Given the ubiquity of modularity in biological systems, module-level regulation analysis is vital for understanding biological systems across various levels and their dynamics. Current statistical analysis on biological modules predominantly focuses on either detecting the functional modules in biological networks or sub-group regression on the biological features without using the network data. This paper proposes a novel network-based neighborhood regression framework whose regression functions depend on both the global community-level information and local connectivity structures among entities. An efficient community-wise least square optimization approach is developed to uncover the strength of regulation among the network modules while enabling asymptotic inference. With random graph theory, we derive non-asymptotic estimation error bounds for the proposed estimator, achieving exact minimax optimality. Unlike the root-n consistency typical in canonical linear regression, our model exhibits linear consistency in the number of nodes n, highlighting the advantage of incorporating neighborhood information. The effectiveness of the proposed framework is further supported by extensive numerical experiments. Application to whole-exome sequencing and RNA-sequencing Autism datasets demonstrates the usage of the proposed method in identifying the association between the gene modules of genetic variations and the gene modules of genomic differential expressions.

Online platform businesses can be identified by using web-scraped texts. This is a classification problem that combines elements of natural language processing and rare event detection. Because online platforms are rare, accurately identifying them with Machine Learning algorithms is challenging. Here, we describe the development of a Machine Learning-based text classification approach that reduces the number of false positives as much as possible. It greatly reduces the bias in the estimates obtained by using calibrated probabilities and ensembles.

A core objective of physical design is to minimize wirelength (WL) when placing chip components on a canvas. Computing the minimal WL of a placement requires finding rectilinear Steiner minimum trees (RSMTs), an NP-hard problem. We propose NeuroSteiner, a neural model that distills GeoSteiner, an optimal RSMT solver, to navigate the cost--accuracy frontier of WL estimation. NeuroSteiner is trained on synthesized nets labeled by GeoSteiner, alleviating the need to train on real chip designs. Moreover, NeuroSteiner's differentiability allows to place by minimizing WL through gradient descent. On ISPD 2005 and 2019, NeuroSteiner can obtain 0.3% WL error while being 60% faster than GeoSteiner, or 0.2% and 30%.

Electroencephalography (EEG) data is often collected from diverse contexts involving different populations and EEG devices. This variability can induce distribution shifts in the data $X$ and in the biomedical variables of interest $y$, thus limiting the application of supervised machine learning (ML) algorithms. While domain adaptation (DA) methods have been developed to mitigate the impact of these shifts, such methods struggle when distribution shifts occur simultaneously in $X$ and $y$. As state-of-the-art ML models for EEG represent the data by spatial covariance matrices, which lie on the Riemannian manifold of Symmetric Positive Definite (SPD) matrices, it is appealing to study DA techniques operating on the SPD manifold. This paper proposes a novel method termed Geodesic Optimization for Predictive Shift Adaptation (GOPSA) to address test-time multi-source DA for situations in which source domains have distinct $y$ distributions. GOPSA exploits the geodesic structure of the Riemannian manifold to jointly learn a domain-specific re-centering operator representing site-specific intercepts and the regression model. We performed empirical benchmarks on the cross-site generalization of age-prediction models with resting-state EEG data from a large multi-national dataset (HarMNqEEG), which included $14$ recording sites and more than $1500$ human participants. Compared to state-of-the-art methods, our results showed that GOPSA achieved significantly higher performance on three regression metrics ($R^2$, MAE, and Spearman's $\rho$) for several source-target site combinations, highlighting its effectiveness in tackling multi-source DA with predictive shifts in EEG data analysis. Our method has the potential to combine the advantages of mixed-effects modeling with machine learning for biomedical applications of EEG, such as multicenter clinical trials.

The minimax risk is often considered as a gold standard against which we can compare specific statistical procedures. Nevertheless, as has been observed recently in robust and heavy-tailed estimation problems, the inherent reduction of the (random) loss to its expectation may entail a significant loss of information regarding its tail behaviour. In an attempt to avoid such a loss, we introduce the notion of a minimax quantile, and seek to articulate its dependence on the quantile level. To this end, we develop high-probability variants of the classical Le Cam and Fano methods, as well as a technique to convert local minimax risk lower bounds to lower bounds on minimax quantiles. To illustrate the power of our framework, we deploy our techniques on several examples, recovering recent results in robust mean estimation and stochastic convex optimisation, as well as obtaining several new results in covariance matrix estimation, sparse linear regression, nonparametric density estimation and isotonic regression. Our overall goal is to argue that minimax quantiles can provide a finer-grained understanding of the difficulty of statistical problems, and that, in wide generality, lower bounds on these quantities can be obtained via user-friendly tools.

Two competing paradigms exist for self-supervised learning of data representations. Joint Embedding Predictive Architecture (JEPA) is a class of architectures in which semantically similar inputs are encoded into representations that are predictive of each other. A recent successful approach that falls under the JEPA framework is self-distillation, where an online encoder is trained to predict the output of the target encoder, sometimes using a lightweight predictor network. This is contrasted with the Masked AutoEncoder (MAE) paradigm, where an encoder and decoder are trained to reconstruct missing parts of the input in the data space rather, than its latent representation. A common motivation for using the JEPA approach over MAE is that the JEPA objective prioritizes abstract features over fine-grained pixel information (which can be unpredictable and uninformative). In this work, we seek to understand the mechanism behind this empirical observation by analyzing the training dynamics of deep linear models. We uncover a surprising mechanism: in a simplified linear setting where both approaches learn similar representations, JEPAs are biased to learn high-influence features, i.e., features characterized by having high regression coefficients. Our results point to a distinct implicit bias of predicting in latent space that may shed light on its success in practice.

With the surge of large-scale pre-trained models (PTMs), adapting these models to numerous downstream tasks becomes a crucial problem. Consequently, parameter-efficient transfer learning (PETL) of large models has grasped huge attention. While PETL methods show impressive performance, they commonly rely on two optimistic assumptions: 1) the entire parameters of a PTM are available, and 2) a sufficiently large memory capacity is equipped for caching all the intermediate activations to compute gradients. However, in most real-world applications, PTMs are served as black-box APIs or proprietary software without explicit parameter accessibility. Besides, it is hard to meet a large memory requirement for modern PTMs. This work proposes black-box visual prompting (BlackVIP), which efficiently adapts the PTMs without knowledge about model architectures and parameters. BlackVIP has two components; 1) Coordinator and 2) simultaneous perturbation stochastic approximation with gradient correction (SPSA-GC). The Coordinator designs input-dependent visual prompts, which allow the target PTM to adapt in the wild. SPSA-GC efficiently estimates the gradient of PTM to update the Coordinator. Besides, we propose a variant, BlackVIP-SE, which significantly reduces the runtime and computational cost of BlackVIP. Extensive experiments on 19 datasets demonstrate that BlackVIPs enable robust adaptation to diverse domains and tasks with minimal memory requirements. We further provide theoretical analysis on the generalization of visual prompting methods by presenting their connection to the certified robustness of randomized smoothing.

This study employs cutting-edge wearable monitoring technology to conduct high-precision, high-temporal-resolution (1-second interval) cognitive load assessment on electroencephalogram (EEG) data from the FP1 channel and heart rate variability (HRV) data of secondary vocational students. By jointly analyzing these two critical physiological indicators, the research delves into their application value in assessing cognitive load among secondary vocational students and their utility across various tasks. The study designed two experiments to validate the efficacy of the proposed approach: Initially, a random forest classification model, developed using the N-BACK task, enabled the precise decoding of physiological signal characteristics in secondary vocational students under different levels of cognitive load, achieving a classification accuracy of 97%. Subsequently, this classification model was applied in a cross-task experiment involving the National Computer Rank Examination (Level-1), demonstrating the method's significant applicability and cross-task transferability in diverse learning contexts. Conducted with high portability, this research holds substantial theoretical and practical significance for optimizing teaching resource allocation in secondary vocational education, as well as for cognitive load assessment methods and monitoring. Currently, the research findings are undergoing trial implementation in the school.

Task-specific functional MRI (fMRI) images provide excellent modalities for studying the neuronal basis of cognitive processes. We use fMRI data to formulate and solve the problem of deconvolving task-specific aggregate neuronal networks into a set of basic building blocks called canonical networks, to use these networks for functional characterization, and to characterize the physiological basis of these responses by mapping them to regions of the brain. Our results show excellent task-specificity of canonical networks, i.e., the expression of a small number of canonical networks can be used to accurately predict tasks; generalizability across cohorts, i.e., canonical networks are conserved across diverse populations, studies, and acquisition protocols; and that canonical networks have strong anatomical and physiological basis. From a methods perspective, the problem of identifying these canonical networks poses challenges rooted in the high dimensionality, small sample size, acquisition variability, and noise. Our deconvolution technique is based on non-negative matrix factorization (NMF) that identifies canonical networks as factors of a suitably constructed matrix. We demonstrate that our method scales to large datasets, yields stable and accurate factors, and is robust to noise.

AI-enabled capabilities are reaching the requisite level of maturity to be deployed in the real world, yet do not always make correct or safe decisions. One way of addressing these concerns is to leverage AI control systems alongside and in support of human decisions, relying on the AI control system in safe situations while calling on a human co-decider for critical situations. We extend a methodology for adversarial explanations (AE) to state-of-the-art reinforcement learning frameworks, including MuZero. Multiple improvements to the base agent architecture are proposed. We demonstrate how this technology has two applications: for intelligent decision tools and to enhance training / learning frameworks. In a decision support context, adversarial explanations help a user make the correct decision by highlighting those contextual factors that would need to change for a different AI-recommended decision. As another benefit of adversarial explanations, we show that the learned AI control system demonstrates robustness against adversarial tampering. Additionally, we supplement AE by introducing strategically similar autoencoders (SSAs) to help users identify and understand all salient factors being considered by the AI system. In a training / learning framework, this technology can improve both the AI's decisions and explanations through human interaction. Finally, to identify when AI decisions would most benefit from human oversight, we tie this combined system to our prior art on statistically verified analyses of the criticality of decisions at any point in time.