This paper demonstrates that in classification problems, fully connected neural networks (FCNs) and residual neural networks (ResNets) cannot be approximated by kernel logistic regression based on the Neural Tangent Kernel (NTK) under overtraining (i.e., when training time approaches infinity). Specifically, when using the cross-entropy loss, regardless of how large the network width is (as long as it is finite), the empirical NTK diverges from the NTK on the training samples as training time increases. To establish this result, we first demonstrate the strictly positive definiteness of the NTKs for multi-layer FCNs and ResNets. Then, we prove that during training, % with the cross-entropy loss, the neural network parameters diverge if the smallest eigenvalue of the empirical NTK matrix (Gram matrix) with respect to training samples is bounded below by a positive constant. This behavior contrasts sharply with the lazy training regime commonly observed in regression problems. Consequently, using a proof by contradiction, we show that the empirical NTK does not uniformly converge to the NTK across all times on the training samples as the network width increases. We validate our theoretical results through experiments on both synthetic data and the MNIST classification task. This finding implies that NTK theory is not applicable in this context, with significant theoretical implications for understanding neural networks in classification problems.

In statistical applications it has become increasingly common to encounter data structures that live on non-linear spaces such as manifolds. Classical linear regression, one of the most fundamental methodologies of statistical learning, captures the relationship between an independent variable and a response variable which both are assumed to live in Euclidean space. Thus, geodesic regression emerged as an extension where the response variable lives on a Riemannian manifold. The parameters of geodesic regression, as with linear regression, capture the relationship of sensitive data and hence one should consider the privacy protection practices of said parameters. We consider releasing Differentially Private (DP) parameters of geodesic regression via the K-Norm Gradient (KNG) mechanism for Riemannian manifolds. We derive theoretical bounds for the sensitivity of the parameters showing they are tied to their respective Jacobi fields and hence the curvature of the space. This corroborates recent findings of differential privacy for the Fr\'echet mean. We demonstrate the efficacy of our methodology on the sphere, $\mbS^2\subset\mbR^3$ and, since it is general to Riemannian manifolds, the manifold of Euclidean space which simplifies geodesic regression to a case of linear regression. Our methodology is general to any Riemannian manifold and thus it is suitable for data in domains such as medical imaging and computer vision.

Tensor dimensionality reduction is one of the fundamental tools for modern data science. To address the high computational overhead, fiber-wise sampled subtensors that preserve the original tensor rank are often used in designing efficient and scalable tensor dimensionality reduction. However, the theory of property inheritance for subtensors is still underdevelopment, that is, how the essential properties of the original tensor will be passed to its subtensors. This paper theoretically studies the property inheritance of the two key tensor properties, namely incoherence and condition number, under the tensor train setting. We also show how tensor train rank is preserved through fiber-wise sampling. The key parameters introduced in theorems are numerically evaluated under various settings. The results show that the properties of interest can be well preserved to the subtensors formed via fiber-wise sampling. Overall, this paper provides several handy analytic tools for developing efficient tensor analysis

Generalized Probabilistic Canonical Correlation Analysis for Multi-modal Data Integration with Full or Partial Observations Tianjian Y ang 1 and Wei Vivian Li 1,* 1 Department of Statistics, University of California, Riverside * T o whom correspondence should be addressed: weil@ucr.edu Abstract Background: The integration and analysis of multi-modal data are increasingly essential across various domains including bioinformatics. As the volume and complexity of such data grow, there is a pressing need for computational models that not only integrate diverse modalities but also leverage their complementary information to improve clustering accuracy and insights, especially when dealing with partial observations with missing data. Results: We propose Generalized Probabilistic Canonical Correlation Analysis (GPCCA), an unsupervised method for the integration and joint dimensionality reduction of multi-modal data. GPCCA addresses key challenges in multi-modal data analysis by handling missing values within the model, enabling the integration of more than two modalities, and identifying informative features while accounting for correlations within individual modalities. The model demonstrates robustness to various missing data patterns and provides low-dimensional embeddings that facilitate downstream clustering and analysis. In a range of simulation settings, GPCCA outperforms existing methods in capturing essential patterns across modalities. Additionally, we demonstrate its applicability to multi-omics data from TCGA cancer datasets and a multi-view image dataset. Conclusion: GPCCA offers a useful framework for multi-modal data integration, effectively handling missing data and providing informative low-dimensional embeddings. Its performance across cancer genomics and multi-view image data highlights its robustness and potential for broad application. T o make the method accessible to the wider research community, we have released an R package, GPCCA, which is available at https://github.com/Kaversoniano/ GPCCA . 1 Introduction Many real-world datasets can be described from multiple perspectives, where each perspective, typically represented as a matrix, corresponds to a data modality . A dataset that is consisted of multiple modalities collected from the same set of individuals is termed a multi-modal dataset [1]. Examples include medical imaging data combining computed tomography (CT) and magnetic 1 arXiv:2504.11610v1 T echnological advances have made the collection of multi-modal data increasingly prevalent, enabling integrative analyses that leverage information across modalities.

Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However, limitations of the technology such as the relatively low resolution and comparatively insufficient sequencing depth make it difficult to reliably extract real biological signals from these data. To alleviate this challenge, we propose a novel transfer learning framework, referred to as TransST, to adaptively leverage the cell-labeled information from external sources in inferring cell-level heterogeneity of a target spatial transcriptomics data. Results: Applications in several real studies as well as a number of simulation settings show that our approach significantly improves existing techniques. For example, in the breast cancer study, TransST successfully identifies five biologically meaningful cell clusters, including the two subgroups of cancer in situ and invasive cancer; in addition, only TransST is able to separate the adipose tissues from the connective issues among all the studied methods. Conclusions: In summary, the proposed method TransST is both effective and robust in identifying cell subclusters and detecting corresponding driving biomarkers in spatial transcriptomics data.

While deep neural networks (DNNs) are widely used for prediction, inference on DNN-estimated subject-specific means for categorical or exponential family outcomes remains underexplored. We address this by proposing a DNN estimator under generalized nonparametric regression models (GNRMs) and developing a rigorous inference framework. Unlike existing approaches that assume independence between prediction errors and inputs to establish the error bound, a condition often violated in GNRMs, we allow for dependence and our theoretical analysis demonstrates the feasibility of drawing inference under GNRMs. To implement inference, we consider an Ensemble Subsampling Method (ESM) that leverages U-statistics and the Hoeffding decomposition to construct reliable confidence intervals for DNN estimates. We show that, under GNRM settings, ESM enables model-free variance estimation and accounts for heterogeneity among individuals in the population. Through simulations under nonparametric logistic, Poisson, and binomial regression models, we demonstrate the effectiveness and efficiency of our method. We further apply the method to the electronic Intensive Care Unit (eICU) dataset, a large-scale collection of anonymized health records from ICU patients, to predict ICU readmission risk and offer patient-centric insights for clinical decision-making.

Image representations are often evaluated through disjointed, task-specific protocols, leading to a fragmented understanding of model capabilities. For instance, it is unclear whether an image embedding model adept at clustering images is equally good at retrieving relevant images given a piece of text. We introduce the Massive Image Embedding Benchmark (MIEB) to evaluate the performance of image and image-text embedding models across the broadest spectrum to date. MIEB spans 38 languages across 130 individual tasks, which we group into 8 high-level categories. We benchmark 50 models across our benchmark, finding that no single method dominates across all task categories. We reveal hidden capabilities in advanced vision models such as their accurate visual representation of texts, and their yet limited capabilities in interleaved encodings and matching images and texts in the presence of confounders. We also show that the performance of vision encoders on MIEB correlates highly with their performance when used in multimodal large language models. Our code, dataset, and leaderboard are publicly available at https://github.com/embeddings-benchmark/mteb.

Foundation models (FMs) trained on electronic health records (EHRs) have shown strong performance on a range of clinical prediction tasks. However, adapting these models to local health systems remains challenging due to limited data availability and resource constraints. In this study, we investigated what these models learn and evaluated the transferability of an FM trained on MIMIC-IV to an institutional EHR dataset at the University of Chicago Medical Center. We assessed their ability to identify outlier patients and examined representation-space patient trajectories in relation to future clinical outcomes. We also evaluated the performance of supervised fine-tuned classifiers on both source and target datasets. Our findings offer insights into the adaptability of FMs across different healthcare systems, highlight considerations for their effective implementation, and provide an empirical analysis of the underlying factors that contribute to their predictive performance.

Predicting phenotype from genotype is a central challenge in genetics. Traditional approaches in quantitative genetics typically analyze this problem using methods based on linear regression. These methods generally assume that the genetic architecture of complex traits can be parameterized in terms of an additive model, where the effects of loci are independent, plus (in some cases) pairwise epistatic interactions between loci. However, these models struggle to analyze more complex patterns of epistasis or subtle gene-environment interactions. Recent advances in machine learning, particularly attention-based models, offer a promising alternative. Initially developed for natural language processing, attention-based models excel at capturing context-dependent interactions and have shown exceptional performance in predicting protein structure and function. Here, we apply attention-based models to quantitative genetics. We analyze the performance of this attention-based approach in predicting phenotype from genotype using simulated data across a range of models with increasing epistatic complexity, and using experimental data from a recent quantitative trait locus mapping study in budding yeast. We find that our model demonstrates superior out-of-sample predictions in epistatic regimes compared to standard methods. We also explore a more general multi-environment attention-based model to jointly analyze genotype-phenotype maps across multiple environments and show that such architectures can be used for "transfer learning" - predicting phenotypes in novel environments with limited training data.

Tissue-of-origin signals dominate pan-cancer gene expression, often obscuring molecular features linked to patient survival. This hampers the discovery of generalizable biomarkers, as models tend to overfit tissue-specific patterns rather than capture survival-relevant signals. To address this, we propose a Domain-Adversarial Neural Network (DANN) trained on TCGA RNA-seq data to learn representations less biased by tissue and more focused on survival. Identifying tissue-independent genetic profiles is key to revealing core cancer programs. We assess the DANN using: (1) Standard SHAP, based on the original input space and DANN's mortality classifier; (2) A layer-aware strategy applied to hidden activations, including an unsupervised manifold from raw activations and a supervised manifold from mortality-specific SHAP values. Standard SHAP remains confounded by tissue signals due to biases inherent in its computation. The raw activation manifold was dominated by high-magnitude activations, which masked subtle tissue and mortality-related signals. In contrast, the layer-aware SHAP manifold offers improved low-dimensional representations of both tissue and mortality signals, independent of activation strength, enabling subpopulation stratification and pan-cancer identification of survival-associated genes.