The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Data-driven algorithm selection is a powerful approach for choosing effective heuristics for computational problems. It operates by evaluating a set of candidate algorithms on a collection of representative training instances and selecting the one with the best empirical performance. However, running each algorithm on every training instance is computationally expensive, making scalability a central challenge. In practice, a common workaround is to evaluate algorithms on smaller proxy instances derived from the original inputs. However, this practice has remained largely ad hoc and lacked theoretical grounding. We provide the first theoretical foundations for this practice by formalizing the notion of size generalization: predicting an algorithm's performance on a large instance by evaluating it on a smaller, representative instance, subsampled from the original instance. We provide size generalization guarantees for three widely used clustering algorithms (single-linkage, k-means++, and Gonzalez's k-centers heuristic) and two canonical max-cut algorithms (Goemans-Williamson and Greedy). We characterize the subsample size sufficient to ensure that performance on the subsample reflects performance on the full instance, and our experiments support these findings.

Membership inference attacks (MIAs) are used to test practical privacy of machine learning models. MIAs complement formal guarantees from differential privacy (DP) under a more realistic adversary model. We analyze MIA vulnerability of fine-tuned neural networks both empirically and theoretically, the latter using a simplified model of fine-tuning. We show that the vulnerability of non-DP models when measured as the attacker advantage at a fixed false positive rate reduces according to a simple power law as the number of examples per class increases. A similar power-law applies even for the most vulnerable points, but the dataset size needed for adequate protection of the most vulnerable points is very large.

A cascade over a network refers to the diffusion process where behavior changes occurring in one part of an interconnected population lead to a series of sequential changes throughout the entire population. In recent years, there has been a surge in interest and efforts to understand and model cascade mechanisms since they motivate many significant research topics across different disciplines. The propagation structure of cascades is governed by underlying diffusion networks that are often hidden. Inferring diffusion networks thus enables interventions in cascading process to maximize information propagation and provides insights into the Granger causality of interaction mechanisms among individuals. In this project, we propose a novel double network mixture model for inferring latent diffusion network in presence of strong cascade heterogeneity. The new model represents cascade pathways as a distributional mixture over diffusion networks that capture different cascading patterns at the population level. We develop a data-driven optimization method to infer diffusion networks using only visible temporal cascade records, avoiding the need to model complex and heterogeneous individual states. Both statistical and computational guarantees are established for the proposed method. We apply the proposed model to analyze research topic cascades in social sciences across U.S. universities and uncover the latent research topic diffusion network among top U.S. social science programs.

The m-out-of-n bootstrap--proposed by Bickel et al. [1992]--approximates the distribution of a statistic by repeatedly drawing msubsamples (m n) without replacement from an original sample of size n; it is now routinely used for robust inference with heavy-tailed data, bandwidth selection, and other large-sample applications. Despite this broad applicability across econometrics, biostatistics, and machine-learning workflows, rigorous parameter-free guarantees for the soundness of the m-out-of-n bootstrap when estimating sample quantiles have remained elusive. This paper establishes such guarantees by analysing the estimator of sample quantiles obtained from m-out-of-n resampling of a dataset of length n. We first prove a central limit theorem for a fully data-driven version of the estimator that holds under a mild moment condition and involves no unknown nuisance parameters. We then show that the moment assumption is essentially tight by constructing a counter-example in which the CLT fails. Strengthening the assumptions slightly, we derive an Edgeworth expansion that delivers exact convergence rates and, as a corollary, a Berry-Esséen bound on the bootstrap approximation error. Finally, we illustrate the scope of our results by obtaining parameter-free asymptotic distributions for practical statistics, including the quantiles for random walk MH, and rewards of ergodic MDP's, thereby demonstrating the usefulness of our theory in modern estimation and learning tasks.

Large language model (LLM) routers improve the efficiency of multi-model systems by directing each query to the most appropriate model while leveraging the diverse strengths of heterogeneous LLMs. Most existing approaches frame routing as a classification problem based solely on the input query. While this reduces overhead by avoiding inference across all models, it overlooks valuable information that could be gleaned from potential outputs and fails to capture implicit intent or contextual nuances that often emerge only during response generation. These limitations can result in suboptimal routing decisions, particularly for complex or ambiguous queries that require deeper semantic understanding. To address this challenge, we propose Lookahead, a routing framework that "foresees" potential model outputs by predicting their latent representations and uses these predictions to guide model selection, thus enabling more informed routing without full inference. Within this framework, we implement two approaches based on causal and masked language models. Empirical evaluations across seven public benchmarks--spanning instruction following, mathematical reasoning, and code generation--show that Lookahead consistently outperforms existing routing baselines, achieving an average performance gain of 7.7% over the state-of-the-art.

Multimodal large language models (MLLMs) remain vulnerable to transferable adversarial examples. While existing methods typically achieve targeted attacks by aligning global features--such as CLIP's [CLS] token--between adversarial and target samples, they often overlook the rich local information encoded in patch tokens. This leads to suboptimal alignment and limited transferability, particularly for closed-source models. To address this limitation, we propose a targeted transferable adversarial attack method based on feature optimal alignment, called FOA-Attack, to improve adversarial transfer capability. Specifically, at the global level, we introduce a global feature loss based on cosine similarity to align the coarse-grained features of adversarial samples with those of target samples. At the local level, given the rich local representations within Transformers, we leverage clustering techniques to extract compact local patterns to alleviate redundant local features. We then formulate local feature alignment between adversarial and target samples as an optimal transport (OT) problem and propose a local clustering optimal transport loss to refine fine-grained feature alignment. Additionally, we propose a dynamic ensemble model weighting strategy to adaptively balance the influence of multiple models during adversarial example generation, thereby further improving transferability. Extensive experiments across various models demonstrate the superiority of the proposed method, outperforming state-of-the-art methods, especially in transferring to closed-source MLLMs.

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Explicit noise-level conditioning is widely regarded as essential for the effective operation of Graph Diffusion Models (GDMs). In this work, we challenge this assumption by investigating whether denoisers can implicitly infer noise levels directly from corrupted graph structures, potentially eliminating the need for explicit noise conditioning. To this end, we develop a theoretical framework centered on Bernoulli edge-flip corruptions and extend it to encompass more complex scenarios involving coupled structure-attribute noise. Extensive empirical evaluations on both synthetic and real-world graph datasets, using models such as GDSS and DiGress, provide strong support for our theoretical findings. Notably, unconditional GDMs achieve performance comparable or superior to their conditioned counterparts, while also offering reductions in parameters (4 6%) and computation time (8 10%). Our results suggest that the high-dimensional nature of graph data itself often encodes sufficient information for the denoising process, opening avenues for simpler, more efficient GDM architectures.

This work tackles the fundamental challenges in Federated Learning (FL) posed by arbitrary client participation and data heterogeneity, prevalent characteristics in practical FL settings. It is well-established that popular FedAvg-style algorithms struggle with exact convergence and can suffer from slow convergence rates since a decaying learning rate is required to mitigate these scenarios. To address these issues, we introduce the concept of stochastic matrix and the corresponding timevarying graphs as a novel modeling tool to accurately capture the dynamics of arbitrary client participation and the local update procedure. Leveraging this approach, we offer a fresh decentralized perspective on designing FL algorithms and present FOCUS, Federated Optimization with Exact Convergence via Push-pull Strategy, a provably convergent algorithm designed to effectively overcome the previously mentioned two challenges. More specifically, we provide a rigorous proof demonstrating that FOCUS achieves exact convergence with a linear rate regardless of the arbitrary client participation, establishing it as the first work to demonstrate this significant result.