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Current physics-informed (standard or operator) neural networks still rely on accurately learning the initial conditions of the system they are solving. In contrast, standard numerical methods evolve such initial conditions without needing to learn these. In this study, we propose to improve current physics-informed deep learning strategies such that initial conditions do not need to be learned and are represented exactly in the predicted solution. Moreover, this method guarantees that when a DeepONet is applied multiple times to time step a solution, the resulting function is continuous.

Iterative refinement (IR) is a popular scheme for solving a linear system of equations based on gradually improving the accuracy of an initial approximation. Originally developed to improve upon the accuracy of Gaussian elimination, interest in IR has been revived because of its suitability for execution on fast low-precision hardware such as analog devices and graphics processing units. IR generally converges when the error associated with the solution method is small, but is known to diverge when this error is large. We propose and analyze a novel enhancement to the IR algorithm by adding a line search optimization step that guarantees the algorithm will not diverge. Numerical experiments verify our theoretical results and illustrate the effectiveness of our proposed scheme.

Unveiling the underlying governing equations of nonlinear dynamic systems remains a significant challenge, especially when encountering noisy observations and no prior knowledge available. This study proposes R-DISCOVER, a framework designed to robustly uncover open-form partial differential equations (PDEs) from limited and noisy data. The framework operates through two alternating update processes: discovering and embedding. The discovering phase employs symbolic representation and a reinforcement learning (RL)-guided hybrid PDE generator to efficiently produce diverse open-form PDEs with tree structures. A neural network-based predictive model fits the system response and serves as the reward evaluator for the generated PDEs. PDEs with superior fits are utilized to iteratively optimize the generator via the RL method and the best-performing PDE is selected by a parameter-free stability metric. The embedding phase integrates the initially identified PDE from the discovering process as a physical constraint into the predictive model for robust training. The traversal of PDE trees automates the construction of the computational graph and the embedding process without human intervention. Numerical experiments demonstrate our framework's capability to uncover governing equations from nonlinear dynamic systems with limited and highly noisy data and outperform other physics-informed neural network-based discovery methods. This work opens new potential for exploring real-world systems with limited understanding.

Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.

Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.

We consider the split-preconditioned FGMRES method in a mixed precision framework, in which four potentially different precisions can be used for computations with the coefficient matrix, application of the left preconditioner, application of the right preconditioner, and the working precision. Our analysis is applicable to general preconditioners. We obtain bounds on the backward and forward errors in split-preconditioned FGMRES. Our analysis further provides insight into how the various precisions should be chosen; under certain assumptions, a suitable selection guarantees a backward error on the order of the working precision.

Confounder selection, namely choosing a set of covariates to control for confounding between a treatment and an outcome, is arguably the most important step in the design of observational studies. Previous methods, such as Pearl's celebrated back-door criterion, typically require pre-specifying a causal graph, which can often be difficult in practice. We propose an interactive procedure for confounder selection that does not require pre-specifying the graph or the set of observed variables. This procedure iteratively expands the causal graph by finding what we call "primary adjustment sets" for a pair of possibly confounded variables. This can be viewed as inverting a sequence of latent projections of the underlying causal graph. Structural information in the form of primary adjustment sets is elicited from the user, bit by bit, until either a set of covariates are found to control for confounding or it can be determined that no such set exists. We show that if the user correctly specifies the primary adjustment sets in every step, our procedure is both sound and complete.

The modeling and simulation of high-dimensional multiscale systems is a critical challenge across all areas of science and engineering. It is broadly believed that even with today's computer advances resolving all spatiotemporal scales described by the governing equations remains a remote target. This realization has prompted intense efforts to develop model order reduction techniques. In recent years, techniques based on deep recurrent neural networks have produced promising results for the modeling and simulation of complex spatiotemporal systems and offer large flexibility in model development as they can incorporate experimental and computational data. However, neural networks lack interpretability, which limits their utility and generalizability across complex systems. Here we propose a novel framework of Interpretable Learning Effective Dynamics (iLED) that offers comparable accuracy to state-of-the-art recurrent neural network-based approaches while providing the added benefit of interpretability. The iLED framework is motivated by Mori-Zwanzig and Koopman operator theory, which justifies the choice of the specific architecture. We demonstrate the effectiveness of the proposed framework in simulations of three benchmark multiscale systems. Our results show that the iLED framework can generate accurate predictions and obtain interpretable dynamics, making it a promising approach for solving high-dimensional multiscale systems.

It is crucial to detect when an instance lies downright too far from the training samples for the machine learning model to be trusted, a challenge known as out-of-distribution (OOD) detection. For neural networks, one approach to this task consists of learning a diversity of predictors that all can explain the training data. This information can be used to estimate the epistemic uncertainty at a given newly observed instance in terms of a measure of the disagreement of the predictions. Evaluation and certification of the ability of a method to detect OOD require specifying instances which are likely to occur in deployment yet on which no prediction is available. Focusing on regression tasks, we choose a simple yet insightful model for this OOD distribution and conduct an empirical evaluation of the ability of various methods to discriminate OOD samples from the data. Moreover, we exhibit evidence that a diversity of parameters may fail to translate to a diversity of predictors. Based on the choice of an OOD distribution, we propose a new way of estimating the entropy of a distribution on predictors based on nearest neighbors in function space. This leads to a variational objective which, combined with the family of distributions given by a generative neural network, systematically produces a diversity of predictors that provides a robust way to detect OOD samples.

The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.