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Tensor networks are a compressed format for multi-dimensional data. One-dimensional tensor networks -- often referred to as tensor trains (TT) or matrix product states (MPS) -- are increasingly being used as a numerical ansatz for continuum functions by "quantizing" the inputs into discrete binary digits. Here we demonstrate the power of more general tree tensor networks for this purpose. We provide direct constructions of a number of elementary functions as generic tree tensor networks and interpolative constructions for more complicated functions via a generalization of the tensor cross interpolation algorithm. For a range of multi-dimensional functions we show how more structured tree tensor networks offer a significantly more efficient ansatz than the commonly used tensor train. We demonstrate an application of our methods to solving multi-dimensional, non-linear Fredholm equations, providing a rigorous bound on the rank of the solution which, in turn, guarantees exponentially scaling accuracy with the size of the tree tensor network for certain problems.

Rationally identifying variables responsible for changes to a biological system can enable myriad applications in disease understanding and cell engineering. From a causality perspective, we are given two datasets generated by the same causal model, one observational (control) and one interventional (perturbed). The goal is to isolate the subset of measured variables (e.g. genes) that were the targets of the intervention, i.e. those whose conditional independencies have changed. Knowing the causal graph would limit the search space, allowing us to efficiently pinpoint these variables. However, current algorithms that infer causal graphs in the presence of unknown intervention targets scale poorly to the hundreds or thousands of variables in biological data, as they must jointly search the combinatorial spaces of graphs and consistent intervention targets. In this work, we propose a causality-inspired approach for predicting perturbation targets that decouples the two search steps. First, we use an amortized causal discovery model to separately infer causal graphs from the observational and interventional datasets. Then, we learn to map these paired graphs to the sets of variables that were intervened upon, in a supervised learning framework. This approach consistently outperforms baselines for perturbation modeling on seven single-cell transcriptomics datasets, each with thousands of measured variables. We also demonstrate significant improvements over six causal discovery algorithms in predicting intervention targets across a variety of tractable, synthetic datasets.

Recently introduced by some of the authors, the in-context identification paradigm aims at estimating, offline and based on synthetic data, a meta-model that describes the behavior of a whole class of systems. Once trained, this meta-model is fed with an observed input/output sequence (context) generated by a real system to predict its behavior in a zero-shot learning fashion. In this paper, we enhance the original meta-modeling framework through three key innovations: by formulating the learning task within a probabilistic framework; by managing non-contiguous context and query windows; and by adopting recurrent patching to effectively handle long context sequences. The efficacy of these modifications is demonstrated through a numerical example focusing on the Wiener-Hammerstein system class, highlighting the model's enhanced performance and scalability.

To solve many problems on graphs, graph traversals are used, the usual variants of which are the depth-first search and the breadth-first search. Implementing a graph traversal we consequently reach all vertices of the graph that belong to a connected component. The breadth-first search is the usual choice when constructing efficient algorithms for finding connected components of a graph. Methods of simple iteration for solving systems of linear equations with modified graph adjacency matrices and with the properly specified right-hand side can be considered as graph traversal algorithms. These traversal algorithms, generally speaking, turn out to be non-equivalent neither to the depth-first search nor the breadth-first search. The example of such a traversal algorithm is the one associated with the Gauss-Seidel method. For an arbitrary connected graph, to visit all its vertices, the algorithm requires not more iterations than that is required for BFS. For a large number of instances of the problem, fewer iterations will be required.

In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review \rv{33} state-of-the-art methods, categorizing SVGs into three types: overall, cell-type-specific, and spatial-domain-marker SVGs. Our review explains the intuitions underlying these methods, summarizes their applications, and categorizes the hypothesis tests they use in the trade-off between generality and specificity for SVG detection. We discuss challenges in SVG detection and propose future directions for improvement. Our review offers insights for method developers and users, advocating for category-specific benchmarking.

Randomized matrix algorithms have become workhorse tools in scientific computing and machine learning. To use these algorithms safely in applications, they should be coupled with posterior error estimates to assess the quality of the output. To meet this need, this paper proposes two diagnostics: a leave-one-out error estimator for randomized low-rank approximations and a jackknife resampling method to estimate the variance of the output of a randomized matrix computation. Both of these diagnostics are rapid to compute for randomized low-rank approximation algorithms such as the randomized SVD and randomized Nystr\"om approximation, and they provide useful information that can be used to assess the quality of the computed output and guide algorithmic parameter choices.

We propose a method utilizing physics-informed neural networks (PINNs) to solve Poisson equations that serve as control variates in the computation of transport coefficients via fluctuation formulas, such as the Green--Kubo and generalized Einstein-like formulas. By leveraging approximate solutions to the Poisson equation constructed through neural networks, our approach significantly reduces the variance of the estimator at hand. We provide an extensive numerical analysis of the estimators and detail a methodology for training neural networks to solve these Poisson equations. The approximate solutions are then incorporated into Monte Carlo simulations as effective control variates, demonstrating the suitability of the method for moderately high-dimensional problems where fully deterministic solutions are computationally infeasible.

In molecular dynamics, transport coefficients measure the sensitivity of the invariant probability measure of the stochastic dynamics at hand with respect to some perturbation. They are typically computed using either the linear response of nonequilibrium dynamics, or the Green--Kubo formula. The estimators for both approaches have large variances, which motivates the study of variance reduction techniques for computing transport coefficients. We present an alternative approach, called the \emph{transient subtraction technique} (inspired by early work by Ciccotti and Jaccucci in 1975), which amounts to simulating a transient dynamics, from which we subtract a sensibly coupled equilibrium trajectory, resulting in an estimator with smaller variance. We present the mathematical formulation of the transient subtraction technique, give error estimates on the bias and variance of the associated estimator, and demonstrate the relevance of the method through numerical illustrations for various systems.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.