Table of Contents

• Interpretable Metadata-Based Microbial Risk Prediction Using Large Language ModelsHyunwoo Yoo, Gail Rosen. [doi]
• ATHENA: Atherosclerosis through Hierarchical Explainable Neural Network AnalysisIrsyad Adam, Steven Swee, Erika Yilin Zheng, Ethan Ji, William Speier, Ding Wang, Alex A. T. Bui, Wei Wang, Karol E. Watson, Peipei Ping. [doi]
• Network-Oriented Genome-Wide DNA Methylation Study of Circulating CD4+ T Lymphocytes of Patients with Heart Failure: DNA Methylation and Heart FailureGiuditta Benincasa, Claudio Napoli. [doi]
• A novel approach to highly variable genes selection for scRNA-Seq analysisEnos Dk Kakwambi, Tuan Nguyen, Suryaveer Kapoor, Marmar R. Moussa. [doi]
• Developing Fairness-Aware Task Decomposition to Improve Equity in Post-Spinal Fusion Complication PredictionYining Yuan, J. Ben Tamo, Wenqi Shi, Yishan Zhong, Micky C. Nnamdi, B. Randall Brenn, Steven W. Hwang, May Dongmei Wang. [doi]
• PhenoGPT2: A Multimodal Fine-tuned Large Language Models for Phenotype Extraction and Normalization from Clinical Text and Facial ImagesQuan Minh Nguyen, Mian Umair Ahsan, Zhanliang Wang, Kai Wang. [doi]
• TrialPred: an interpretability model based on multimodal data for predicting the duration of clinical trialsTianxing Zhou, Jialiang Huang, Chenxi Wang, Andreu Paredes-Gallardo, Eryu Xia, Yinghua Zhou, Guangzhong Sun. [doi]
• GamELY: Human-in-the loop Framework for Scaling Human Evaluation of LLMs in HealthcareRaghav Awasthi, Nishant Singh, Shreya Mishra, Atharva Bhattad, Moises Auron, Charumathi Raghu Subramanian, Ashish Atreja, Kamal Maheshwari, Dwarikanath Mahapatra, Jacek B. Cywinski, Ashish K. Khanna, Francis A. Papay, Piyush Mathur. [doi]
• ATOMS: An Action Theory Of Moran SystemEllen A Huang, Xing Tan. [doi]
• Early Assessment of Parkinson's Disease Using Spatiotemporal Analysis of Ground Reaction Forces From a Wearable SensorRithik Vir. [doi]
• Enabling Few-Shot Alzheimer's Disease Diagnosis on Biomarker Data with Tabular LLMsSophie Kearney, Shu Yang 0009, Zixuan Wen, Bojian Hou, Duy Duong Tran, Tianlong Chen 0001, Jason H. Moore, Marylyn D. Ritchie, Li Shen 0001. [doi]
• Local Structural Features Analysis of Hemispheres for AD Diagnosis from Brain sMRIYanteng Zhang, Zibo Zhao, Chuanyi Zhang, Lipei Zhang, Yuxiang Wei 0004, Vince D. Calhoun. [doi]
• A Million Nectin-1 Permutations Reveal an Order-Driven Feature LandscapeTia Pope, Ahmad Patooghy. [doi]
• Distributed Iterative Multi-k-mer Metagenome Assembly with Progressive Graph Simplification and GC-Aware ClusteringGauri D. Ket, William Winnett, Arghya Kusum Das. [doi]
• Fine-Grained Interaction and Task-Driven Fusion of Histology Images and Genomics for Multimodal Cancer Survival PredictionXulin Chen, JunZhou Huang. [doi]
• CSMSA: Cross-Space Multiscale Adaptive Link Prediction for ceRNA-Mediated Multimolecular Disease Regulatory NetworksJunqi Long, Jianqiang Li 0002, Guangzhi Qu, Kun Liu, Bo Liu 0024. [doi]
• Controllable Flow-based Hybrid Space Protein GenerationShiv Shankar. [doi]
• Augmenting Randomized Controlled Trials with Foundation Models as Synthetic UnitsShiv Shankar, Madalina Fiterau. [doi]
• Graph-Based Spatio-temporal Attention and Multi-Scale Fusion for Clinically Interpretable, High-Fidelity Fetal ECG ExtractionChang Wang, Ming Zhu, Shengjie Zhai, Buddhadeb Dawn, Shahram Latifi. [doi]
• Improved Spatial Transcriptomics Clustering with Nested Graph Neural NetworksAtishay Jain, David H. Laidlaw, Ying Ma, Ritambhara Singh. [doi]
• Investigating Pace of Biological Aging as a Mental and Physical Health Biomarker in Youth with Perinatally-Acquired HIVHansoo Chang, Ashni Kumar, Joshua Suh, Kevin Street, Ana Ferariu, Alexei Taylor, Kunjal Patel, Sean Brummel, Paige Williams, Lei Wang, Fengqing Zhang. [doi]
• Uncovering Disease-Relevant Regulatory Modules in Bulk RNA-Seq via GRN Clustering, Text Mining, and Enrichment: A Case Study in SHS-Induced PreeclampsiaArcharlie Chou, Juan Arroyo, Brett E. Pickett. [doi]
• A Hybrid Deep Learning Framework for Automated Cobb Angle Estimation in Scoliosis AssessmentShaun Qien Yeau Tan, Shaunna Wang, Chia-Pei Wang, Alexandru C. Florea, Isabella W. Wang, Degel S. Agoreyo, Joline J. Speck, Micky C. Nnamdi, J. Ben Tamo, Benoit Louis Marteau, Yishan Zhong, Selina Poon, May Dongmei Wang. [doi]
• Thermodynamically Consistent Neural Models of Protein Folding KineticsFnu Hridyanshu. [doi]
• Comorbidity Extraction for In-Hospital Mortality Analysis: a Comparison of Regular Expressions and Large Language ModelsAyca Begum Tascioglu, Flavio Bertini 0001, Laura Pistore, Andrea Fabbri, Danilo Montesi. [doi]
• VERIRAG: Healthcare Claim Verification via Statistical Audit in Retrieval-Augmented GenerationShubham Mohole, Hongjun Choi, Shusen Liu 0001, Christine Klymko, Shashank Kushwaha, Derek Shi, Wesam A. Sakla, Sainyam Galhotra, Ruben Glatt. [doi]
• Enhancing Medical AI Safety Through Multi-Agent Evaluation and Iterative RefinementZainab Ghafoor, Md Shafiqul Islam, Koushik Howlader, Md Rasel Khondokar, Tanusree Bhattacharjee, Sayantan Chakroborty, Adrito Roy, Ushashi Bhattacharjee, Tirtho Roy. [doi]
• FlowGRN: Scalable and Dropout-Robust Gene Regulatory Network Inference via Flow Matching-Based Trajectory ReconstructionTsz Pan Tong, Jun Pang 0001. [doi]
• ChiralRetro: Chirality-Sensitive Encoding and Enhanced Pathway Strategies in RetrosynthesisZheyi Cai, Yinghui Jiang, Changzhi Jiang, Lian Shen, Hongpeng Qiu, Yuan Lin, Juan Liu, Xiangrong Liu. [doi]
• Towards optimal selection of ultra-deep sequencing reads for de novo genome assemblySakshar Chakravarty, Stefano Lonardi. [doi]
• Mapping Interneuron Fate Decisions in the Medial Ganglionic Eminence with Single-Cell RNA SequencingJessica Schmilovich, Amanda Zint, Anna Katharina Schlusche, Shawn Singh, Margaret Elizabeth Ross, Vanessa Aguiar-Pulido. [doi]
• Examining Radiation Therapy Planning Knowledge in Large Language ModelsOuldouz Ghorbani, Ahmed Helmy, Qingrong Jackie Wu, Yaorong Ge. [doi]
• Longitudinal Tumor Generation in Mammograms via Dual Encoder GAN and Learnable BlendingAfsana Ahsan Jeny, Sahand Hamzehei, Mostafa Karami, Stephen Andrew Baker, Tucker Van Rathe, Clifford Yang, Sheida Nabavi. [doi]
• HyMaTE: A Hybrid Mamba and Transformer Model for EHR Representation LearningMd Mozaharul Mottalib, Thao-Ly T. Phan, Rahmatollah Beheshti. [doi]
• Benchmarking Dimensionality Reduction Techniques for Spatial TranscriptomicsMd Ishtyaq Mahmud, Veena Kochat, Suresh Satpati, Jagan Mohan Reddy Dwarampudi, Kunal Rai, Tania Banerjee. [doi]
• Reward Hacking Mitigation using Verifiable Composite RewardsMirza Farhan Bin Tarek, Rahmatollah Beheshti. [doi]
• Transformer-based Prediction of Microbial Growth Rates from Genomic DataIyanu Oduwole, Mengling He, Ratish Kumar Chandrakant Jha, Adrienne Hoarfrost, Andrew D. Steen, Scott J. Emrich. [doi]
• Interpretable Neural Networks Reveal Gene Interactions Underlying Autoimmune Disease RiskMonica Isgut, Andrew Hornback, Karan Samel, Logan Gloster, Neha Jain, Kyungbeom Kim, May Dongmei Wang. [doi]
• scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell DataJiaqi Zhang, Manav Chakravarthy, Ritambhara Singh. [doi]
• Deconvolving Complex Neuronal Networks into Interpretable Task-Specific ConnectomesYifan Wang, Ananth Grama, Vikram Ravindra. [doi]
• The Effect of Electrospun Polyacrylonitrile on Antifungal Drug Sensitivity in Candida albicansNooshin KianvashRad, Dennis LaJeunesse, Lifeng Zhang. [doi]
• VECTr: Visualizing Distance Measures for Clonal TreesThea Traw, Quoc Nguyen, Layla Oesper, Eric Carlson Alexander. [doi]
• Species detection for microbiomes with TIPP-SDChengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow. [doi]
• A Novel AI Approach to Analyze the Cardiovascular Effects of Artificial Sweeteners Using Daphnia magnaZooey Lan. [doi]
• Climate Change Drives the Evolution of Influenza A VirusesMatthieu Vilain, Rasha Mghabghab, Stéphane Aris-Brosou. [doi]
• Identifying master transcriptional regulators with single-cell-based networksEwura-Esi Manful, Yasin Uzun. [doi]
• Extending Fairness in Single-Cell AI: Evaluating Age, Sex, and Ethnicity Bias with Synthetic Data AugmentationFernando Peralta Castro, Jiaqi Zhang, Ritambhara Singh. [doi]
• EpiCRISPR: Improving CRISPR/Cas9 on- and off-target prediction by flanking sequences, epigenetic marks, and high-throughput datasetsAlon Luboshitz, Michal Rahimi, Ayal Hendel, Yaron Orenstein. [doi]
• CTSuggest: An LLM-powered Open Source Application to support Clinical Trial Design by Suggesting Baseline FeaturesSoumeek Mishra, Corey Curran, Tianyan Lin, John S. Erickson, Kristin P. Bennett. [doi]
• Bioinformatics-Driven Lipidomics and Network Modeling Reveal Cardiolipin Remodeling as a Regulatory Switch in OsteogenesisPraveen Kumar Guttula, Maria Iftesum, Manas Ranjan Gartia. [doi]
• Novel Graph Neural Network Method for Differential Network Analysis in Biological DataMarianna Milano, Pietro Hiram Guzzi. [doi]
• Large-Scale Stance Analysis of Public Discourse on Anti-Obesity Drugs Using Locally Deployed LLMsShengtian Huang, Qing Qin, Dawei Liu. [doi]
• MicroTraitLLM: A RAG-based, Microbe-focused LLM for ResearchersGlen Rogers, James R. Brown, Bahrad A. Sokhansanj, Joshua Chang Mell, Gail L. Rosen. [doi]
• Pan-cancer Outcome Prediction using Multi-classifier SystemsSakhawat Hossain Saimon, Tanzira Najnin, Jianhua Ruan. [doi]
• SegJointGene: Joint Cell Segmentation and Spatially Gene Prioritization by an Iterative Deep Learning FrameworkHaotian Ma, Daifeng Wang. [doi]
• Enhancing Agent-Based Models with Real-Time Movement Data to Assess Impacts of Biosecurity Interventions on Disease Exposure in Healthcare SettingsRavi Chandra Thota, Yusuf Sarwar Uddin, Majid Bani-Yaghoub, Mohamed Nezar Abourraja, Gary Sutkin, Susanna Paschal. [doi]
• Hidden in protein sequences: Predicting cryptic binding sitesVít Skrhák, Hamza Gamouh, David Hoksza. [doi]
• Movi Color: fast and accurate taxonomic classification with the move structureSteven Tan, Sina Majidian, Benjamin Thomas Langmead, Mohsen Zakeri. [doi]
• AtlasCollect: A Single Cell Data Atlas platform and Unified Platform for Datasets Collection and IntegrationSriram Boddeda, Marmar R. Moussa, Olajumoke B. Oladapo, Youla Ali, Nicholas Louque, Suryaveer Kapoor. [doi]
• MoE-MSC: Mixture of Experts with Multi-Stream Connector for Modality-Aware Medical Image CaptioningAl Shahriar Rubel, Frank Y. Shih, Fadi P. Deek. [doi]
• GCVAE: A graph conditional variational autoencoder for feature dependency guided synthetic metabolomic data generationKowshika Sarker, ChengXiang Zhai. [doi]
• DeepPH : A Multimodal Deep Learning Model for Predicting Enzyme Optimal pH RangeWei Wang, Po-yu Liang, Jun Bai. [doi]
• Using Diffusion Planner for Cell Fate ReprogrammingShiv Shankar. [doi]
• Predicting T-Cell Receptor Specificity and Phenotype Using Integrated Classical and Pre-Trained Protein Language ModelsMarmar R. Moussa, Mohamed Abdelnaby. [doi]
• Multi-Objective Loss Function For Free Energy CalculationsLibina Bovan Thomas, Ali Risheh, Negin Forouzesh. [doi]
• Evaluating the Impact of Human Segmentation on AI-Based Pancreatic Cancer Detection in CT ScansLang Leo Xiong. [doi]
• Learning the native-like codons with a 5'UTR and RNA secondary structure aided species-informed transformer modelQiuyue Hu, Rui Zhou, ZhiHao Wang, Liangzhen Zheng, Yanjie Wei. [doi]
• Multi-Agent LLM Reasoning for Clinical Procedure Sequencing from High-Granularity EHR DataYishan Zhong, Wenqi Shi, J. Ben Tamo, Micky C. Nnamdi, Yining Yuan, May Dongmei Wang. [doi]
• PLATO: Predicting Longitudinally-Aligned Time Observations of biological networksTamim Khatib, Shahaddin Gafarov, Justin Strikowski, Mehmet Turan, Tamer Kahveci. [doi]
• Identification of Condition-Specific Exosomal miRNA Modules Using a Bayesian FrameworkYin Liu, Daniel J. Wu, Sarah Bounds, Jiyang Cai. [doi]
• A Dual Graph Encoder Approach to Structure-Based TCR-pMHC Binding PredictionA. N. M. Nafiz Abeer, Xiaoning Qian, Byung-Jun Yoon. [doi]
• MT-UGAN: Multi-task GANs for Automatic Segmentation and Identification of Hippocampal RegionsSayed Mehedi Azim, Renuka Kumar, Brian Corbett, Iman Dehzangi. [doi]
• RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis TechniquesFurkan Eris, Ulysse McConnell, Can Firtina, Onur Mutlu. [doi]
• Identifying Top Performing Providers: A Sheaf-theoretic Approach on Healthcare NetworksCorey Verkouteren, Djalil Sawadogo, Esra Akbas, Mehmet Emin Aktas. [doi]
• Vision transformer supported Kolmogorov-Arnold networks for survival prediction in lung cancerMert Gökpinar, Yasin Almalioglu, Mustafa Taha Koçyigit, Tamer Kahveci, Derya Demir, Kayhan Basak, Mehmet Turan. [doi]
• Retrospective Inference of Evolutionary Parameters in the Moran Process Using ChatGPTFrank Tan, Isaac Huang, Jimmy Xiangji Huang. [doi]
• Privacy-Preserving Collaborative Population Stratification with Dynamic Algorithm and Hyperparameter SelectionMaryam Ghasemian, Lynette Hammond Gerido, Erman Ayday. [doi]
• Benchmarking and Improving Foundation Model Dietary Estimates from Meal ImagesYongcheng Mu, Jiangwen Sun, Jing He 0002. [doi]
• Rational Multi-Modal Transformers for TCR-pMHC PredictionJiarui Li, Zixiang Yin, Zhengming Ding, Samuel J. Landry, Ramgopal R. Mettu. [doi]
• Efficient and effective methods for variant selectionSrinivas Aluru, Anne Benoit, Bora Uçar. [doi]
• Characterizing Amyloid Pathogenic Spread in Alzheimer's Disease Through A Network Diffusion ModelFrederick H. Xu, Duy Duong Tran, Heng Huang, Andrew J. Saykin, Paul M. Thompson, Christos Davatzikos, Yize Zhao, Li Shen 0001. [doi]
• An explainable approach to learning feature representations of omics data using optimal transport to improve phenotype stratificationNandini Amit Gadhia, Soumyadip Ghosh, Ritesh Krishna, Anh Nguyen 0003, Michalis Smyrnakis. [doi]
• Predicting Brain Age in Functional Neuroimages using Node Centrality MeasuresMonireh Taimouri, Vikram Ravindra. [doi]
• Unsupervised Latent Pattern Analysis for Estimating Type 2 Diabetes Risk in Undiagnosed PopulationsPraveen Kumar, Vincent T. Metzger, Scott Alexander Malec. [doi]
• Predicting Pneumococcal Meningitis from Demographics and Early AMR SignalsMichael Aaron G. Sy, Garrett Ellward, Daniel M. Czyz, Vidhu Kariyawasam, Panayiotis V. Benos, Simone Marini. [doi]
• Automated Clinical Problem Detection from SOAP Notes using a Collaborative Multi-Agent LLM ArchitectureYeawon Lee, Xiaoyang Wang, Christopher Yang. [doi]
• MADSurv: An Uncertainty-Aware Framework for Multimodal Cancer Survival AnalysisEnshi Zhang, Varun Sai Raigir, Christian Poellabauer, Adrian Kohut, John Michael Templeton, Ananda Mondal, Lexi Weintraub. [doi]
• ICU-Length of Stay Prediction on Electronic Health Records using Graph Neural Networks and Homogeneous Similarity GraphsAhmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman, Rishabh Kapoor, Preetam Ghosh. [doi]
• From Association to Mechanism: Causal Graph-Based Fine-Mapping of Regulatory SNPs for Functional ValidationNishant Singh Chouhan, J. Ben Tamo, Oankar R. Patil, Wenqi Shi, Micky C. Nnamdi, Steven Randall Hwang, Kamran W. Shazand, May Dongmei Wang. [doi]
• Network Analysis of Methylomics in Patients with Brugada: DNA Methylation and Brugada SyndromeGiuditta Benincasa, Claudio Napoli. [doi]
• BioRSP: Angular Scanning for Directional Gene Expression Enrichment in Single-Cell EmbeddingsZeyu Yao, Jake Y. Chen. [doi]
• Protein-Protein Interface Angle Change (∆FA) as a Descriptor of Mutation-Induced Structural PerturbationsLogan Nicholas Day, Filip Jagodzinski, James Tessmer, Bogdan Trigubov, Emelia Galante. [doi]
• Data-Driven Symbolic Higher-Order Epistasis Discovery with Kolmogorov-Arnold NetworksOankar R. Patil, Benoit Louis Marteau, Kamran Shazand, Yuxuan Shen, May Dongmei Wang. [doi]
• Graph Neural Network with Pretrained Embeddings for Cancer and miRNA Regulator DiscoveryLi Sa, Tianle Ma. [doi]
• Cell-Type-Aware Single-Cell ML Reveals Distinct Biomarkers for Sarcoidosis Prognosis and CBD DifferentiationSaaketh Bhojanam, Sohum Mehta. [doi]
• KindSleep: Knowledge-Informed Diagnosis of Obstructive Sleep Apnea from OximetryMicky C. Nnamdi, Wenqi Shi, Cheng Wan, J. Ben Tamo, Benjamin M. Smith, Chad Purnell, May Dongmei Wang. [doi]
• Retrieval-Reasoning Large Language Model-based Synthetic Clinical Trial GenerationZerui Xu, Fang Wu 0002, Yingzhou Lu, Yuanyuan Zhang, Yue Zhao 0016. [doi]
• MoE-Health: A Mixture of Experts Framework for Robust Multimodal Healthcare PredictionXiaoyang Wang, Christopher C. Yang. [doi]
• Rare Disease Phenotyping via Self-Supervised Multimodal LearningKhartik Uppalapati, Bora Yimenicioglu, Adan Eftekhari, Shakeel Abdulkareem. [doi]
• RDS: A ReCIPE for Overlapping Community Detection in Biological NetworksFaith Abiria Ocitti, Charlotte Versavel, Samuel Sledzieski, Lenore Cowen. [doi]
• Deconvolution-Enhanced Contrastive Pretraining of Histology Images and Gene Expressions in Spatial TranscriptomicsXulin Chen, JunZhou Huang. [doi]
• Characterizing Gene Regulatory Network Ensembles in Kidney Injury and RepairEitan Tannenbaum, Dana Markiewitz, Tomer Kalisky, Hillel Kugler. [doi]
• MCL-DMD: Multi-modal Contrastive Learning for Drug-Microbe-Disease Association PredictionNiecia Say, Farhan Tanvir, Moctar Keita, Lilia Chebbah, Muhammad Ifte Khairul Islam, Esra Akbas. [doi]
• Fair CCA for Fair Representation Learning: An ADNI StudyBojian Hou, Zhanliang Wang, Zhuoping Zhou, Boning Tong, Zexuan Wang, Jingxuan Bao, Duy Duong Tran, Qi Long, Li Shen 0001. [doi]
• Addressing COVID-19 Data Imbalance Issue with Multimodal Image GenerationMaxwell Sam, Hailemicael Lulseged Yimer, Salil Desai, Xiaohong Yuan, Jinsheng Xu, Huiming Anna Yu, Letu Qingge. [doi]
• Privacy-Preserving Genomic Similarity Search via Enhanced Homomorphic Encryption with BLAST-Concordant AlgorithmsSaaketh Bhojanam, Sohum Mehta. [doi]