Computer Science Faculty Publications
Explore our Open Access Publications to discover research freely available to the public.
You can also view All Research Publications by the department, including both open access and subscription-based work over the past 36 months.
Submissions from 2026
Lightweight Privacy-First Federated Learning for Medical AI, Al Amin, Kamrul Hasan, Liang Hong, Sergei Chuprov, Rohan Thompson, Azubike D. Okpalaeze, Primo Abena, Tariqul Islam, and Imtiaz Ahmed
Reachability in Interactive Chemical Reaction Networks, Aberto Avila-Jimenez, Bin Fu, Elise Grizzell, Robert Schweller, and Tim Wylie
Tile-based knot assembly with Celtic!, Divya Bajaj, Ryan Knobel, Juan Manuel Perez, Rene Reyes, Ramiro Santos, and Tim Wylie
What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Tara Sudhadevi, Anantha Harijith, Marzieh Ayati, Mehmet Koyutürk, and Mark R. Chance
Why Text Prevails: Vision May Undermine Multimodal Medical Decision Making, Siyuan Dai, Lunxiao Li, Kun Zhao, Eardi Lila, Paul K. Crane, Heng Huang, Dongkuan Xu, and Haoteng Tang
Constrained multiview contrastive learning for jointly supervised representation learning, Siyuan Dai, Kai Ye, Kun Zhao, Yang Du, Haoteng Tang, and Liang Zhan
A Machine Learning Framework for Contractor Scope Matching Using Profile Characteristics and Work Package Vector Similarity, Pedro Fonseca and Sergei Chuprov
Minimizing Makespan in Sublinear Time via Weighted Random Sampling, Bin Fu, Yumei Huo, and Hairong Zhao
A Visitation Grid for Complete Coverage Foraging in Robot Swarms, Arturo Gonzalez, Yifeng Gao, Li Zhang, and Qi Lu
Integrating Multi-scale and Multi-filtration Topological Features for Medical Image Classification, Pengfei Gu, Huimin Li, Haoteng Tang, Dongkuan Xu, Erik Enriquez, Dongchul Kim, Bin Fu, and Danny Z. Chen
Fractals in seeded tile automata, Asher Haun, Ryan Knobel, Adrian Salinas, Ramiro Santos, Robert Schweller, and Tim Wylie
Quantitative Phosphocreatine Mapping with a Transformer-Based Regression Network, Qi Huang, Haoteng Tang, Han Tang, Caleb Berberet, Liya Dai, and Thomas H. Schindler
Redox Stoichiometry at the Single-Residue Level Using Mass Spectrometry Reveals Dynamic Methionine Sulfoxide Speciation in Actin and Calmodulin during Brain Aging, Jiwoo Hwang, Madeleine F. Clore, Filipa Blasco Tavares Pereira Lopes, Marzieh Ayati, Daniela Schlatzer, Xin Qi, Rihua Wang, Mehmet Koyutürk, and Mark R. Chance
Submissions from 2025
Gradient-based Model Shortcut Detection for Time Series Classification, Salomon Ibarra, Frida Cantu, Kaixiong Zhou, and Li Zhang
Submissions from 2026
Polynomial Simulations of CRN Models with Trimolecular Void Step-Cycle CRNs, Austin Luchsinger, Aiden J. Massie, Robert Schweller, Evan Tomai, and Tim Wylie
A Granularity-Centered Taxonomy of Personalized Federated Learning, Ei Ei Nyein Chan, Sergei Chuprov, Pretom Roy Ovi, and Kamrul Hasan
Improving PID Control with Bayesian Optimization for Adversarially Robust Federated Learning, Adrian Pena, Sergei Chuprov, Raman Zatsarenko, and Leon Reznik
When Swin Transformer Meets KANs: An Improved Transformer Architecture for Medical Image Segmentation, Nishchal Sapkota, Haoyan Shi, Yejia Zhang, Xianshi Ma, Bofang Zheng, and Fabian Vazquez Jr.
Short-term Electricity Price Forecasting with Constrained Regressors, Mucun Sun, Li Zhang, and Yifeng Gao
SynM-FPP: Few-Shot Learning on Synthmorph-Based Motion Correction Framework for Myocardial First-Pass Perfusion, Han Tang, Qi Huang, Haoteng Tang, Liya Dai, Caleb Berberet, and Scott Bugenhagen
Learning with Geometric Priors in U-Net Variants for Polyp Segmentation, Fabian Vazquez, Jose A. Nuñez, Diego Adame, Alissen Moreno, Augustin Zhan, Huimin Li, Jinghao Yang, Haoteng Tang, Bin Fu, and Pengfei Gu
Interpretable multimodal learning for integrating neuroimaging and genetic data in Alzheimer’s disease, Kun Zhao, Siyuan Dai, Yingying Zhang, Guodong Liu, Pengfei Gu, Chenghua Lin, Paul M. Thompson, Alex D. Leow, Heng Huang, and Haoteng Tang
Who Matters More in Radiology Report Generation: Vision Encoders or Language Models?, Kun Zhao, Yang Du, Rhianna Zhang, Liang Zhan, Dongkuan Xu, Pengfei Gu, and Haoteng Tang
Submissions from 2025
Topo-VM-UNetV2: Encoding Topology Into Vision Mamba UNet for Polyp Segmentation, Diego Adame, Jose Angel Nunez, Fabian Vazquez Jr., Nayeli Gurrola, Huimin Li, and Haoteng Tang
Hierarchical Log Bayesian Neural Network for Enhanced Aorta Segmentation, Delin An, Pan Du, Pengfei Gu, Jian-Xun Wang, and Chaoli Wang
A Novel Digital Twin Driven Multi-Camera Edge Computing Sensing System for Additive Manufacturing, Martha Asare, Joel Mathew, Efren Saenz, Hongkai Yu, and Jinghao Yang
An Efficient Self-Supervised Learning Framework for Swarm Robot Trajectory Analysis, Brooklyn Berry, Gaukhar Nurbek, Juan Manuel Perez, Richard Tapia, Qi Lu, and Yifeng Gao
Training Robot Swarms for Adaptive Foraging in Environments with Obstacles, Pigar Biteng, Tameem Uz Zaman, and Qi Lu
Uniform robot relocation is hard in only two directions even without obstacles, David Caballero, Angel A. Cantu, Timothy Gomez, Austin Luchsinger, Robert Schweller, and Tim Wylie
An Unsupervised Time Series Anomaly Detection Approach for Efficient Online Process Monitoring of Additive Manufacturing, Frida Cantu, Salomon Ibarra, Arturo Gonzales, Jesus Barreda, Chenang Liu, and Li Zhang
Zeus: zero-shot LLM instruction for union segmentation in multimodal medical imaging, Siyuan Dai, Kai Ye, Guodong Liu, Haoteng Tang, and Liang Zhan
SIN-Seg: A joint spatial-spectral information fusion model for medical image segmentation, Siyuan Dai, Kai Ye, Charlie Zhan, Haoteng Tang, and Liang Zhan
Inferred global dense residue transition graphs from primary structure sequences enable protein interaction prediction via directed graph convolutional neural networks, Islam A. Ebeid, Haoteng Tang, and Pengfei Gu
Streaming Algorithms for Scheduling Jobs with Priorities, Bin Fu, Yumei Huo, and Hairong Zhao
Sublinear Algorithms for Scheduling with Chain Precedence Constraints, Bin Fu, Yumei Huo, and Hairong Zhao
Sublinear time approximation schemes for makespan minimization on parallel machines, Bin Fu, Yumei Huo, and Hairong Zhao
Symbol-Temporal Consistency Self-supervised Learning for Robust Time Series Classification, Kevin Garcia, Cassandra Garza, Brooklyn Berry, and Yifeng Gao
Congestion Mitigation for Foraging Robot Swarms Using Spiral Path Strategies, Arturo Gonzalez and Qi Lu
Adapting a Segmentation Foundation Model for Medical Image Classification, Pengfei Gu, Haoteng Tang, Islam A. Ebeid, Jose Angel Nunez, Fabian Vazquez Jr., and Diego Adame
TopoImages: Incorporating Local Topology Encoding into Deep Learning Models for Medical Image Classification, Pengfei Gu, Hongxiao Wang, Yejia Zhang, Huimin Li, Chaoli Wang, and Danny Z. Chen
Some Remarks on Fibonacci-type Recursive Polynomials, Kristen Hallas, Joan Mattle, Deanna Perez, and Aklilu Zeleke
Model-based self-supervised learning for quantitative assessment of myocardial oxygen extraction fraction and myocardial blood volume, Qi Huang, Haoteng Tang, Keyan Wang, Ran Li, Cihat Eldeniz, Natalie Nguyen, Thomas H. Schindler, Linda R. Peterson, Yang Yang, and Yan Yan
Personalized Chemotherapy Dosing Through Offline Reinforcement Learning, Hector Lugo III, Angel Antonio Peredo, Christian Ivan Narcia-Macias, Jose Espinoza, Daniel Masamba, Adan Gandarilla, Erik Enriquez, and Dongchul Kim
Robust Mitigation Strategy for Misleading Pheromone Trails in Foraging Robot Swarms, Ryan Luna and Qi Lu
Pi-talk: Edge-Only, Adapter-Tuned Multimodal Small Language Model for Safe, Real-Time In-Vehicle Dialogue, Alex Pissinou Makki, Vahid Tarokh, Louis Lago Enamorado, Carlos Carroz, Miguel Garcia, and Niki Pissinou
Intelligent Soccer Event Detection and Highlights Generation with Broadcast Cues Integration, Anirudh Narayanan, Sergei Chuprov, Leon Reznik, Raman Zatsarenko, and Dmitrii Korobeinikov
White Light Specular Reflection Data Augmentation for Deep Learning Polyp Detection, Jose Angel Nuñez, Fabian Vazquez Jr., Diego Adame, Xiaoyan Fu, Pengfei Gu, and Bin Fu
Offline Reinforcement Learning Approaches for Safe and Effective Smart Grid Control, Angel Antonio Peredo, Hector Lugo III, Christian Ivan Narcia-Macias, Jose Espinoza, Daniel Masamba, Adan Gandarilla, Erik Enriquez, and Dong-Chul Kim
Adaptive von Mises–Fisher Likelihood Loss for Supervised Deep Time Series Hashing, Juan Manuel Perez, Kevin Garcia, Brooklyn Berry, Dongjin Song, and Yifeng Gao
Precision-Weighted Federated Learning, Jonatan Reyes, Lisa Di Jorio, Cecile Low-Kam, and Marta Kersten-Oertel
Auction Consensus Algorithm with Loss Mechanism for Decentralized Task Allocation, Jose Rodriguez, Wenjie Dong, Constantine Tarawneh, and Qi Lu
Blockchain-Aided Intrusion Detection in Marine Tactical Network Using Reinforcement Learning, Md Raihan Subhan, Md Mahinur Alam, Mohtasin Golam, Md Facklasur Rahaman, and Taesoo Jun
Exploring transfer learning for deep learning polyp detection in colonoscopy images using YOLOv8, Fabian Vazquez Jr., Jose Angel Nuñez, Xiaoyan Fu, Pengfei Gu, and Bin Fu
BPEN: Brain Posterior Evidential Network for trustworthy brain imaging analysis, Kai Ye, Haoteng Tang, Siyuan Dai, Igor Fortel, Paul M. Thompson, R. Scott Mackin, Alex Leow, Heng Huang, and Liang Zhan
Evolving Adaptive Foraging Robot Swarms with NEAT in Environments with Obstacles, Tameem Uz Zaman, Pigar Biteng, and Qi Lu
Evaluating Time Series Models with Knowledge Discovery, Li Zhang
A General Paradigm for Fine-Tuning Large Language Models in Alzheimer’s Disease Diagnosis, Marcus Zhan, Kun Zhao, Guodong Liu, and Haoteng Tang
Submissions from 2024
Computing Threshold Circuits with Bimolecular Void Reactions in Step Chemical Reaction Networks, Rachel Anderson, Bin Fu, Aiden Massie, Gourab Mukhopadhyay, Adrian Salinas, Robert Schweller, Evan Tomai, and Tim Wylie
A Simple Proof that Ricochet Robots is PSPACE-Complete, Jose Balanza-Martinez, Angel A. Cantu, Robert Schweller, and Tim Wylie
COSCO: A Sharpness-Aware Training Framework for Few-shot Multivariate Time Series Classification, Jesus Barreda, Ashley Gomez, Ruben Puga, Kaixiong Zhou, and Li Zhang
Methionine Sulfoxide Speciation in Mouse Hippocampus Revealed by Global Proteomics Exhibits Age- and Alzheimer’s Disease-Dependent Changes Targeted to Mitochondrial and Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, and Mark R. Chance
Methionine Sulfoxide Speciation in Mouse Hippocampus Revealed by Global Proteomics Exhibits Age- and Alzheimer’s Disease-Dependent Changes Targeted to Mitochondrial and Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, and Mark R. Chance
Verification and computation in restricted Tile Automata, David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie
Data Quality Based Intelligent Instrument Selection with Security Integration, Sergei Chuprov, Raman Zatsarenko, Leon Reznik, and Igor Khokhlov
Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds, Erik D. Demaine, Elize Grizzell, Jayson Lynch, Ahmed Shalaby, Timothy Gomez, Markus Hecher, Robert Schweller, and Damien Woods
Efficient High-Resolution Time Series Classification via Attention Kronecker Decomposition, Aosong Feng, Jialin Chen, Juan Garza, Brooklyn Berry, Francisco Salazar, Yifeng Gao, Rex Ying, and Leandros Tassiulas
Speeding Up Constrained k-Means Through 2-Means, Qilong Feng and Bin Fu
Possible Role of Correlation Coefficients and Network Analysis of Multiple Intracellular Proteins in Blood Cells of Patients with Bipolar Disorder in Studying the Mechanism of Lithium Responsiveness: A Proof-Concept Study, Keming Gao, Marzieh Ayati, Nicholas M. Kaye, Mehmet Koyutürk, Joseph R. Calabrese, Eric Christian, Hillard M. Lazarus, and David Kaplan
Efficient Hierarchical Contrastive Self-supervising Learning for Time Series Classification via Importance-aware Resolution Selection, Kevin Garcia, Juan M. Perez, and Yifeng Gao
Self Pre-training with Topology- and Spatiality-aware Masked Autoencoders for 3D Medical Image Segmentation, Pengfei Gu, Yejia Zhang, Huimin Li, Chaoli Wang, and Danny Z. Chen
Controlling Adversarial Pheromone-Based Infections via Quarantine Strategies in Foraging Robot Swarms, Ryan Luna and Qi Lu
Detection and Mitigation of Misleading Pheromone Trails in Foraging Robot Swarms, Ryan Luna and Qi Lu
IntelliBeeHive: An Automated Honey Bee, Pollen, and Varroa Destructor Monitoring System, Christian I. Narcia-Macias, Joselito Guardado, Jocell Rodriguez, Joanne Rampersad, Erik Enriquez, and Dong-Chul Kim
Tuning PID Controller for Quadrotor Using Particle Swarm Optimization, Eric X. Rodriguez and Qi Lu
Ex-Vivo Hippocampus Segmentation Using Diffusion-Weighted MRI, Haoteng Tang, Siyuan Dai, Eric M. Zou, Guodong Liu, Ryan Ahearn, Ryan Krafty, Michel Modo, and Liang Zhan
Interpretable Spatio-Temporal Embedding for Brain Structural-Effective Network with Ordinary Differential Equation, Haoteng Tang, Guodong Liu, Siyuan Dai, Kai Ye, Kun Zhao, Wenlu Wang, Carl Yang, Lifang He, Alex D. Leow, and Paul Thompson
The use of generated 3D models in teaching the development of AR/VR applications, Parassat Tazabekova, Askar Nurbekov, Zhanat Nurbekova, and Talgat Sembayev
Efficient and Accurate Similarity-Aware Graph Neural Network for Semi-supervised Time Series Classification, Wenjie Xi, Arnav Jain, Li Zhang, and Jessica Lin
Efficient and Accurate Similarity-Aware Graph Neural Network for Semi-supervised Time Series Classification, Wenjie Xi, Arnav Jain, Li Zhang, and Jessica Lin
Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data, Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Marzieh Ayati, Mark R. Chance, and Mehmet Koyutürk
Submissions from 2023
Exploring Spectral Bias in Time Series Long Sequence Forecasting, Kofi Nketia Ackaah-Gyasi, Sergio Valdez, Yifeng Gao, and Li Zhang
Security Attacks and Countermeasures in Smart Homes, Hasibul Alam and Emmett Tomai
Complexity of Reconfiguration in Surface Chemical Reaction Networks, Robert M. Alaniz, Josh Brunner, Michael Coulombe, Erik D. Demaine, Yevhenii Diomidov, Ryan Knobel, Timothy Gomez, Elise Grizzell, Jayson Lynch, Andrew Rodriguez, Robert Schweller, and Tim Wylie
Building squares with optimal state complexity in restricted active self-assembly, Robert M. Alaniz, David Caballero, Sonya C. Cirlos, Timothy Gomez, Elize Grizzell, Andrew Rodriguez, Robert Schweller, Armando Tenorio, and Tim Wylie
Covert Computation in the Abstract Tile-Assembly Model, Robert M. Alaniz, Timothy Gomez, Andrew Rodriguez, Tim Wylie, David Caballero, Elize Grizzell, and Robert Schweller
A Fast and Responsive Web-based Framework for Visualizing HPC Application Usage, Ved Arora, Nayeli Gurrola, Amiya K. Maji, and Guangzhen Jin
Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites, Marzieh Ayati, Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Mark R. Chance, and Mehmet Koyutürk
Uniform Robot Relocation Is Hard in only Two Directions Even Without Obstacles, David Caballero, Angel A. Cantu, Timothy Gomez, Austin Luchsinger, Robert Schweller, and Tim Wylie
Complexity of verification in self-assembly with prebuilt assemblies, David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie
Unique Assembly Verification in Two-Handed Self-Assembly, David Caballero, Timothy Gomez, Robert Schweller, and Tim Wylie
Simulation of Multiple Stages in Single Bin Active Tile Self-assembly, Sonya C. Cirlos, Timothy Gomez, Elise Grizzell, Andrew Rodriguez, Robert Schweller, and Tim Wylie
Machine-Learning-Based Model for Hurricane Storm Surge Forecasting in the Lower Laguna Madre, Cesar E. Davila Hernandez, Jungseok Ho, Dong-Chul Kim, and Abdoul Oubeidillah
Sublinear Time Motif Discovery from Multiple Sequences, Bin Fu, Yunhui Fu, and Yuan Xue
Multitasking scheduling with shared processing, Bin Fu, Yumei Huo, and Hairong Zhao
Streaming approximation scheme for minimizing total completion time on parallel machines subject to varying processing capacity, Bin Fu, Yumei Huo, and Hairong Zhao
Differences in intracellular protein levels in monocytes and CD4+ lymphocytes between bipolar depressed patients and healthy controls: A pilot study with tyramine-based signal-amplified flow cytometry, Keming Gao, Marzieh Ayati, Nicholas M. Kaye, Mehmet Koyutürk, Joseph R. Calabrese, Stephen J. Ganocy, Hillard M. Lazarus, Eric Christian, and David Kaplan
Divergent Directionality of Immune Cell-Specific Protein Expression between Bipolar Lithium Responders and Non-Responders Revealed by Enhanced Flow Cytometry, Keming Gao, Nicholas M. Kaye, Marzieh Ayati, Mehmet Koyuturk, Joseph R. Calabrese, Eric Christian, Hillard M. Lazarus, and David Kaplan
Adaptive Resolution Loss: An Efficient and Effective Loss for Time Series Self-Supervised Learning Framework, Kevin Garcia, Juan Manuel Perez, and Yifeng Gao
Poster: No Fly-Zone: Drone Policies for Ensuring Safe Operations in Restricted Areas, Arturo Gonzalez, Amani Davidson, and Carlos Rubio-Medrano
Computational and experimental study on undoped and Er-doped lithium tantalate nanofluorescent probes, Mkhitar A. Hobosyan, Andrea Pelayo Carvajal, Bhupendra B. Srivastava, Tamanna Zakia, Mohammed Uddin, Karen S. Martirosyan, Eric Rodriguez, Kofi Nketia Ackaah-Gyasi, and Nicholas Dimakis
