Table of Contents

• NeuralTE: an accurate approach for Transposable Element superfamily classification with multi-feature fusionKang Hu, Minghua Xu 0005, Xin Gao 0001, Jianxin Wang 0001. [doi]
• Robinson-Foulds distance between phylogenetic networks and gene treesNatalia Rutecka, Agnieszka Mykowiecka 0002, Jaroslaw Paszek, Pawel Górecki 0001. [doi]
• Building Personality-Adaptive Conversational AI for Mental Health TherapySugam Jaiswal, Joyce Lee, Joe Berria, Raviteja Tanikella, Annuska Zolyomi, Muhammad Aurangzeb Ahmad, Dong-Si. [doi]
• Rethinking Radiology Report Generation via Causal Inspired Counterfactual AugmentationXiao Song 0003, Jiafan Liu, Yan Liu, Yun Li, Wenbin Lei, Ruxin Wang. [doi]
• Heterogeneous Treatment Effects of Spinal Fusion Surgery for Adolescent Idiopathic Scoliosis PatientsJ. Ben Tamo, Micky C. Nnamdi, Andrew Hornback, Matthew Chen, Wenqi Shi, Yuanda Zhu, Henry J. Iwinski, May D. Wang. [doi]
• DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expressionYixian Huang, Huacong Wu, Ying Cai, Danhong Dong, Sicong Yu, Yigang Chen 0001, Zihao Zhu, Yang-Chi-Dung Lin, Hsien-Da Huang, Hsi-Yuan Huang. [doi]
• RBVS: Database of the Receptor-Based Virtual ScreeningSenbiao Fang, Huimin Zhu, Yongfan Ming, Kunying Niu, Baoying Zhao, Min Li 0007. [doi]
• GCLNSTDA: Predicting tsRNA-Disease Association Based on Contrastive Learning and Negative SamplingWei Lan, Wenyi Chen, Chunling Li, Qingfeng Chen, Yi-Ping Phoebe Chen, Yi Pan 0001. [doi]
• ICDFGF: Identification of potential circRNA-disease associations based on feature graph factorizationYuchen Zhang 0003, Xiujuan Lei, Zhengfeng Wang, Yi Pan 0001. [doi]
• TrialDura: Hierarchical Attention Transformer for Interpretable Clinical Trial Duration PredictionLing Yue, Sixue Xing, Jonathan Li 0010, Md. Zabirul Islam, Bolun Xia, Jintai Chen, Tianfan Fu. [doi]
• SVMPT: A Hybrid Approach to Sparse and Irregular Clinical Data Learning with Selective Variable-wise Message Passing and TransformerRongqin Chen, Dan Wu 0002, Leong Hou U, Ye Li 0002. [doi]
• Dual-view jointly learning improves personalized drug synergy predictionXueliang Li, Bihan Shen, Fangyoumin Feng, Kunshi Li, Liangxiao Ma, Hong Li. [doi]
• Peptide Sequencing Via Protein Language ModelsThuong Le Hoai Pham, Jillur Rahman Saurav, Aisosa A. Omere, Calvin J. Heyl, Mohammad Sadegh Nasr 0001, Cody Tyler Reynolds, Jai Prakash Yadav Veerla, Helen H. Shang, Justyn Jaworski, Alison Ravenscraft, Joseph Anthony Buonomo, Jacob M. Luber. [doi]
• Dynamic Knowledge-Prior for Few-Shot Drug-Drug Interaction Events PredictionPengfei Liu, Jun Tao 0002, Zhixiang Ren. [doi]
• Fast-scBatch: Batch Effect Correction Using Neural Network-Driven Distance Matrix AdjustmentFu Chen, Leqi Tian, Teng Fei, Tianwei Yu. [doi]
• scDBImpute: Dual-branch imputation for single-cell RNA-seq data dropoutsLin Zhang 0015, Feng Wang, Jiani Ma, Hui Liu 0024. [doi]
• FHIRViz: Multi-Agent Platform for FHIR Visualization to Advance Healthcare AnalyticsMariam Almutairi, Lulwah Alkulaib, Shengkun Wang, Zhiqian Chen, Youssif ALMutairi, Thamer M. Alenazi, Kurt Luther, Chang-Tien Lu. [doi]
• CCVAN: A Conditional Molecular Generation Model based on conditional VAE and Wasserstein GANJianqiang Zheng, Ziqi Xu, Junwen Huang, Xiaochuan Chen, Yuetong Li, Yanjie Wei, Huiling Zhang. [doi]
• A Co-contrastive Learning Method to Fuse Multi-modal Phenotypes and Identify Genetic Risk VariationsMuheng Shang, Yan Yang, Jin Zhang, Daoqiang Zhang, Lei Du 0001. [doi]
• Deciphering Bladder Cancer-Related circRNA Biomarkers: An Ensemble Model Integrating Deep Learning and Statistics for circRNA AnalysisYulian Ding, Yi Pan 0001, Ronald C. Geyer, Franco J. Vizeacoumar, Frederick S. Vizeacoumar, Fang-Xiang Wu. [doi]
• DVL-CC: A Novel Dual-View Learning Framework for Compound Cocrystal Prediction Boosted by View Consistency and ComplementarityHaoyang Yu, Bei Zhu, Bing-Xue Du, Xue-Xin Wei, Hui Yu 0011, Jian-Yu Shi. [doi]
• Normalized Compression Distance for DNA ClassificationGavin L. A. Hearne, Mohammad S. Refahi, Haozhe Neil Duan, James R. Brown, Gail L. Rosen. [doi]
• Enhancing Privacy Protection for Human Genome Synthesis Using Gradient ClippingKohei Hashimoto, Kana Shimizu. [doi]
• Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity ClustersManas Jyoti Das, Praveen Rao 0001, Lisong Xu. [doi]
• Distilling Multi-Modal Genomic Knowledge for Drug Response PredictionShuang Ge, Shuqing Sun, Huan Xu, Zhixiang Ren. [doi]
• AlphaEpi: Enhancing B Cell Epitope Prediction with AlphaFold 3Feng Jiang, Yuzhi Guo, Hehuan Ma, Saiyang Na, Weizhi An, Bing Song, Yi Han, Jean Gao, Tao Wang, JunZhou Huang. [doi]
• New Spatial Phenotypes from Imaging Uncover Survival Differences for Breast Cancer PatientsMahmudul Hasan 0006, Ariadna Kim Silva, Shahira Abousamra, Shao-Jun Tang, Prateek Prasanna, Joel H. Saltz, Kevin Gardner, Chao Chen 0012, Alisa Yurovsky. [doi]
• GMF-MGCN-LDA: Prediction of IncRNA-disease association based on novel generalized matrix factorization and graph neural networksQi Gao, Guosheng Han, Jialin Li, Li Zeng. [doi]
• TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep & Cross Network and Large Language ModelsLing Yue, Sixue Xing, Jintai Chen, Tianfan Fu. [doi]
• A Comparison of Representation Learning Methods for Medical Concepts in EHR DatabasesZhangdaihong Liu, Xuan Wu, Yang Yang, David A. Clifton. [doi]
• gPSRM: A generative propensity score-based replay memory for deep reinforcement learningsJiang Liu, Chan Zhou, Yuwen Chen, Yihao Xie, Kunhua Zhong, Qilong Sun, Yujie Li, Bin Yi. [doi]
• Causality-based Subject and Task Fingerprints using fMRI Time-series DataDachuan Song, Li Shen 0001, Duy Duong Tran, Xuan Wang 0013. [doi]
• Towards Instructing Disease-Drug Link Prediction with Social Determinants of HealthYashaswi Galhotra, Ying Ding 0003, Li Shen 0001, Huanmei Wu, Tianlong Chen, Kaixiong Zhou. [doi]
• Graph learning of disentangled representation for accurately aligning multiple spatial slicesJianing Chen, Yuansong Zeng, Ningyuan Shangguan, Wenhao Zhou, Wenbing Li, Yuedong Yang. [doi]
• EpiUNet: Stain-Style Transfer Model for Histology Image Based on Generative Adversarial NetworkZhengze Gong, Wenhui Wang, Xiaocong Tan, Mengkun Gan, Weijie Xie. [doi]
• ClinicalAgent: Clinical Trial Multi-Agent System with Large Language Model-based ReasoningLing Yue, Sixue Xing, Jintai Chen, Tianfan Fu. [doi]
• One-shot Biomedical Named Entity Recognition via Knowledge-Inspired Large Language ModelJunyi Bian, Jiaxuan Zheng, Yuyi Zhang, Hong Zhou, Shanfeng Zhu. [doi]
• Deep Learning for Autism Spectrum Disorder Identification Based on Children's Facial Images: A Multi-Feature Fusion PerspectiveWondimagegn Bekele Munto, Mengying Zhou, Yi Pan 0001, Yanjie Wei, Wenhui Xi. [doi]
• MFMF: Multiple Foundation Model Fusion Networks for Whole Slide Image ClassificationThao M. Dang, Yuzhi Guo, Hehuan Ma, Qifeng Zhou, Saiyang Na, Jean Gao, JunZhou Huang. [doi]
• Leveraging Mutual Information for Functional Annotation Analysis of Microglia in Alzheimer's DiseaseChenyu Zhang, Qingli Hu, Honglin Wang, Seung-Hyun Hong, Riqiang Yan, Dong-Guk Shin. [doi]
• MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic ModelingRuohan Wang, Zilong Wang, Ziyang Song, David Buckeridge, Yue Li. [doi]
• FiSSC: Finding smallest sequence covers to sets of degenerate reads with applications to RNA editingIdo Tziony, Jonathan Mandl, Kobi Shapira, Eli Eisenberg, Ely Porat, Yaron Orenstein. [doi]
• DANTE: Determining Adaptation trajectories in biological Networks Through Evolutionary mappingTamim Khatib, Oscar Diaz de la Rua, Kawthar Moria, Tamer Kahveci. [doi]
• The Algorithms of Predicting DNA Binding Site with Combined Feature Encoding and Optimum DecisionZhendong Liu, Jun Liu, Dongqing Wei, Yanjie Wei, Rongjun Man. [doi]
• Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoringSangam Buddhacharya, Noël Lefevre, Elain S. Fu, Stephen A. Ramsey. [doi]
• EEG-DIF: Early Warning of Epileptic Seizures through Generative Diffusion Model-based Multi-channel EEG Signals ForecastingZekun Jiang, Wei Dai, Qu Wei, Ziyuan Qin 0001, Kang Li 0004, Le Zhang 0004. [doi]
• BactAG: a novel method resolving bacterial ancient genomes precisely and automaticallyYiwei Wang, Peijun Chen, Yejun Wang. [doi]
• ChatASD: A Dialogue Framework for LLMs Enhanced by Autism Knowledge Graph RetrievalLei Chu, Hongyan Wu, Yi Pan 0001. [doi]
• Detecting and Subtyping Anomalous Single Cells with M2ASDAKaichen Xu, Kainan Liu, Linjie Wang, Yueyang Ding, Yan Lu, Hao Wu 0003, Xiaobo Sun. [doi]
• Operonome: the concept and application in bacterial systems biologyLeting Sun, Zhixuan Deng, Yejun Wang. [doi]
• Cutting-Edge Algorithms in Genomics: From Theory to PracticeXuefeng Cui. [doi]
• TimelyGPT: Extrapolatable Transformer Pre-training for Long-term Time-Series Forecasting in HealthcareZiyang Song, Qincheng Lu, Hao Xu, He Zhu, David Buckeridge, Yue Li. [doi]
• PathoEye: a novel deep learning framework for histopathological image analysis of skin tissueYusen Lin, Feiyan Lin, Yongjun Zhang, Jiajian Zhou. [doi]
• Med-PRSIMD: Enhanced Complex Disease Risk Prediction through Integrative Analysis of Multi-Type Data and Medical History RecordsZeming Li, Yu Xu, Debajyoti Chowdhury, Hip Fung Yip, Chonghao Wang, Lu Zhang 0061. [doi]
• PepGPL: A Multi-Task Framework for Identifying Peptide-Protein Interactions and Corresponding Binding ResiduesRuikang Zhou, Haochen Zhao, Jian Zhong, Guihua Duan. [doi]
• Large Language Models for Cuffless Blood Pressure Measurement From Wearable BiosignalsZengding Liu, Chen Chen, Jiannong Cao 0001, Minglei Pan, Jikui Liu, Nan Li 0011, Fen Miao, Ye Li 0002. [doi]
• STAPFormer: A New 3D Human Pose Estimation Framework in Sports and HealthZhongteng Zhang, Qing Peng, Liu Zhang, Zihao Zhang, Weihong Huang. [doi]
• Optimal protospacer sequences recommended by ensemble deep learning for high-efficiency base editingHui Peng, Xiaocai Zhang, Yuansheng Liu, Yi Pan 0001, Wilson Wen Bin Goh, Jinyan Li. [doi]
• Static and multivariate-temporal attentive fusion transformer for readmission risk prediction of ICU patientsRunzhi Li, Zhe Sun, Jing Wang 0080, Gang Chen 0037, Siyu Yan, Lihong Ma 0004. [doi]
• MCWCM: Multi-Criteria Ranking and Weighted Control Model for Identifying Key Drivers in cancerBolin Chen, Zhengyu Wang, Ziyuan Li. [doi]
• MLPA: A Multi-scale Digital Twin Framework for Personalized Cancer Simulation and Treatment OptimizationJames Gu, Jake Y. Chen. [doi]
• iDNA-EBT: An ensemble model based on multi-scale secondary fine-tuned BERTWei Peng, Yueran Hu, Zihan Zhao, Jingwen Yan, HongWei Xia, Xiaolei Zhu. [doi]
• Spatiotemporal attention boosts calling of complicated variations from long reads' alignment dataYing Shi 0004, Shifu Luo, Yi Pan 0001, Hao Wu 0003, Wenjian Wang, Jinyan Li. [doi]
• CAPTURE: A Clustered Adaptive Patchwork Technique for Unified Registration Enhancement in Biological ImagingSahand Hamzehei, Gianna Raimondi, Mostafa Karami, Linnaea Ostroff, Sheida Nabavi. [doi]
• Efficient Federated Learning with Multi-Teacher Knowledge Distillation for COVID-19 DetectionRichard Annan, Hong Qin 0003, Xiaohong Yuan, Kaushik Roy 0003, Robert H. Newman, Letu Qingge. [doi]
• Com-DNB: A novel method for identifying critical states of complex biological processes and its parallelizationLetian Wang, Yanbing Zhu, Xiaohua Wan, Yiming Zhang, Shuang Feng, Chang Li, Fa Zhang 0001, Bin Hu 0001. [doi]
• AttCON-Homo: Attention and PLMs-enhanced Neural Networks for Predicting Inter-chain Contacts and Distances in Homo-oligomeric Protein ComplexesChe Zhao, Shunfang Wang. [doi]
• PANACEA: Towards Influence-driven Profiling of Drug Target Combinations in Cancer Signaling NetworksBaihui Xu, Sourav S. Bhowmick, Jiancheng Hu. [doi]
• MVFormer: Predicting the pathogenicity of missense variants using gated transformersZongxuan Li, Wenkui Huang, Hong-Dong Li. [doi]
• MIXER: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing DataTao Deng, Mengqian Huang, Kaichen Xu, Yan Lu, Siyu Chen, Yucheng Xu, Nina Xie, Hao Wu 0003, Xiaobo Sun. [doi]
• DeePSP-GIN: identification and classification of phage structural proteins using predicted protein structure, pretrained protein language model, and graph isomorphism networkMuhit Islam Emon, Badhan Das, Ashrith Reddy Thukkaraju, Liqing Zhang 0002. [doi]
• scMoE: single-cell mixture of experts for learning hierarchical, cell-type-specific, and interpretable representations from heterogeneous scRNA-seq dataMichael Huang, Yue Li. [doi]
• Revealing Multi-biological Subtypes of Schizophrenia through a Data-Driven ClusteringYuran Wang, Kai Wu 0002. [doi]
• 13th Workshop on Parallel and AI-based Bioinformatics and Biomedicine (ParBio): EditorialGiuseppe Agapito, Mario Cannataro, Wes J. Lloyd, Chiara Zucco. [doi]
• L2 Normalization and Geodesic Distance for Enhanced Information Preservation in Visualizing High-dimensional Single-cell Sequencing DataZiqi Rong, Jinpu Cai, Jiahao Qiu, Pengcheng Xu, Lana X. Garmire, Qiuyu Lian, Hongyi Xin. [doi]
• PCMA: A New Mediation Analysis Method Effectively Identifies Relevant Pathways Connecting Microbiota and DiseasesWeimiao Kong, Yuqi Lin, Yejun Wang. [doi]
• A High Performance Parametric Model for 3D Gingiva-Tooth Boundary via Generalized CylindersYuanhao Gong. [doi]
• DynPred: A Multimodal Deep Learning Approach for Protein Dynamics PredictionAaditya Shah, Sugyan Dixit. [doi]
• DCCNV: Enhanced CNV Detection in Single-Cell Sequencing Using Diffusion Process and Contrastive LearningMostafa Karami, Bingjun Li, Samson Weiner, Sahand Hamzehei, Sheida Nabavi. [doi]
• MetaphorPrompt - An Analogical Reasoning Approach for Extracting Causal Links from Biological TextParth Patel, Yu-Chiao Chiu, Yufei Hunag, Jianqiu Zhang 0002. [doi]
• Asymmetric Mutual Learning for Decentralized Federated Medical ImagingJiaqi Wang 0002, Houping Xiao, Fenglong Ma. [doi]
• Learning Structured Sparsity for Efficient Nanopore DNA Basecalling Using Delayed MaskingMees Frensel, Zaid Al-Ars, H. Peter Hofstee. [doi]
• Cox-Path: Biological Pathway-Informed Graph Neural Network for Cancer Survival PredictionTeng Ma, Haochen Zhao, Qichang Zhao, Jianxin Wang 0001. [doi]
• SeqBench: A Benchmark Suite for Lossless and Lossy Compression of Sequence DataTaolue Yang, Youyuan Liu, Chong Li, Xinhua Mindy Shi, Sian Jin. [doi]
• Integrated analysis of gut microbiome compositional and genomic alterations reveals strain diversity and actionable biomarkers across multiple colorectal cancer cohortsChao Yang, Jingjing Wang, Lu Zhang 0061. [doi]
• mm2-gb: GPU Accelerated Minimap2 for Long Read DNA MappingJuechu Dong, Xueshen Liu, Harisankar Sadasivan, Sriranjani Sitaraman, Satish Narayanasamy. [doi]
• PMSA-Net: A parallel multi-scale attention network for MI-BCI classificationMingzhe Cui, Tao Chen, Yang Jiao, Qian Zheng, Yi Pan 0001, Lei Xie 0007. [doi]
• Improved genetic algorithm for readmission risk index optimizationShuo Feng, Zhe Sun, Runzhi Li, Siyu Yan, Lihong Ma 0004. [doi]
• Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRIRuimin Ma, Ying Huang, Yi Pan 0001, Yanlin Wang, Yanjie Wei. [doi]
• Drug-gene Associations with Graph LearningJiayang Wu, Wensheng Gan, Jinqi Lai, Guoting Chen, Philip S. Yu. [doi]
• A Multi-task Learning Approach for Predicting Spatio-temporal Patient VariablesKaniz Fatema Madhobi, Eric Lofgren, Ananth Kalyanaraman. [doi]
• Comparative Analysis of Prominent AI Models for Enhanced Diabetes Diagnosis & PredictionRudransh Pathak. [doi]
• Missense Mutation Effect Prediction using Categorical Boosting Optimized with Sparrow Search AlgorithmHuiling Zhang, Jingjing Zhang, Ganzhang Zheng, Xiaochuan Chen, ZaoQing Liang, Haiyan Wang, Yanjie Wei. [doi]
• MPDF-UNET: Modality Priors and Dynamic Features Fusion U-Net for Incomplete Multimodal Brain Tumor SegmentationYutian Xiao, Xiaomao Fan, Chongguang Yang, Yang Zhao 0009. [doi]
• Towards Smartphone-Based Monitoring of Micronutrient StatusAndrew Balch, Afsaneh Doryab. [doi]
• CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairsJianing Wang, Jin A, Hanjun Pan, Ruiqing Zheng, Chaojin Wu, Min Li 0007. [doi]
• ISGDRP: a multi-modal learning method for drug response predictionHaochen Zhao, Xiaoyu Zhang, Qichang Zhao, Guihua Duan. [doi]
• Uncovering Key Features of Individuals Who Benefit from Polygenic Risk Scores in Prostate Cancer PredictionAndrew Hornback, Monica Isgut, Anirudh Jaishankar, Harinishree Sathu, Pavithra Avula, May D. Wang. [doi]