Graph neural networks (GNNs) take as input the graph structure and the feature vectors associated with the nodes. Both contain noisy information about the labels. Here we propose joint denoising and rewiring (JDR)--an algorithm to jointly denoise the graph structure and features, which can improve the performance of any downstream algorithm. We do this by defining and maximizing the alignment between the leading eigenspaces of graph and feature matrices. To approximately solve this computationally hard problem, we propose a heuristic that efficiently handles real-world graph datasets with many classes and different levels of homophily or heterophily. We experimentally verify the effectiveness of our approach on synthetic data and real-world graph datasets. The results show that JDR consistently outperforms existing rewiring methods on node classification tasks using GNNs as downstream models.

Relational inference aims to identify interactions between parts of a dynamical system from the observed dynamics. Current state-of-the-art methods fit the dynamics with a graph neural network (GNN) on a learnable graph. They use one-step message-passing GNNs -- intuitively the right choice since non-locality of multi-step or spectral GNNs may confuse direct and indirect interactions. But the \textit{effective} interaction graph depends on the sampling rate and it is rarely localized to direct neighbors, leading to poor local optima for the one-step model. In this work, we propose a \textit{graph dynamics prior} (GDP) for relational inference. GDP constructively uses error amplification in non-local polynomial filters to steer the solution to the ground-truth graph. To deal with non-uniqueness, GDP simultaneously fits a ``shallow'' one-step model and a polynomial multi-step model with shared graph topology. Experiments show that GDP reconstructs graphs far more accurately than earlier methods, with remarkable robustness to under-sampling. Since appropriate sampling rates for unknown dynamical systems are not known a priori, this robustness makes GDP suitable for real applications in scientific machine learning. Reproducible code is available at https://github.com/DaDaCheng/GDP.

Phase association groups seismic wave arrivals according to their originating earthquakes. It is a fundamental task in a seismic data processing pipeline, but challenging to perform for smaller, high-rate seismic events which carry fundamental information about earthquake dynamics, especially with a commonly assumed inaccurate wave speed model. As a consequence, most association methods focus on larger events that occur at a lower rate and are thus easier to associate, even though microseismicity provides a valuable description of the elastic medium properties in the subsurface. In this paper, we show that association is possible at rates much higher than previously reported even when the wave speed is unknown. We propose Harpa, a high-rate seismic phase association method which leverages deep neural fields to build generative models of wave speeds and associated travel times, and first solves a joint spatio--temporal source localization and wave speed recovery problem, followed by association. We obviate the need for associated phases by interpreting arrival time data as probability measures and using an optimal transport loss to enforce data fidelity. The joint recovery problem is known to admit a unique solution under certain conditions but due to the non-convexity of the corresponding loss a simple gradient scheme converges to poor local minima. We show that this is effectively mitigated by stochastic gradient Langevin dynamics (SGLD). Numerical experiments show that \harpa~efficiently associates high-rate seismicity clouds over complex, unknown wave speeds and graciously handles noisy and missing picks.

Graph neural networks are among the most successful machine learning models for relational datasets like metabolic, transportation, and social networks. Yet the determinants of their strong generalization for diverse interactions encoded in the data are not well understood. Methods from statistical learning theory do not explain emergent phenomena such as double descent or the dependence of risk on the nature of interactions. We use analytical tools from statistical physics and random matrix theory to precisely characterize generalization in simple graph convolution networks on the contextual stochastic block model. The derived curves are phenomenologically rich: they explain the distinction between learning on homophilic and heterophilic and they predict double descent whose existence in GNNs has been questioned by recent work. We show how risk depends on the interplay between the noise in the graph, noise in the features, and the proportion of nodes used for training. Our analysis predicts qualitative behavior not only of a stylized graph learning model but also to complex GNNs on messy real-world datasets. As a case in point, we use these analytic insights about heterophily and self-loop signs to improve performance of state-of-the-art graph convolution networks on several heterophilic benchmarks by a simple addition of negative self-loop filters.

FDA has been promoting enrollment practices that could enhance the diversity of clinical trial populations, through broadening eligibility criteria. However, how to broaden eligibility remains a significant challenge. We propose an AI approach to Cohort Optimization (AICO) through transformer-based natural language processing of the eligibility criteria and evaluation of the criteria using real-world data. The method can extract common eligibility criteria variables from a large set of relevant trials and measure the generalizability of trial designs to real-world patients. It overcomes the scalability limits of existing manual methods and enables rapid simulation of eligibility criteria design for a disease of interest. A case study on breast cancer trial design demonstrates the utility of the method in improving trial generalizability.

Grouping objects into clusters based on similarities or weights between them is one of the most important problems in science and engineering. In this work, by extending message passing algorithms and spectral algorithms proposed for unweighted community detection problem, we develop a non-parametric method based on statistical physics, by mapping the problem to Potts model at the critical temperature of spin glass transition and applying belief propagation to solve the marginals corresponding to the Boltzmann distribution. Our algorithm is robust to over-fitting and gives a principled way to determine whether there are significant clusters in the data and how many clusters there are. We apply our method to different clustering tasks and use extensive numerical experiments to illustrate the advantage of our method over existing algorithms. In the community detection problem in weighted and directed networks, we show that our algorithm significantly outperforms existing algorithms. In the clustering problem when the data was generated by mixture models in the sparse regime we show that our method works to the theoretical limit of detectability and gives accuracy very close to that of the optimal Bayesian inference. In the semi-supervised clustering problem, our method only needs several labels to work perfectly in classic datasets. Finally, we further develop Thouless-Anderson-Palmer equations which reduce heavily the computation complexity in dense-networks but gives almost the same performance as belief propagation.