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This work introduces a novel framework for dynamic factor model-based data integration of multiple subjects, called GRoup Integrative DYnamic factor models (GRIDY). The framework facilitates the determination of inter-subject differences between two pre-labeled groups by considering a combination of group spatial information and individual temporal dependence. Furthermore, it enables the identification of intra-subject differences over time by employing different model configurations for each subject. Methodologically, the framework combines a novel principal angle-based rank selection algorithm and a non-iterative integrative analysis framework. Inspired by simultaneous component analysis, this approach also reconstructs identifiable latent factor series with flexible covariance structures. The performance of the framework is evaluated through simulations conducted under various scenarios and the analysis of resting-state functional MRI data collected from multiple subjects in both the Autism Spectrum Disorder group and the control group.

This paper investigates the problem of efficient constrained global optimization of hybrid models that are a composition of a known white-box function and an expensive multi-output black-box function subject to noisy observations, which often arises in real-world science and engineering applications. We propose a novel method, Constrained Upper Quantile Bound (CUQB), to solve such problems that directly exploits the composite structure of the objective and constraint functions that we show leads substantially improved sampling efficiency. CUQB is a conceptually simple, deterministic approach that avoid constraint approximations used by previous methods. Although the CUQB acquisition function is not available in closed form, we propose a novel differentiable sample average approximation that enables it to be efficiently maximized. We further derive bounds on the cumulative regret and constraint violation under a non-parametric Bayesian representation of the black-box function. Since these bounds depend sublinearly on the number of iterations under some regularity assumptions, we establis bounds on the convergence rate to the optimal solution of the original constrained problem. In contrast to most existing methods, CUQB further incorporates a simple infeasibility detection scheme, which we prove triggers in a finite number of iterations when the original problem is infeasible (with high probability given the Bayesian model). Numerical experiments on several test problems, including environmental model calibration and real-time optimization of a reactor system, show that CUQB significantly outperforms traditional Bayesian optimization in both constrained and unconstrained cases. Furthermore, compared to other state-of-the-art methods that exploit composite structure, CUQB achieves competitive empirical performance while also providing substantially improved theoretical guarantees.

Existing error-bounded lossy compression techniques control the pointwise error during compression to guarantee the integrity of the decompressed data. However, they typically do not explicitly preserve the topological features in data. When performing post hoc analysis with decompressed data using topological methods, preserving topology in the compression process to obtain topologically consistent and correct scientific insights is desirable. In this paper, we introduce TopoSZ, an error-bounded lossy compression method that preserves the topological features in 2D and 3D scalar fields. Specifically, we aim to preserve the types and locations of local extrema as well as the level set relations among critical points captured by contour trees in the decompressed data. The main idea is to derive topological constraints from contour-tree-induced segmentation from the data domain, and incorporate such constraints with a customized error-controlled quantization strategy from the classic SZ compressor.Our method allows users to control the pointwise error and the loss of topological features during the compression process with a global error bound and a persistence threshold.

We provide a unified operational framework for the study of causality, non-locality and contextuality, in a fully device-independent and theory-independent setting. Our work has its roots in the sheaf-theoretic framework for contextuality by Abramsky and Brandenburger, which it extends to include arbitrary causal orders (be they definite, dynamical or indefinite). We define a notion of causal function for arbitrary spaces of input histories, and we show that the explicit imposition of causal constraints on joint outputs is equivalent to the free assignment of local outputs to the tip events of input histories. We prove factorisation results for causal functions over parallel, sequential, and conditional sequential compositions of the underlying spaces. We prove that causality is equivalent to continuity with respect to the lowerset topology on the underlying spaces, and we show that partial causal functions defined on open sub-spaces can be bundled into a presheaf. In a striking departure from the Abramsky-Brandenburger setting, however, we show that causal functions fail, under certain circumstances, to form a sheaf. We define empirical models as compatible families in the presheaf of probability distributions on causal functions, for arbitrary open covers of the underlying space of input histories. We show the existence of causally-induced contextuality, a phenomenon arising when the causal constraints themselves become context-dependent, and we prove a no-go result for non-locality on total orders, both static and dynamical.

A geometric graph is an abstract graph along with an embedding of the graph into the Euclidean plane which can be used to model a wide range of data sets. The ability to compare and cluster such objects is required in a data analysis pipeline, leading to a need for distances or metrics on these objects. In this work, we study the interleaving distance on geometric graphs, where functor representations of data can be compared by finding pairs of natural transformations between them. However, in many cases, particularly those of the set-valued functor variety, computation of the interleaving distance is NP-hard. For this reason, we take inspiration from the work of Robinson to find quality measures for families of maps that do not rise to the level of a natural transformation. Specifically, we call collections $\phi = \{\phi_U\mid U\}$ and $\psi = \{\psi_U\mid U\}$ which do not necessarily form a true interleaving an \textit{assignment}. In the case of embedded graphs, we impose a grid structure on the plane, treat this as a poset endowed with the Alexandroff topology $K$, and encode the embedded graph data as functors $F: \mathbf{Open}(K) \to \mathbf{Set}$ where $F(U)$ is the set of connected components of the graph inside of the geometric realization of the set $U$. We then endow the image with the extra structure of a metric space and define a loss function $L(\phi,\psi)$ which measures how far the required diagrams of an interleaving are from commuting. Then for a pair of assignments, we use this loss function to bound the interleaving distance, with an eye toward computation and approximation of the distance. We expect these ideas are not only useful in our particular use case of embedded graphs, but can be extended to a larger class of interleaving distance problems where computational complexity creates a barrier to use in practice.

Counterfactual examples have emerged as an effective approach to produce simple and understandable post-hoc explanations. In the context of graph classification, previous work has focused on generating counterfactual explanations by manipulating the most elementary units of a graph, i.e., removing an existing edge, or adding a non-existing one. In this paper, we claim that such language of explanation might be too fine-grained, and turn our attention to some of the main characterizing features of real-world complex networks, such as the tendency to close triangles, the existence of recurring motifs, and the organization into dense modules. We thus define a general density-based counterfactual search framework to generate instance-level counterfactual explanations for graph classifiers, which can be instantiated with different notions of dense substructures. In particular, we show two specific instantiations of this general framework: a method that searches for counterfactual graphs by opening or closing triangles, and a method driven by maximal cliques. We also discuss how the general method can be instantiated to exploit any other notion of dense substructures, including, for instance, a given taxonomy of nodes. We evaluate the effectiveness of our approaches in 7 brain network datasets and compare the counterfactual statements generated according to several widely-used metrics. Results confirm that adopting a semantic-relevant unit of change like density is essential to define versatile and interpretable counterfactual explanation methods.

We study the reverse shortest path problem on disk graphs in the plane. In this problem we consider the proximity graph of a set of $n$ disks in the plane of arbitrary radii: In this graph two disks are connected if the distance between them is at most some threshold parameter $r$. The case of intersection graphs is a special case with $r=0$. We give an algorithm that, given a target length $k$, computes the smallest value of $r$ for which there is a path of length at most $k$ between some given pair of disks in the proximity graph. Our algorithm runs in $O^*(n^{5/4})$ randomized expected time, which improves to $O^*(n^{6/5})$ for unit disk graphs, where all the disks have the same radius. Our technique is robust and can be applied to many variants of the problem. One significant variant is the case of weighted proximity graphs, where edges are assigned real weights equal to the distance between the disks or between their centers, and $k$ is replaced by a target weight $w$; that is, we seek a path whose length is at most $w$. In other variants, we want to optimize a parameter different from $r$, such as a scale factor of the radii of the disks. The main technique for the decision version of the problem (determining whether the graph with a given $r$ has the desired property) is based on efficient implementations of BFS (for the unweighted case) and of Dijkstra's algorithm (for the weighted case), using efficient data structures for maintaining the bichromatic closest pair for certain bicliques and several distance functions. The optimization problem is then solved by combining the resulting decision procedure with enhanced variants of the interval shrinking and bifurcation technique of [4].

Empirical Bayes shrinkage methods usually maintain a prior independence assumption: The unknown parameters of interest are independent from the known precision of the estimates. This assumption is theoretically questionable and empirically rejected, and imposing it inappropriately may harm the performance of empirical Bayes methods. We instead model the conditional distribution of the parameter given the standard errors as a location-scale family, leading to a family of methods that we call CLOSE. We establish that (i) CLOSE is rate-optimal for squared error Bayes regret, (ii) squared error regret control is sufficient for an important class of economic decision problems, and (iii) CLOSE is worst-case robust. We use our method to select high-mobility Census tracts targeting a variety of economic mobility measures in the Opportunity Atlas (Chetty et al., 2020; Bergman et al., 2023). Census tracts selected by close are more mobile on average than those selected by the standard shrinkage method. For 6 out of 15 mobility measures considered, the gain of close over the standard shrinkage method is larger than the gain of the standard method over selecting Census tracts uniformly at random.

Generative Adversarial Networks (GANs) have recently achieved impressive results for many real-world applications, and many GAN variants have emerged with improvements in sample quality and training stability. However, they have not been well visualized or understood. How does a GAN represent our visual world internally? What causes the artifacts in GAN results? How do architectural choices affect GAN learning? Answering such questions could enable us to develop new insights and better models. In this work, we present an analytic framework to visualize and understand GANs at the unit-, object-, and scene-level. We first identify a group of interpretable units that are closely related to object concepts using a segmentation-based network dissection method. Then, we quantify the causal effect of interpretable units by measuring the ability of interventions to control objects in the output. We examine the contextual relationship between these units and their surroundings by inserting the discovered object concepts into new images. We show several practical applications enabled by our framework, from comparing internal representations across different layers, models, and datasets, to improving GANs by locating and removing artifact-causing units, to interactively manipulating objects in a scene. We provide open source interpretation tools to help researchers and practitioners better understand their GAN models.

In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.