arXiv subjects

Heidi Hanson

Publications and source records attributed to Heidi Hanson.

9 recordsLinked to original sources

arXiv2026

Score-Based Generative Data Assimilation for Integrating Aggregated Surveillance Data into Agent-Based Models in Epidemic Tracking

Reliable epidemic monitoring often requires inferring regional infection burden and transmission heterogeneity from noisy, spatially aggregated, and potentially sparse surveillance data. Agent-based models (ABMs) are attractive for this task because they represent individual behavior, contact heterogeneity, and localized interventions, but these same features make them difficult to calibrate online. We develop a generative AI-based data-assimilation (GenDA) framework for partially observed epidemic ABMs that estimates both the epidemic state and a heterogeneous parameter field while respecting the gap between observable macrostates and latent agent-level microstates. GenDA combines a training-free, score-based generative update for macrostate correction with a direct parameter update based on macrostate discrepancies, followed by a macro-micro reassignment step that restores consistency with the ABM. In controlled and geographically explicit synthetic experiments, the framework recovers regional epidemic burden, dominant hotspot structures, and effective transmission heterogeneity from aggregated observations, while improving post-assimilation forecasts relative to state-only assimilation.

math.NA↗

arXiv2026

Decoupled I/O-Dominant Pipelines for Large-Scale Whole-Slide Image Embedding Extraction

Whole-slide images (WSIs) are central to computational pathology but are prohibitively large, making patch-based processing the practical unit for foundation model inference. At scale, however, generating and handling massive numbers of patches on quickly introduces significant I/O and orchestration overhead, often dominating end-to-end performance. We present a decoupled, I/O-aware pipeline for large-scale WSI embedding extraction that decomposes the workflow into three stages: (1) patch generation and staging, (2) embarrassingly parallel embedding inference, and (3) sharded vector database ingestion. This design isolates data movement from compute, enabling efficient patch delivery, scalable multi-node inference with minimal communication. The resulting system produces a distributed vector database where embeddings are persistently coupled with rich metadata (e.g., patient, slide, and patch attributes), enabling efficient filtering, retrieval, and downstream reuse. This representation database is compact and reusable for tasks such as retrieval, classification, and few-shot learning, particularly benefiting low-resource environments. We show that decoupling I/O, computation, and ingestion enables high-throughput WSI embedding extraction at scale. By characterizing the scaling envelope, we demonstrate that storage dominates beyond moderate concurrency, reframing WSI embedding extraction as a data-centric systems problem rather than a purely compute-bound workload.

cs.DC↗

arXiv2026

LLM-powered reasoning in agent-based modeling

Agent-based modeling (ABM) has the capability to model millions of individuals and their interactions, which is useful for policy making. However, ABMs have traditionally relied on static prior, which prevents the models from adapting to real-time changes. Our research provides a novel approach to addressing this information gap. Large language models (LLMs) offer new opportunities to predict human decision-making. Here, we introduce a scalable Hybrid Agent-based and Language-driven Epidemic (HALE) modeling framework that leverages LLMs to predict human decision-making in an ABM simulation. As a proof-of-concept, we use HALE to simulate COVID-19 and its effects in Salt Lake County, UT.

cs.AI↗

arXiv2026

In-Domain Supervised Pathology Report Classification: A Reproducible Pipeline from Data Curation to Production-Matched Evaluation

We introduce an in-domain supervised pipeline designed to counter the out-of-distribution performance drop that hampers supervised biomedical NLP models, a problem observed when models trained on pathology reports are moved across cancer registries. Our contribution is a reproducible recipe for training a supervised classifier from routinely collected cancer registry data. It describes how to build the in-domain training set and a production-matched holdout, and to choose operating points that keep the false-negative rate (FNR) very low while keeping reviewer workload manageable. The pipeline standardizes data curation with facility-stratified sampling and separate handling of reports linked to registry cases, and includes a blinded manual audit to estimate positive-case prevalence and label noise. On a 418k-report holdout set, the Kentucky model achieved FNR 0.003 and false-positive rate (FPR) 0.097, improving over the Seattle-trained MOSSAIC OncoID baseline (FNR 0.010, FPR 0.183) and raising F1 from 0.860 to 0.922. In a blinded manual review of 600 reports, estimated positive prevalence declined from 0.500 to 0.398, indicating substantial label noise with errors concentrated in rare primary sites.

cs.CL↗

arXiv2026

STAMP: Selective Task-Aware Mechanism for Text Privacy

We present STAMP (Selective Task-Aware Mechanism for Text Privacy), a new framework for task-aware text privatization that achieves an improved privacy-utility trade-off. STAMP selectively allocates privacy budgets across tokens by jointly considering (i) each token's importance to the downstream task (as measured via a task- or query-specific representation), and (ii) its privacy sensitivity (e.g., names, dates, identifiers). This token-level partitioning enables fine-grained, group-wise control over the level of noise applied to different parts of the input, balancing privacy protection with task relevance. To privatize individual token embeddings, we introduce the polar mechanism, which perturbs only the direction of embeddings on the unit sphere while preserving their magnitude. Decoding is performed via cosine nearest-neighbor search, aligning the perturbation geometry with the decoding geometry. Unlike isotropic noise mechanisms, the polar mechanism maintains semantic neighborhoods in the embedding space and better preserves downstream utility. Experimental evaluations on SQuAD, Yelp, and AG News datasets demonstrate that STAMP, when combined with the normalized polar mechanism, consistently achieves superior privacy-utility trade-offs across varying per-token privacy budgets.

cs.LG↗

arXiv2026

Resource-Adaptive Federated Text Generation with Differential Privacy

In cross-silo federated learning (FL), sensitive text datasets remain confined to local organizations due to privacy regulations, making repeated training for each downstream task both communication-intensive and privacy-demanding. A promising alternative is to generate differentially private (DP) synthetic datasets that approximate the global distribution and can be reused across tasks. However, pretrained large language models (LLMs) often fail under domain shift, and federated finetuning is hindered by computational heterogeneity: only resource-rich clients can update the model, while weaker clients are excluded, amplifying data skew and the adverse effects of DP noise. We propose a flexible participation framework that adapts to client capacities. Strong clients perform DP federated finetuning, while weak clients contribute through a lightweight DP voting mechanism that refines synthetic text. To ensure the synthetic data mirrors the global dataset, we apply control codes (e.g., labels, topics, metadata) that represent each client's data proportions and constrain voting to semantically coherent subsets. This two-phase approach requires only a single round of communication for weak clients and integrates contributions from all participants. Experiments show that our framework improves distribution alignment and downstream robustness under DP and heterogeneity.

cs.LG↗

arXiv2025

Learning to Diagnose Privately: DP-Powered LLMs for Radiology Report Classification

Large Language Models (LLMs) are increasingly adopted across domains such as education, healthcare, and finance. In healthcare, LLMs support tasks including disease diagnosis, abnormality classification, and clinical decision-making. Among these, multi-abnormality classification of radiology reports is critical for clinical workflow automation and biomedical research. Leveraging strong natural language processing capabilities, LLMs enable efficient processing of unstructured medical text and reduce the administrative burden of manual report analysis. To improve performance, LLMs are often fine-tuned on private, institution-specific datasets such as radiology reports. However, this raises significant privacy concerns: LLMs may memorize training data and become vulnerable to data extraction attacks, while sharing fine-tuned models risks exposing sensitive patient information. Despite growing interest in LLMs for medical text classification, privacy-preserving fine-tuning for multi-abnormality classification remains underexplored. To address this gap, we propose a differentially private (DP) fine-tuning framework for multi-abnormality classification from free-text radiology reports. Our approach integrates differential privacy with Low-Rank Adaptation (LoRA) to efficiently fine-tune LLMs on sensitive clinical data while mitigating leakage risks. We further employ labels generated by a larger LLM to train smaller models, enabling efficient inference under strong privacy guarantees. Experiments on MIMIC-CXR and CT-RATE demonstrate the effectiveness of our DP-LoRA framework across varying privacy regimes. On MIMIC-CXR, our method achieves weighted F1-scores up to 0.89 under moderate privacy budgets, approaching non-private LoRA (0.90) and full fine-tuning (0.96), confirming that strong privacy can be achieved with only modest performance trade-offs.

cs.CR↗

arXiv2025

Radon Exposure Dataset

Exposure to elevated radon levels in the home is one of the leading causes of lung cancer in the world. The following study describes the creation of a comprehensive, state-level dataset designed to enable the modeling and prediction of household radon concentrations at Zip Code Tabulation Area (ZCTA) and sub-kilometer scales. Details include the data collection and processing involved in compiling physical and demographic factors for Pennsylvania and Utah. Attempting to mitigate this risk requires identifying the underlying geological causes and the populations that might be at risk. This work focuses on identifying at-risk populations throughout Pennsylvania and Utah, where radon levels are some of the highest in the country. The resulting dataset harmonizes geological and demographic factors from various sources and spatial resolutions, including temperature, geochemistry, and soil characteristics. Demographic variables such as the household heating fuel used, the age of building, and the housing type provide further insight into which populations could be most susceptible in areas with potentially high radon levels. This dataset also serves as a foundational resource for two other studies conducted by the authors. The resolution of the data provides a novel approach to predicting potential radon exposure, and the data processing conducted for these states can be scaled up to larger spatial resolutions (e.g., the Contiguous United States [CONUS]) and allow for a broad reclassification of radon exposure potential in the United States.

cs.CE↗

arXiv2023

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.

cs.AI↗