Publications

A Unified Solution to Diverse Heterogeneities in One-Shot Federated Learning
Jun Bai
Yiliao Song
Di Wu
Atul Sajjanhar
Yong Xiang
Wei Zhou
Xiaohui Tao
Yan Li
Yue Li
One-Shot Federated Learning (OSFL) restricts communication between the server and clients to a single round, significantly reducing communic… (see more)ation costs and minimizing privacy leakage risks compared to traditional Federated Learning (FL), which requires multiple rounds of communication. However, existing OSFL frameworks remain vulnerable to distributional heterogeneity, as they primarily focus on model heterogeneity while neglecting data heterogeneity. To bridge this gap, we propose FedHydra, a unified, data-free, OSFL framework designed to effectively address both model and data heterogeneity. Unlike existing OSFL approaches, FedHydra introduces a novel two-stage learning mechanism. Specifically, it incorporates model stratification and heterogeneity-aware stratified aggregation to mitigate the challenges posed by both model and data heterogeneity. By this design, the data and model heterogeneity issues are simultaneously monitored from different aspects during learning. Consequently, FedHydra can effectively mitigate both issues by minimizing their inherent conflicts. We compared FedHydra with five SOTA baselines on four benchmark datasets. Experimental results show that our method outperforms the previous OSFL methods in both homogeneous and heterogeneous settings. The code is available at https://github.com/Jun-B0518/FedHydra.
2025-08-02
Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2 (published)
doi.org
arxiv.org
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models
Darcy Elizabeth Wagner
Hani N. Alsafadi
Nilay Mitash
Aurelien Justet
Qianjiang Hu
Ricardo Pineda
Claudia Staab-Weijnitz
Martina Korfei
Nika Gvazava
Kristin Wannemo
Ugochi Onwuka
Molly Mozurak
Adriana Estrada-Bernal
Juan Cala Garcia
Katrin Mutze
Rita Costa
Deniz Bölükbas
John Stegmayr
Wioletta Skronska-Wasek
Stephan Klee … (see 14 more)
Chiharu Ota
Hoeke A. Baarsma
Jingtao Wang
John Sembrat
Anne Hilgendorff
Jun Ding
Andreas Günther
Rachel Chambers
Ivan O Rosas
Stijn de Langhe
Naftali Kaminski
Mareike Lehmann
Oliver Eickelberg
Melanie Königshoff
Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current … (see more)IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX expression in experimental lung fibrosis in vivo and in human fibrotic tissue ex vivo. We thus identify YAP-TEAD/LOX inhibition in alveolar type II cells as a promising potential therapy for IPF patients.
2025-08-01
Nature Communications (published)
doi.org
ConvNTC: convolutional neural tensor completion for detecting “A–A–B” type biological triplets
Pei Liu
Xiao Liang
Yuemei Li
Jiawei Luo
Abstract Systematically investigating interactions among molecules of the same type across different contexts is crucial for unraveling dise… (see more)ase mechanisms and developing potential therapeutic strategies. The “A–A–B” triplet paradigm provides a principled approach to model such context-specific interactions, and leveraging third-order tensor to capture such type ternary relationships is an efficient strategy. However, effectively modeling both multilinear and nonlinear characteristics to accurately identify such triplets using tensor-based methods remains a challenge. In this paper, we propose a novel Convolutional Neural Tensor Completion (ConvNTC) framework that collaboratively learns the multilinear and nonlinear representations to model triplet-based network interactions. ConvNTC consists of a multilinear module and a nonlinear module. The former is a tensor decomposition approach that integrates multiple constraints to learn the tensor factor embeddings. The latter contains three components: an embedding generator to produce position-specific index embeddings for each tensor entry in addition to the factor embeddings, a convolutional encoder to perform nonlinear feature mapping while preserving the tensor’s rank-one property, and a Kolmogorov–Arnold Network (KAN) based predictor to effectively capture high-dimensional relationships aligned with the intrinsic structure of real-world data. We evaluate ConvNTC on two types triplet datasets of the “A–A–B” type: miRNA–miRNA–disease and drug–drug–cell. Comprehensive experiments against 11 state-of-the-art methods demonstrate the superiority of ConvNTC in terms of triplet prediction. ConvNTC reveals promising prognostic values of the miRNA–miRNA interactions on breast cancer and detects synergistic drug combinations in cancer cell lines.
2025-07-31
Briefings in Bioinformatics (published)
doi.org
Data Visualization using Functional Data Analysis
Haozhe Chen
Andres Duque Correa
Guy Wolf
Kevin R. Moon
Data visualization via dimensionality reduction is an important tool in exploratory data analysis. However, when the data are noisy, many ex… (see more)isting methods fail to capture the underlying structure of the data. Furthermore, existing methods that can theoretically eliminate all noise are difficult to implement in high dimensions. Here we propose a new data visualization method called Functional Information Geometry (FIG) for dynamical processes that denoises the data by leveraging time information and mitigates the curse of dimensionality using approaches from functional data analysis. We experimentally demonstrate that FIG outperforms other methods in terms of capturing the true structure, hyperparameter robustness, and computational speed. We then use our method to visualize EEG brain measurements of sleep activity.
2025-07-31
2025 International Conference on Sampling Theory and Applications (SampTA) (published)
doi.org
openreview.net
Efficient Deep Reinforcement Learning-Based Supplementary Damping Control with a Coordinated RMS Training and EMT Testing Scheme
Tao Xue
Mingxuan Zhao
Ilhan Kocar
Mohsen Ghafouri
Antoine Lesage-Landry
Siqi Bu
Ziqing Zhu
2025-07-31
IEEE Transactions on Power Delivery (published)
doi.org
Towards an Interpretable Machine Learning Model for Predicting Antimicrobial Resistance
Mohamed Mediouni
Vladimir Makarenkov
Abdoulaye Banire Diallo
2025-07-31
Journal of Global Antimicrobial Resistance (published)
doi.org
Zero-Shot Anomaly Detection with Dual-Branch Prompt Learning
Zihan Wang
S Ebrahimi Kahou
Narges Armanfard
Zero-shot anomaly detection (ZSAD) enables identifying and localizing defects in unseen categories by relying solely on generalizable featur… (see more)es rather than requiring any labeled examples of anomalies. However, existing ZSAD methods, whether using fixed or learned prompts, struggle under domain shifts because their training data are derived from limited training domains and fail to generalize to new distributions. In this paper, we introduce PILOT, a framework designed to overcome these challenges through two key innovations: (1) a novel dual-branch prompt learning mechanism that dynamically integrates a pool of learnable prompts with structured semantic attributes, enabling the model to adaptively weight the most relevant anomaly cues for each input image; and (2) a label-free test-time adaptation strategy that updates the learnable prompt parameters using high-confidence pseudo-labels from unlabeled test data. Extensive experiments on 13 industrial and medical benchmarks demonstrate that PILOT achieves state-of-the-art performance in both anomaly detection and localization under domain shift.
2025-07-31
ArXiv (preprint)
doi.org
arxiv.org
Advancing science- and evidence-based AI policy.
Rishi Bommasani
Sanjeev Arora
Jennifer Chayes
Yejin Choi
Mariano-Florentino Cuéllar
Li Fei-Fei
Daniel E. Ho
Dan Jurafsky
Sanmi Koyejo
Hima Lakkaraju
Arvind Narayanan
Alondra Nelson
Emma Pierson
Joelle Pineau
Scott Singer
Gael Varoquaux
Suresh Venkatasubramanian
Ion Stoica
Percy Liang
Dawn Song
2025-07-30
Science (published)
doi.org
arxiv.org
Computing Approximate Nash Equilibria for Integer Programming Games
Aloïs Duguet
Margarida Carvalho
Gabriele Dragotto
Sandra-ulrich Ngueveu
2025-07-30
Optimization Letters (published)
doi.org
arxiv.org
Evaluating and Improving LitLLMs with Deep Research
Gaurav Sahu
Shubham Agarwal
Abhay Puri
Issam Hadj Laradji
Krishnamurthy Dj Dvijotham
Jason Stanley
Laurent Charlin
Christopher Pal
Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially du… (see more)e to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: (1) Retrieving related works given a query abstract and (2) Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Particularly, our ``Deep Research" retrieval variant improves coverage by over 5x compared to standard keyword search, addressing a key bottleneck in the pipeline. Further, we demonstrate that our planning-based approach achieves higher-quality reviews by minimizing hallucinated references in the generated review by 18-26\% compared to existing simpler LLM-based generation methods.
2025-07-30
colmweb.org/COLM/2025/Workshop/LM4Sci (published)
openreview.net
openreview.net
Capacity-Constrained Continual Learning
Zheng Wen
Doina Precup
Benjamin Van Roy
Satinder Singh
2025-07-28
ArXiv (preprint)
doi.org
arxiv.org
Latent brain subtypes of chronotype reveal unique behavioral and health profiles: an across-cohort validation
Le Zhou
Karin Saltoun
Justin Marotta
Shambhavi Aggarwal
Jakub Kopal
Julie Carrier
Kai-Florian Storch
Robin Dunbar
Danilo Bzdok
Chronotype is shaped by the complex interplay of endogenous and exogenous factors. This trait ties into various behaviors in the wider socie… (see more)ty and is linked to the prevalence of psychiatric and metabolic conditions. Despite its multifaceted nature, prior research has treated chronotype as a monolithic trait across the population, risking overlooking substantial heterogeneity in neural and behavioral fingerprints of both early risers and night owls. To test for such hidden subgroups, we developed a supervised pattern-learning framework for trait subtyping, integrating three complementary brain-imaging modalities with deep behavior, diagnosis, and drug prescription profiling from 27,030 UK Biobank participants. We identified and characterized five distinct biologically valid chronotype subtypes: (1) typical eveningness, (2) depression-associated eveningness, (3) typical morningness, (4) morningness with greater expression in females, and (5) eveningness with greater expression in males. Each uncovered subtype showed unique patterns across brain, behavioral and health profiles. We finally externally validated these subtypes in 10,550 US children from the ABCD Study® cohort, which revealed reversed age distributions and replicated sex-associated brain-behavioral patterns, underscoring the fact that potential divergences between chronotype traits observed throughout adulthood may begin to emerge early in life. These findings highlight underappreciated sources of population variation that echo the rhythm of people’s inner clock.
2025-07-28
Research Square (preprint)
doi.org