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Fitness functions map large combinatorial spaces of biological sequences to properties of interest. Inferring these multimodal functions from experimental data is a central task in modern protein engineering. Global epistasis models are an effective and physically-grounded class of models for estimating fitness functions from observed data. These models assume that a sparse latent function is transformed by a monotonic nonlinearity to emit measurable fitness. Here we demonstrate that minimizing contrastive loss functions, such as the Bradley-Terry loss, is a simple and flexible technique for extracting the sparse latent function implied by global epistasis. We argue by way of a fitness-epistasis uncertainty principle that the nonlinearities in global epistasis models can produce observed fitness functions that do not admit sparse representations, and thus may be inefficient to learn from observations when using a Mean Squared Error (MSE) loss (a common practice). We show that contrastive losses are able to accurately estimate a ranking function from limited data even in regimes where MSE is ineffective. We validate the practical utility of this insight by showing contrastive loss functions result in consistently improved performance on benchmark tasks.

We consider the application of the generalized Convolution Quadrature (gCQ) to approximate the solution of an important class of sectorial problems. The gCQ is a generalization of Lubich's Convolution Quadrature (CQ) that allows for variable steps. The available stability and convergence theory for the gCQ requires non realistic regularity assumptions on the data, which do not hold in many applications of interest, such as the approximation of subdiffusion equations. It is well known that for non smooth enough data the original CQ, with uniform steps, presents an order reduction close to the singularity. We generalize the analysis of the gCQ to data satisfying realistic regularity assumptions and provide sufficient conditions for stability and convergence on arbitrary sequences of time points. We consider the particular case of graded meshes and show how to choose them optimally, according to the behaviour of the data. An important advantage of the gCQ method is that it allows for a fast and memory reduced implementation. We describe how the fast and oblivious gCQ can be implemented and illustrate our theoretical results with several numerical experiments.

Modelling noisy data in a network context remains an unavoidable obstacle; fortunately, random matrix theory may comprehensively describe network environments effectively. Thus it necessitates the probabilistic characterisation of these networks (and accompanying noisy data) using matrix variate models. Denoising network data using a Bayes approach is not common in surveyed literature. This paper adopts the Bayesian viewpoint and introduces a new matrix variate t-model in a prior sense by relying on the matrix variate gamma distribution for the noise process, following the Gaussian graphical network for the cases when the normality assumption is violated. From a statistical learning viewpoint, such a theoretical consideration indubitably benefits the real-world comprehension of structures causing noisy data with network-based attributes as part of machine learning in data science. A full structural learning procedure is provided for calculating and approximating the resulting posterior of interest to assess the considered model's network centrality measures. Experiments with synthetic and real-world stock price data are performed not only to validate the proposed algorithm's capabilities but also to show that this model has wider flexibility than originally implied in Billio et al. (2021).

We analyze a goal-oriented adaptive algorithm that aims to efficiently compute the quantity of interest $G(u^\star)$ with a linear goal functional $G$ and the solution $u^\star$ to a general second-order nonsymmetric linear elliptic partial differential equation. The current state of the analysis of iterative algebraic solvers for nonsymmetric systems lacks the contraction property in the norms that are prescribed by the functional analytic setting. This seemingly prevents their application in the optimality analysis of goal-oriented adaptivity. As a remedy, this paper proposes a goal-oriented adaptive iteratively symmetrized finite element method (GOAISFEM). It employs a nested loop with a contractive symmetrization procedure, e.g., the Zarantonello iteration, and a contractive algebraic solver, e.g., an optimal multigrid solver. The various iterative procedures require well-designed stopping criteria such that the adaptive algorithm can effectively steer the local mesh refinement and the computation of the inexact discrete approximations. The main results consist of full linear convergence of the proposed adaptive algorithm and the proof of optimal convergence rates with respect to both degrees of freedom and total computational cost (i.e., optimal complexity). Numerical experiments confirm the theoretical results and investigate the selection of the parameters.

Given an $m\times n$ binary matrix $M$ with $|M|=p\cdot mn$ (where $|M|$ denotes the number of 1 entries), define the discrepancy of $M$ as $\mbox{disc}(M)=\displaystyle\max_{X\subset [m], Y\subset [n]}\big||M[X\times Y]|-p|X|\cdot |Y|\big|$. Using semidefinite programming and spectral techniques, we prove that if $\mbox{rank}(M)\leq r$ and $p\leq 1/2$, then $$\mbox{disc}(M)\geq \Omega(mn)\cdot \min\left\{p,\frac{p^{1/2}}{\sqrt{r}}\right\}.$$ We use this result to obtain a modest improvement of Lovett's best known upper bound on the log-rank conjecture. We prove that any $m\times n$ binary matrix $M$ of rank at most $r$ contains an $(m\cdot 2^{-O(\sqrt{r})})\times (n\cdot 2^{-O(\sqrt{r})})$ sized all-1 or all-0 submatrix, which implies that the deterministic communication complexity of any Boolean function of rank $r$ is at most $O(\sqrt{r})$.

We propose novel optimal and parameter-free algorithms for computing an approximate solution with small (projected) gradient norm. Specifically, for computing an approximate solution such that the norm of its (projected) gradient does not exceed $\varepsilon$, we obtain the following results: a) for the convex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{L\|x_0 - x^*\|/\varepsilon}$, where $L$ is the Lipschitz constant of the gradient and $x^*$ is any optimal solution; b) for the strongly convex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{L/\mu}\log(\|\nabla f(x_0)\|/\epsilon)$, where $\mu$ is the strong convexity modulus; and c) for the nonconvex case, the total number of gradient evaluations is bounded by $O(1)\sqrt{Ll}(f(x_0) - f(x^*))/\varepsilon^2$, where $l$ is the lower curvature constant. Our complexity results match the lower complexity bounds of the convex and strongly cases, and achieve the above best-known complexity bound for the nonconvex case for the first time in the literature. Moreover, for all the convex, strongly convex, and nonconvex cases, we propose parameter-free algorithms that do not require the input of any problem parameters. To the best of our knowledge, there do not exist such parameter-free methods before especially for the strongly convex and nonconvex cases. Since most regularity conditions (e.g., strong convexity and lower curvature) are imposed over a global scope, the corresponding problem parameters are notoriously difficult to estimate. However, gradient norm minimization equips us with a convenient tool to monitor the progress of algorithms and thus the ability to estimate such parameters in-situ.

We study the statistical capacity of the classical binary perceptrons with general thresholds $\kappa$. After recognizing the connection between the capacity and the bilinearly indexed (bli) random processes, we utilize a recent progress in studying such processes to characterize the capacity. In particular, we rely on \emph{fully lifted} random duality theory (fl RDT) established in \cite{Stojnicflrdt23} to create a general framework for studying the perceptrons' capacities. Successful underlying numerical evaluations are required for the framework (and ultimately the entire fl RDT machinery) to become fully practically operational. We present results obtained in that directions and uncover that the capacity characterizations are achieved on the second (first non-trivial) level of \emph{stationarized} full lifting. The obtained results \emph{exactly} match the replica symmetry breaking predictions obtained through statistical physics replica methods in \cite{KraMez89}. Most notably, for the famous zero-threshold scenario, $\kappa=0$, we uncover the well known $\alpha\approx0.8330786$ scaled capacity.

In inverse scattering problems, a model that allows for the simultaneous recovery of both the domain shape and an impedance boundary condition covers a wide range of problems with impenetrable domains, including recovering the shape of sound-hard and sound-soft obstacles and obstacles with thin coatings. This work develops an optimization framework for recovering the shape and material parameters of a penetrable, dissipative obstacle in the multifrequency setting, using a constrained class of curvature-dependent impedance function models proposed by Antoine, Barucq, and Vernhet. We find that this constrained model improves the robustness of the recovery problem, compared to more general models, and provides meaningfully better obstacle recovery than simpler models. We explore the effectiveness of the model for varying levels of dissipation, for noise-corrupted data, and for limited aperture data in the numerical examples.

Three variants of the statistical complexity function, which is used as a criterion in the problem of detection of a useful signal in the signal-noise mixture, are considered. The probability distributions maximizing the considered variants of statistical complexity are obtained analytically and conclusions about the efficiency of using one or another variant for detection problem are made. The comparison of considered information characteristics is shown and analytical results are illustrated on an example of synthesized signals. A method is proposed for selecting the threshold of the information criterion, which can be used in decision rule for useful signal detection in the signal-noise mixture. The choice of the threshold depends a priori on the analytically obtained maximum values. As a result, the complexity based on the total variation demonstrates the best ability of useful signal detection.

Graph-centric artificial intelligence (graph AI) has achieved remarkable success in modeling interacting systems prevalent in nature, from dynamical systems in biology to particle physics. The increasing heterogeneity of data calls for graph neural architectures that can combine multiple inductive biases. However, combining data from various sources is challenging because appropriate inductive bias may vary by data modality. Multimodal learning methods fuse multiple data modalities while leveraging cross-modal dependencies to address this challenge. Here, we survey 140 studies in graph-centric AI and realize that diverse data types are increasingly brought together using graphs and fed into sophisticated multimodal models. These models stratify into image-, language-, and knowledge-grounded multimodal learning. We put forward an algorithmic blueprint for multimodal graph learning based on this categorization. The blueprint serves as a way to group state-of-the-art architectures that treat multimodal data by choosing appropriately four different components. This effort can pave the way for standardizing the design of sophisticated multimodal architectures for highly complex real-world problems.