Digital Commons Network^™

Predicting Food Prices In Kenya Using Machine Learning: A Hybrid Model Approach With Xgboost And Gradient Boosting, Benard O. Ogol, Evans Omondi, John Olukuru, Betsy Muriithi, Kennedy Senagi

All Peer-Reviewed Publications

Introduction: Food price volatility continues to be a significant concern in Kenya's economic development, posing challenges to the country's economic stability. Methodology: This study examines the application of machine learning methods, employing a hybrid approach that combines XGBoost and gradient boosting, to predict food prices in Kenya. The food prices data from the World Food Programme, covering the period from January 2006 to September 2024, as well as currency exchange rates data from the Central Bank of Kenya in US dollars (USD) and inflation rates data, were collated and preprocessed to be ready for analytics and machine learning. The augmented …

An Assessment Of Vegetable Production Constraints, Trait Preferences And Willingness To Adopt Sustainable Intensification Options In Kenya And Uganda, Rose N. Okoma, Evanson R. Omuse, Daniel M. Mutyambai, Dennis Beesigamukama, Marius F. Murongo, Sevgan Subramanian, Frank Chidawanyika

All Peer-Reviewed Publications

Global food production systems are under pressure due to population increase, limited farmland, biotic and abiotic constrains, and ongoing climate change. Sustainable intensification is needed to increase agricultural productivity with minimal adverse environmental and social impacts. Vegetable-integrated push pull (VIPP) technology coupled with black soldier fly (BSF) frass offer such opportunities to smallholder farmers. However, farmers’ vegetable preferences and willingness to adopt these innovations remain unknown and are variable across various geographic scales. Focus group discussions (FGDs) and in-person interviews with smallholder farmers were conducted to assess vegetable production constraints and select vegetables to be integrated into VIPP coupled with …

Selective Lure For Bactrocera Dorsalis Based On Shared Palpal And Antennal Responses Across Three Economically Important Tephritid Species, Tibebe Dejene Biasazin, Raphael Njurai Miano, Xavier Cheseto, Shepard Ndlela, Samira A. Mohamed, Teun Dekker

All Peer-Reviewed Publications

The oriental fruit fly Bactrocera dorsalis is a highly destructive and invasive pest that threatens global horticulture, causing economic losses due to fruit damage and quarantine regulations. While attract-and-kill baits are widely used to suppress fly populations, these baits also impact many non-target species. To achieve ecological sustainability, our study aimed to develop a method that selectively targets female fruit flies. Using gas chromatography coupled to electro-antennal or palpal detection (GC-EAD/GC-EPD), we identified compounds that elicited responses in the maxillary palp and antenna of three different fruit flies including B. dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae. As previous studies indicated …

If You Have Nothing To Hide, You Still Have Something To Fear: How Libraries Can Support Alternative Information Channels, Abbie Steuhm

Annual Research Symposium

Libraries in the U.S. have seen massive increases in book challenges in recent years. Since books are one of the library’s vital resources, censoring books can have a great impact on libraries and patrons. To counteract the effects of censorship, libraries need to adopt and support alternative information channels so information can still be accessed through other channels even if one is shut down.

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 …

Delivery Of Medical Supplies To Remote Locations Via Unmanned Aerial Vehicles: Approaches, Challenges, And Solutions, Meshari Aljohani, Ravi Mukkamala, Stephanie Olariu

Computer Science Faculty Publications

Unmanned Aerial Vehicles (UAVs) are becoming more important in improving healthcare logistics, in particular due to their cost effectiveness, minimized risk, and versatile operational capabilities. This study explores the deployment of autonomous UAVs to deliver medical supplies to remote areas. Advances in ledger technology, smart contracts, and machine learning have transformed tasks previously managed by human teams or manually controlled UAVs into fully autonomous missions. We present a comprehensive analysis of the challenges and initial solutions vital for the effective use of autonomous UAVs in the delivery of medical supplies. In addition, we propose a machine-learning model to optimize UAV …

Nexus: Network Exploration For Exploiting Unsafe Sequences In Multi-Turn Llm Jailbreaks, Javad Rafiei Asl, Sidhant Narula, Mohammad Ghasemigol, Eduardo Blanco, Daniel Takabi

Computer Science Faculty Publications

Large Language Models (LLMs) have revolutionized natural language processing, yet remain vulnerable to jailbreak attacks—particularly multi-turn jailbreaks that distribute malicious intent across benign exchanges, thereby bypassing alignment mechanisms. Existing approaches often suffer from limited exploration of the adversarial space, rely on hand-crafted heuristics, or lack systematic query refinement. We propose NEXUS (Network Exploration for eXploiting Unsafe Sequences), a modular framework for constructing, refining, and executing optimized multi-turn attacks. NEXUS comprises: (1) ThoughtNet, which hierarchically expands a harmful intent into a structured semantic network of topics, entities, and query chains; (2) a feedback-driven Simulator that iteratively refines and prunes these chains …

Privshap: A Finer-Granularity Network Linearization Method For Private Inference, Xiangrui Xu, Zhenzhen Wang, Rui Ning, Chunsheng Xiu, Hongyi Wu

Computer Science Faculty Publications

Private inference applies cryptographic techniques like homomorphic encryption, garble circuit and secret sharing to keep both sides privacy in a client-server setting during inference. It is often hindered by the high communication overheads, especially at non-linear activation layers such as ReLU. Hence ReLU pruning has been widely recognized as an efficient way to accelerate private inference. Existing approaches to ReLU pruning typically rely on coarse hypothesis, which assume an inverse correlation between the importance of ReLU and linear layers or shallow activation layers have less importance for universal models, to assign the budgets according to the layer while preserving the …

Lrtm Left-Right Transition Matrices For Molecular Interaction Prediction, Kaitlin Zheng, Guihua Duan, Mengyun Yang, Wei Wu, Yao-Hang Li, Jianxin Wang

Computer Science Faculty Publications

Molecular interactions are central to most biological processes. The discovery and identification of potential associations between molecules can provide insights into biological exploration, diagnostic and therapeutic interventions, and drug development. So far many relevant computational methods have been proposed, but most of them are usually limited to specific domains and rely on complex preprocessing procedures, which restricts the models’ ability to be applied to other tasks. Therefore, it remains a challenge to explore a generalized approach to accurately predicting potential associations. In this study, We propose Left-Right Transition Matrices (LRTM) for molecular interaction prediction. From the perspective on the diffusion …

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 …

Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang

Computer Science Faculty Publications

With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs …

Gramseq-Dta: A Grammar-Based Drug-Target Affinity Prediction Approach Fusing Gene Expression Information, Kasul Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug–target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common approach that has demonstrated good results in drug–target affinity prediction. However, these approach lacks information on the relative position of the atoms and bonds. To address this limitation, graph-based representations have been used to some extent. However, solely considering the structural aspect of drugs and targets may be insufficient for accurate DTA prediction. Integrating the functional aspect of these drugs at the genetic level can enhance …

An Analytical Review Of Preprocessing Techniques In Bengali Natural Language Processing, Sovon Chakraborty, Protiva Das, Shakib Mahmud Dipto, Md Aktaruzzaman Pramanik, Jannatun Noor

Computer Science Faculty Publications

Research in Bengali Natural Language Processing (BNLP) is rapidly expanding. Despite being one of the most widely spoken languages in the world, BNLP research remains insufficient, particularly in Bengali speech recognition. The languages rich morphology, agglutinative structure, and diverse dialects make text and speech processing especially challenging. However, these challenges can be addressed with effective preprocessing techniques. Various organizations in Bangladesh and West Bengal are integrating Natural Language Processing (NLP) into their services, but without a thorough understanding of preprocessing, these implementations remain incomplete. Applying proper preprocessing techniques to the Bengali language will serve as a foundation for developing robust …

Prompt-Based Learning For Few-Shot Class-Incremental Learning, Jicheng Yuan, Hang Chen, Songsong Tian, Wenfa Li, Lusi Li, Enhao Ning, Yugui Zhang

Computer Science Faculty Publications

Few-Shot Class-Incremental Learning (FSCIL) aims to enable deep neural networks to incrementally learn new tasks from a limited number of labeled samples, while retaining knowledge of previously learned tasks, mimicking the way humans learn. In this paper, we introduce a novel approach called Prompt Learning for FSCIL (PL-FSCIL), which leverages the power of prompts alongside a pre-trained Vision Transformer (ViT) model to effectively tackle the challenges of FSCIL. Our approach explores the feasibility of directly applying visual prompts in FSCIL, using a simplified model architecture. PL-FSCIL integrates two key prompts: the Domain Prompt and the FSCIL Prompt. Both are tensors …

Not Here, Go There: Analyzing Redirection Patterns On The Web, Kritika Garg, Sawood Alam, Dietrich Ayala, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

URI redirections are integral to web management, supporting structural changes, SEO optimization, and security. However, their complexities affect usability, SEO performance, and digital preservation. This study analyzed 11 million unique redirecting URIs, following redirections up to 10 hops per URI, to uncover patterns and implications of redirection practices. Our findings revealed that 50% of the URIs terminated successfully, while 50% resulted in errors, including 0.06% exceeding 10 hops. Canonical redirects, such as HTTP to HTTPS transitions, were prevalent, reflecting adherence to SEO best practices. Non-canonical redirects, often involving domain or path changes, highlighted significant web migrations, rebranding, and security risks. …

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. …

Vaim-Cff: A Variational Autoencoder Inverse Mapper Solution To Compton Form Factor Extraction From Deeply Virtual Compton Scattering, Manal Almaeen, Tareq Alghamdi, Brandon Kriesten, Douglas Adams, Yaohang Li, Huey-Wen Lin, Simonetta Liuti

Computer Science Faculty Publications

We develop a new methodology for extracting Compton form factors (CFFs) from deeply virtual exclusive reactions such as the unpolarized DVCS cross section using a specialized inverse problem solver, a variational autoencoder inverse mapper (VAIM). The VAIM-CFF framework not only allows us access to a fitted solution set possibly containing multiple solutions in the extraction of all 8 CFFs from a single cross section measurement, but also accesses the lost information contained in the forward mapping from CFFs to cross section. We investigate various assumptions and their effects on the predicted CFFs such as cross section organization, number of extracted …

Position: Benchmarking Is Broken - Don't Let Ai Be Its Own Judge, Zerui Cheng, Stella Wohnig, Ruchika Gupta, Samiul Alam, Tassallah Abdullahi, João Alves Ribeiro, Christian Nielsen-Garcia, Saif Mir, Siran Li, Jason Orender, Seyed Ali Bahrainian, Daniel Kirste, Aaron Gokaslan, Carsten Eickhoff, Pramod Viswanath, Ruben Wolff

Computer Science Faculty Publications

The meteoric rise of Artificial Intelligence (AI), with its rapidly expanding market capitalization, presents both transformative opportunities and critical challenges. Chief among these is the urgent need for a new, unified paradigm for trustworthy evaluation, as current benchmarks increasingly reveal critical vulnerabilities. Issues like data contamination and selective reporting by model developers fuel hype, while inadequate data quality control can lead to biased evaluations that, even if unintentionally, may favor specific approaches. As a flood of participants enters the AI space, this "Wild West" of assessment makes distinguishing genuine progress from exaggerated claims exceptionally difficult. Such ambiguity blurs scientific signals …

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 …

Github Repository Complexity Leads To Diminished Web Archive Availability, David Calano, Michael Nelson, Michele Weigle

Computer Science Faculty Publications

Software is often developed using versioned controlled software, such as Git, and hosted on centralized Web hosts, such as GitHub and GitLab. These Web hosted software repositories are made available to users in the form of traditional HTML Web pages for each source file and directory, as well as a presentational home page and various descriptive pages. We examined more than 12,000 Web hosted Git repository project home pages, primarily from GitHub, to measure how well their presentational components are preserved in the Internet Archive, as well as the source trees of the collected GitHub repositories to assess the extent …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …

Human Perception Of Ai Capabilities At Classifying Perturbed Roadway Signs, Katherine R. Garcia, Jing Chen, Yanru Xiao, Scott Mishler, Cong Wang, Bin Hu

Computer Science Faculty Publications

Artificial Intelligence (AI) is crucial to numerous functions required for driving automation systems, including the computer vision techniques used to detect the roadway environment and make real-time decisions. However, the images used as inputs to the AI system may be maliciously perturbed, or manipulated, causing the AI system to make an incorrect classification. In this study, we examined humans’ perception of the AI’s computer vision capability of classifying various road sign images, including the original images, images with two different types of malicious attacks, and images that are scrambled randomly at the pixel level. Our results showed that participants rated …

Uncertainty-Aware Deep Learning Framework For Forecasting Coastal Water Level In Virginia Beach, Md Mahmudul Hasan, Malachi Schram, Sridhar Katragadda, Diana Mcspadden, Alisa N. Udomvisawakul, Heather Richter, Frank Liu

Computer Science Faculty Publications

Coastal areas like Virginia Beach, USA, are increasingly vulnerable to flooding. To mitigate the impact of flooding, it is crucial for the City of Virginia Beach to have reliable 72-hour-ahead (3 days) forecasts of water levels at key gauge locations. To support this effort, several sensors have been installed throughout the city to monitor water levels and other environmental parameters such as wind speed, precipitation, and atmospheric pressure. Leveraging sensor data from one of these locations, we developed an uncertainty-aware deep learning model to forecast water levels. We employed deep quantile regression (DQR) to quantify variability in the predictions and …

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 Real-Time Approach To Capture Ambient And Focal Attention In Visual Search, Gavindya Jayawardena, Yasith Jayawardana, Yasasi Abeysinghe, Bhanuka Mahanama, Sampath Jayarathna, Jacek Gwizdka

Computer Science Faculty Publications

During visual search, individuals’ attention shifts between ambient and focal states in response to task demands and stimuli. The ambient/focal coefficient K is a statistically validated measure of these states, computed offline from fixation duration and saccade amplitude data. While current methods compute K offline, real-time computation could enable applications such as monitoring user attention, creating attention-adaptive user interfaces, and optimizing graphics rendering. However, real-time computation of K requires stable estimates for the parameters of fixation duration and saccade amplitude distributions. Since these distributions are heavy-tailed, the real-time estimates exhibit high variance and slow convergence. To overcome this, we propose …

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 …

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 …

Ai For Nuclear Physics: The Exclaim Project, S. Liuti, D. Adams, M. Boër, G. W. Chern, M. Cuic, M. Engelhardt, G. R. Goldstein, B. Kriesten, Y. Li, H. W. Lin, M. Sievert, D. Sivers

Computer Science Faculty Publications

An overview of the recent activity of the newly funded EXCLusives with AI and Machine learning (EXCLAIM) collaboration is presented. The main goal of the collaboration is to develop a framework to implement AI and machine learning techniques in problems emerging from the phenomenology of high energy exclusive scattering processes from nucleons and nuclei, maximizing the information that can be extracted from various sets of experimental data, while implementing theoretical constraints from lattice QCD. A specific perspective embraced by EXCLAIM is to use the methods of theoretical physics to understand the working of ML, beyond its standardized applications to physics …

Normalizing Images In Various Weather And Lighting Conditions Using Colorpix2pix Generative Adversarial Network, Sanjida Tasnim, Ashif Mahmud Mostafa, Azmain Morshed, Namreen Shaiyaz, Shakib Mahmud Dipto, Saad Aloteibi, Mohammad Ali Moni, Md. Golam Rabiul Alam, Md. Ashraful Alam

Computer Science Faculty Publications

Autonomous vehicles (AVs) are widely regarded as the future of transportation due to their tremendous benefits and user comfort. However, the AVs have been struggling with very crucial challenges, such as achieving reliable accuracy in object detection as well as faster computation required for quick decision-making. In recent years, perception systems in driverless cars have been significantly enhanced, mainly due to advances in deep-learning-based object detection systems. However, these perception systems are still heavily affected by environmental variables, such as changes in illumination, refractive interference, and adverse weather conditions, which may compromise their reliability and safety. This research proposes an …