@article{13315, abstract = {How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.}, author = {Barbier, Jean and Camilli, Francesco and Mondelli, Marco and Sáenz, Manuel}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {30}, publisher = {National Academy of Sciences}, title = {{Fundamental limits in structured principal component analysis and how to reach them}}, doi = {10.1073/pnas.2302028120}, volume = {120}, year = {2023}, } @article{14037, abstract = {Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.}, author = {Vardi, Ofek and Maroudas-Sklare, Naama and Kolodny, Yuval and Volosniev, Artem and Saragovi, Amijai and Galili, Nir and Ferrera, Stav and Ghazaryan, Areg and Yuran, Nir and Affek, Hagit P. and Luz, Boaz and Goldsmith, Yonaton and Keren, Nir and Yochelis, Shira and Halevy, Itay and Lemeshko, Mikhail and Paltiel, Yossi}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {32}, publisher = {National Academy of Sciences}, title = {{Nuclear spin effects in biological processes}}, doi = {10.1073/pnas.2300828120}, volume = {120}, year = {2023}, } @article{12683, abstract = {We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.}, author = {Dubach, Guillaume and Erdös, László}, issn = {1083-589X}, journal = {Electronic Communications in Probability}, pages = {1--13}, publisher = {Institute of Mathematical Statistics}, title = {{Dynamics of a rank-one perturbation of a Hermitian matrix}}, doi = {10.1214/23-ECP516}, volume = {28}, year = {2023}, } @article{12761, abstract = {We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine the fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent multiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {1050-5164}, journal = {Annals of Applied Probability}, number = {1}, pages = {447--489}, publisher = {Institute of Mathematical Statistics}, title = {{Functional central limit theorems for Wigner matrices}}, doi = {10.1214/22-AAP1820}, volume = {33}, year = {2023}, } @article{8682, abstract = {It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.}, author = {Browning, Timothy D and Boudec, Pierre Le and Sawin, Will}, issn = {0003-486X}, journal = {Annals of Mathematics}, number = {3}, pages = {1115--1203}, publisher = {Princeton University}, title = {{The Hasse principle for random Fano hypersurfaces}}, doi = {10.4007/annals.2023.197.3.3}, volume = {197}, year = {2023}, } @article{12706, abstract = {Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.}, author = {Mckerral, Jody C. and Kleshnina, Maria and Ejov, Vladimir and Bartle, Louise and Mitchell, James G. and Filar, Jerzy A.}, issn = {1932-6203}, journal = {PLoS One}, number = {2}, pages = {e0279838}, publisher = {Public Library of Science}, title = {{Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations}}, doi = {10.1371/journal.pone.0279838}, volume = {18}, year = {2023}, } @article{13202, abstract = {Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons.}, author = {Eguchi, Kohgaku and Le Monnier, Elodie and Shigemoto, Ryuichi}, issn = {1529-2401}, journal = {The Journal of Neuroscience}, number = {23}, pages = {4197--4216}, publisher = {Society for Neuroscience}, title = {{Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons}}, doi = {10.1523/JNEUROSCI.1514-22.2023}, volume = {43}, year = {2023}, } @article{12916, abstract = {We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface. }, author = {Bonolis, Dante and Browning, Timothy D}, issn = {2036-2145}, journal = {Annali della Scuola Normale Superiore di Pisa - Classe di Scienze}, number = {1}, pages = {173--204}, publisher = {Scuola Normale Superiore - Edizioni della Normale}, title = {{Uniform bounds for rational points on hyperelliptic fibrations}}, doi = {10.2422/2036-2145.202010_018}, volume = {24}, year = {2023}, } @phdthesis{14422, abstract = {Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of changes in the brain throughout adulthood, regrouped under the term "plasticity". Some cells in the brain —neurons— and specifically changes in the connections between neurons, the synapses, were shown to be crucial for the formation, selection, and consolidation of memories from past experiences. These ongoing changes of synapses across time are called synaptic plasticity. Understanding how a myriad of biochemical processes operating at individual synapses can somehow work in concert to give rise to meaningful changes in behavior is a fascinating problem and an active area of research. However, the experimental search for the precise plasticity mechanisms at play in the brain is daunting, as it is difficult to control and observe synapses during learning. Theoretical approaches have thus been the default method to probe the plasticity-behavior connection. Such studies attempt to extract unifying principles across synapses and model all observed synaptic changes using plasticity rules: equations that govern the evolution of synaptic strengths across time in neuronal network models. These rules can use many relevant quantities to determine the magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic action potentials, the recent neuronal activity levels, the state of neighboring synapses, etc. However, analytical studies rely heavily on human intuition and are forced to make simplifying assumptions about plasticity rules. In this thesis, we aim to assist and augment human intuition in this search for plasticity rules. We explore whether a numerical approach could automatically discover the plasticity rules that elicit desired behaviors in large networks of interconnected neurons. This approach is dubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make neuronal networks learn how to solve a desired task. We first write all the potential plasticity mechanisms to consider using a single expression with adjustable parameters. We then optimize these plasticity parameters using evolutionary strategies or Bayesian inference on tasks known to involve synaptic plasticity, such as familiarity detection and network stabilization. We show that these automated approaches are powerful tools, able to complement established analytical methods. By comprehensively screening plasticity rules at all synapse types in realistic, spiking neuronal network models, we discover entire sets of degenerate plausible plasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more robust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity rules, and provide fresh insights on synaptic plasticity in spiking network models. }, author = {Confavreux, Basile J}, issn = {2663 - 337X}, pages = {148}, publisher = {Institute of Science and Technology Austria}, title = {{Synapseek: Meta-learning synaptic plasticity rules}}, doi = {10.15479/at:ista:14422}, year = {2023}, } @phdthesis{14374, abstract = {Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary. BCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries. For Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary. Second, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality. In the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.}, author = {Roos, Barbara}, issn = {2663 - 337X}, pages = {206}, publisher = {Institute of Science and Technology Austria}, title = {{Boundary superconductivity in BCS theory}}, doi = {10.15479/at:ista:14374}, year = {2023}, } @article{13207, abstract = {We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity.}, author = {Hainzl, Christian and Roos, Barbara and Seiringer, Robert}, issn = {1664-0403}, journal = {Journal of Spectral Theory}, number = {4}, pages = {1507–1540}, publisher = {EMS Press}, title = {{Boundary superconductivity in the BCS model}}, doi = {10.4171/JST/439}, volume = {12}, year = {2023}, } @article{14452, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√⁠. We illustrate our results with some numerical examples.}, author = {Barton, Nicholas H and Etheridge, Alison M. and Véber, Amandine}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Oxford Academic}, title = {{The infinitesimal model with dominance}}, doi = {10.1093/genetics/iyad133}, volume = {225}, year = {2023}, } @misc{12949, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, } @inproceedings{14461, abstract = {Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.}, author = {Markov, Ilia and Vladu, Adrian and Guo, Qi and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {24020--24044}, publisher = {ML Research Press}, title = {{Quantized distributed training of large models with convergence guarantees}}, volume = {202}, year = {2023}, } @inproceedings{14462, abstract = {We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount . Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error.}, author = {Fichtenberger, Hendrik and Henzinger, Monika H and Upadhyay, Jalaj}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {10072--10092}, publisher = {ML Research Press}, title = {{Constant matters: Fine-grained error bound on differentially private continual observation}}, volume = {202}, year = {2023}, } @inproceedings{14459, abstract = {Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.}, author = {Shevchenko, Aleksandr and Kögler, Kevin and Hassani, Hamed and Mondelli, Marco}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {31151--31209}, publisher = {ML Research Press}, title = {{Fundamental limits of two-layer autoencoders, and achieving them with gradient methods}}, volume = {202}, year = {2023}, } @inproceedings{14460, abstract = {We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware.}, author = {Nikdan, Mahdi and Pegolotti, Tommaso and Iofinova, Eugenia B and Kurtic, Eldar and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {26215--26227}, publisher = {ML Research Press}, title = {{SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge}}, volume = {202}, year = {2023}, } @inproceedings{14457, abstract = {Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n). In this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise. }, author = {Hoffmann, Charlotte and Simkin, Mark}, booktitle = {8th International Conference on Cryptology and Information Security in Latin America}, isbn = {9783031444685}, issn = {1611-3349}, location = {Quito, Ecuador}, pages = {215--228}, publisher = {Springer Nature}, title = {{Stronger lower bounds for leakage-resilient secret sharing}}, doi = {10.1007/978-3-031-44469-2_11}, volume = {14168}, year = {2023}, } @inproceedings{14458, abstract = {We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.}, author = {Frantar, Elias and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, issn = {2640-3498}, location = {Honolulu, Hawaii, HI, United States}, pages = {10323--10337}, publisher = {ML Research Press}, title = {{SparseGPT: Massive language models can be accurately pruned in one-shot}}, volume = {202}, year = {2023}, } @article{14451, abstract = {We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.}, author = {Cornalba, Federico and Disselkamp, Constantin and Scassola, Davide and Helf, Christopher}, issn = {1433-3058}, journal = {Neural Computing and Applications}, publisher = {Springer Nature}, title = {{Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading}}, doi = {10.1007/s00521-023-09033-7}, year = {2023}, } @article{14442, abstract = {In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter.}, author = {Rojas Vega, Mauricio Nicolas and De Castro, Pablo and Soto, Rodrigo}, issn = {1292-895X}, journal = {The European Physical Journal E}, number = {10}, publisher = {Springer Nature}, title = {{Mixtures of self-propelled particles interacting with asymmetric obstacles}}, doi = {10.1140/epje/s10189-023-00354-y}, volume = {46}, year = {2023}, } @article{14444, abstract = {We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare) is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN , where N is the number of intercalates in a uniformly random order- n Latin square. In fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2)) and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)). Finally, as an application of some new general tools for studying substructures in random Latin squares, we show that in almost all order- n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices with the same arrangement of symbols) is of order n4, which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring ``how associative'' the quasigroup associated with the Latin square is.}, author = {Kwan, Matthew Alan and Sah, Ashwin and Sawhney, Mehtaab and Simkin, Michael}, issn = {1565-8511}, journal = {Israel Journal of Mathematics}, number = {2}, pages = {363--416}, publisher = {Springer Nature}, title = {{Substructures in Latin squares}}, doi = {10.1007/s11856-023-2513-9}, volume = {256}, year = {2023}, } @inproceedings{14454, abstract = {As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples.}, author = {Henzinger, Thomas A and Kueffner, Konstantin and Mallik, Kaushik}, booktitle = {23rd International Conference on Runtime Verification}, isbn = {9783031442667}, issn = {1611-3349}, location = {Thessaloniki, Greece}, pages = {291--311}, publisher = {Springer Nature}, title = {{Monitoring algorithmic fairness under partial observations}}, doi = {10.1007/978-3-031-44267-4_15}, volume = {14245}, year = {2023}, } @article{14446, abstract = {Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal.}, author = {Jakubík, Jozef and Bui Thi Mai, Phuong and Chvosteková, Martina and Krakovská, Anna}, issn = {1335-8871}, journal = {Measurement Science Review}, number = {4}, pages = {175--183}, publisher = {Sciendo}, title = {{Against the flow of time with multi-output models}}, doi = {10.2478/msr-2023-0023}, volume = {23}, year = {2023}, } @article{14443, abstract = {Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known. Observations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse. Conclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness.}, author = {Schumann, Gunter and Andreassen, Ole A. and Banaschewski, Tobias and Calhoun, Vince D. and Clinton, Nicholas and Desrivieres, Sylvane and Brandlistuen, Ragnhild Eek and Feng, Jianfeng and Hese, Soeren and Hitchen, Esther and Hoffmann, Per and Jia, Tianye and Jirsa, Viktor and Marquand, Andre F. and Nees, Frauke and Nöthen, Markus M. and Novarino, Gaia and Polemiti, Elli and Ralser, Markus and Rapp, Michael and Schepanski, Kerstin and Schikowski, Tamara and Slater, Mel and Sommer, Peter and Stahl, Bernd Carsten and Thompson, Paul M. and Twardziok, Sven and Van Der Meer, Dennis and Walter, Henrik and Westlye, Lars}, issn = {2168-6238}, journal = {JAMA Psychiatry}, number = {10}, pages = {1066--1074}, publisher = {American Medical Association}, title = {{Addressing global environmental challenges to mental health using population neuroscience: A review}}, doi = {10.1001/jamapsychiatry.2023.2996}, volume = {80}, year = {2023}, } @article{14441, abstract = {We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation.}, author = {Brooks, Morris and Seiringer, Robert}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {287--337}, publisher = {Springer Nature}, title = {{The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy}}, doi = {10.1007/s00220-023-04841-3}, volume = {404}, year = {2023}, } @inproceedings{14448, abstract = {We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.}, author = {Kolmogorov, Vladimir}, booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, isbn = {9798350301298}, issn = {1063-6919}, location = {Vancouver, Canada}, pages = {11980--11989}, publisher = {IEEE}, title = {{Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions}}, doi = {10.1109/CVPR52729.2023.01153}, volume = {2023}, year = {2023}, } @article{12672, abstract = {Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.}, author = {Lyons, David B. and Briffa, Amy and He, Shengbo and Choi, Jaemyung and Hollwey, Elizabeth and Colicchio, Jack and Anderson, Ian and Feng, Xiaoqi and Howard, Martin and Zilberman, Daniel}, issn = {2211-1247}, journal = {Cell Reports}, number = {3}, publisher = {Elsevier}, title = {{Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons}}, doi = {10.1016/j.celrep.2023.112132}, volume = {42}, year = {2023}, } @article{13178, abstract = {We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.}, author = {Mitrouskas, David Johannes and Mysliwy, Krzysztof and Seiringer, Robert}, issn = {2050-5094}, journal = {Forum of Mathematics}, pages = {1--52}, publisher = {Cambridge University Press}, title = {{Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron}}, doi = {10.1017/fms.2023.45}, volume = {11}, year = {2023}, } @article{14484, abstract = {Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling.}, author = {Kicheva, Anna and Briscoe, James}, issn = {1530-8995}, journal = {Annual Review of Cell and Developmental Biology}, pages = {91--121}, publisher = {Annual Reviews}, title = {{Control of tissue development by morphogens}}, doi = {10.1146/annurev-cellbio-020823-011522}, volume = {39}, year = {2023}, } @article{14488, abstract = {Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.}, author = {Rao, Pramod and Mallikarjun, B. R. and Fox, Gereon and Weyrich, Tim and Bickel, Bernd and Pfister, Hanspeter and Matusik, Wojciech and Zhan, Fangneng and Tewari, Ayush and Theobalt, Christian and Elgharib, Mohamed}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, publisher = {Springer Nature}, title = {{A deeper analysis of volumetric relightiable faces}}, doi = {10.1007/s11263-023-01899-3}, year = {2023}, } @article{14487, abstract = {High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified.}, author = {Buri, Pascal and Fatichi, Simone and Shaw, Thomas and Miles, Evan S. and Mccarthy, Michael and Fyffe, Catriona Louise and Fugger, Stefan and Ren, Shaoting and Kneib, Marin and Jouberton, Achille and Steiner, Jakob and Fujita, Koji and Pellicciotti, Francesca}, issn = {1944-7973}, journal = {Water Resources Research}, number = {10}, publisher = {Wiley}, title = {{Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment}}, doi = {10.1029/2022WR033841}, volume = {59}, year = {2023}, } @inproceedings{14485, abstract = {Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching. In this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct "data" and "index" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is "close" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.}, author = {Aksenov, Vitaly and Anoprenko, Michael and Fedorov, Alexander and Spear, Michael}, booktitle = {37th International Symposium on Distributed Computing}, isbn = {9783959773010}, issn = {1868-8969}, location = {L'Aquila, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Brief announcement: BatchBoost: Universal batching for concurrent data structures}}, doi = {10.4230/LIPIcs.DISC.2023.35}, volume = {281}, year = {2023}, } @article{14486, abstract = {We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites.}, author = {Koutentakis, Georgios and Ghazaryan, Areg and Lemeshko, Mikhail}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Rotor lattice model of ferroelectric large polarons}}, doi = {10.1103/PhysRevResearch.5.043016}, volume = {5}, year = {2023}, } @article{14313, abstract = {To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.}, author = {Fiedler, Lukas and Friml, Jiří}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, number = {10}, publisher = {Elsevier}, title = {{Rapid auxin signaling: Unknowns old and new}}, doi = {10.1016/j.pbi.2023.102443}, volume = {75}, year = {2023}, } @misc{14494, abstract = {We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023). Buri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841}, author = {Buri, Pascal and Fatichi, Simone and Shaw, Thomas and Miles, Evan and McCarthy, Michael and Fyffe, Catriona Louise and Fugger, Stefan and Ren, Shaoting and Kneib, Marin and Jouberton, Achille and Steiner, Jakob and Fujita, Koji and Pellicciotti, Francesca}, publisher = {Zenodo}, title = {{Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"}}, doi = {10.5281/ZENODO.8402426}, year = {2023}, } @article{14499, abstract = {An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables. The proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes.}, author = {Kwan, Matthew Alan and Sah, Ashwin and Sauermann, Lisa and Sawhney, Mehtaab}, issn = {2050-5086}, journal = {Forum of Mathematics, Pi}, keywords = {Discrete Mathematics and Combinatorics, Geometry and Topology, Mathematical Physics, Statistics and Probability, Algebra and Number Theory, Analysis}, publisher = {Cambridge University Press}, title = {{Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture}}, doi = {10.1017/fmp.2023.17}, volume = {11}, year = {2023}, } @article{14281, abstract = {In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.}, author = {Praetorius, Florian M and Leung, Philip J. Y. and Tessmer, Maxx H. and Broerman, Adam and Demakis, Cullen and Dishman, Acacia F. and Pillai, Arvind and Idris, Abbas and Juergens, David and Dauparas, Justas and Li, Xinting and Levine, Paul M. and Lamb, Mila and Ballard, Ryanne K. and Gerben, Stacey R. and Nguyen, Hannah and Kang, Alex and Sankaran, Banumathi and Bera, Asim K. and Volkman, Brian F. and Nivala, Jeff and Stoll, Stefan and Baker, David}, issn = {1095-9203}, journal = {Science}, number = {6659}, pages = {754--760}, publisher = {American Association for the Advancement of Science}, title = {{Design of stimulus-responsive two-state hinge proteins}}, doi = {10.1126/science.adg7731}, volume = {381}, year = {2023}, } @unpublished{14294, abstract = {Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.}, author = {Edman, Natasha I and Redler, Rachel L and Phal, Ashish and Schlichthaerle, Thomas and Srivatsan, Sanjay R and Etemadi, Ali and An, Seong and Favor, Andrew and Ehnes, Devon and Li, Zhe and Praetorius, Florian M and Gordon, Max and Yang, Wei and Coventry, Brian and Hicks, Derrick R and Cao, Longxing and Bethel, Neville and Heine, Piper and Murray, Analisa N and Gerben, Stacey and Carter, Lauren and Miranda, Marcos and Negahdari, Babak and Lee, Sangwon and Trapnell, Cole and Stewart, Lance and Ekiert, Damian C and Schlessinger, Joseph and Shendure, Jay and Bhabha, Gira and Ruohola-Baker, Hannele and Baker, David}, booktitle = {bioRxiv}, title = {{Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies}}, doi = {10.1101/2023.03.14.532666}, year = {2023}, } @article{14513, abstract = {Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems.}, author = {Mistakidis, S. I. and Volosniev, Artem and Barfknecht, R. E. and Fogarty, T. and Busch, Th and Foerster, A. and Schmelcher, P. and Zinner, N. T.}, issn = {0370-1573}, journal = {Physics Reports}, pages = {1--108}, publisher = {Elsevier}, title = {{Few-body Bose gases in low dimensions - A laboratory for quantum dynamics}}, doi = {10.1016/j.physrep.2023.10.004}, volume = {1042}, year = {2023}, } @misc{12869, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. }, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for: A stochastic cellular automaton model of culture formation}}, doi = {10.15479/AT:ISTA:12869}, year = {2023}, } @article{12890, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.}, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, issn = {2470-0053}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Stochastic cellular automaton model of culture formation}}, doi = {10.1103/PhysRevE.108.054307}, volume = {108}, year = {2023}, } @inproceedings{14516, abstract = {We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.}, author = {Beaver, Donald and Kelkar, Mahimna and Lewi, Kevin and Nikolaenko, Valeria and Sonnino, Alberto and Chalkias, Konstantinos and Kokoris Kogias, Eleftherios and Naurois, Ladi De and Roy, Arnab}, booktitle = {5th Conference on Advances in Financial Technologies}, isbn = {9783959773034}, issn = {1868-8969}, location = {Princeton, NJ, United States}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{STROBE: Streaming Threshold Random Beacons}}, doi = {10.4230/LIPIcs.AFT.2023.7}, volume = {282}, year = {2023}, } @article{14517, abstract = {State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. }, author = {Zemlicka, Martin and Redchenko, Elena and Peruzzo, Matilda and Hassani, Farid and Trioni, Andrea and Barzanjeh, Shabir and Fink, Johannes M}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {4}, publisher = {American Physical Society}, title = {{Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses}}, doi = {10.1103/PhysRevApplied.20.044054}, volume = {20}, year = {2023}, } @article{14515, abstract = {Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.}, author = {Reinhardt, Manuel and Tkačik, Gašper and Ten Wolde, Pieter Rein}, issn = {2160-3308}, journal = {Physical Review X}, number = {4}, publisher = {American Physical Society}, title = {{Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories}}, doi = {10.1103/PhysRevX.13.041017}, volume = {13}, year = {2023}, } @article{14514, abstract = {The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta V. and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James E. and Souslov, Anton}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Modeling Leidenfrost levitation of soft elastic solids}}, doi = {10.1103/PhysRevLett.131.168201}, volume = {131}, year = {2023}, } @misc{14523, abstract = {see Readme file}, author = {Binysh, Jack and Chakraborty, Indrajit and Chubynsky, Mykyta and Diaz Melian, Vicente L and Waitukaitis, Scott R and Sprittles, James and Souslov, Anton}, publisher = {Zenodo}, title = {{SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1}}, doi = {10.5281/ZENODO.8329143}, year = {2023}, } @inproceedings{14518, abstract = {We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.}, author = {Avni, Guy and Meggendorfer, Tobias and Sadhukhan, Suman and Tkadlec, Josef and Zikelic, Dorde}, booktitle = {Frontiers in Artificial Intelligence and Applications}, isbn = {9781643684369}, issn = {0922-6389}, location = {Krakow, Poland}, pages = {141--148}, publisher = {IOS Press}, title = {{Reachability poorman discrete-bidding games}}, doi = {10.3233/FAIA230264}, volume = {372}, year = {2023}, } @article{13096, abstract = {Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.}, author = {Degen, Morris and Santos, José Carlos and Pluhackova, Kristyna and Cebrero, Gonzalo and Ramos, Saray and Jankevicius, Gytis and Hartenian, Ella and Guillerm, Undina and Mari, Stefania A. and Kohl, Bastian and Müller, Daniel J. and Schanda, Paul and Maier, Timm and Perez, Camilo and Sieben, Christian and Broz, Petr and Hiller, Sebastian}, issn = {1476-4687}, journal = {Nature}, pages = {1065--1071}, publisher = {Springer Nature}, title = {{Structural basis of NINJ1-mediated plasma membrane rupture in cell death}}, doi = {10.1038/s41586-023-05991-z}, volume = {618}, year = {2023}, } @article{13041, abstract = {A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance.}, author = {Farag, Nadia L. and Jethwa, Rajesh B and Beardmore, Alice E. and Insinna, Teresa and O'Keefe, Christopher A. and Klusener, Peter A.A. and Grey, Clare P. and Wright, Dominic S.}, issn = {1864-564X}, journal = {ChemSusChem}, number = {13}, publisher = {Wiley}, title = {{Triarylamines as catholytes in aqueous organic redox flow batteries}}, doi = {10.1002/cssc.202300128}, volume = {16}, year = {2023}, }