BiomedParse: a biomedical foundation model for image parsing of everything everywhere all at once. Theodore Zhao, Yu Gu, Jianwei Yang, Naoto Usuyama, Ho Hin Lee, Tristan Naumann, Jianfeng Gao, Angela Crabtree, Brian Piening, Carlo Bifulco, Mu Wei#, Hoifung Poon#,Sheng Wang# arxiv
BiomedCLIP: a multimodal biomedical foundation model pretrained from fifteen million scientific image-text pairs. Sheng Zhang, Yanbo Xu, Naoto Usuyama, Hanwen Xu, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, Andrea Tupini, Yu Wang, Matt Mazzola, Swadheen Shukla, Lars Liden, Jianfeng Gao, Matthew P. Lungren, Tristan Naumann, Sheng Wang#, Hoifung Poon#.
arxiv Under review.
Training Small Multimodal Models to Bridge Biomedical Competency Gap: A Case Study in Radiology Imaging. Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu, Hanwen Xu, Naoto Usuyama, Sheng Zhang, Fei Wang, Yujia Xie, Mahmoud Khademi, Ziyi Yang, Hany Awadalla, Julia Gong, Houdong Hu, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Yu Gu, Cliff Wong, Mu Wei, Tristan Naumann, Muhao Chen, Matthew P. Lungren, Serena Yeung-Levy, Curtis P. Langlotz, Sheng Wang#, Hoifung Poon#.
arxiv
Pisces: A multi-modal data augmentation approach for drug combination synergy prediction. Hanwen Xu*, Jiacheng Lin*, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang# bioRxiv In revision at Cell Genomics.
Poisoning scientific knowledge using large language models. Junwei Yang, Hanwen Xu, Srbuhi Mirzoyan, Tong Chen, Zixuan Liu, Wei Ju, Luchen Liu, Ming Zhang#, Sheng Wang# bioRxiv In revision at Nature Machine Intelligence.
A foundation model for bioactivity prediction using pairwise meta-learning. Bin Feng, Zequn Liu, Nanlan Huang, Zhiping Xiao, Haomiao Zhang, Srbuhi Mirzoyan, Hanwen Xu, Jiaran Hao, Yinghui Xu#, Ming Zhang#, Sheng Wang# bioRxiv In revision at Nature Machine Intelligence.
Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model. Tangqi Fang*, Yifeng Liu*, Addie Woicik*, Minsi Lu, Anupama Jha, Xiao Wang, Gang Li, Borislav Hristov, Zixuan Liu, Hanwen Xu, William S. Noble#, Sheng Wang# ISMB, 2024. bioRxiv
MMICL: Empowering Vision-language Model with Multi-Modal In-Context Learning. Haozhe Zhao, Zefan Cai, Shuzheng Si, Xiaojian Ma, Kaikai An, Liang Chen, Zixuan Liu,Sheng Wang, Wenjuan Han, Baobao Chang
ICLR, 2024.
Retrieval augmentation of large language models for lay language generation. Yue Guo, Wei Qiu, Gondy Leroy, Sheng Wang, and Trevor Cohen
Journal of Biomedical Informatics, 2024.
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Shixuan Liu, Camille Ezran, Michael FZ Wang, Zhengda Li, Kyle Awayan, Jonathan Z Long, Iwijn De Vlaminck, Sheng Wang, Jacques Epelbaum, Christin S Kuo, Jérémy Terrien, Mark A Krasnow, James E Ferrell Jr
Nature communications, 2024.
Foreseer: Product aspect forecasting using temporal graph embedding. Zixuan Liu, Gaurush Hiranandani, Kun Qian, Edward W Huang, Yi Xu, Belinda Zeng, Karthik Subbian, Sheng Wang# CIKM, 2023.
Sagittarius: Extrapolating Heterogeneous Time-Series Gene Expression Data. Addie Woicik, Mingxin Zhang, Janelle Chan, Jianzhu Ma, Sheng Wang# Nature Machine Intelligence, 2023. Link to view-only full text.
Gemini: Memory-efficient integration of hundreds of gene networks with high-order pooling. Addie Woicik, Mingxin Zhang, Hanwen Xu, Sara Mostafavi, Sheng Wang# ISMB, 2023
Supervised biological network alignment with graph neural networks. Kerr Ding, Sheng Wang, Yunan Luo
ISMB, 2023
POPDx: An Automated Framework for Patient Phenotyping across 392,246 Individuals in the UK Biobank Study.
Lu Yang, Sheng Wang, Russ Altman
Journal of the American Medical Informatics Association (JAMIA), 2023
MetaFill: Text Infilling for Meta-Path Generation on Heterogeneous Information Networks.
Zequn Liu, Kefei Duan, Junwei Yang, Hanwen Xu, Ming Zhang#, Sheng Wang# EMNLP, 2022
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models.
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma
NeurIPS, 2022
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Tabula Sapiens Consortium Science, 2022
Cell types of origin of the cell-free transcriptome.
Vorperian, Sevahn K., Mira N. Moufarrej, Tabula Sapiens Consortium, and Stephen R Quake.
Nature biotechnology, 2022
RNA splicing programs define tissue compartments and cell types at single-cell resolution.
Julia Eve Olivieri, Roozbeh Dehghannasiri, Peter L Wang, SoRi Jang, Antoine de Morree, Serena Y Tan, Jingsi Ming, Angela Ruohao Wu, Tabula Sapiens Consortium Elife, 2022
Brain-Aware Replacements for Supervised Contrastive Learning in Detection of Alzheimer's Disease
Mehmet Saygın Seyfioğlu, Zixuan Liu, Pranav Kamath, Sadjyot Gangolli, Sheng Wang, Thomas Grabowski, Linda Shapiro
MICCAI, 2022
DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning
Yuepeng Jiang, Stefano Rensi, Sheng Wang#, Russ B. Altman#
RECOMB, 2021 bioRxiv Code
Disease GenePrediction with Privileged Information and Heteroscedastic Dropout
Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma.
The international conference on molecular biology (ISMB), 2021
Publications (before tenure-track at UW)
Leveraging the Cell Ontology to classify unseen cell types Sheng Wang*, Angela Oliveira Pisco*, Aaron McGeever, Maria Brbic, Marinka Zitnik, Spyros Darmanis, Jure Leskovec, Jim Karkanias, Russ B. Altman
Nature Communications Code Project website
Opportunities and challenges for the computational interpretation of rare variation in clinically important genes
Gregory McInnes, Andrew G Sharo, Megan L Koleske, Julia EH Brown, Matthew Norstad, Aashish N Adhikari, Sheng Wang, Steven E Brenner, Jodi Halpern, Barbara A Koenig, David C Magnus, Renata C Gallagher, Kathleen M Giacomini, Russ B Altman
The American Journal of Human Genetics
Set2Gaussian: Embedding GeneSets as Gaussian Distributions for Large-scale Gene Set Analysis Sheng Wang, Emily Flynn, Russ B. Altman
Nature Machine Intelligence News & Views in Nature Machine Intelligence
DisenHAN: Disentangled Heterogeneous Graph Attention Network for Recommendation
Yifan Wang, Suyao Tang, Yuntong Lei, Weiping Song, Sheng Wang and Ming Zhang
The Conference on Information and Knowledge Management (CIKM), 2020
GRep: Gene Set Representation via Gaussian Embedding Sheng Wang, Emily Flynn, Russ B. Altman RECOMB, 2019
Identification of Pathways Associated with Chemosensitivity through Network Embedding Sheng Wang, Edward Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha PLoS computational biology, 2019 (selected in AMIA Year-In-Review 2020)
Community assessment to advance computational prediction of cancer drugcombinations in a pharmacogenomic screen
Michael Menden et al. Nature Communications, 2019 (Our team ranked 5th/160 teams in Dream Drug Combo Challenge)
Typing tumors using pathways selected by somatic evolution Sheng Wang*, Jianzhu Ma*, Wei Zhang, John Paul Shen, Justin Huang, Jian Peng, Trey Ideker Nature Communications, 2018
Annotating gene sets by mining large literature collections with protein networks Sheng Wang*, Jianzhu Ma*, Michael Ku Yu, Fan Zheng, Edward W Huang, Jiawei Han, Jian Peng, Trey Ideker Pacific Symposium on Biocomputing (PSB), 2018
VisAGE: Integrating ExternalKnowledge into Electronic Medical Record Visualization
Edward Huang, Sheng Wang, ChengXiang Zhai Pacific Symposium on Biocomputing (PSB), 2018
Large-Scale Integration ofHeterogeneous Pharmacogenomic Data for Identifying Drug Mechanism of Action
Yunan Luo,Sheng Wang, Jinfeng Xiao, Jian Peng. Pacific Symposium on Biocomputing (PSB), 2018
HEMnet: Integration of Electronic Medical Records with Molecular Interaction Networks and Domain Knowledge for Survival Analysis
Edward W Huang, Sheng Wang, Bingxue Li, Ran Zhang, Baoyan Liu, Runshun Zhang,Jie Liu, Xuezhong Zhou, Hongsheng Lin, ChengXiang Zhai ACM BCB, 2018
Network-assisted target identification for haploinsufficiency and homozygous profiling screens Sheng Wang, Jian Peng PLOS Computational Biology, 2017
ProSNet: integrating homology with molecular networks for protein function prediction Sheng Wang, Meng Qu, Jian Peng Pacific Symposium on Biocomputing (PSB), 2017
PaReCat: Patient Record Subcategorization for PrecisionTraditional Chinese Medicine
Edward Huang, Sheng Wang, Runshun Zhang, Baoyan Liu, Xuezhong Zhou,ChengXiang Zhai. ACM BCB, 2017
Prediction of overall survival for patients with metastatic castration-resistantprostate cancer: development of a prognostic model through a crowdsourcedchallenge with open clinical trial data
Justin Guinney et al. The Lancet Oncology, 2017 (Our team is the co-winner of Dream Prostate Cancer Challenge)
Framing Electronic Medical Records as Polylingual Documents in Query Expansion
Edward W Huang, Sheng Wang, Doris Jung-lin Lee, Runshun Zhang, Baoyan Liu, Xuezhong Zhou, ChengXiang Zhai AMIA , 2017
proTCM: An Asymmetric Probabilistic Model for the Joint Analysis of Symptoms, Diseases, and Herbs in Traditional Chinese Medicine Clinical Data Sheng Wang, Edward Huang, Bingxue Li, Ran Zhang, Xiaoping Zhang, Baoyan Liu, Jie Liu, Runshun Zhang, Xuezhong Zhou, ChengXiang Zhai BIBM, 2017.
Exploiting Ontology Graph for Predicting Sparsely Annotated Gene Function Sheng Wang*, Hyunghoon Cho*, ChengXiang Zhai, Bonnie Berger, Jian Peng ISMB/ECCB, 2015. Bioinformatics, 2015. (Candidate of Outstanding Student Paper Award)
Early Identification of Adverse Drug Reactions from Search Log Data
Ryen W. White, Sheng Wang, Apurv Pant, Rave Harpaz, Pushpraj Shukla, Walter Sun, William DuMouchel, Eric Horvitz. Journal of Biomedical Informatics,2016. (Editors' Choice Award)
DWCox: A Density-Weighted Cox Model for Robust Prediction of Prostate Cancer Survival
Jinfeng Xiao, Sheng Wang, Jingbo Shang, Henry Lin, Doris Xin, Xiang Ren, Jiawei Han, Jian Peng F1000Research, 2016
SideEffectPTM: An Unsupervised Topic Model to Mine Adverse Drug Reactions from Health Forums Sheng Wang, Yanen Li, Duncan Ferguson, Chengxiang Zhai ACM BCB, 2014
SUIT: A Supervised User-Item based Topic model for Sentiment Analysis
Fangtao Li,Sheng Wang, Shenghua Liu, Ming Zhang AAAI, 2014
Supervised Topic Model with Consideration of User and Item Sheng Wang, Fangtao Li, Ming Zhang. AAAI Late breaking paper, 2014
Please Spread: RecommendingTweets for Retweeting with Implicit Feedback Sheng Wang, Xiaobo Zhou, Ziqi Wang, Ming Zhang CIKM workshop, 2012