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The estimation of directed couplings between the nodes of a network from indirect measurements is a central methodological challenge in scientific fields such as neuroscience, systems biology and economics. Unfortunately, the problem is generally ill-posed due to the possible presence of unknown delays in the measurements. In this paper, we offer a solution of this problem by using a variational Bayes framework, where the uncertainty over the delays is marginalized in order to obtain conservative coupling estimates. To overcome the well-known overconfidence of classical variational methods, we use a hybrid-VI scheme where the (possibly flat or multimodal) posterior over the measurement parameters is estimated using a forward KL loss while the (nearly convex) conditional posterior over the couplings is estimated using the highly scalable gradient-based VI. In our ground-truth experiments, we show that the network provides reliable and conservative estimates of the couplings, greatly outperforming similar methods such as regression DCM.

Identifying predictive biomarkers, which forecast individual treatment effectiveness, is crucial for personalized medicine and informs decision-making across diverse disciplines. These biomarkers are extracted from pre-treatment data, often within randomized controlled trials, and have to be distinguished from prognostic biomarkers, which are independent of treatment assignment. Our study focuses on the discovery of predictive imaging biomarkers, aiming to leverage pre-treatment images to unveil new causal relationships. Previous approaches relied on labor-intensive handcrafted or manually derived features, which may introduce biases. In response, we present a new task of discovering predictive imaging biomarkers directly from the pre-treatment images to learn relevant image features. We propose an evaluation protocol for this task to assess a model's ability to identify predictive imaging biomarkers and differentiate them from prognostic ones. It employs statistical testing and a comprehensive analysis of image feature attribution. We explore the suitability of deep learning models originally designed for estimating the conditional average treatment effect (CATE) for this task, which previously have been primarily assessed for the precision of CATE estimation, overlooking the evaluation of imaging biomarker discovery. Our proof-of-concept analysis demonstrates promising results in discovering and validating predictive imaging biomarkers from synthetic outcomes and real-world image datasets.

This paper presents an agent-based model of mobility choice, influenced by human factors such as habits and perception biases. It is implemented in a Netlogo simulator, calibrated from results of an online survey about perceptions of mobility. The simulator can be played online. It allows to modify urban infrastructure and observe modal report.

Ongoing advances in microbiome profiling have allowed unprecedented insights into the molecular activities of microbial communities. This has fueled a strong scientific interest in understanding the critical role the microbiome plays in governing human health, by identifying microbial features associated with clinical outcomes of interest. Several aspects of microbiome data limit the applicability of existing variable selection approaches. In particular, microbiome data are high-dimensional, extremely sparse, and compositional. Importantly, many of the observed features, although categorized as different taxa, may play related functional roles. To address these challenges, we propose a novel compositional regression approach that leverages the data-adaptive clustering and variable selection properties of the spiked Dirichlet process to identify taxa that exhibit similar functional roles. Our proposed method, Bayesian Regression with Agglomerated Compositional Effects using a dirichLET process (BRACElet), enables the identification of a sparse set of features with shared impacts on the outcome, facilitating dimension reduction and model interpretation. We demonstrate that BRACElet outperforms existing approaches for microbiome variable selection through simulation studies and an application elucidating the impact of oral microbiome composition on insulin resistance.

The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work uses only genetic data for species delimitation, often employing some kind of cluster analysis. This can be misleading, because geographically distant groups of individuals can be genetically quite different even if they belong to the same species. We investigate the problem of testing whether two potentially separated groups of individuals can belong to a single species or not based on genetic and spatial data. Existing methods such as the partial Mantel test and jackknife-based distance-distance regression are considered. New approaches, i.e., an adaptation of a mixed effects model, a bootstrap approach, and a jackknife version of partial Mantel, are proposed. All these methods address the issue that distance data violate the independence assumption for standard inference regarding correlation and regression; a standard linear regression is also considered. The approaches are compared on simulated meta-populations generated with SLiM and GSpace - two software packages that can simulate spatially-explicit genetic data at an individual level. Simulations show that the new jackknife version of the partial Mantel test provides a good compromise between power and respecting the nominal type I error rate. Mixed-effects models have larger power than jackknife-based methods, but tend to display type I error rates slightly above the significance level. An application on brassy ringlets concludes the paper.

Spiking neural networks play an important role in brain-like neuromorphic computations and in studying working mechanisms of neural circuits. One drawback of training a large scale spiking neural network is that updating all weights is quite expensive. Furthermore, after training, all information related to the computational task is hidden into the weight matrix, prohibiting us from a transparent understanding of circuit mechanisms. Therefore, in this work, we address these challenges by proposing a spiking mode-based training protocol, where the recurrent weight matrix is explained as a Hopfield-like multiplication of three matrices: input, output modes and a score matrix. The first advantage is that the weight is interpreted by input and output modes and their associated scores characterizing the importance of each decomposition term. The number of modes is thus adjustable, allowing more degrees of freedom for modeling the experimental data. This significantly reduces the training cost because of significantly reduced space complexity for learning. Training spiking networks is thus carried out in the mode-score space. The second advantage is that one can project the high dimensional neural activity (filtered spike train) in the state space onto the mode space which is typically of a low dimension, e.g., a few modes are sufficient to capture the shape of the underlying neural manifolds. We successfully apply our framework in two computational tasks -- digit classification and selective sensory integration tasks. Our method accelerate the training of spiking neural networks by a Hopfield-like decomposition, and moreover this training leads to low-dimensional attractor structures of high-dimensional neural dynamics.

Topology optimization is used to systematically design contact-aided thermo-mechanical regulators, i.e. components whose effective thermal conductivity is tunable by mechanical deformation and contact. The thermo-mechanical interactions are modeled using a fully coupled non-linear thermo-mechanical finite element framework. To obtain the intricate heat transfer response, the components leverage self-contact, which is modeled using a third medium contact method. The effective heat transfer properties of the regulators are tuned by solving a topology optimization problem using a traditional gradient based algorithm. Several designs of thermo-mechanical regulators in the form of switches, diodes and triodes are presented.

Diffusion models have emerged as effective distribution estimators in vision, language, and reinforcement learning, but their use as priors in downstream tasks poses an intractable posterior inference problem. This paper studies amortized sampling of the posterior over data, $\mathbf{x}\sim p^{\rm post}(\mathbf{x})\propto p(\mathbf{x})r(\mathbf{x})$, in a model that consists of a diffusion generative model prior $p(\mathbf{x})$ and a black-box constraint or likelihood function $r(\mathbf{x})$. We state and prove the asymptotic correctness of a data-free learning objective, relative trajectory balance, for training a diffusion model that samples from this posterior, a problem that existing methods solve only approximately or in restricted cases. Relative trajectory balance arises from the generative flow network perspective on diffusion models, which allows the use of deep reinforcement learning techniques to improve mode coverage. Experiments illustrate the broad potential of unbiased inference of arbitrary posteriors under diffusion priors: in vision (classifier guidance), language (infilling under a discrete diffusion LLM), and multimodal data (text-to-image generation). Beyond generative modeling, we apply relative trajectory balance to the problem of continuous control with a score-based behavior prior, achieving state-of-the-art results on benchmarks in offline reinforcement learning.

We derive information-theoretic generalization bounds for supervised learning algorithms based on the information contained in predictions rather than in the output of the training algorithm. These bounds improve over the existing information-theoretic bounds, are applicable to a wider range of algorithms, and solve two key challenges: (a) they give meaningful results for deterministic algorithms and (b) they are significantly easier to estimate. We show experimentally that the proposed bounds closely follow the generalization gap in practical scenarios for deep learning.

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.