arXiv subjects

Zilinghan Li

Publications and source records attributed to Zilinghan Li.

At least 19 recordsLinked to original sources

arXiv2026

Towards Global Federated Genome-Wide Association Meta-Analysis Using GA4GH TES

Genome-wide association studies (GWAS) gain statistical power from large, ancestrally diverse cohorts, but privacy regulations and data-residency constraints often prevent genomic data from being centrally pooled across institutional or national borders. We present a privacy-preserving federated GWAS meta-analysis pipeline built on the APPFL framework, in which each site computes local GWAS summary statistics and transmits only aggregate results, never individual-level genotypes. Analysis is executed through a global network of Global Alliance for Genomics and Health (GA4GH) Task Execution Service (TES) endpoints, which allows computation to move to the data rather than the reverse. The server performs inverse-variance-weighted fixed-effect meta-analysis and returns aggregated results to all sites, while HiveWatch, our developed geographic observability toolkit, provides real-time monitoring of distributed task execution. In a five-site simulation over 100,000 synthetic individuals and roughly 240,000 variants for Type 2 Diabetes and Body Mass Index, the federated meta-analysis reproduces the association signal expected from a pooled analysis without centralizing any genotype data, showing that standards-based task execution and federated learning enables a practical privacy-preserving infrastructure for international GWAS meta-analysis.

cs.DC↗

arXiv2026

Federated Learning on the American Science Cloud using APPFL

The American Science Cloud (AmSC), established under the Genesis Mission of the U.S. Department of Energy (DOE), aims to integrate DOE high-performance computing systems, experimental facilities, and data resources into a single, coordinated, AI-driven discovery platform. AmSC's early services focus on curated artifacts, such as gated inference access to hosted models, experiment tracking, and function execution across computing facilities. However, what these services lack is a means to train a model across organizational boundaries where data cannot be centralized due to policy, privacy, or scale. This is, by definition, a use case for federated learning (FL) and a growing class of scientific AI. In this paper, we show that this gap can be bridged by deploying the orchestration logic of the Advanced Privacy-Preserving Federated Learning (APPFL) framework as a scalable cloud service on top of the primitives AmSC already provides: project-scoped authentication that supports secure and reliable federation membership, function execution that drives distributed training at each site, experiment tracking that records round-level performance, and finally, the model-hosting and inference infrastructure that can be leveraged to distribute the federated trained models to authorized participants. We argue that offering federated computing as an important AmSC service would unlock privacy-constrained scientific collaborations, enabling public-private partnerships in model building while exercising and enhancing the platform's own federated infrastructure.

cs.DC↗

arXiv2026

FedQueue: Queue-Aware Federated Learning for Cross-Facility HPC Training

Federated learning (FL) across multiple HPC facilities faces stochastic admission delays from batch schedulers that dominate wall-clock time. Synchronous FL suffers from severe stragglers, while asynchronous FL accumulates stale updates when queues spike. We propose FedQueue, a queue-aware FL protocol that incorporates scheduler delays directly into training and aggregation, which (i) predicts per-facility queue delays online to budget local work, (ii) applies cutoff-based admission that buffers late arrivals to bound staleness, and (iii) performs staleness-aware aggregation to stabilize heterogeneous local workloads. We prove the convergence for non-convex objectives at rate $\mathcal{O}(1/\sqrt{R})$ under bounded staleness, and show that the admission controls yield bounded staleness with high probability under queue-prediction error. Real-world cross-facility deployment of FedQueue shows 20.5% improvement over baseline algorithms. Controlled queue simulations demonstrate robust improvement over the baselines; in particular, up to 60% reduction in time to reach a target accuracy level under high queue variance and non-IID partitions.

cs.DC↗

arXiv2026

Scalable Cross-Facility Federated Learning for Scientific Foundation Models on Multiple Supercomputers

Artificial Intelligence for scientific applications increasingly requires training large models on data that cannot be centralized due to privacy constraints, data sovereignty, or the sheer volume of data generated. Federated learning (FL) addresses this by enabling collaborative training without centralizing raw data, but scientific applications demand model scales that requires extensive computing resources, typically offered at High Performance Computing (HPC) facilities. Deploying FL experiments across HPC facilities introduces challenges beyond cloud or enterprise settings. We present a comprehensive cross-facility FL framework for heterogeneous HPC environments, built on Advanced Privacy-Preserving Federated Learning (APPFL) framework with Globus Compute and Transfer orchestration, and evaluate it across four U.S. Department of Energy (DOE) leadership-class supercomputers. We demonstrate that FL experiments across HPC facilities are practically achievable, characterize key sources of heterogeneity impacting the training performance, and show that algorithmic choices matter significantly under realistic HPC scheduling conditions. We validate the scientific applicability by fine-tuning a large language model on a chemistry instruction dataset, and identify scheduler-aware algorithm design as a critical open challenge for future deployments.

cs.LG↗

arXiv2025

TICON: A Slide-Level Tile Contextualizer for Histopathology Representation Learning

The interpretation of small tiles in large whole slide images (WSI) often needs a larger image context. We introduce TICON, a transformer-based tile representation contextualizer that produces rich, contextualized embeddings for ''any'' application in computational pathology. Standard tile encoder-based pipelines, which extract embeddings of tiles stripped from their context, fail to model the rich slide-level information essential for both local and global tasks. Furthermore, different tile-encoders excel at different downstream tasks. Therefore, a unified model is needed to contextualize embeddings derived from ''any'' tile-level foundation model. TICON addresses this need with a single, shared encoder, pretrained using a masked modeling objective to simultaneously unify and contextualize representations from diverse tile-level pathology foundation models. Our experiments demonstrate that TICON-contextualized embeddings significantly improve performance across many different tasks, establishing new state-of-the-art results on tile-level benchmarks (i.e., HEST-Bench, THUNDER, CATCH) and slide-level benchmarks (i.e., Patho-Bench). Finally, we pretrain an aggregator on TICON to form a slide-level foundation model, using only 11K WSIs, outperforming SoTA slide-level foundation models pretrained with up to 350K WSIs.

cs.CV↗

arXiv2025

Experiences Building Enterprise-Level Privacy-Preserving Federated Learning to Power AI for Science

Federated learning (FL) is a promising approach to enabling collaborative model training without centralized data sharing, a crucial requirement in scientific domains where data privacy, ownership, and compliance constraints are critical. However, building user-friendly enterprise-level FL frameworks that are both scalable and privacy-preserving remains challenging, especially when bridging the gap between local prototyping and distributed deployment across heterogeneous client computing infrastructures. In this paper, based on our experiences building the Advanced Privacy-Preserving Federated Learning (APPFL) framework, we present our vision for an enterprise-grade, privacy-preserving FL framework designed to scale seamlessly across computing environments. We identify several key capabilities that such a framework must provide: (1) Scalable local simulation and prototyping to accelerate experimentation and algorithm design; (2) seamless transition from simulation to deployment; (3) distributed deployment across diverse, real-world infrastructures, from personal devices to cloud clusters and HPC systems; (4) multi-level abstractions that balance ease of use and research flexibility; and (5) comprehensive privacy and security through techniques such as differential privacy, secure aggregation, robust authentication, and confidential computing. We further discuss architectural designs to realize these goals. This framework aims to bridge the gap between research prototypes and enterprise-scale deployment, enabling scalable, reliable, and privacy-preserving AI for science.

cs.DC↗

arXiv2025

RADAR-Radio Afterglow Detection and AI-driven Response: A Federated Framework for Gravitational Wave Event Follow-Up

The landmark detection of both gravitational waves (GWs) and electromagnetic (EM) radiation from the binary neutron star merger GW170817 has spurred efforts to streamline the follow-up of GW alerts in current and future observing runs of ground-based GW detectors. Within this context, the radio band of the EM spectrum presents unique challenges. Sensitive radio facilities capable of detecting the faint radio afterglow seen in GW170817, and with sufficient angular resolution, have small fields of view compared to typical GW localization areas. Additionally, theoretical models predict that the radio emission from binary neutron star mergers can evolve over weeks to years, necessitating long-term monitoring to probe the physics of the various post-merger ejecta components. These constraints, combined with limited radio observing resources, make the development of more coordinated follow-up strategies essential -- especially as the next generation of GW detectors promise a dramatic increase in detection rates. Here, we present RADAR, a framework designed to address these challenges by promoting community-driven information sharing, federated data analysis, and system resilience, while integrating AI methods for both GW signal identification and radio data aggregation. We show that it is possible to preserve data rights while sharing models that can help design and/or update follow-up strategies. We demonstrate our approach through a case study of GW170817, and discuss future directions for refinement and broader application.

astro-ph.HE↗

arXiv2025

CDG-MAE: Cross-view Masked Modeling using Diffusion Generated Views

Cross-view masked autoencoding has emerged as a powerful pretext task for learning dense correspondences, which are essential for applications such as video label propagation. The cross-view pretext task is modeled with a masked autoencoder, where a masked target view is reconstructed from an anchor view. However, acquiring effective training data remains a challenge - collecting diverse video datasets is costly, while simple image crops lack the necessary pose variations, underperforming video-based methods. This paper introduces CDG-MAE, a novel MAE-based self-supervised method that uses diverse synthetic views generated from static images via an image-conditioned diffusion model. We present a quantitative method to evaluate the local and global consistency of the generated views to choose the right diffusion model for cross-view self-supervised pretraining. These generated views exhibit substantial changes in pose and perspective, providing a rich training signal that overcomes the limitations of video and crop-based anchors. Furthermore, we enhance the standard single-anchor MAE setting to a multi-anchor masking strategy to increase the difficulty of the pretext task. CDG-MAE substantially narrows the gap to video-based MAE methods, while maintaining the data advantages of image-only MAEs.

cs.CV↗

arXiv2025

PixCell: A generative foundation model for digital histopathology images

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, there are unique problems in pathology, such as annotated data scarcity, privacy regulations in data sharing, and inherently generative tasks like virtual staining. Generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address these problems through image synthesis. We introduce PixCell, the first generative foundation model for histopathology images. PixCell is a diffusion model trained on PanCan-30M, a large, diverse dataset derived from 69,184 H&E-stained whole slide images of various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any human-annotated data. By conditioning on real slides, the synthetic images capture the properties of the real data and can be used as data augmentation for small-scale datasets to boost classification performance. We prove the foundational versatility of PixCell by applying it to two generative downstream tasks: privacy-preserving synthetic data generation and virtual IHC staining. PixCell's high-fidelity conditional generation enables institutions to use their private data to synthesize highly realistic, site-specific surrogate images that can be shared in place of raw patient data. Furthermore, using datasets of roughly paired H&E-IHC tiles, we learn to translate PixCell's conditioning from H&E to multiple IHC stains, allowing the generation of IHC images from H&E inputs. Our trained models are publicly released to accelerate research in computational pathology.

eess.IV↗

arXiv2025

CADRE: Customizable Assurance of Data Readiness in Privacy-Preserving Federated Learning

Privacy-Preserving Federated Learning (PPFL) is a decentralized machine learning approach where multiple clients train a model collaboratively. PPFL preserves the privacy and security of a client's data without exchanging it. However, ensuring that data at each client is of high quality and ready for federated learning (FL) is a challenge due to restricted data access. In this paper, we introduce CADRE (Customizable Assurance of Data Readiness) for federated learning (FL), a novel framework that allows users to define custom data readiness (DR) metrics, rules, and remedies tailored to specific FL tasks. CADRE generates comprehensive DR reports based on the user-defined metrics, rules, and remedies to ensure datasets are prepared for FL while preserving privacy. We demonstrate a practical application of CADRE by integrating it into an existing PPFL framework. We conducted experiments across six datasets and addressed seven different DR issues. The results illustrate the versatility and effectiveness of CADRE in ensuring DR across various dimensions, including data quality, privacy, and fairness. This approach enhances the performance and reliability of FL models as well as utilizes valuable resources.

cs.CR↗

arXiv2025

FedCostAware: Enabling Cost-Aware Federated Learning on the Cloud

Federated learning (FL) is a distributed machine learning (ML) approach that allows multiple clients to collaboratively train ML models without exchanging original training data, offering a solution that is particularly valuable in sensitive domains such as biomedicine. However, training robust FL models often requires substantial computing resources from participating clients, which may not be readily available at institutions such as hospitals. While cloud platforms offer on-demand access to such resources, their usage can incur significant costs, particularly in distributed training scenarios where poor coordination strategies can lead to substantial resource wastage. To address this, we introduce FedCostAware, a cost-aware scheduling algorithm designed to optimize synchronous FL on cloud spot instances. FedCostAware addresses the challenges of training on spot instances and different client budgets by employing intelligent management of the lifecycle of spot instances. This approach minimizes resource idle time and overall expenses. Comprehensive experiments across multiple datasets demonstrate that FedCostAware significantly reduces cloud computing costs compared to conventional spot and on-demand schemes, enhancing the accessibility and affordability of FL.

cs.DC↗

arXiv2025

Pathology Image Compression with Pre-trained Autoencoders

The growing volume of high-resolution Whole Slide Images in digital histopathology poses significant storage, transmission, and computational efficiency challenges. Standard compression methods, such as JPEG, reduce file sizes but often fail to preserve fine-grained phenotypic details critical for downstream tasks. In this work, we repurpose autoencoders (AEs) designed for Latent Diffusion Models as an efficient learned compression framework for pathology images. We systematically benchmark three AE models with varying compression levels and evaluate their reconstruction ability using pathology foundation models. We introduce a fine-tuning strategy to further enhance reconstruction fidelity that optimizes a pathology-specific learned perceptual metric. We validate our approach on downstream tasks, including segmentation, patch classification, and multiple instance learning, showing that replacing images with AE-compressed reconstructions leads to minimal performance degradation. Additionally, we propose a K-means clustering-based quantization method for AE latents, improving storage efficiency while maintaining reconstruction quality. We provide the weights of the fine-tuned autoencoders at https://huggingface.co/collections/StonyBrook-CVLab/pathology-fine-tuned-aes-67d45f223a659ff2e3402dd0.

eess.IV↗

arXiv2025

EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

cs.AI↗

arXiv2024

Gen-SIS: Generative Self-augmentation Improves Self-supervised Learning

Self-supervised learning (SSL) methods have emerged as strong visual representation learners by training an image encoder to maximize similarity between features of different views of the same image. To perform this view-invariance task, current SSL algorithms rely on hand-crafted augmentations such as random cropping and color jittering to create multiple views of an image. Recently, generative diffusion models have been shown to improve SSL by providing a wider range of data augmentations. However, these diffusion models require pre-training on large-scale image-text datasets, which might not be available for many specialized domains like histopathology. In this work, we introduce Gen-SIS, a diffusion-based augmentation technique trained exclusively on unlabeled image data, eliminating any reliance on external sources of supervision such as text captions. We first train an initial SSL encoder on a dataset using only hand-crafted augmentations. We then train a diffusion model conditioned on embeddings from that SSL encoder. Following training, given an embedding of the source image, this diffusion model can synthesize its diverse views. We show that these `self-augmentations', i.e. generative augmentations based on the vanilla SSL encoder embeddings, facilitate the training of a stronger SSL encoder. Furthermore, based on the ability to interpolate between images in the encoder latent space, we introduce the novel pretext task of disentangling the two source images of an interpolated synthetic image. We validate Gen-SIS's effectiveness by demonstrating performance improvements across various downstream tasks in both natural images, which are generally object-centric, as well as digital histopathology images, which are typically context-based.

cs.CV↗

arXiv2024

FedSpaLLM: Federated Pruning of Large Language Models

Large Language Models (LLMs) achieve state-of-the-art performance but are challenging to deploy due to their high computational and storage demands. Pruning can reduce model size, yet existing methods assume public access to calibration data, which is impractical for privacy-sensitive applications. To address the challenge of pruning LLMs in privacy-preserving settings, we propose FedSpaLLM, the first federated learning framework designed specifically for pruning LLMs. FedSpaLLM enables clients to prune their models locally based on private data while accounting for system heterogeneity and maintaining communication efficiency. Our framework introduces several key innovations: (1) a novel $\ell_0$-norm aggregation function that ensures only non-zero weights are averaged across clients, preserving important model parameters; (2) an adaptive mask expansion technique that meets global sparsity targets while accommodating client-specific pruning decisions; and (3) a layer sampling strategy that reduces communication overhead and personalizes the pruning process based on client resources. Extensive experiments show that FedSpaLLM improves pruning performance in diverse federated settings.

cs.LG↗

arXiv2024

Advances in Privacy Preserving Federated Learning to Realize a Truly Learning Healthcare System

The concept of a learning healthcare system (LHS) envisions a self-improving network where multimodal data from patient care are continuously analyzed to enhance future healthcare outcomes. However, realizing this vision faces significant challenges in data sharing and privacy protection. Privacy-Preserving Federated Learning (PPFL) is a transformative and promising approach that has the potential to address these challenges by enabling collaborative learning from decentralized data while safeguarding patient privacy. This paper proposes a vision for integrating PPFL into the healthcare ecosystem to achieve a truly LHS as defined by the Institute of Medicine (IOM) Roundtable.

cs.CR↗

arXiv2024

Advances in APPFL: A Comprehensive and Extensible Federated Learning Framework

Federated learning (FL) is a distributed machine learning paradigm enabling collaborative model training while preserving data privacy. In today's landscape, where most data is proprietary, confidential, and distributed, FL has become a promising approach to leverage such data effectively, particularly in sensitive domains such as medicine and the electric grid. Heterogeneity and security are the key challenges in FL, however, most existing FL frameworks either fail to address these challenges adequately or lack the flexibility to incorporate new solutions. To this end, we present the recent advances in developing APPFL, an extensible framework and benchmarking suite for federated learning, which offers comprehensive solutions for heterogeneity and security concerns, as well as user-friendly interfaces for integrating new algorithms or adapting to new applications. We demonstrate the capabilities of APPFL through extensive experiments evaluating various aspects of FL, including communication efficiency, privacy preservation, computational performance, and resource utilization. We further highlight the extensibility of APPFL through case studies in vertical, hierarchical, and decentralized FL. APPFL is fully open-sourced on GitHub at https://github.com/APPFL/APPFL.

cs.LG↗

arXiv2024

Secure Federated Learning Across Heterogeneous Cloud and High-Performance Computing Resources -- A Case Study on Federated Fine-tuning of LLaMA 2

Federated learning enables multiple data owners to collaboratively train robust machine learning models without transferring large or sensitive local datasets by only sharing the parameters of the locally trained models. In this paper, we elaborate on the design of our Advanced Privacy-Preserving Federated Learning (APPFL) framework, which streamlines end-to-end secure and reliable federated learning experiments across cloud computing facilities and high-performance computing resources by leveraging Globus Compute, a distributed function as a service platform, and Amazon Web Services. We further demonstrate the use case of APPFL in fine-tuning a LLaMA 2 7B model using several cloud resources and supercomputers.

cs.DC↗