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ORCID15th BCB 2024: Shenzhen, China
- Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2024, Shenzhen, China, November 22-25, 2024. ACM 2024, ISBN 979-8-4007-1302-6
Regular Papers
- Manas Jyoti Das, Praveen Rao, Lisong Xu:
Impact of the Networking Infrastructure on the Performance of Variant Calling on Human Genomes in Commodity Clusters. 1:1-1:11 - Yulian Ding, Yi Pan, Ronald C. Geyer, Franco J. Vizeacoumar, Frederick S. Vizeacoumar, Fang-Xiang Wu:
Deciphering Bladder Cancer-Related circRNA Biomarkers: An Ensemble Model Integrating Deep Learning and Statistics for circRNA Analysis. 2:1-2:10 - Jianing Wang, Jin A, Hanjun Pan, Ruiqing Zheng, Chaojin Wu, Min Li:
CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs. 3:1-3:7 - Senbiao Fang, Huimin Zhu, Yongfan Ming, Kunying Niu, Baoying Zhao, Min Li:
RBVS: Database of the Receptor-Based Virtual Screening. 4:1-4:9 - Xiao Song, Jiafan Liu, Yan Liu, Yun Li, Wenbin Lei, Ruxin Wang:
Rethinking Radiology Report Generation via Causal Inspired Counterfactual Augmentation. 5:1-5:10 - J. Ben Tamo, Micky C. Nnamdi, Andrew Hornback, Matthew Chen, Wenqi Shi, Yuanda Zhu, Henry J. Iwinski, May D. Wang:
Heterogeneous Treatment Effects of Spinal Fusion Surgery for Adolescent Idiopathic Scoliosis Patients. 6:1-6:10 - Natalia Rutecka, Agnieszka Mykowiecka, Jaroslaw Paszek, Pawel Górecki:
Robinson-Foulds distance between phylogenetic networks and gene trees. 7:1-7:10 - Wei Lan, Wenyi Chen, Chunling Li, Qingfeng Chen, Yi-Ping Phoebe Chen, Yi Pan:
GCLNSTDA: Predicting tsRNA-Disease Association Based on Contrastive Learning and Negative Sampling. 8:1-8:7 - Yuchen Zhang, Xiujuan Lei, Zhengfeng Wang, Yi Pan:
ICDFGF: Identification of potential circRNA-disease associations based on feature graph factorization. 9:1-9:10 - Yixian Huang, Huacong Wu, Ying Cai, Danhong Dong, Sicong Yu, Yigang Chen, Zihao Zhu, Yang-Chi-Dung Lin, Hsien-Da Huang, Hsi-Yuan Huang:
DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expression. 10:1-10:10 - Ling Yue, Sixue Xing, Jintai Chen, Tianfan Fu:
ClinicalAgent: Clinical Trial Multi-Agent System with Large Language Model-based Reasoning. 11:1-11:10 - Mees Frensel, Zaid Al-Ars, H. Peter Hofstee:
Learning Structured Sparsity for Efficient Nanopore DNA Basecalling Using Delayed Masking. 12:1-12:9 - Ido Tziony, Jonathan Mandl, Kobi Shapira, Eli Eisenberg, Ely Porat, Yaron Orenstein:
FiSSC: Finding smallest sequence covers to sets of degenerate reads with applications to RNA editing. 13:1-13:10 - Chenyu Zhang, Qingli Hu, Honglin Wang, Seung-Hyun Hong, Riqiang Yan, Dong-Guk Shin:
Leveraging Mutual Information for Functional Annotation Analysis of Microglia in Alzheimer's Disease. 14:1-14:10 - Kaniz Fatema Madhobi, Eric Lofgren, Ananth Kalyanaraman:
A Multi-task Learning Approach for Predicting Spatio-temporal Patient Variables. 15:1-15:10 - Ziyang Song, Qincheng Lu, Hao Xu, He Zhu, David Buckeridge, Yue Li:
TimelyGPT: Extrapolatable Transformer Pre-training for Long-term Time-Series Forecasting in Healthcare. 16:1-16:10 - Mahmudul Hasan, Ariadna Kim Silva, Shahira Abousamra, Shao-Jun Tang, Prateek Prasanna, Joel H. Saltz, Kevin Gardner, Chao Chen, Alisa Yurovsky:
New Spatial Phenotypes from Imaging Uncover Survival Differences for Breast Cancer Patients. 17:1-17:12 - Dachuan Song, Li Shen, Duy Duong-Tran, Xuan Wang:
Causality-based Subject and Task Fingerprints using fMRI Time-series Data. 18:1-18:10 - Ying Shi, Shifu Luo, Yi Pan, Hao Wu, Wenjian Wang, Jinyan Li:
Spatiotemporal attention boosts calling of complicated variations from long reads' alignment data. 19:1-19:10 - Zhongteng Zhang, Qing Peng, Liu Zhang, Zihao Zhang, Weihong Huang:
STAPFormer: A New 3D Human Pose Estimation Framework in Sports and Health. 20:1-20:10 - Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Guihua Duan:
ISGDRP: a multi-modal learning method for drug response prediction. 21:1-21:8 - Ruikang Zhou, Haochen Zhao, Jian Zhong, Guihua Duan:
PepGPL: A Multi-Task Framework for Identifying Peptide-Protein Interactions and Corresponding Binding Residues. 22:1-22:9 - Rongqin Chen, Dan Wu, Leong Hou U, Ye Li:
SVMPT: A Hybrid Approach to Sparse and Irregular Clinical Data Learning with Selective Variable-wise Message Passing and Transformer. 23:1-23:8 - Juechu Dong, Xueshen Liu, Harisankar Sadasivan, Sriranjani Sitaraman, Satish Narayanasamy:
mm2-gb: GPU Accelerated Minimap2 for Long Read DNA Mapping. 24:1-24:9 - Jiaqi Wang, Houping Xiao, Fenglong Ma:
Asymmetric Mutual Learning for Decentralized Federated Medical Imaging. 25:1-25:9 - Junyi Bian, Jiaxuan Zheng, Yuyi Zhang, Hong Zhou, Shanfeng Zhu:
One-shot Biomedical Named Entity Recognition via Knowledge-Inspired Large Language Model. 26:1-26:10 - Zengding Liu, Chen Chen, Jiannong Cao, Minglei Pan, Jikui Liu, Nan Li, Fen Miao, Ye Li:
Large Language Models for Cuffless Blood Pressure Measurement From Wearable Biosignals. 27:1-27:11 - Qi Gao, Guosheng Han, Jialin Li, Li Zeng:
GMF-MGCN-LDA: Prediction of IncRNA-disease association based on novel generalized matrix factorization and graph neural networks. 28:1-28:10 - Letian Wang, Yanbing Zhu, Xiaohua Wan, Yiming Zhang, Shuang Feng, Chang Li, Fa Zhang, Bin Hu:
Com-DNB: A novel method for identifying critical states of complex biological processes and its parallelization. 29:1-29:10 - Ziqi Rong, Jinpu Cai, Jiahao Qiu, Pengcheng Xu, Lana X. Garmire, Qiuyu Lian, Hongyi Xin:
L2 Normalization and Geodesic Distance for Enhanced Information Preservation in Visualizing High-dimensional Single-cell Sequencing Data. 30:1-30:11 - Hui Peng, Xiaocai Zhang, Yuansheng Liu, Yi Pan, Wilson Wen Bin Goh, Jinyan Li:
Optimal protospacer sequences recommended by ensemble deep learning for high-efficiency base editing. 31:1-31:10 - Haoyang Yu, Bei Zhu, Bing-Xue Du, Xue-Xin Wei, Hui Yu, Jian-Yu Shi:
DVL-CC: A Novel Dual-View Learning Framework for Compound Cocrystal Prediction Boosted by View Consistency and Complementarity. 32:1-32:9 - Kang Hu, Minghua Xu, Xin Gao, Jianxin Wang:
NeuralTE: an accurate approach for Transposable Element superfamily classification with multi-feature fusion. 33:1-33:10 - Kaichen Xu, Kainan Liu, Linjie Wang, Yueyang Ding, Yan Lu, Hao Wu, Xiaobo Sun:
Detecting and Subtyping Anomalous Single Cells with M2ASDA. 34:1 - Tao Deng, Mengqian Huang, Kaichen Xu, Yan Lu, Siyu Chen, Yucheng Xu, Nina Xie, Hao Wu, Xiaobo Sun:
MIXER: Identifying Co-expressed Genes in Multimodal Transcriptomic Sequencing Data. 35:1
Short Papers
- Lei Chu, Hongyan Wu, Yi Pan:
ChatASD: A Dialogue Framework for LLMs Enhanced by Autism Knowledge Graph Retrieval. 36:1-36:8 - Kohei Hashimoto, Kana Shimizu:
Enhancing Privacy Protection for Human Genome Synthesis Using Gradient Clipping. 37:1-37:6 - Mariam Almutairi, Lulwah Alkulaib, Shengkun Wang, Zhiqian Chen, Youssif ALMutairi, Thamer M. Alenazi, Kurt Luther, Chang-Tien Lu:
FHIRViz: Multi-Agent Platform for FHIR Visualization to Advance Healthcare Analytics. 38:1-38:7 - Zhendong Liu, Jun Liu, Dongqing Wei, Yanjie Wei, Rongjun Man:
The Algorithms of Predicting DNA Binding Site with Combined Feature Encoding and Optimum Decision. 39:1-39:8 - Thuong Le Hoai Pham, Jillur Rahman Saurav, Aisosa A. Omere, Calvin J. Heyl, Mohammad Sadegh Nasr, Cody Tyler Reynolds, Jai Prakash Yadav Veerla, Helen H. Shang, Justyn Jaworski, Alison Ravenscraft, Joseph Anthony Buonomo, Jacob M. Luber:
Peptide Sequencing Via Protein Language Models. 40:1-40:8 - Yashaswi Galhotra, Ying Ding, Li Shen, Huanmei Wu, Tianlong Chen, Kaixiong Zhou:
Towards Instructing Disease-Drug Link Prediction with Social Determinants of Health. 41:1-41:6 - Muhit Islam Emon, Badhan Das, Ashrith Reddy Thukkaraju, Liqing Zhang:
DeePSP-GIN: identification and classification of phage structural proteins using predicted protein structure, pretrained protein language model, and graph isomorphism network. 42:1-42:6 - Ling Yue, Sixue Xing, Jintai Chen, Tianfan Fu:
TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep & Cross Network and Large Language Models. 43:1-43:9 - Zhengze Gong, Wenhui Wang, Xiaocong Tan, Mengkun Gan, Weijie Xie:
EpiUNet: Stain-Style Transfer Model for Histology Image Based on Generative Adversarial Network. 44:1-44:6 - Jiang Liu, Chan Zhou, Yuwen Chen, Yihao Xie, Kunhua Zhong, Qilong Sun, Yujie Li, Bin Yi:
gPSRM: A generative propensity score-based replay memory for deep reinforcement learnings. 45:1-45:8 - Yusen Lin, Feiyan Lin, Yongjun Zhang, Jiajian Zhou:
PathoEye: a novel deep learning framework for histopathological image analysis of skin tissue. 46:1-46:6 - Andrew Hornback, Monica Isgut, Anirudh Jaishankar, Harinishree Sathu, Pavithra Avula, May D. Wang:
Uncovering Key Features of Individuals Who Benefit from Polygenic Risk Scores in Prostate Cancer Prediction. 47:1-47:6 - Mostafa Karami, Bingjun Li, Samson Weiner, Sahand Hamzehei, Sheida Nabavi:
DCCNV: Enhanced CNV Detection in Single-Cell Sequencing Using Diffusion Process and Contrastive Learning. 48:1-48:6 - Parth Patel, Yu-Chiao Chiu, Yufei Hunag, Jianqiu Zhang:
MetaphorPrompt - An Analogical Reasoning Approach for Extracting Causal Links from Biological Text. 49:1-49:6 - Che Zhao, Shunfang Wang:
AttCON-Homo: Attention and PLMs-enhanced Neural Networks for Predicting Inter-chain Contacts and Distances in Homo-oligomeric Protein Complexes. 50:1-50:6 - Wei Peng, Yueran Hu, Zihan Zhao, Jingwen Yan, Hongwei Xia, Xiaolei Zhu:
iDNA-EBT: An ensemble model based on multi-scale secondary fine-tuned BERT. 51:1-51:6 - Tamim Khatib, Oscar Diaz de la Rua, Kawthar Moria, Tamer Kahveci:
DANTE: Determining Adaptation trajectories in biological Networks Through Evolutionary mapping. 52:1-52:6 - Ruohan Wang, Zilong Wang, Ziyang Song, David Buckeridge, Yue Li:
MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling. 53:1-53:8 - Mingzhe Cui, Tao Chen, Yang Jiao, Qian Zheng, Yi Pan, Lei Xie:
PMSA-Net: A parallel multi-scale attention network for MI-BCI classification. 54:1-54:6 - Sangam Buddhacharya, Noël Lefevre, Elain S. Fu, Stephen A. Ramsey:
Evaluation of multi-feature machine-learning models for analyzing electrochemical signals for drug monitoring. 55:1-55:9 - Richard Annan, Hong Qin, Xiaohong Yuan, Kaushik Roy, Robert H. Newman, Letu Qingge:
Efficient Federated Learning with Multi-Teacher Knowledge Distillation for COVID-19 Detection. 56:1-56:6 - Michael Huang, Yue Li:
scMoE: single-cell mixture of experts for learning hierarchical, cell-type-specific, and interpretable representations from heterogeneous scRNA-seq data. 57:1-57:8 - Taolue Yang, Youyuan Liu, Chong Li, Xinhua Mindy Shi, Sian Jin:
SeqBench: A Benchmark Suite for Lossless and Lossy Compression of Sequence Data. 58:1-58:7 - Jianing Chen, Yuansong Zeng, Ningyuan Shangguan, Wenhao Zhou, Wenbing Li, Yuedong Yang:
Graph learning of disentangled representation for accurately aligning multiple spatial slices. 59:1-59:8 - Bolin Chen, Zhengyu Wang, Ziyuan Li:
MCWCM: Multi-Criteria Ranking and Weighted Control Model for Identifying Key Drivers in cancer. 60:1-60:6 - Jiayang Wu, Wensheng Gan, Jinqi Lai, Guoting Chen, Philip S. Yu:
Drug-gene Associations with Graph Learning. 61:1-61:6 - Sahand Hamzehei, Gianna Raimondi, Mostafa Karami, Linnaea Ostroff, Sheida Nabavi:
CAPTURE: A Clustered Adaptive Patchwork Technique for Unified Registration Enhancement in Biological Imaging. 62:1-62:6 - Zongxuan Li, Wenkui Huang, Hong-Dong Li:
MVFormer: Predicting the pathogenicity of missense variants using gated transformers. 63:1-63:6 - Thao M. Dang, Yuzhi Guo, Hehuan Ma, Qifeng Zhou, Saiyang Na, Jean Gao, Junzhou Huang:
MFMF: Multiple Foundation Model Fusion Networks for Whole Slide Image Classification. 64:1-64:8 - Yutian Xiao, Xiaomao Fan, Chongguang Yang, Yang Zhao:
MPDF-UNET: Modality Priors and Dynamic Features Fusion U-Net for Incomplete Multimodal Brain Tumor Segmentation. 65:1-65:6 - Fu Chen, Leqi Tian, Teng Fei, Tianwei Yu:
Fast-scBatch: Batch Effect Correction Using Neural Network-Driven Distance Matrix Adjustment. 66:1-66:6 - Feng Jiang, Yuzhi Guo, Hehuan Ma, Saiyang Na, Weizhi An, Bing Song, Yi Han, Jean Gao, Tao Wang, Junzhou Huang:
AlphaEpi: Enhancing B Cell Epitope Prediction with AlphaFold 3. 67:1-67:8 - Muheng Shang, Yan Yang, Jin Zhang, Daoqiang Zhang, Lei Du:
A Co-contrastive Learning Method to Fuse Multi-modal Phenotypes and Identify Genetic Risk Variations. 68:1-68:6 - Baihui Xu, Sourav S. Bhowmick, Jiancheng Hu:
PANACEA: Towards Influence-driven Profiling of Drug Target Combinations in Cancer Signaling Networks. 69:1-69:6 - Teng Ma, Haochen Zhao, Qichang Zhao, Jianxin Wang:
Cox-Path: Biological Pathway-Informed Graph Neural Network for Cancer Survival Prediction. 70:1-70:6 - Zekun Jiang, Wei Dai, Qu Wei, Ziyuan Qin, Kang Li, Le Zhang:
EEG-DIF: Early Warning of Epileptic Seizures through Generative Diffusion Model-based Multi-channel EEG Signals Forecasting. 71:1
Poster Presentations
- Xueliang Li, Bihan Shen, Fangyoumin Feng, Kunshi Li, Liangxiao Ma, Hong Li:
Dual-view jointly learning improves personalized drug synergy prediction. 72:1 - Yuran Wang, Kai Wu:
Revealing Multi-biological Subtypes of Schizophrenia through a Data-Driven Clustering. 73:1 - Wondimagegn Bekele Munto, Mengying Zhou, Yi Pan, Yanjie Wei, Wenhui Xi:
Deep Learning for Autism Spectrum Disorder Identification Based on Children's Facial Images: A Multi-Feature Fusion Perspective. 74:1 - Ruimin Ma, Ying Huang, Yi Pan, Yanlin Wang, Yanjie Wei:
Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRI. 75:1 - James Gu, Jake Y. Chen:
MLPA: A Multi-scale Digital Twin Framework for Personalized Cancer Simulation and Treatment Optimization. 76:1 - Yiwei Wang, Peijun Chen, Yejun Wang:
BactAG: a novel method resolving bacterial ancient genomes precisely and automatically. 77:1 - Leting Sun, Zhixuan Deng, Yejun Wang:
Operonome: the concept and application in bacterial systems biology. 78:1 - Weimiao Kong, Yuqi Lin, Yejun Wang:
PCMA: A New Mediation Analysis Method Effectively Identifies Relevant Pathways Connecting Microbiota and Diseases. 79:1 - Aaditya Shah, Sugyan Dixit:
DynPred: A Multimodal Deep Learning Approach for Protein Dynamics Prediction. 80:1 - Shuang Ge, Shuqing Sun, Huan Xu, Zhixiang Ren:
Distilling Multi-Modal Genomic Knowledge for Drug Response Prediction. 81:1 - Pengfei Liu, Jun Tao, Zhixiang Ren:
Dynamic Knowledge-Prior for Few-Shot Drug-Drug Interaction Events Prediction. 82:1 - Rudransh Pathak:
Comparative Analysis of Prominent AI Models for Enhanced Diabetes Diagnosis & Prediction. 83:1 - Shuo Feng, Zhe Sun, Runzhi Li, Siyu Yan, Lihong Ma:
Improved genetic algorithm for readmission risk index optimization. 84:1 - Ling Yue, Sixue Xing, Jonathan Li, Md. Zabirul Islam, Bolun Xia, Jintai Chen, Tianfan Fu:
TrialDura: Hierarchical Attention Transformer for Interpretable Clinical Trial Duration Prediction. 85:1 - Runzhi Li, Zhe Sun, Jing Wang, Gang Chen, Siyu Yan, Lihong Ma:
Static and multivariate-temporal attentive fusion transformer for readmission risk prediction of ICU patients. 86:1 - Jianqiang Zheng, Ziqi Xu, Junwen Huang, Xiaochuan Chen, Yuetong Li, Yanjie Wei, Huiling Zhang:
CCVAN: A Conditional Molecular Generation Model based on conditional VAE and Wasserstein GAN. 87:1 - Chao Yang, Jingjing Wang, Lu Zhang:
Integrated analysis of gut microbiome compositional and genomic alterations reveals strain diversity and actionable biomarkers across multiple colorectal cancer cohorts. 88:1 - Lin Zhang, Feng Wang, Jiani Ma, Hui Liu:
scDBImpute: Dual-branch imputation for single-cell RNA-seq data dropouts. 89:1 - Andrew Balch, Afsaneh Doryab:
Towards Smartphone-Based Monitoring of Micronutrient Status. 90:1
Workshop Abstracts: 13th Workshop on Parallel and AI-based Bioinformatics and Biomedicine (ParBio)
- Yuanhao Gong:
A High Performance Parametric Model for 3D Gingiva-Tooth Boundary via Generalized Cylinders. 91:1 - Sugam Jaiswal, Joyce Lee, Joe Berria, Raviteja Tanikella, Annuska Zolyomi, Muhammad Aurangzeb Ahmad, Dong Si:
Building Personality-Adaptive Conversational AI for Mental Health Therapy. 92:1 - Gavin L. A. Hearne, Mohammad S. Refahi, Haozhe Neil Duan, James R. Brown, Gail L. Rosen:
Normalized Compression Distance for DNA Classification. 93:1 - Zhangdaihong Liu, Xuan Wu, Yang Yang, David A. Clifton:
A Comparison of Representation Learning Methods for Medical Concepts in EHR Databases. 94:1 - Giuseppe Agapito, Mario Cannataro, Wes J. Lloyd, Chiara Zucco:
13th Workshop on Parallel and AI-based Bioinformatics and Biomedicine (ParBio): Editorial. 95:1
Workshop Abstracts: Cutting-edge Algorithms in Genomics: From Theory to Practice
- Xuefeng Cui:
Cutting-Edge Algorithms in Genomics: From Theory to Practice. 96:1 - Zeming Li, Yu Xu, Debajyoti Chowdhury, Hip Fung Yip, Chonghao Wang, Lu Zhang:
Med-PRSIMD: Enhanced Complex Disease Risk Prediction through Integrative Analysis of Multi-Type Data and Medical History Records. 97:1 - Huiling Zhang, Jingjing Zhang, Ganzhang Zheng, Xiaochuan Chen, Zaoqing Liang, Haiyan Wang, Yanjie Wei:
Missense Mutation Effect Prediction using Categorical Boosting Optimized with Sparrow Search Algorithm. 98:1
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