Digital Commons Network^™

Revised Final Multi-Pathway Residential Metals Abatement Program Plan, Atlantic Richfield Company, Butte Silver Bow

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

A Data-Driven Sliding-Window Pairwise Comparative Approach For The Estimation Of Transmission Fitness Of Sars-Cov-2 Variants And The Construction Of The Evolution Fitness Landscape, Md Jubair Pantho, Richard Annan, Landen Alexander Bauder, Sophia Huang, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here, we introduce a sliding-window data-driven pairwise comparison method, the differential population growth rate (DPGR) that uses viral strains as internal controls to mitigate sampling biases. DPGR is applicable in time windows in which the logarithmic ratio of two variant subpopulations is approximately linear. We apply DPGR to genomic surveillance data and focus on variants of concern (VOCs) in multiple countries and regions. …

The Invisible Influencer In Information Infrastructure, Herbert Van De Sompel, Michael L. Nelson

Computer Science Faculty Publications

The UPS Prototype was a proof-of-concept web portal built in preparation for the Universal Preprint Service Meeting held in October 1999 in Santa Fe, New Mexico. The portal provided search functionality for a set of metadata records that had been aggregated from a range of repositories that hosted preprints, working papers, and technical reports. Every search result was overlaid with a dynamically generated menu, called an SFX-menu, that provided a selection of value-adding links for the described scholarly work. The meeting eventually led to the Open Archives Initiative and its Protocol for Metadata Harvesting (OAI-PMH), which remains widely used in …

Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …

Coming Back Differently: An Exploratory Case Study Of Near Death Experiences Of Webpages, Lesley Frew, Michael L. Nelson, Michele Weigle

Computer Science Faculty Publications

In this case study, we use web archives to analyze 8,824 webpages that were taken offline and subsequently put back online, thus experiencing a “near death experience.” We enumerate the stages of a webpage’s near death experience, including the change from a successful HTTP status code to non-successful and back, the intermediate stage with markers such as an under construction banner, and an analysis of how the pages came back differently.

From Philosophy To Nlu: Evolving Definitions With Research Hypotheses, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Over the past decades, alongside advancements in natural language processing, significant attention has been paid to training models to automatically extract, understand, test, and generate hypotheses in open and scientific domains. However, interpretations of the term hypothesis for various natural language understanding (NLU) tasks have migrated from traditional definitions in the natural, social, and formal sciences. Even within NLU, we observe differences defining hypotheses across literature. In this paper, we overview and delineate various definitions of hypothesis. Especially, we discern the nuances of definitions across recently published NLU tasks. We highlight the importance of well-structured and well-defined hypotheses, particularly as …

From Philosophy To Nlu: Evolving Definitions Of Research Hypotheses, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Over the past decades, alongside advancements in natural language processing, significant attention has been paid to training models to automatically extract, understand, test, and generate hypotheses in open and scientific domains. However, interpretations of the term hypothesis for various natural language understanding (NLU) tasks have migrated from traditional definitions in the natural, social, and formal sciences. Even within NLU, we observe differences defining hypotheses across literature. In this paper, we overview and delineate various definitions of hypothesis. Especially, we discern the nuances of definitions across recently published NLU tasks. We highlight the importance of well-structured and well-defined hypotheses, particularly as …

Optiselect And Enshap: Integrating Machine Learning And Game Theory For Ischemic Stroke Prediction, Pritam Chakraborty, Anjan Bandyopadhyay, Sricheta Parul, Sujata Swain, Partha Sarathy Banerjee, Tapas Si, Hong Qin, Saurav Mallik

Computer Science Faculty Publications

Stroke analysis using game theory and machine learning techniques. The study investigates the use of the Shapley value in predictive ischemic brain stroke analysis. Initially, preference algorithms identify the most important features in various machine learning models, including logistic regression, K-nearest neighbor, decision tree, support vector machine (linear kernel), support vector machine ( RBF kernel), neural networks, etc. For each sample, the top 3, 4, and 5 features are evaluated and selected to evaluate their performance. The Shapley value method was used to rank the models using their best four features based on their predictive capabilities. As a result, better-performing …

Neural Topic Modeling Via Contextual And Graph Information Fusion, Jiyuan Liu, Jiaxing Yan, Chunjiang Zhu, Xingyu Liu, Qing Li, Yanghui Rao

Computer Science Faculty Publications

Topic modeling is a powerful unsupervised tool for knowledge discovery. However, existing work struggles with generating limited-quality topics that are uninformative and incoherent, which hindering interpretable insights from managing textual data. In this paper, we improve the original variational autoencoder framework by incorporating contextual and graph information to address the above issues. First, the encoder utilizes topic fusion techniques to combine contextual and bag-of-words information well, and meanwhile exploits the constraints of topic alignment and topic sharpening to generate informative topics. Second, we develop a simple word co-occurrence graph information fusion strategy that efficiently increases topic coherence. On three benchmark …

Understanding Pii Leakage In Large Language Models: A Systematic Survey, Shuai Cheng, Zhao Li, Shu Meng, Mengxia Ren, Haitao Xu, Shuai Hao, Chuan Yue, Fang Zhang

Computer Science Faculty Publications

Large Language Models (LLMs) have demonstrated exceptional success across a variety of tasks, particularly in natural language processing, leading to their growing integration into numerous facets of daily life. However, this widespread deployment has raised substantial privacy concerns, especially regarding personally identifiable information (PII), which can be directly associated with specific individuals. The leakage of such information presents significant real-world privacy threats. In this paper, we conduct a systematic investigation into existing research on PII leakage in LLMs, encompassing commonly utilized PII datasets, evaluation metrics, and current studies on both PII leakage attacks and defensive strategies. Finally, we identify unresolved …

Humans Vs. Llms On Open Domain Scientific Claim Verification: A Baseline Study, Benjamin Curtis, Stefania Dzhaman, Matthew Maisonave, Jian Wu

Computer Science Faculty Publications

Verifying scientific claims is challenging for the general public because most people lack domain knowledge. Manual verification by subject domain experts is accurate, but it is obviously not scalable to meet the rising number of scientific claims on the Web. Whether the emerging large language models and large reasoning models can be used for scientific claim verification, and how their performances compare to humans, are still research questions. To this end, we developed a new benchmark MSVEC2 that consists of 138 claims from credible fact verification websites and science news outlets. Two tasks were given to both human and LLM …

Draft Final Silver Bow Creek Conservation Area Repository Data Gap Data Summary Report (Dsr), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

This Silver Bow Creek Conservation Area (SBCCA) Repository Data Gap Data Summary Report (DSR) presents the results from the soil sampling activities conducted as specified in the SBCCA Repository Data Gap Quality Assurance Project Plan (QAPP) (referred to herein as the SBCCA Repository Data Gap QAPP; Atlantic Richfield Company, 2024). The information presented in this DSR includes laboratory analytical results from subsurface soil sampling collected from Buffalo Gulch (BG), Butte Reduction Works (BRW), Diggings East (DE), and Northside Tailings (NST) within the SBCCA. This DSR was prepared by Pioneer Technical Services, Inc. (Pioneer), 1101 S. Montana Street, Butte, Montana 59701 …

Draft Final Butte Priority Soils Operable Unit (Bpsou) Unreclaimed Sites: Ur-03 Site Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Final Horseshoe Bend Effluent Line (Hbel) Discharge Structure Surface Enhancements Work Plan, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria

Computer Science Faculty Publications

Brain metastases (BMs) are the most common adult central nervous system malignancy, affecting 20–40% of cancer patients. Accurate segmentation of metastatic lesions in multi-modal MRI is essential for treatment planning and prognosis however, manual delineation is time consuming and prone to variability. Traditional deep learning models such as U-Net, have improved segmentation accuracy but capture limited long-range dependencies and struggle with variations in metastasis size, shape, and distribution. This study introduces the Adaptive Integrated Multi-modal Segmentation (AIMS) model, an adaptive self-attention framework within a hybrid U-Net and Transformer architecture to enhance BM segmentation by leveraging multi-modal MRI integration. The proposed …

A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …

Decode The Workload: Training Deep Learning Models For Efficient Compute Cluster Representation, Ahmed Hossam Mohammed, Mark Jones, Diana Mcspadden, Malachi Schram, Bryan Hess, Kishansingh Rajput

Computer Science Faculty Publications

In this study, we address the mounting challenge of monitoring high throughput computing clusters running computationally intensive jobs, which increasingly strains system administrators. We develop autoencoders that analyze traces of Linux kernel CPU metrics to capture salient system features by producing robust compressed embeddings for various downstream tasks. In addition, we employ graph neural networks to incorporate contextual information from surrounding CPUs and assess their performance. We also demonstrate the enhanced job differentiation achieved by increasing the sampling rate of these traces. Our models are evaluated based on their ability to generate meaningful latent representations, detect anomalies, and distinguish between …

Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …

Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Accurate quantifying dietary contents, such as calories, proteins, carbohydrates, and fats, from an image of a meal plate is vital for managing diabetes. Recently, Large Multimodal Models (LMMs) have excelled in complex vision-language tasks due to their use of very large, highly diverse data. This study benchmarked the use of seven LMMs that include full and lightweight models of GPT, Gemini, and Llama for nutrition estimation based on Google's Nutrition5k dataset and our own phone-collected DonateAndLearn dataset. We analyzed the performance of LMMs and the RGB-D fusion model, in which the RGB-D model was specifically trained using Nutrition5k data. On …

Effective Pii Extraction From Llms Through Augmented Few-Shot Learning, Shuai Cheng, Shu Meng, Haitao Xu, Haoran Zhang, Shuai Hao, Chuan Yue, Wenrui Ma, Meng Han, Fang Zhang, Zhao Li

Computer Science Faculty Publications

Large Language Models (LLMs) exhibit strong natural language processing capabilities but also pose significant privacy risks, particularly regarding the leakage of Personally Identifiable Information (PII) embedded in their training data. Existing PII extraction methods suffer from the limitations of low success rates or impracticality for large-scale PII extraction. In this study, we propose a novel PII extraction approach based on enhanced few-shot learning techniques, which achieves efficient and cost-effective PII retrieval without relying on fine-tuning or jailbreaking. We evaluated our approach on both open-source and closed-source LLMs. The experimental results demonstrate that, for non-targeted PII extraction, the attack success rate …

Icu-Length Of Stay Prediction On Electronic Health Records Using Graph Neural Networks And Homogeneous Similarity Graphs, Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman Iv, Rishabh Kapoor, Preetam Ghosh

Computer Science Faculty Publications

Predicting the length of stay (LoS) is important for hospital administration, as it helps allocate proper resources, such as bed management and hospital staffing. Patients' Electronic Health Records (EHRs) contain highly relevant data for LoS prediction; however, their integration and effective use in predictive modeling for accurately estimating LoS remain challenging. To address this, we propose a homogeneous Graph Neural Network (GNN)-based framework for predicting LoS. This method employs a comprehensive data fusion strategy based on the hospital Visit-based Similarity Graph (VSG), which integrates diverse multi-modal clinical features into a coherent, homogeneous graph representation. Next, this VSG is fed into …

Characterizing Language Use In Online Accessibility Discussion Forums, Nithiya Venkatraman, Anand Ravi Aiyer, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Discussion forums are one of the favored platforms for knowledge sharing. Given their popularity, copious research exists on understanding the linguistic and behavioral characteristics of forum conversations, so as to inform the design of many downstream applications including discourse visualization, sentiment analysis, and question answering. However, prior investigations have mainly focused on general forums designed primarily for sighted users, and as such the applicability of their findings to dedicated accessibility discussion forums frequented by blind screen reader users remains unanswered. To bridge this knowledge gap and facilitate the development of better-informed assistive technologies for blind people, we investigated language use …

Colorado River Insights, 2025: Dancing With Deadpool, Colorado River Research Group

Books, Reports, and Studies

No abstract provided.

The Response Of Tropopause Phenomena To Stratospheric Variability: Rossby Wave Breaking And Tropopause Polar Vortices, Cameron R. Paquette

Electronic Theses & Dissertations (2024 - present)

Variability in the high-latitude wintertime stratospheric flow, often referred to as the stratospheric polar vortex, can precede anomalous conditions in tropospheric flow on subseasonal-to-seasonal (S2S) timescales and impact surface weather. The range of stratospheric impacts on tropospheric conditions range from shifts in the North Atlantic storm tracks, formation of cold spells, and development of extreme precipitation. Impacts of stratospheric variability are known to persist for up to 60 days, providing ample windows of opportunity in forecasting on S2S timescales. This dissertation focuses on the stratospheric impacts on tropopause-level processes, such as Rossby wave breaking (RWB) events and tropopause polar vortices …

Large Scale Machine Learning Over Knowledge Graphs, Bedirhan Gergin

Electronic Theses & Dissertations (2024 - present)

Knowledge graphs (KGs) have become popular across various fields, providing convenient access to web-based knowledge while storing and formalizing domain-specific information. By analyzing KGs, patterns, connections, and dependencies can be identified across different data sources, enabling the inference of new knowledge from given facts. As the use of KGs expands, the size of modern KGs has grown significantly, making them impossible to process within the main memory of a single computer. Distributed computing offers a viable solution to this challenge by leveraging the combined capabilities of multiple servers within a cluster. This thesis explores how distributed computing can be effectively …

Food Rescue, Food Waste, And Policy In New York: A Mixed-Methods Study Of Food System Impacts, Mariana Torres Arroyo

Electronic Theses & Dissertations (2024 - present)

This dissertation investigates how food donation policies in New York State influence the recovery, redistribution, and waste of surplus fresh produce, with a focus on fruits and vegetables. Using an interdisciplinary, systems-based approach that integrates system dynamics modeling with qualitative, community-engaged research, the study analyzes the effectiveness and unintended consequences of three major policies: Nourish New York, the Farm to Food Bank tax credit, and the Food Donation and Food Scraps Recycling Law.

Chapter 2 uses simulation modeling to examine how the tax credit and waste ban affect produce recovery and redistribution. Results show that while both policies can boost …

Safeguard Cyberspace In Ransomware Era: Risk Analysis & Cyber Insurance, Li Huang

Electronic Theses & Dissertations (2024 - present)

The increasing frequency and severity of ransomware attacks pose significant challenges for organizational cybersecurity. Fragmentation across disciplines in cyber defense has created practical gaps in the development of the necessary capabilities needed to address rapidly evolving cyber threats. This study explores the impact of ransomware attacks and the evolving role of cyber insurance as a proactive cybersecurity partner. Bridging the gap between actuarial science and cyber risk management, it proposes an interdisciplinary framework that quantifies the impact of ransomware and integrates cyber insurance into cybersecurity strategies.

The primary contribution of this study is methodology. We present a framework that remains …

Theoretical Foundations And Applied Performance Of Periodicity-Aware Imputation: Variable Bandpass Block Bootstrap Methods For Incomplete Time Series, Asmaa Ahmad

Electronic Theses & Dissertations (2024 - present)

Time series data are prevalent across a wide range of disciplines, including health surveillance, public policy, and environmental monitoring. In the presence of underlying cyclical patterns, the integrity of time series analysis depends critically on the ability to detect, model, and impute structured missing data without compromising the temporal structure. This dissertation introduces and validates a novel imputation framework that integrates the Variable Bandpass Periodic Block Bootstrap (VBPBB) into multiple imputation procedures, improving the accuracy, robustness, and interpretability of time series models under high rates of missingness and noise. The overarching goal of this dissertation was to develop and evaluate …