TY - JOUR AB - Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures. AU - Rzadkowski, Wojciech AU - Defenu, N AU - Chiacchiera, S AU - Trombettoni, A AU - Bighin, Giacomo ID - 8644 IS - 9 JF - New Journal of Physics SN - 13672630 TI - Detecting composite orders in layered models via machine learning VL - 22 ER - TY - JOUR AB - We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model. AU - Mysliwy, Krzysztof AU - Seiringer, Robert ID - 8705 IS - 12 JF - Annales Henri Poincare SN - 1424-0637 TI - Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit VL - 21 ER - TY - JOUR AB - We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance. AU - Nickovic, Dejan AU - Lebeltel, Olivier AU - Maler, Oded AU - Ferrere, Thomas AU - Ulus, Dogan ID - 10861 IS - 6 JF - International Journal on Software Tools for Technology Transfer KW - Information Systems KW - Software SN - 1433-2779 TI - AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic VL - 22 ER - TY - JOUR AB - Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed. Results: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively. AU - Stark, Stefan G AU - Ficek, Joanna AU - Locatello, Francesco AU - Bonilla, Ximena AU - Chevrier, Stéphane AU - Singer, Franziska AU - Aebersold, Rudolf AU - Al-Quaddoomi, Faisal S AU - Albinus, Jonas AU - Alborelli, Ilaria AU - Andani, Sonali AU - Attinger, Per-Olof AU - Bacac, Marina AU - Baumhoer, Daniel AU - Beck-Schimmer, Beatrice AU - Beerenwinkel, Niko AU - Beisel, Christian AU - Bernasconi, Lara AU - Bertolini, Anne AU - Bodenmiller, Bernd AU - Bonilla, Ximena AU - Casanova, Ruben AU - Chevrier, Stéphane AU - Chicherova, Natalia AU - D'Costa, Maya AU - Danenberg, Esther AU - Davidson, Natalie AU - gan, Monica-Andreea Dră AU - Dummer, Reinhard AU - Engler, Stefanie AU - Erkens, Martin AU - Eschbach, Katja AU - Esposito, Cinzia AU - Fedier, André AU - Ferreira, Pedro AU - Ficek, Joanna AU - Frei, Anja L AU - Frey, Bruno AU - Goetze, Sandra AU - Grob, Linda AU - Gut, Gabriele AU - Günther, Detlef AU - Haberecker, Martina AU - Haeuptle, Pirmin AU - Heinzelmann-Schwarz, Viola AU - Herter, Sylvia AU - Holtackers, Rene AU - Huesser, Tamara AU - Irmisch, Anja AU - Jacob, Francis AU - Jacobs, Andrea AU - Jaeger, Tim M AU - Jahn, Katharina AU - James, Alva R AU - Jermann, Philip M AU - Kahles, André AU - Kahraman, Abdullah AU - Koelzer, Viktor H AU - Kuebler, Werner AU - Kuipers, Jack AU - Kunze, Christian P AU - Kurzeder, Christian AU - Lehmann, Kjong-Van AU - Levesque, Mitchell AU - Lugert, Sebastian AU - Maass, Gerd AU - Manz, Markus AU - Markolin, Philipp AU - Mena, Julien AU - Menzel, Ulrike AU - Metzler, Julian M AU - Miglino, Nicola AU - Milani, Emanuela S AU - Moch, Holger AU - Muenst, Simone AU - Murri, Riccardo AU - Ng, Charlotte KY AU - Nicolet, Stefan AU - Nowak, Marta AU - Pedrioli, Patrick GA AU - Pelkmans, Lucas AU - Piscuoglio, Salvatore AU - Prummer, Michael AU - Ritter, Mathilde AU - Rommel, Christian AU - Rosano-González, María L AU - Rätsch, Gunnar AU - Santacroce, Natascha AU - Castillo, Jacobo Sarabia del AU - Schlenker, Ramona AU - Schwalie, Petra C AU - Schwan, Severin AU - Schär, Tobias AU - Senti, Gabriela AU - Singer, Franziska AU - Sivapatham, Sujana AU - Snijder, Berend AU - Sobottka, Bettina AU - Sreedharan, Vipin T AU - Stark, Stefan AU - Stekhoven, Daniel J AU - Theocharides, Alexandre PA AU - Thomas, Tinu M AU - Tolnay, Markus AU - Tosevski, Vinko AU - Toussaint, Nora C AU - Tuncel, Mustafa A AU - Tusup, Marina AU - Drogen, Audrey Van AU - Vetter, Marcus AU - Vlajnic, Tatjana AU - Weber, Sandra AU - Weber, Walter P AU - Wegmann, Rebekka AU - Weller, Michael AU - Wendt, Fabian AU - Wey, Norbert AU - Wicki, Andreas AU - Wollscheid, Bernd AU - Yu, Shuqing AU - Ziegler, Johanna AU - Zimmermann, Marc AU - Zoche, Martin AU - Zuend, Gregor AU - Rätsch, Gunnar AU - Lehmann, Kjong-Van ID - 14125 IS - Supplement_2 JF - Bioinformatics KW - Computational Mathematics KW - Computational Theory and Mathematics KW - Computer Science Applications KW - Molecular Biology KW - Biochemistry KW - Statistics and Probability TI - SCIM: Universal single-cell matching with unpaired feature sets VL - 36 ER - TY - CONF AB - The goal of the unsupervised learning of disentangled representations is to separate the independent explanatory factors of variation in the data without access to supervision. In this paper, we summarize the results of Locatello et al., 2019, and focus on their implications for practitioners. We discuss the theoretical result showing that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases and the practical challenges it entails. Finally, we comment on our experimental findings, highlighting the limitations of state-of-the-art approaches and directions for future research. AU - Locatello, Francesco AU - Bauer, Stefan AU - Lucic, Mario AU - Rätsch, Gunnar AU - Gelly, Sylvain AU - Schölkopf, Bernhard AU - Bachem, Olivier ID - 14186 IS - 9 SN - 9781577358350 T2 - The 34th AAAI Conference on Artificial Intelligence TI - A commentary on the unsupervised learning of disentangled representations VL - 34 ER - TY - CONF AB - Intelligent agents should be able to learn useful representations by observing changes in their environment. We model such observations as pairs of non-i.i.d. images sharing at least one of the underlying factors of variation. First, we theoretically show that only knowing how many factors have changed, but not which ones, is sufficient to learn disentangled representations. Second, we provide practical algorithms that learn disentangled representations from pairs of images without requiring annotation of groups, individual factors, or the number of factors that have changed. Third, we perform a large-scale empirical study and show that such pairs of observations are sufficient to reliably learn disentangled representations on several benchmark data sets. Finally, we evaluate our learned representations and find that they are simultaneously useful on a diverse suite of tasks, including generalization under covariate shifts, fairness, and abstract reasoning. Overall, our results demonstrate that weak supervision enables learning of useful disentangled representations in realistic scenarios. AU - Locatello, Francesco AU - Poole, Ben AU - Rätsch, Gunnar AU - Schölkopf, Bernhard AU - Bachem, Olivier AU - Tschannen, Michael ID - 14188 T2 - Proceedings of the 37th International Conference on Machine Learning TI - Weakly-supervised disentanglement without compromises VL - 119 ER - TY - CONF AB - We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient) algorithm for constrained smooth finite-sum minimization with a generalized linear prediction/structure. This class of problems includes empirical risk minimization with sparse, low-rank, or other structured constraints. The proposed method is simple to implement, does not require step-size tuning, and has a constant per-iteration cost that is independent of the dataset size. Furthermore, as a byproduct of the method we obtain a stochastic estimator of the Frank-Wolfe gap that can be used as a stopping criterion. Depending on the setting, the proposed method matches or improves on the best computational guarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several datasets highlight different regimes in which the proposed method exhibits a faster empirical convergence than related methods. Finally, we provide an implementation of all considered methods in an open-source package. AU - Négiar, Geoffrey AU - Dresdner, Gideon AU - Tsai, Alicia AU - Ghaoui, Laurent El AU - Locatello, Francesco AU - Freund, Robert M. AU - Pedregosa, Fabian ID - 14187 T2 - Proceedings of the 37th International Conference on Machine Learning TI - Stochastic Frank-Wolfe for constrained finite-sum minimization VL - 119 ER - TY - JOUR AB - The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000 models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets. AU - Locatello, Francesco AU - Bauer, Stefan AU - Lucic, Mario AU - Rätsch, Gunnar AU - Gelly, Sylvain AU - Schölkopf, Bernhard AU - Bachem, Olivier ID - 14195 JF - Journal of Machine Learning Research TI - A sober look at the unsupervised learning of disentangled representations and their evaluation VL - 21 ER - TY - JOUR AB - Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models. AU - Grah, Rok AU - Friedlander, Tamar ID - 7569 IS - 2 JF - PLOS Computational Biology SN - 1553-7358 TI - The relation between crosstalk and gene regulation form revisited VL - 16 ER - TY - GEN AB - In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation. AU - Santini, Laura AU - Halbritter, Florian AU - Titz-Teixeira, Fabian AU - Suzuki, Toru AU - Asami, Maki AU - Ramesmayer, Julia AU - Ma, Xiaoyan AU - Lackner, Andreas AU - Warr, Nick AU - Pauler, Florian AU - Hippenmeyer, Simon AU - Laue, Ernest AU - Farlik, Matthias AU - Bock, Christoph AU - Beyer, Andreas AU - Perry, Anthony C. F. AU - Leeb, Martin ID - 8813 T2 - bioRxiv TI - Novel imprints in mouse blastocysts are predominantly DNA methylation independent ER - TY - GEN AU - Grah, Rok AU - Friedlander, Tamar ID - 9777 TI - Maximizing crosstalk ER - TY - THES AB - Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks. In a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning. In a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. Our approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step. AU - Kragl, Bernhard ID - 8332 SN - 2663-337X TI - Verifying concurrent programs: Refinement, synchronization, sequentialization ER - TY - CONF AB - Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks. AU - Locatello, Francesco AU - Weissenborn, Dirk AU - Unterthiner, Thomas AU - Mahendran, Aravindh AU - Heigold, Georg AU - Uszkoreit, Jakob AU - Dosovitskiy, Alexey AU - Kipf, Thomas ID - 14326 SN - 9781713829546 T2 - Advances in Neural Information Processing Systems TI - Object-centric learning with slot attention VL - 33 ER - TY - JOUR AB - We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric. AU - Gladbach, Peter AU - Kopfer, Eva AU - Maas, Jan ID - 71 IS - 3 JF - SIAM Journal on Mathematical Analysis SN - 00361410 TI - Scaling limits of discrete optimal transport VL - 52 ER - TY - JOUR AB - We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms. AU - Hikaru, Ibayashi AU - Wojtan, Christopher J AU - Thuerey, Nils AU - Igarashi, Takeo AU - Ando, Ryoichi ID - 5681 IS - 6 JF - IEEE Transactions on Visualization and Computer Graphics SN - 10772626 TI - Simulating liquids on dynamically warping grids VL - 26 ER - TY - THES AB - The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment. In this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath. With this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. For the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules. AU - Li, Xiang ID - 8958 SN - 2663-337X TI - Rotation of coupled cold molecules in the presence of a many-body environment ER - TY - THES AB - Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical quantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures— our design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints were taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting. AU - Zhang, Ran ID - 8386 SN - 2663-337X TI - Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability ER - TY - THES AB - Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization. Here we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element resonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity. AU - Kukucka, Josip ID - 7996 SN - 2663-337X TI - Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing ER - TY - CONF AB - We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies. AU - Chatterjee, Krishnendu AU - Katoen, Joost P AU - Weininger, Maximilian AU - Winkler, Tobias ID - 8272 SN - 03029743 T2 - International Conference on Computer Aided Verification TI - Stochastic games with lexicographic reachability-safety objectives VL - 12225 ER - TY - CHAP AB - The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material. AU - Dos Santos Caldas, Paulo R AU - Radler, Philipp AU - Sommer, Christoph M AU - Loose, Martin ED - Tran, Phong ID - 7572 SN - 0091679X T2 - Methods in Cell Biology TI - Computational analysis of filament polymerization dynamics in cytoskeletal networks VL - 158 ER - TY - JOUR AB - Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site. AU - Baranova, Natalia S. AU - Radler, Philipp AU - Hernández-Rocamora, Víctor M. AU - Alfonso, Carlos AU - Lopez Pelegrin, Maria D AU - Rivas, Germán AU - Vollmer, Waldemar AU - Loose, Martin ID - 7387 JF - Nature Microbiology SN - 2058-5276 TI - Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins VL - 5 ER - TY - JOUR AB - Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces. AU - Vegter, Gert AU - Wintraecken, Mathijs ID - 8163 IS - 2 JF - Studia Scientiarum Mathematicarum Hungarica SN - 0081-6906 TI - Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes VL - 57 ER - TY - JOUR AB - We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. AU - Shakiba, A. AU - Goharshady, Amir Kafshdar AU - Hooshmandasl, M.R. AU - Alambardar Meybodi, M. ID - 8671 IS - 2 JF - Iranian Journal of Mathematical Sciences and Informatics SN - 1735-4463 TI - A note on belief structures and s-approximation spaces VL - 15 ER - TY - JOUR AB - The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients. AU - Dareiotis, Konstantinos AU - Gerencser, Mate ID - 6359 JF - Electronic Journal of Probability TI - On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift VL - 25 ER - TY - THES AB - Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction for tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually dissimilar domains. AU - Royer, Amélie ID - 8390 SN - 2663-337X TI - Leveraging structure in Computer Vision tasks for flexible Deep Learning models ER - TY - CONF AB - Numerous methods have been proposed for probabilistic generative modelling of 3D objects. However, none of these is able to produce textured objects, which renders them of limited use for practical tasks. In this work, we present the first generative model of textured 3D meshes. Training such a model would traditionally require a large dataset of textured meshes, but unfortunately, existing datasets of meshes lack detailed textures. We instead propose a new training methodology that allows learning from collections of 2D images without any 3D information. To do so, we train our model to explain a distribution of images by modelling each image as a 3D foreground object placed in front of a 2D background. Thus, it learns to generate meshes that when rendered, produce images similar to those in its training set. A well-known problem when generating meshes with deep networks is the emergence of self-intersections, which are problematic for many use-cases. As a second contribution we therefore introduce a new generation process for 3D meshes that guarantees no self-intersections arise, based on the physical intuition that faces should push one another out of the way as they move. We conduct extensive experiments on our approach, reporting quantitative and qualitative results on both synthetic data and natural images. These show our method successfully learns to generate plausible and diverse textured 3D samples for five challenging object classes. AU - Henderson, Paul M AU - Tsiminaki, Vagia AU - Lampert, Christoph ID - 8186 T2 - Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition TI - Leveraging 2D data to learn textured 3D mesh generation ER - TY - JOUR AB - Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements. AU - Sinclair, Scott A AU - Krämer, U. ID - 7416 IS - 1 JF - Plant Signaling & Behavior SN - 1559-2324 TI - Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation VL - 15 ER - TY - JOUR AB - In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces. AU - Hensel, Sebastian AU - Rosati, Tommaso ID - 9196 IS - 3 JF - Studia Mathematica KW - General Mathematics SN - 0039-3223 TI - Modelled distributions of Triebel–Lizorkin type VL - 252 ER - TY - JOUR AB - Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly. AU - Dick, Robert A. AU - Xu, Chaoyi AU - Morado, Dustin R. AU - Kravchuk, Vladyslav AU - Ricana, Clifton L. AU - Lyddon, Terri D. AU - Broad, Arianna M. AU - Feathers, J. Ryan AU - Johnson, Marc C. AU - Vogt, Volker M. AU - Perilla, Juan R. AU - Briggs, John A. G. AU - Schur, Florian KM ID - 7464 IS - 1 JF - PLOS Pathogens SN - 1553-7374 TI - Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly VL - 16 ER - TY - JOUR AB - The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process. AU - Tkadlec, Josef AU - Pavlogiannis, Andreas AU - Chatterjee, Krishnendu AU - Nowak, Martin A. ID - 7212 JF - PLoS computational biology TI - Limits on amplifiers of natural selection under death-Birth updating VL - 16 ER - TY - THES AB - In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time. AU - Tkadlec, Josef ID - 7196 TI - A role of graphs in evolutionary processes ER - TY - CONF AB - The optimization of multilayer neural networks typically leads to a solution with zero training error, yet the landscape can exhibit spurious local minima and the minima can be disconnected. In this paper, we shed light on this phenomenon: we show that the combination of stochastic gradient descent (SGD) and over-parameterization makes the landscape of multilayer neural networks approximately connected and thus more favorable to optimization. More specifically, we prove that SGD solutions are connected via a piecewise linear path, and the increase in loss along this path vanishes as the number of neurons grows large. This result is a consequence of the fact that the parameters found by SGD are increasingly dropout stable as the network becomes wider. We show that, if we remove part of the neurons (and suitably rescale the remaining ones), the change in loss is independent of the total number of neurons, and it depends only on how many neurons are left. Our results exhibit a mild dependence on the input dimension: they are dimension-free for two-layer networks and depend linearly on the dimension for multilayer networks. We validate our theoretical findings with numerical experiments for different architectures and classification tasks. AU - Shevchenko, Alexander AU - Mondelli, Marco ID - 9198 T2 - Proceedings of the 37th International Conference on Machine Learning TI - Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks VL - 119 ER - TY - JOUR AB - Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy. AU - Akopyan, Arseniy AU - Edelsbrunner, Herbert ID - 9157 IS - 1 JF - Computational and Mathematical Biophysics SN - 2544-7297 TI - The weighted mean curvature derivative of a space-filling diagram VL - 8 ER - TY - JOUR AB - The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy. AU - Akopyan, Arseniy AU - Edelsbrunner, Herbert ID - 9156 IS - 1 JF - Computational and Mathematical Biophysics SN - 2544-7297 TI - The weighted Gaussian curvature derivative of a space-filling diagram VL - 8 ER - TY - JOUR AB - We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity. AU - Redig, Frank AU - Saada, Ellen AU - Sau, Federico ID - 8973 JF - Electronic Journal of Probability TI - Symmetric simple exclusion process in dynamic environment: Hydrodynamics VL - 25 ER - TY - JOUR AB - An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed. AU - Browning, Timothy D AU - Heath Brown, Roger ID - 179 IS - 16 JF - Duke Mathematical Journal SN - 0012-7094 TI - Density of rational points on a quadric bundle in ℙ3×ℙ3 VL - 169 ER - TY - GEN AB - Data and mathematica notebooks for plotting figures from Language learning with communication between learners AU - Ibsen-Jensen, Rasmus AU - Tkadlec, Josef AU - Chatterjee, Krishnendu AU - Nowak, Martin ID - 9814 TI - Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners ER - TY - JOUR AB - We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively. AU - Malia, Benjamin K. AU - Martínez-Rincón, Julián AU - Wu, Yunfan AU - Hosten, Onur AU - Kasevich, Mark A. ID - 8285 IS - 4 JF - Physical Review Letters SN - 0031-9007 TI - Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit VL - 125 ER - TY - CONF AB - We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient. AU - Lambert, Nicholas J. AU - Mobassem, Sonia AU - Rueda Sanchez, Alfredo R AU - Schwefel, Harald G.L. ID - 10328 SN - 9-781-5575-2820-9 T2 - OSA Quantum 2.0 Conference TI - New designs and noise channels in electro-optic microwave to optical up-conversion ER - TY - CONF AB - The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions. AU - Confavreux, Basile J AU - Zenke, Friedemann AU - Agnes, Everton J. AU - Lillicrap, Timothy AU - Vogels, Tim P ID - 9633 SN - 1049-5258 T2 - Advances in Neural Information Processing Systems TI - A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network VL - 33 ER - TY - JOUR AB - The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds. AU - Tan, Shutang AU - Di Donato, Martin AU - Glanc, Matous AU - Zhang, Xixi AU - Klíma, Petr AU - Liu, Jie AU - Bailly, Aurélien AU - Ferro, Noel AU - Petrášek, Jan AU - Geisler, Markus AU - Friml, Jiří ID - 8943 IS - 9 JF - Cell Reports TI - Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development VL - 33 ER - TY - JOUR AB - Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer. AU - Xu, Duo AU - Varshney, Atul AU - Ma, Xingyu AU - Song, Baofang AU - Riedl, Michael AU - Avila, Marc AU - Hof, Björn ID - 7932 IS - 21 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 00278424 TI - Nonlinear hydrodynamic instability and turbulence in pulsatile flow VL - 117 ER - TY - JOUR AB - We study the unique solution m of the Dyson equation \( -m(z)^{-1} = z\1 - a + S[m(z)] \) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases. AU - Alt, Johannes AU - Erdös, László AU - Krüger, Torben H ID - 14694 JF - Documenta Mathematica KW - General Mathematics SN - 1431-0635 TI - The Dyson equation with linear self-energy: Spectral bands, edges and cusps VL - 25 ER - TY - THES AB - We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry. AU - Avvakumov, Sergey ID - 8156 SN - 2663-337X TI - Topological methods in geometry and discrete mathematics ER - TY - JOUR AB - We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space. AU - Lewin, Mathieu AU - Lieb, Elliott H. AU - Seiringer, Robert ID - 14891 IS - 1 JF - Pure and Applied Analysis SN - 2578-5893 TI - The local density approximation in density functional theory VL - 2 ER - TY - JOUR AB - Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord. AU - Salamatina, Alina AU - Yang, Jerry H AU - Brenner-Morton, Susan AU - Bikoff, Jay B AU - Fang, Linjing AU - Kintner, Christopher R AU - Jessell, Thomas M AU - Sweeney, Lora Beatrice Jaeger ID - 8914 JF - Neuroscience SN - 0306-4522 TI - Differential loss of spinal interneurons in a mouse model of ALS VL - 450 ER - TY - DATA AB - This data collection contains the transport data for figures presented in the 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). AU - Katsaros, Georgios ID - 8834 TI - Enhancement of proximity induced superconductivity in planar Germanium ER - TY - DATA AB - Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology. AU - Kavcic, Bor ID - 8097 KW - Escherichia coli KW - antibiotic combinations KW - translation KW - growth laws KW - drug interactions KW - bacterial physiology KW - translation inhibitors TI - Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics" ER - TY - DATA AB - Here are the research data underlying the publication "Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)". Further information are summed up in the README document. The files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192. AU - Arathoon, Louise S ID - 8254 TI - Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus) ER - TY - JOUR AB - Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon. AU - Gao, Fei AU - Wang, Jian-Huan AU - Watzinger, Hannes AU - Hu, Hao AU - Rančić, Marko J. AU - Zhang, Jie-Yin AU - Wang, Ting AU - Yao, Yuan AU - Wang, Gui-Lei AU - Kukucka, Josip AU - Vukušić, Lada AU - Kloeffel, Christoph AU - Loss, Daniel AU - Liu, Feng AU - Katsaros, Georgios AU - Zhang, Jian-Jun ID - 7541 IS - 16 JF - Advanced Materials SN - 0935-9648 TI - Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling VL - 32 ER -