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A fundamental aspect of statistics is the integration of data from different sources. Classically, Fisher and others were focused on how to integrate homogeneous (or only mildly heterogeneous) sets of data. More recently, as data is becoming more accessible, the question of if data sets from different sources should be integrated is becoming more relevant. The current literature treats this as a question with only two answers: integrate or don't. Here we take a different approach, motivated by information-sharing principles coming from the shrinkage estimation literature. In particular, we deviate from the do/don't perspective and propose a dial parameter that controls the extent to which two data sources are integrated. How far this dial parameter should be turned is shown to depend, for example, on the informativeness of the different data sources as measured by Fisher information. In the context of generalized linear models, this more nuanced data integration framework leads to relatively simple parameter estimates and valid tests/confidence intervals. Moreover, we demonstrate both theoretically and empirically that setting the dial parameter according to our recommendation leads to more efficient estimation compared to other binary data integration schemes.

There are now many comprehension algorithms for understanding the decisions of a machine learning algorithm. Among these are those based on the generation of counterfactual examples. This article proposes to view this generation process as a source of creating a certain amount of knowledge that can be stored to be used, later, in different ways. This process is illustrated in the additive model and, more specifically, in the case of the naive Bayes classifier, whose interesting properties for this purpose are shown.

Gene set analysis is a mainstay of functional genomics, but it relies on manually curated databases of gene functions that are incomplete and unaware of biological context. Here we evaluate the ability of OpenAI's GPT-4, a Large Language Model (LLM), to develop hypotheses about common gene functions from its embedded biomedical knowledge. We created a GPT-4 pipeline to label gene sets with names that summarize their consensus functions, substantiated by analysis text and citations. Benchmarking against named gene sets in the Gene Ontology, GPT-4 generated very similar names in 50% of cases, while in most remaining cases it recovered the name of a more general concept. In gene sets discovered in 'omics data, GPT-4 names were more informative than gene set enrichment, with supporting statements and citations that largely verified in human review. The ability to rapidly synthesize common gene functions positions LLMs as valuable functional genomics assistants.

Multiscale stochastic dynamical systems have been widely adopted to scientific and engineering problems due to their capability of depicting complex phenomena in many real world applications. This work is devoted to investigating the effective reduced dynamics for a slow-fast stochastic dynamical system. Given observation data on a short-term period satisfying some unknown slow-fast stochastic system, we propose a novel algorithm including a neural network called Auto-SDE to learn invariant slow manifold. Our approach captures the evolutionary nature of a series of time-dependent autoencoder neural networks with the loss constructed from a discretized stochastic differential equation. Our algorithm is also proved to be accurate, stable and effective through numerical experiments under various evaluation metrics.

Model selection aims to identify a sufficiently well performing model that is possibly simpler than the most complex model among a pool of candidates. However, the decision-making process itself can inadvertently introduce non-negligible bias when the cross-validation estimates of predictive performance are marred by excessive noise. In finite data regimes, cross-validated estimates can encourage the statistician to select one model over another when it is not actually better for future data. While this bias remains negligible in the case of few models, when the pool of candidates grows, and model selection decisions are compounded (as in forward search), the expected magnitude of selection-induced bias is likely to grow too. This paper introduces an efficient approach to estimate and correct selection-induced bias based on order statistics. Numerical experiments demonstrate the reliability of our approach in both estimating selection-induced bias and quantifying the degree of over-fitting along compounded model selection decisions, with specific application to forward search. This work represents a light-weight alternative to more computationally expensive approaches to correcting selection-induced bias, such as nested cross-validation and the bootstrap. Our approach rests on several theoretic assumptions, and we provide a diagnostic to help understand when these may not be valid, and when to fall back on safer, albeit more computationally expensive approaches. The accompanying code facilitates its practical implementation and fosters further exploration in this area.

The utility of reinforcement learning is limited by the alignment of reward functions with the interests of human stakeholders. One promising method for alignment is to learn the reward function from human-generated preferences between pairs of trajectory segments, a type of reinforcement learning from human feedback (RLHF). These human preferences are typically assumed to be informed solely by partial return, the sum of rewards along each segment. We find this assumption to be flawed and propose modeling human preferences instead as informed by each segment's regret, a measure of a segment's deviation from optimal decision-making. Given infinitely many preferences generated according to regret, we prove that we can identify a reward function equivalent to the reward function that generated those preferences, and we prove that the previous partial return model lacks this identifiability property in multiple contexts. We empirically show that our proposed regret preference model outperforms the partial return preference model with finite training data in otherwise the same setting. Additionally, we find that our proposed regret preference model better predicts real human preferences and also learns reward functions from these preferences that lead to policies that are better human-aligned. Overall, this work establishes that the choice of preference model is impactful, and our proposed regret preference model provides an improvement upon a core assumption of recent research. We have open sourced our experimental code, the human preferences dataset we gathered, and our training and preference elicitation interfaces for gathering a such a dataset.

We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.

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.

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.