arXiv subjects

Samuel E. Armstrong

Publications and source records attributed to Samuel E. Armstrong.

10 recordsLinked to original sources

arXiv2025

Toward an AI Reasoning-Enabled System for Patient-Clinical Trial Matching

Screening patients for clinical trial eligibility remains a manual, time-consuming, and resource-intensive process. We present a secure, scalable proof-of-concept system for Artificial Intelligence (AI)-augmented patient-trial matching that addresses key implementation challenges: integrating heterogeneous electronic health record (EHR) data, facilitating expert review, and maintaining rigorous security standards. Leveraging open-source, reasoning-enabled large language models (LLMs), the system moves beyond binary classification to generate structured eligibility assessments with interpretable reasoning chains that support human-in-the-loop review. This decision support tool represents eligibility as a dynamic state rather than a fixed determination, identifying matches when available and offering actionable recommendations that could render a patient eligible in the future. The system aims to reduce coordinator burden, intelligently broaden the set of trials considered for each patient and guarantee comprehensive auditability of all AI-generated outputs.

cs.AI↗

arXiv2025

Semantic Nutrition Estimation: Predicting Food Healthfulness from Text Descriptions

Accurate nutritional assessment is critical for public health, but existing profiling systems require detailed data often unavailable or inaccessible from colloquial text descriptions of food. This paper presents a machine learning pipeline that predicts the comprehensive Food Compass Score 2.0 (FCS) from text descriptions. Our approach uses multi-headed neural networks to process hybrid feature vectors that combine semantic text embeddings, lexical patterns, and domain heuristics, alongside USDA Food and Nutrient Database for Dietary Studies (FNDDS) data. The networks estimate the nutrient and food components necessary for the FCS algorithm. The system demonstratedstrong predictive power, achieving a median R^2 of 0.81 for individual nutrients. The predicted FCS correlated strongly with published values (Pearson's r = 0.77), with a mean absolute difference of 14.0 points. While errors were largest for ambiguous or processed foods, this methodology translates language into actionable nutritional information, enabling scalable dietary assessment for consumer applications and research.

cs.LG↗

arXiv2025

Vision Foundry: A System for Training Foundational Vision AI Models

Self-supervised learning (SSL) leverages vast unannotated medical datasets, yet steep technical barriers limit adoption by clinical researchers. We introduce Vision Foundry, a code-free, HIPAA-compliant platform that democratizes pre-training, adaptation, and deployment of foundational vision models. The system integrates the DINO-MX framework, abstracting distributed infrastructure complexities while implementing specialized strategies like Magnification-Aware Distillation (MAD) and Parameter-Efficient Fine-Tuning (PEFT). We validate the platform across domains, including neuropathology segmentation, lung cellularity estimation, and coronary calcium scoring. Our experiments demonstrate that models trained via Vision Foundry significantly outperform generic baselines in segmentation fidelity and regression accuracy, while exhibiting robust zero-shot generalization across imaging protocols. By bridging the gap between advanced representation learning and practical application, Vision Foundry enables domain experts to develop state-of-the-art clinical AI tools with minimal annotation overhead, shifting focus from engineering optimization to clinical discovery.

q-bio.QM↗

arXiv2025

Leveraging LLMs for Structured Data Extraction from Unstructured Patient Records

Manual chart review remains an extremely time-consuming and resource-intensive component of clinical research, requiring experts to extract often complex information from unstructured electronic health record (EHR) narratives. We present a secure, modular framework for automated structured feature extraction from clinical notes leveraging locally deployed large language models (LLMs) on institutionally approved, Health Insurance Portability and Accountability Act (HIPPA)-compliant compute infrastructure. This system integrates retrieval augmented generation (RAG) and structured response methods of LLMs into a widely deployable and scalable container to provide feature extraction for diverse clinical domains. In evaluation, the framework achieved high accuracy across multiple medical characteristics present in large bodies of patient notes when compared against an expert-annotated dataset and identified several annotation errors missed in manual review. This framework demonstrates the potential of LLM systems to reduce the burden of manual chart review through automated extraction and increase consistency in data capture, accelerating clinical research.

cs.AI↗

arXiv2025

Institutional Platform for Secure Self-Service Large Language Model Exploration

This paper introduces a user-friendly platform developed by the University of Kentucky Center for Applied AI, designed to make large, customized language models (LLMs) more accessible. By capitalizing on recent advancements in multi-LoRA inference, the system efficiently accommodates custom adapters for a diverse range of users and projects. The paper outlines the system's architecture and key features, encompassing dataset curation, model training, secure inference, and text-based feature extraction. We illustrate the establishment of a tenant-aware computational network using agent-based methods, securely utilizing islands of isolated resources as a unified system. The platform strives to deliver secure LLM services, emphasizing process and data isolation, end-to-end encryption, and role-based resource authentication. This contribution aligns with the overarching goal of enabling simplified access to cutting-edge AI models and technology in support of scientific discovery.

cs.CR↗

arXiv2025

SmartState: An Automated Research Protocol Adherence System

Developing and enforcing study protocols is crucial in medical research, especially as interactions with participants become more intricate. Traditional rules-based systems struggle to provide the automation and flexibility required for real-time, personalized data collection. We introduce SmartState, a state-based system designed to act as a personal agent for each participant, continuously managing and tracking their unique interactions. Unlike traditional reporting systems, SmartState enables real-time, automated data collection with minimal oversight. By integrating large language models to distill conversations into structured data, SmartState reduces errors and safeguards data integrity through built-in protocol and participant auditing. We demonstrate its utility in research trials involving time-dependent participant interactions, addressing the increasing need for reliable automation in complex clinical studies.

cs.HC↗

arXiv2024

Toward Automated Clinical Transcriptions

Administrative documentation is a major driver of rising healthcare costs and is linked to adverse outcomes, including physician burnout and diminished quality of care. This paper introduces a secure system that applies recent advancements in speech-to-text transcription and speaker-labeling (diarization) to patient-provider conversations. This system is optimized to produce accurate transcriptions and highlight potential errors to promote rapid human verification, further reducing the necessary manual effort. Applied to over 40 hours of simulated conversations, this system offers a promising foundation for automating clinical transcriptions.

eess.AS↗

arXiv2024

State-Based Automation for Time-Restricted Eating Adherence

Developing and enforcing study protocols is a foundational component of medical research. As study complexity for participant interactions increases, translating study protocols to supporting application code becomes challenging. A collaboration exists between the University of Kentucky and Arizona State University to determine the efficacy of time-restricted eating in improving metabolic risk among postmenopausal women. This study utilizes a graph-based approach to monitor and support adherence to a designated schedule, enabling the validation and step-wise audit of participants' statuses to derive dependable conclusions. A texting service, driven by a participant graph, automatically manages interactions and collects data. Participant data is then accessible to the research study team via a website, which enables viewing, management, and exportation. This paper presents a system for automatically managing participants in a time-restricted eating study that eliminates time-consuming interactions with participants.

cs.HC↗

arXiv2024

Multi-Modal Machine Learning Framework for Automated Seizure Detection in Laboratory Rats

A multi-modal machine learning system uses multiple unique data sources and types to improve its performance. This article proposes a system that combines results from several types of models, all of which are trained on different data signals. As an example to illustrate the efficacy of the system, an experiment is described in which multiple types of data are collected from rats suffering from seizures. This data includes electrocorticography readings, piezoelectric motion sensor data, and video recordings. Separate models are trained on each type of data, with the goal of classifying each time frame as either containing a seizure or not. After each model has generated its classification predictions, these results are combined. While each data signal works adequately on its own for prediction purposes, the significant imbalance in class labels leads to increased numbers of false positives, which can be filtered and removed by utilizing all data sources. This paper will demonstrate that, after postprocessing and combination techniques, classification accuracy is improved with this multi-modal system when compared to the performance of each individual data source.

cs.LG↗

arXiv2023

CLASSify: A Web-Based Tool for Machine Learning

Machine learning classification problems are widespread in bioinformatics, but the technical knowledge required to perform model training, optimization, and inference can prevent researchers from utilizing this technology. This article presents an automated tool for machine learning classification problems to simplify the process of training models and producing results while providing informative visualizations and insights into the data. This tool supports both binary and multiclass classification problems, and it provides access to a variety of models and methods. Synthetic data can be generated within the interface to fill missing values, balance class labels, or generate entirely new datasets. It also provides support for feature evaluation and generates explainability scores to indicate which features influence the output the most. We present CLASSify, an open-source tool for simplifying the user experience of solving classification problems without the need for knowledge of machine learning.

cs.LG↗