazato, Kaio and Kitsis, Richard N. and Kittler, Josef T. and Kjaerulff, Ole and Klein, Peter S. and Klopstock, Thomas and Klucken, Jochen and Knævelsrud, Helene and Knorr, Roland L. and Ko, Ben C.B. and Ko, Fred and Ko, Jiunn Liang and Kobayashi, Hotaka and Kobayashi, Satoru and Koch, Ina and Koch, Jan C. and Koenig, Ulrich and Kögel, Donat and Koh, Young Ho and Koike, Masato and Kohlwein, Sepp D. and Kocaturk, Nur M. and Komatsu, Masaaki and König, Jeannette and Kono, Toru and Kopp, Benjamin T. and Korcsmaros, Tamas and Korkmaz, Gözde and Korolchuk, 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Charlie and Kenchappa, Chandra Shekar and Li, Zuguo and Lin, Yong and Oshima, Shigeru and Rong, Yueguang and Sluimer, Judith C. and Stallings, Christina L. and Tong, Chun Kit}, issn = {1554-8635}, journal = {Autophagy}, number = {1}, pages = {1--382}, publisher = {Taylor & Francis}, title = {{Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)}}, doi = {10.1080/15548627.2020.1797280}, volume = {17}, year = {2021}, } @article{8742, abstract = {We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros.}, author = {Browning, Timothy D and Heath-Brown, Roger}, issn = {1435-5337}, journal = {Forum Mathematicum}, number = {1}, pages = {147--165}, publisher = {De Gruyter}, title = {{The geometric sieve for quadrics}}, doi = {10.1515/forum-2020-0074}, volume = {33}, year = {2021}, } @phdthesis{10035, abstract = {Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for "graph-building" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).}, author = {Klein, Karen}, issn = {2663-337X}, pages = {276}, publisher = {Institute of Science and Technology Austria}, title = {{On the adaptive security of graph-based games}}, doi = {10.15479/at:ista:10035}, year = {2021}, } @inproceedings{10410, abstract = {The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.}, author = {Kamath Hosdurg, Chethan and Klein, Karen and Pietrzak, Krzysztof Z and Walter, Michael}, booktitle = {19th International Conference}, isbn = {9-783-0309-0452-4}, issn = {1611-3349}, location = {Raleigh, NC, United States}, pages = {550--581}, publisher = {Springer Nature}, title = {{The cost of adaptivity in security games on graphs}}, doi = {10.1007/978-3-030-90453-1_19}, volume = {13043}, year = {2021}, } @inproceedings{10048, abstract = {The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques. }, author = {Kamath Hosdurg, Chethan and Klein, Karen and Pietrzak, Krzysztof Z and Walter, Michael}, booktitle = {19th Theory of Cryptography Conference 2021}, location = {Raleigh, NC, United States}, publisher = {International Association for Cryptologic Research}, title = {{The cost of adaptivity in security games on graphs}}, year = {2021}, } @article{10738, abstract = {We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2.}, author = {Leopold, Nikolai K and Rademacher, Simone Anna Elvira and Schlein, Benjamin and Seiringer, Robert}, issn = {1948-206X}, journal = {Analysis and PDE}, number = {7}, pages = {2079--2100}, publisher = {Mathematical Sciences Publishers}, title = {{ The Landau–Pekar equations: Adiabatic theorem and accuracy}}, doi = {10.2140/APDE.2021.14.2079}, volume = {14}, year = {2021}, } @phdthesis{10429, abstract = {The scalability of concurrent data structures and distributed algorithms strongly depends on reducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures such as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.}, author = {Nadiradze, Giorgi}, issn = {2663-337X}, pages = {132}, publisher = {Institute of Science and Technology Austria}, title = {{On achieving scalability through relaxation}}, doi = {10.15479/at:ista:10429}, year = {2021}, } @inproceedings{10435, abstract = {Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \emph{SwarmSGD} still converges in this setting, even if \emph{non-blocking communication}, \emph{quantization}, and \emph{local steps} are all applied \emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks.}, author = {Nadiradze, Giorgi and Sabour, Amirmojtaba and Davies, Peter and Li, Shigang and Alistarh, Dan-Adrian}, booktitle = {35th Conference on Neural Information Processing Systems}, location = {Sydney, Australia}, publisher = {Neural Information Processing Systems Foundation}, title = {{Asynchronous decentralized SGD with quantized and local updates}}, year = {2021}, } @inproceedings{10593, abstract = {We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance.}, author = {Mondelli, Marco and Venkataramanan, Ramji}, booktitle = {35th Conference on Neural Information Processing Systems}, isbn = {9781713845393}, issn = {1049-5258}, location = {Virtual}, pages = {29616--29629}, publisher = {Neural Information Processing Systems Foundation}, title = {{PCA initialization for approximate message passing in rotationally invariant models}}, volume = {35}, year = {2021}, } @inproceedings{10594, abstract = {The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold.}, author = {Nguyen, Quynh and Bréchet, Pierre and Mondelli, Marco}, booktitle = {35th Conference on Neural Information Processing Systems}, isbn = {9781713845393}, issn = {1049-5258}, location = {Virtual}, publisher = {Neural Information Processing Systems Foundation}, title = {{When are solutions connected in deep networks?}}, volume = {35}, year = {2021}, } @article{9815, abstract = {The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.}, author = {Mobassem, Sonia and Lambert, Nicholas J. and Rueda Sanchez, Alfredo R and Fink, Johannes M and Leuchs, Gerd and Schwefel, Harald G.L.}, issn = {2058-9565}, journal = {Quantum Science and Technology}, number = {4}, publisher = {IOP Publishing}, title = {{Thermal noise in electro-optic devices at cryogenic temperatures}}, doi = {10.1088/2058-9565/ac0f36}, volume = {6}, year = {2021}, } @unpublished{9978, abstract = {Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.}, author = {Cao, Deqing and Shen, Xiaoxiao and Wang, Aiping and Yu, Fengjiao and Wu, Yuping and Shi, Siqi and Freunberger, Stefan Alexander and Chen, Yuhui}, booktitle = {Research Square}, issn = {2693-5015}, keywords = {Catalysis, Energy engineering, Materials theory and modeling}, pages = {21}, publisher = {Research Square}, title = {{Sharp kinetic acceleration potentials during mediated redox catalysis of insulators}}, doi = {10.21203/rs.3.rs-750965/v1}, year = {2021}, } @article{8730, abstract = {P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors.}, author = {Tournier, N and Goutal, S and Mairinger, S and Lozano, IH and Filip, T and Sauberer, M and Caillé, F and Breuil, L and Stanek, J and Freeman, AF and Novarino, Gaia and Truillet, C and Wanek, T and Langer, O}, issn = {1559-7016}, journal = {Journal of Cerebral Blood Flow and Metabolism}, number = {7}, pages = {1634--1646}, publisher = {SAGE Publications}, title = {{Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib}}, doi = {10.1177/0271678X20965500}, volume = {41}, year = {2021}, } @article{9383, abstract = {A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.}, author = {Stankowski, Sean and Ravinet, Mark}, issn = {1558-5646}, journal = {Evolution}, number = {6}, pages = {1256--1273}, publisher = {Oxford University Press}, title = {{Defining the speciation continuum}}, doi = {10.1111/evo.14215}, volume = {75}, year = {2021}, } @article{10223, abstract = {Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.}, author = {Li, Lanxin and Verstraeten, Inge and Roosjen, Mark and Takahashi, Koji and Rodriguez Solovey, Lesia and Merrin, Jack and Chen, Jian and Shabala, Lana and Smet, Wouter and Ren, Hong and Vanneste, Steffen and Shabala, Sergey and De Rybel, Bert and Weijers, Dolf and Kinoshita, Toshinori and Gray, William M. and Friml, Jiří}, issn = {14764687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7884}, pages = {273--277}, publisher = {Springer Nature}, title = {{Cell surface and intracellular auxin signalling for H+ fluxes in root growth}}, doi = {10.1038/s41586-021-04037-6}, volume = {599}, year = {2021}, } @article{9379, abstract = {When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.}, author = {Bolger-Munro, Madison and Choi, Kate and Cheung, Faith and Liu, Yi Tian and Dang-Lawson, May and Deretic, Nikola and Keane, Connor and Gold, Michael R.}, issn = {2296-634X}, journal = {Frontiers in Cell and Developmental Biology}, keywords = {B cell, actin, immune synapse, cell spreading, cofilin, WDR1 (AIP1), LIM domain kinase, B cell receptor (BCR)}, publisher = {Frontiers Media}, title = {{The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse}}, doi = {10.3389/fcell.2021.649433}, volume = {9}, year = {2021}, } @article{9362, abstract = {A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics.}, author = {Chalk, Matthew J and Tkačik, Gašper and Marre, Olivier}, issn = {19326203}, journal = {PLoS ONE}, number = {4}, publisher = {Public Library of Science}, title = {{Inferring the function performed by a recurrent neural network}}, doi = {10.1371/journal.pone.0248940}, volume = {16}, year = {2021}, } @article{9986, abstract = {Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.}, author = {Velasquez, Silvia Melina and Guo, Xiaoyuan and Gallemi, Marçal and Aryal, Bibek and Venhuizen, Peter and Barbez, Elke and Dünser, Kai Alexander and Darino, Martin and Pӗnčík, Aleš and Novák, Ondřej and Kalyna, Maria and Mouille, Gregory and Benková, Eva and Bhalerao, Rishikesh P. and Mravec, Jozef and Kleine-Vehn, Jürgen}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, keywords = {auxin, growth, cell wall, xyloglucans, hypocotyls, gravitropism}, number = {17}, publisher = {MDPI}, title = {{Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants}}, doi = {10.3390/ijms22179222}, volume = {22}, year = {2021}, } @article{9189, abstract = {Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.}, author = {Zhao, Y and Wu, L and Fu, Q and Wang, D and Li, J and Yao, B and Yu, S and Jiang, L and Qian, J and Zhou, X and Han, L and Zhao, S and Ma, C and Zhang, Y and Luo, C and Dong, Q and Li, S and Zhang, L and Jiang, X and Li, Y and Luo, H and Li, K and Yang, J and Luo, Q and Li, L and Peng, S and Huang, H and Zuo, Z and Liu, C and Wang, L and Li, C and He, X and Friml, Jiří and Du, Y}, issn = {1365-3040}, journal = {Plant, Cell & Environment}, number = {6}, pages = {1846--1857}, publisher = {Wiley}, title = {{INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance}}, doi = {10.1111/pce.14029}, volume = {44}, year = {2021}, } @unpublished{9792, abstract = {This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.}, author = {Feliciangeli, Dario and Gerolin, Augusto and Portinale, Lorenzo}, booktitle = {arXiv}, title = {{A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature}}, doi = {10.48550/arXiv.2106.11217}, year = {2021}, } @article{10655, abstract = {Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency. }, author = {Maes, Margaret E and Wögenstein, Gabriele M. and Colombo, Gloria and Casado Polanco, Raquel and Siegert, Sandra}, issn = {2329-0501}, journal = {Molecular Therapy - Methods and Clinical Development}, pages = {210--224}, publisher = {Elsevier}, title = {{Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment}}, doi = {10.1016/j.omtm.2021.09.006}, volume = {23}, year = {2021}, } @article{10565, abstract = {Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).}, author = {Venturino, Alessandro and Siegert, Sandra}, issn = {2666-1667}, journal = {STAR Protocols}, number = {4}, publisher = {Elsevier ; Cell Press}, title = {{Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain}}, doi = {10.1016/j.xpro.2021.101012}, volume = {2}, year = {2021}, } @article{10321, abstract = {Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).}, author = {Amberg, Nicole and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, number = {4}, publisher = {Cell Press}, title = {{Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers}}, doi = {10.1016/j.xpro.2021.100939}, volume = {2}, year = {2021}, } @article{10290, abstract = {A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.}, author = {Dimchev, Georgi A and Amiri, Behnam and Fäßler, Florian and Falcke, Martin and Schur, Florian KM}, issn = {1047-8477}, journal = {Journal of Structural Biology}, keywords = {Structural Biology}, number = {4}, publisher = {Elsevier }, title = {{Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data}}, doi = {10.1016/j.jsb.2021.107808}, volume = {213}, year = {2021}, } @inproceedings{9969, abstract = {Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths.}, author = {Pietrzak, Krzysztof Z and Salem, Iosif and Schmid, Stefan and Yeo, Michelle X}, isbn = {978-1-6654-4501-6}, issn = {1861-2288}, location = {Espoo and Helsinki, Finland}, publisher = {IEEE}, title = {{LightPIR: Privacy-preserving route discovery for payment channel networks}}, doi = {10.23919/IFIPNetworking52078.2021.9472205}, year = {2021}, } @inproceedings{9644, abstract = {We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.}, author = {Chatterjee, Krishnendu and Goharshady, Ehsan Kafshdar and Novotný, Petr and Zikelic, Dorde}, booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation}, isbn = {9781450383912}, location = {Online}, pages = {1033--1048}, publisher = {Association for Computing Machinery}, title = {{Proving non-termination by program reversal}}, doi = {10.1145/3453483.3454093}, year = {2021}, } @article{9760, abstract = {The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent the issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.}, author = {Sack, Stefan and Serbyn, Maksym}, issn = {2521-327X}, journal = {Quantum}, publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften}, title = {{Quantum annealing initialization of the quantum approximate optimization algorithm}}, doi = {10.22331/Q-2021-07-01-491}, volume = {5}, year = {2021}, } @inproceedings{10414, abstract = {We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.}, author = {Chatterjee, Krishnendu and Goharshady, Ehsan Kafshdar and Novotný, Petr and Zárevúcky, Jiří and Zikelic, Dorde}, booktitle = {24th International Symposium on Formal Methods}, isbn = {9-783-0309-0869-0}, issn = {1611-3349}, location = {Virtual}, pages = {619--639}, publisher = {Springer Nature}, title = {{On lexicographic proof rules for probabilistic termination}}, doi = {10.1007/978-3-030-90870-6_33}, volume = {13047}, year = {2021}, } @article{14800, abstract = {Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. }, author = {Chang, Cheng and Chen, Wei and Chen, Ye and Chen, Yonghua and Chen, Yu and Ding, Feng and Fan, Chunhai and Fan, Hong Jin and Fan, Zhanxi and Gong, Cheng and Gong, Yongji and He, Qiyuan and Hong, Xun and Hu, Sheng and Hu, Weida and Huang, Wei and Huang, Yuan and Ji, Wei and Li, Dehui and Li, Lain Jong and Li, Qiang and Lin, Li and Ling, Chongyi and Liu, Minghua and Liu, Nan and Liu, Zhuang and Loh, Kian Ping and Ma, Jianmin and Miao, Feng and Peng, Hailin and Shao, Mingfei and Song, Li and Su, Shao and Sun, Shuo and Tan, Chaoliang and Tang, Zhiyong and Wang, Dingsheng and Wang, Huan and Wang, Jinlan and Wang, Xin and Wang, Xinran and Wee, Andrew T.S. and Wei, Zhongming and Wu, Yuen and Wu, Zhong Shuai and Xiong, Jie and Xiong, Qihua and Xu, Weigao and Yin, Peng and Zeng, Haibo and Zeng, Zhiyuan and Zhai, Tianyou and Zhang, Han and Zhang, Hui and Zhang, Qichun and Zhang, Tierui and Zhang, Xiang and Zhao, Li Dong and Zhao, Meiting and Zhao, Weijie and Zhao, Yunxuan and Zhou, Kai Ge and Zhou, Xing and Zhou, Yu and Zhu, Hongwei and Zhang, Hua and Liu, Zhongfan}, issn = {1001-4861}, journal = {Acta Physico-Chimica Sinica}, number = {12}, publisher = {Peking University}, title = {{Recent progress on two-dimensional materials}}, doi = {10.3866/PKU.WHXB202108017}, volume = {37}, year = {2021}, } @inproceedings{10206, abstract = {Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.}, author = {Lukina, Anna and Schilling, Christian and Henzinger, Thomas A}, booktitle = {21st International Conference on Runtime Verification}, isbn = {9-783-0308-8493-2}, issn = {1611-3349}, keywords = {monitoring, neural networks, novelty detection}, location = {Virtual}, pages = {42--61}, publisher = {Springer Nature}, title = {{Into the unknown: active monitoring of neural networks}}, doi = {10.1007/978-3-030-88494-9_3}, volume = {12974 }, year = {2021}, } @article{14889, abstract = {We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2.}, author = {Leopold, Nikolai K and Mitrouskas, David Johannes and Rademacher, Simone Anna Elvira and Schlein, Benjamin and Seiringer, Robert}, issn = {2578-5885}, journal = {Pure and Applied Analysis}, number = {4}, pages = {653--676}, publisher = {Mathematical Sciences Publishers}, title = {{Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron}}, doi = {10.2140/paa.2021.3.653}, volume = {3}, year = {2021}, } @article{14890, abstract = {We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.}, author = {Bossmann, Lea and Petrat, Sören P and Pickl, Peter and Soffer, Avy}, issn = {2578-5885}, journal = {Pure and Applied Analysis}, number = {4}, pages = {677--726}, publisher = {Mathematical Sciences Publishers}, title = {{Beyond Bogoliubov dynamics}}, doi = {10.2140/paa.2021.3.677}, volume = {3}, year = {2021}, } @article{15013, abstract = {We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge.}, author = {Alt, Johannes and Erdös, László and Krüger, Torben H}, issn = {2690-1005}, journal = {Probability and Mathematical Physics}, number = {2}, pages = {221--280}, publisher = {Mathematical Sciences Publishers}, title = {{Spectral radius of random matrices with independent entries}}, doi = {10.2140/pmp.2021.2.221}, volume = {2}, year = {2021}, } @article{9887, abstract = {Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.}, author = {Johnson, Alexander J and Dahhan, Dana A and Gnyliukh, Nataliia and Kaufmann, Walter and Zheden, Vanessa and Costanzo, Tommaso and Mahou, Pierre and Hrtyan, Mónika and Wang, Jie and Aguilera Servin, Juan L and van Damme, Daniël and Beaurepaire, Emmanuel and Loose, Martin and Bednarek, Sebastian Y and Friml, Jiří}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {51}, publisher = {National Academy of Sciences}, title = {{The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis}}, doi = {10.1073/pnas.2113046118}, volume = {118}, year = {2021}, } @misc{14988, abstract = {Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS}, author = {Johnson, Alexander J}, publisher = {Zenodo}, title = {{Raw data from Johnson et al, PNAS, 2021}}, doi = {10.5281/ZENODO.5747100}, year = {2021}, } @unpublished{10029, abstract = {Superconductor-semiconductor hybrids are platforms for realizing effective p-wave superconductivity. Spin-orbit coupling, combined with the proximity effect, causes the two-dimensional semiconductor to inherit p±ip intraband pairing, and application of magnetic field can then result in transitions to the normal state, partial Bogoliubov Fermi surfaces, or topological phases with Majorana modes. Experimentally probing the hybrid superconductor-semiconductor interface is challenging due to the shunting effect of the conventional superconductor. Consequently, the nature of induced pairing remains an open question. Here, we use the circuit quantum electrodynamics architecture to probe induced superconductivity in a two dimensional Al-InAs hybrid system. We observe a strong suppression of superfluid density and enhanced dissipation driven by magnetic field, which cannot be accounted for by the depairing theory of an s-wave superconductor. These observations are explained by a picture of independent intraband p±ip superconductors giving way to partial Bogoliubov Fermi surfaces, and allow for the first characterization of key properties of the hybrid superconducting system.}, author = {Phan, Duc T and Senior, Jorden L and Ghazaryan, Areg and Hatefipour, M. and Strickland, W. M. and Shabani, J. and Serbyn, Maksym and Higginbotham, Andrew P}, booktitle = {arXiv}, title = {{Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid}}, year = {2021}, } @misc{9291, abstract = {This .zip File contains the transport data for figures presented in the main text and supplementary material of "Enhancement of Proximity Induced Superconductivity in Planar Germanium" by K. Aggarwal, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).}, author = {Katsaros, Georgios}, publisher = {Institute of Science and Technology Austria}, title = {{Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium}}, doi = {10.15479/AT:ISTA:9291}, year = {2021}, } @misc{9636, author = {Higginbotham, Andrew P}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid"}}, year = {2021}, } @article{8910, abstract = {A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.}, author = {Valentini, Marco and Peñaranda, Fernando and Hofmann, Andrea C and Brauns, Matthias and Hauschild, Robert and Krogstrup, Peter and San-Jose, Pablo and Prada, Elsa and Aguado, Ramón and Katsaros, Georgios}, issn = {10959203}, journal = {Science}, number = {6550}, publisher = {American Association for the Advancement of Science}, title = {{Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states}}, doi = {10.1126/science.abf1513}, volume = {373}, year = {2021}, } @misc{9323, abstract = {This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.}, author = {Jirovec, Daniel}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for "A singlet-triplet hole spin qubit planar Ge"}}, doi = {10.15479/AT:ISTA:9323}, year = {2021}, } @misc{9389, abstract = {This .zip File contains the transport data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states" by M. Valentini, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. Instructions of how to read the data are in "Notebook_Valentini.pdf".}, author = {Valentini, Marco}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states"}}, doi = {10.15479/AT:ISTA:9389}, year = {2021}, } @article{10559, abstract = {Hole gases in planar germanium can have high mobilities in combination with strong spin-orbit interaction and electrically tunable g factors, and are therefore emerging as a promising platform for creating hybrid superconductor-semiconductor devices. A key challenge towards hybrid Ge-based quantum technologies is the design of high-quality interfaces and superconducting contacts that are robust against magnetic fields. In this work, by combining the assets of aluminum, which provides good contact to the Ge, and niobium, which has a significant superconducting gap, we demonstrate highly transparent low-disordered JoFETs with relatively large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.}, author = {Aggarwal, Kushagra and Hofmann, Andrea C and Jirovec, Daniel and Prieto Gonzalez, Ivan and Sammak, Amir and Botifoll, Marc and Martí-Sánchez, Sara and Veldhorst, Menno and Arbiol, Jordi and Scappucci, Giordano and Danon, Jeroen and Katsaros, Georgios}, issn = {2643-1564}, journal = {Physical Review Research}, keywords = {general engineering}, number = {2}, publisher = {American Physical Society}, title = {{Enhancement of proximity-induced superconductivity in a planar Ge hole gas}}, doi = {10.1103/physrevresearch.3.l022005}, volume = {3}, year = {2021}, } @article{10166, abstract = {While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.}, author = {Huylmans, Ann K and Macon, Ariana and Hontoria, Francisco and Vicoso, Beatriz}, issn = {1471-2954}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {asexual reproduction, parthenogenesis, sex-biased genes, sexual conflict, automixis, crustaceans}, number = {1959}, publisher = {The Royal Society}, title = {{Transitions to asexuality and evolution of gene expression in Artemia brine shrimp}}, doi = {10.1098/rspb.2021.1720}, volume = {288}, year = {2021}, } @misc{9192, abstract = {Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document.}, author = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H}, publisher = {Institute of Science and Technology Austria}, title = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}}, doi = {10.15479/AT:ISTA:9192}, year = {2021}, } @misc{9949, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp"}}, doi = {10.15479/AT:ISTA:9949}, year = {2021}, } @article{8997, abstract = {Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.}, author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {Modelling and Simulation, Genetics, Molecular Biology, Antibiotics, Drug interactions}, publisher = {Public Library of Science}, title = {{Minimal biophysical model of combined antibiotic action}}, doi = {10.1371/journal.pcbi.1008529}, volume = {17}, year = {2021}, } @article{9283, abstract = {Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.}, author = {Nagy-Staron, Anna A and Tomasek, Kathrin and Caruso Carter, Caroline and Sonnleitner, Elisabeth and Kavcic, Bor and Paixão, Tiago and Guet, Calin C}, issn = {2050-084X}, journal = {eLife}, keywords = {Genetics and Molecular Biology}, publisher = {eLife Sciences Publications}, title = {{Local genetic context shapes the function of a gene regulatory network}}, doi = {10.7554/elife.65993}, volume = {10}, year = {2021}, } @article{10184, abstract = {We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely automatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.}, author = {Alderighi, Thomas and Malomo, Luigi and Bickel, Bernd and Cignoni, Paolo and Pietroni, Nico}, issn = {1557-7368 }, journal = {ACM Transactions on Graphics}, number = {6}, publisher = {Association for Computing Machinery}, title = {{Volume decomposition for two-piece rigid casting}}, doi = {10.1145/3478513.3480555}, volume = {40}, year = {2021}, } @article{9541, abstract = {The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].}, author = {Czumaj, Artur and Davies, Peter and Parter, Merav}, issn = {1549-6333}, journal = {ACM Transactions on Algorithms}, number = {2}, publisher = {Association for Computing Machinery}, title = {{Graph sparsification for derandomizing massively parallel computation with low space}}, doi = {10.1145/3451992}, volume = {17}, year = {2021}, } @article{10134, abstract = {We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics.}, author = {Suzuki, Fumika and Lemeshko, Mikhail and Zurek, Wojciech H. and Krems, Roman V.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {16}, publisher = {American Physical Society }, title = {{Anderson localization of composite particles}}, doi = {10.1103/physrevlett.127.160602}, volume = {127}, year = {2021}, } @inproceedings{9678, abstract = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.}, author = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara}, booktitle = {Annual ACM Symposium on Parallelism in Algorithms and Architectures}, isbn = {9781450380706}, location = { Virtual Event, United States}, pages = {129--139}, title = {{Efficient load-balancing through distributed token dropping}}, doi = {10.1145/3409964.3461785}, year = {2021}, } @article{8286, abstract = {We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. }, author = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Sabour, Amirmojtaba}, issn = {1432-0541}, journal = {Algorithmica}, location = {Virtual, Online; Germany}, publisher = {Springer Nature}, title = {{Dynamic averaging load balancing on cycles}}, doi = {10.1007/s00453-021-00905-9}, year = {2021}, } @phdthesis{9733, abstract = {This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author.}, author = {Feliciangeli, Dario}, issn = {2663-337X}, pages = {180}, publisher = {Institute of Science and Technology Austria}, title = {{The polaron at strong coupling}}, doi = {10.15479/at:ista:9733}, year = {2021}, } @article{9571, abstract = {As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.}, author = {Ramezani-Kebrya, Ali and Faghri, Fartash and Markov, Ilya and Aksenov, Vitalii and Alistarh, Dan-Adrian and Roy, Daniel M.}, issn = {15337928}, journal = {Journal of Machine Learning Research}, number = {114}, pages = {1−43}, publisher = {Journal of Machine Learning Research}, title = {{NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization}}, volume = {22}, year = {2021}, } @article{8544, abstract = {The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.}, author = {Takeo, Yukari H. and Shuster, S. Andrew and Jiang, Linnie and Hu, Miley and Luginbuhl, David J. and Rülicke, Thomas and Contreras, Ximena and Hippenmeyer, Simon and Wagner, Mark J. and Ganguli, Surya and Luo, Liqun}, issn = {1097-4199}, journal = {Neuron}, number = {4}, pages = {P629--644.E8}, publisher = {Elsevier}, title = {{GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells}}, doi = {10.1016/j.neuron.2020.11.028}, volume = {109}, year = {2021}, } @unpublished{9791, abstract = {We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.}, author = {Feliciangeli, Dario and Rademacher, Simone Anna Elvira and Seiringer, Robert}, booktitle = {arXiv}, title = {{The effective mass problem for the Landau-Pekar equations}}, year = {2021}, } @article{7553, abstract = {Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.}, author = {Mlynarski, Wiktor F and Hledik, Michal and Sokolowski, Thomas R and Tkačik, Gašper}, journal = {Neuron}, number = {7}, pages = {1227--1241.e5}, publisher = {Cell Press}, title = {{Statistical analysis and optimality of neural systems}}, doi = {10.1016/j.neuron.2021.01.020}, volume = {109}, year = {2021}, } @inproceedings{10598, abstract = { We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. }, author = {Mondelli, Marco and Venkataramanan, Ramji}, booktitle = {Proceedings of The 24th International Conference on Artificial Intelligence and Statistics}, editor = {Banerjee, Arindam and Fukumizu, Kenji}, issn = {2640-3498}, location = {Virtual, San Diego, CA, United States}, pages = {397--405}, publisher = {ML Research Press}, title = {{Approximate message passing with spectral initialization for generalized linear models}}, volume = {130}, year = {2021}, } @article{8196, abstract = {This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.}, author = {Shehu, Yekini and Dong, Qiao-Li and Liu, Lu-Lu and Yao, Jen-Chih}, issn = {1573-2924}, journal = {Optimization and Engineering}, pages = {2627--2653}, publisher = {Springer Nature}, title = {{New strong convergence method for the sum of two maximal monotone operators}}, doi = {10.1007/s11081-020-09544-5}, volume = {22}, year = {2021}, } @article{8911, abstract = {In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects toward scalable quantum information processing. }, author = {Scappucci, Giordano and Kloeffel, Christoph and Zwanenburg, Floris A. and Loss, Daniel and Myronov, Maksym and Zhang, Jian-Jun and Franceschi, Silvano De and Katsaros, Georgios and Veldhorst, Menno}, issn = {2058-8437}, journal = {Nature Reviews Materials}, pages = {926–943 }, publisher = {Springer Nature}, title = {{The germanium quantum information route}}, doi = {10.1038/s41578-020-00262-z}, volume = {6}, year = {2021}, }