Publications (since tenure-track at UW)

  1. 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

  2. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.
    Tabula Sapiens Consortium
    Science, 2022

  3. 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

  4. 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

  5. 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

  6. Graph-in-Graph Network for Automatic Gene Ontology Description Generation
    Fenglin Liu, Bang Yang, Xian Wu, Shen Ge, Addie Woicik, Sheng Wang#
    KDD, 2022

  7. Pathway2Text: Dataset and Method for Biomedical Pathway Description Generation
    Junwei Yang, Zequn Liu, Ming Zhang#, Sheng Wang#
    NAACL (Findings), 2022

  8. Seed-Guided Topic Discovery with Out-of-Vocabulary Seeds
    Yu Zhang, Yu Meng, Xuan Wang, Sheng Wang, Jiawei Han
    NAACL, 2022

  9. Textomics: A Dataset for Genomics Data Summary Generation
    Mu-Chun Wang*, Zixuan Liu*, Sheng Wang#
    ACL, 2022

  10. Deep Graph Mutual Learning for Cross-domain Recommendation
    Yifan Wang, Yongkang Li, Shuai Li, Weiping Song, Jiangke Fan, Shan Gao, Huan Lou, Bing Cheng, Xunliang Cai, Sheng Wang, and Ming Zhang.
    DASFAA, 2022

  11. scPretrain: Multi-task self-supervised learning for cell type classification
    Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang#, Sheng Wang#
    Bioinformatics, 2022 Code

  12. ProTranslator: zero-shot protein function prediction using textual description
    Hanwen Xu, Sheng Wang#
    RECOMB, 2022

  13. DisenCite: Graph-based Disentangled Representation Learning for Context-specific Citation Generation
    Yifan Wang, Yiping Song, Shuai Li, Chaoran Cheng, Wei Ju, Ming Zhang, Sheng Wang
    AAAI, 2022

  14. Auto-Encoding Knowledge Graph for Unsupervised Medical Report Generation
    Fenglin Liu, Chenyu You, Xian Wu, Shen Ge, Sheng Wang#, Xu Sun#
    NeurIPS, 2021

  15. Graphine: A Dataset for Graph-aware Terminology Definition Generation
    Zequn Liu, Shukai Wang, Yiyang Gu, Ruiyi Zhang, Ming Zhang#, Sheng Wang#
    EMNLP, 2021 Dataset Code

  16. HYPON: embedding biomedical ontology with entity sets
    Zhuoyan Li, Sheng Wang#
    ACM BCB, 2021

  17. 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

  18. 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)

  1. 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

  2. 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

  3. 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

  4. 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

  5. GRep: Gene Set Representation via Gaussian Embedding
    Sheng Wang, Emily Flynn, Russ B. Altman
    RECOMB, 2019

  6. 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)

  7. 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)

  8. 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

  9. 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

  10. VisAGE: Integrating ExternalKnowledge into Electronic Medical Record Visualization
    Edward Huang, Sheng Wang, ChengXiang Zhai
    Pacific Symposium on Biocomputing (PSB), 2018

  11. 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

  12. 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

  13. Network-assisted target identification for haploinsufficiency and homozygous profiling screens
    Sheng Wang, Jian Peng
    PLOS Computational Biology, 2017

  14. ProSNet: integrating homology with molecular networks for protein function prediction
    Sheng Wang, Meng Qu, Jian Peng
    Pacific Symposium on Biocomputing (PSB), 2017

  15. PaReCat: Patient Record Subcategorization for PrecisionTraditional Chinese Medicine
    Edward Huang, Sheng Wang, Runshun Zhang, Baoyan Liu, Xuezhong Zhou,ChengXiang Zhai.
    ACM BCB, 2017

  16. 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)

  17. 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

  18. 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.

  19. 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)

  20. 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)

  21. 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

  22. SideEffectPTM: An Unsupervised Topic Model to Mine Adverse Drug Reactions from Health Forums
    Sheng Wang, Yanen Li, Duncan Ferguson, Chengxiang Zhai
    ACM BCB, 2014

  23. SUIT: A Supervised User-Item based Topic model for Sentiment Analysis
    Fangtao Li,Sheng Wang, Shenghua Liu, Ming Zhang
    AAAI, 2014

  24. Supervised Topic Model with Consideration of User and Item
    Sheng Wang, Fangtao Li, Ming Zhang.
    AAAI Late breaking paper, 2014

  25. Please Spread: RecommendingTweets for Retweeting with Implicit Feedback
    Sheng Wang, Xiaobo Zhou, Ziqi Wang, Ming Zhang
    CIKM workshop, 2012