Skeleton Graph Matching Based on Critical Points Using Path Similarity. - Yao Xu; Bo Wang 044; Wenyu Liu 001; Xiang Bai (ACCV (3), 2009)

Co-transduction for Shape Retrieval. - Xiang Bai; Bo Wang 044; Xinggang Wang; Wenyu Liu 001; Zhuowen Tu (ECCV (3), 2010)

Object Recognition Using Junctions. - Bo Wang 044; Xiang Bai; Xinggang Wang; Wenyu Liu 001; Zhuowen Tu (ECCV (5), 2010)

Shape Classification Using Tree -Unions. - Bo Wang 044; Wei Shen 002; Wenyu Liu 001; Xinge You; Xiang Bai (ICPR, 2010)

Unsupervised metric learning by Self-Smoothing Operator. - Jiayan Jiang; Bo Wang 044; Zhuowen Tu (ICCV, 2011)

Effective Improved Graph Transduction. - Jun Chen 019; Yu Zhou 016; Yajun Gao; Bo Wang 044; Lin-bo Luo 002; Wenyu Liu 001 (J. Softw., 2011)

Unsupervised metric fusion by cross diffusion. - Bo Wang 044; Jiayan Jiang; Wei Wang 028; Zhi-Hua Zhou; Zhuowen Tu (CVPR, 2012)

Affinity learning via self-diffusion for image segmentation and clustering. - Bo Wang 044; Zhuowen Tu (CVPR, 2012)

Co-Transduction for Shape Retrieval. - Xiang Bai; Bo Wang 044; Cong Yao; Wenyu Liu 001; Zhuowen Tu (IEEE Trans. Image Process., 2012)

Early Recurrence Improves Edge Detection. - Xun Shi; Bo Wang 044; John K. Tsotsos (BMVC, 2013)

Sparse Subspace Denoising for Image Manifolds. - Bo Wang 044; Zhuowen Tu (CVPR, 2013)

Dynamic Label Propagation for Semi-supervised Multi-class Multi-label Classification. - Bo Wang 044; Zhuowen Tu; John K. Tsotsos (ICCV, 2013)

Face identification using reference-based features with message passing model. - Wei Shen 002; Bo Wang 044; Yueming Wang; Xiang Bai; Longin Jan Latecki (Neurocomputing, 2013)

Parameter Estimation for ODEs Using a Cross-Entropy Approach. - Bo Wang 044; Wayne Enright (SIAM J. Sci. Comput., 2013)

Gradient-based Laplacian Feature Selection. - Bo Wang 044; Anna Goldenberg (CoRR, 2014)

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data. - Bo Wang 044; Junjie Zhu; Armin Pourshafeie; Oana Ursu; Serafim Batzoglou; Anshul Kundaje (NIPS, 2016)

Reveel: large-scale population genotyping using low-coverage sequencing data. - Lin Huang; Bo Wang 044; Ruitang Chen; Sivan Bercovici; Serafim Batzoglou (Bioinform., 2016)

Dynamic label propagation for semi-supervised multi-class multi-label classification. - Bo Wang 044; John K. Tsotsos (Pattern Recognit., 2016)

SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning. - Bo Wang 044; Daniele Ramazzotti; Luca De Sano; Junjie Zhu; Emma Pierson; Serafim Batzoglou (CoRR, 2017)

Vicus: Exploiting local structures to improve network-based analysis of biological data. - Bo Wang 044; Lin Huang; Yuke Zhu; Anshul Kundaje; Serafim Batzoglou; Anna Goldenberg (PLoS Comput. Biol., 2017)

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. - Bo Wang 044 (2017)

Deep Regression Forests for Age Estimation. - Wei Shen 002; Yilu Guo; Yan Wang 033; Kai Zhao; Bo Wang 044; Alan L. Yuille (CVPR, 2018)

Single-Shot Object Detection With Enriched Semantics. - Zhishuai Zhang; Siyuan Qiao; Cihang Xie; Wei Shen 002; Bo Wang 044; Alan L. Yuille (CVPR, 2018)

Deep Co-Training for Semi-Supervised Image Recognition. - Siyuan Qiao; Wei Shen 002; Zhishuai Zhang; Bo Wang 044; Alan L. Yuille (ECCV (15), 2018)

Gradually Updated Neural Networks for Large-Scale Image Recognition. - Siyuan Qiao; Zhishuai Zhang; Wei Shen 002; Bo Wang 044; Alan L. Yuille (ICML, 2018)

Network Enhancement: a general method to denoise weighted biological networks. - Bo Wang 044; Armin Pourshafeie; Marinka Zitnik; Junjie Zhu; Carlos D. Bustamante; Serafim Batzoglou; Jure Leskovec (CoRR, 2018)

Moment Matching for Multi-Source Domain Adaptation. - Xingchao Peng; Qinxun Bai; Xide Xia; Zijun Huang; Kate Saenko; Bo Wang 044 (ICCV, 2019)

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models. - John M. Giorgi; Xindi Wang 001; Nicola Sahar; Won Young Shin; Gary D. Bader; Bo Wang 044 (CoRR, 2019)

Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities. - Marinka Zitnik; Francis Nguyen; Bo Wang 044; Jure Leskovec; Anna Goldenberg; Michael M. Hoffman (Inf. Fusion, 2019)

Weakly supervised mitosis detection in breast histopathology images using concentric loss. - Chao Li 007; Xinggang Wang; Wenyu Liu 001; Longin Jan Latecki; Bo Wang 044; Junzhou Huang (Medical Image Anal., 2019)

Diversity Transfer Network for Few-Shot Learning. - Mengting Chen; Yuxin Fang; Xinggang Wang; Heng Luo; Yifeng Geng; Xinyu Zhang; Chang Huang; Wenyu Liu 001; Bo Wang 044 (AAAI, 2020)

CDF-Net: Cross-Domain Fusion Network for Accelerated MRI Reconstruction. - Osvald Nitski; Sayan Nag; Chris McIntosh; Bo Wang 044 (MICCAI (2), 2020)

Robust Face Detection via Learning Small Faces on Hard Images. - Zhishuai Zhang; Wei Shen 002; Siyuan Qiao; Yan Wang 033; Bo Wang 044; Alan L. Yuille (WACV, 2020)

DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. - John M. Giorgi; Osvald Nitski; Bo Wang 044; Gary D. Bader (ACL/IJCNLP (1), 2021)

MassFormer: Tandem Mass Spectrum Prediction with Graph Transformers. - Adamo Young; Bo Wang 044; Hannes L. Röst (CoRR, 2021)

Deep Differentiable Random Forests for Age Estimation. - Wei Shen 002; Yilu Guo; Yan Wang 033; Kai Zhao; Bo Wang 044; Alan L. Yuille (IEEE Trans. Pattern Anal. Mach. Intell., 2021)

A sequence-to-sequence approach for document-level relation extraction. - John M. Giorgi; Gary D. Bader; Bo Wang 044 (BioNLP@ACL, 2022)

BigBio: A Framework for Data-Centric Biomedical Natural Language Processing. - Jason A. Fries; Leon Weber; Natasha Seelam; Gabriel Altay; Debajyoti Datta; Samuele Garda; Sunny Kang; Rosaline Su; Wojciech Kusa; Samuel Cahyawijaya; Fabio Barth; Simon Ott; et al. (NeurIPS, 2022)

A graph neural network approach for molecule carcinogenicity prediction. - Philip Fradkin; Adamo Young; Lazar Atanackovic; Brendan J. Frey; Leo J. Lee; Bo Wang 044 (Bioinform., 2022)

BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing. - Jason Alan Fries; Leon Weber; Natasha Seelam; Gabriel Altay; Debajyoti Datta; Samuele Garda; Myungsun Kang; Ruisi Su; Wojciech Kusa; Samuel Cahyawijaya; Fabio Barth; Simon Ott; et al. (CoRR, 2022)

Exploring the Challenges of Open Domain Multi-Document Summarization. - John M. Giorgi; Luca Soldaini; Bo Wang 044; Gary D. Bader; Kyle Lo; Lucy Lu Wang; Arman Cohan (CoRR, 2022)

Developing a random forest algorithm to identify patent foramen ovale and atrial septal defects in Ontario administrative databases. - Laura Oliva; Eric Horlick; Bo Wang 044; Ella Huszti; Ruth Hall; Lusine Abrahamyan (BMC Medical Informatics Decis. Mak., 2022)

The promise of machine learning applications in solid organ transplantation. - Neta Gotlieb; Amirhossein Azhie; Divya Sharma; Ashley Spann; Nan-Ji Suo; Jason Tran; Ani Orchanian-Cheff; Bo Wang 044; Anna Goldenberg; Michael Chassé; Héloïse Cardinal; Joseph Paul Cohen; et al. (npj Digit. Medicine, 2022)

WangLab at MEDIQA-Chat 2023: Clinical Note Generation from Doctor-Patient Conversations using Large Language Models. - John M. Giorgi; Augustin Toma; Ronald Xie; Sondra Chen; Kevin R. An; Grace X. Zheng; Bo Wang 044 (ClinicalNLP@ACL, 2023)

MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition. - Ronald Xie; Kuan Pang; Gary D. Bader; Bo Wang 044 (CVPR, 2023)

Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval. - John M. Giorgi; Luca Soldaini; Bo Wang 044; Gary D. Bader; Kyle Lo; Lucy Lu Wang; Arman Cohan (EMNLP (Findings), 2023)

Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning. - Ronald Xie; Kuan Pang; Sai Chung; Catia Perciani; Sonya MacParland; Bo Wang 044; Gary D. Bader (NeurIPS, 2023)

Moment-alignment domain adaptation in the few-shot and low-resource context. - Lauren Erdman; Mandy Rickard; Kyla N. Velear; Daniel Alvarez; Kunj Sheth; Armando J. Lorenzo; Bo Wang 044; Anna Goldenberg (SIPAIM, 2023)

Clinical Note Generation from Doctor-Patient Conversations using Large Language Models: Insights from MEDIQA-Chat. - John M. Giorgi; Augustin Toma; Ronald Xie; Sondra Chen; Kevin R. An; Grace X. Zheng; Bo Wang 044 (CoRR, 2023)

Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning. - Ronald Xie; Kuan Pang; Gary D. Bader; Bo Wang 044 (CoRR, 2023)

Unleashing the Strengths of Unlabeled Data in Pan-cancer Abdominal Organ Quantification: the FLARE22 Challenge. - Jun Ma 016; Yao Zhang 010; Song Gu; Cheng Ge; Shihao Ma; Adamo Young; Cheng Zhu; Kangkang Meng; Xin Yang 009; Ziyan Huang; Fan Zhang; Wentao Liu; et al. (CoRR, 2023)

The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions. - Jun Ma 016; Ronald Xie; Shamini Ayyadhury; Cheng Ge; Anubha Gupta; Ritu Gupta; Song Gu; Yao Zhang 010; Gihun Lee; Joonkee Kim; Wei Lou; Haofeng Li; et al. (CoRR, 2023)

Splicing Up Your Predictions with RNA Contrastive Learning. - Philip Fradkin; Ruian Shi; Bo Wang 044; Brendan J. Frey; Leo J. Lee (CoRR, 2023)

To Transformers and Beyond: Large Language Models for the Genome. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (CoRR, 2023)

Reusability report: Evaluating reproducibility and reusability of a fine-tuned model to predict drug response in cancer patient samples. - Emily So; Fengqing Yu; Bo Wang 044; Benjamin Haibe-Kains (Nat. Mac. Intell., 2023)

WangLab at MEDIQA-M3G 2024: Multimodal Medical Answer Generation using Large Language Models. - Augustin Toma; Ronald Xie; Steven Palayew; Gary D. Bader; Bo Wang 044 (ClinicalNLP@NAACL, 2024)

WangLab at MEDIQA-CORR 2024: Optimized LLM-based Programs for Medical Error Detection and Correction. - Augustin Toma; Ronald Xie; Steven Palayew; Patrick R. Lawler; Bo Wang 044 (ClinicalNLP@NAACL, 2024)

Towards a personalized pregnancy experience: Forecasting symptoms using graph neural networks and digital health technologies. - Rui Zhu; Jennifer Yu; Stephen H. Friend; Sarah M. Goodday; Bo Wang 044; Anna Goldenberg (ML4H@NeurIPS, 2024)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation. - Jun Ma 016; Feifei Li 010; Bo Wang 044 (CoRR, 2024)

Integrate Any Omics: Towards genome-wide data integration for patient stratification. - Shihao Ma; Andy G. X. Zeng; Benjamin Haibe-Kains; Anna Goldenberg; John E. Dick; Bo Wang 044 (CoRR, 2024)

FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Hannes L. Röst; Russ Greiner (CoRR, 2024)

EVA-X: A Foundation Model for General Chest X-ray Analysis with Self-supervised Learning. - Jingfeng Yao; Xinggang Wang; Yuehao Song; Huangxuan Zhao; Jun Ma 016; Yajie Chen; Wenyu Liu 001; Bo Wang 044 (CoRR, 2024)

Automatic Organ and Pan-cancer Segmentation in Abdomen CT: the FLARE 2023 Challenge. - Jun Ma 016; Yao Zhang 010; Song Gu; Cheng Ge; Ershuai Wang; Qin Zhou; Ziyan Huang; Pengju Lyu; Jian He; Bo Wang 044 (CoRR, 2024)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. - Charlotte Bunne; Yusuf H. Roohani; Yanay Rosen; Ankit Gupta; Xikun Zhang 001; Marcel Roed; Theo Alexandrov; Mohammed AlQuraishi; Patricia Brennan; Daniel B. Burkhardt; Andrea Califano; Jonah Cool; et al. (CoRR, 2024)

Efficient MedSAMs: Segment Anything in Medical Images on Laptop. - Jun Ma 016; Feifei Li 010; Sumin Kim; Reza Asakereh; Bao-Hiep Le; Dang-Khoa Nguyen-Vu; Alexander Pfefferle; Muxin Wei; Ruochen Gao; Donghang Lyu; Songxiao Yang; Lennart Purucker; et al. (CoRR, 2024)

Results from the autoPET challenge on fully automated lesion segmentation in oncologic PET/CT imaging. - Sergios Gatidis; Marcel Früh; Matthias Fabritius; Sijing Gu; Konstantin Nikolaou; Christian La Fougère; Jin Ye 002; Junjun He; Yige Peng; Lei Bi 001; Jun Ma 016; Bo Wang 044; et al. (Nat. Mac. Intell., 2024)

Tandem mass spectrum prediction for small molecules using graph transformers. - Adamo Young; Hannes L. Röst; Bo Wang 044 (Nat. Mac. Intell., 2024)

Improving prognostic accuracy in lung transplantation using unique features of isolated human lung radiographs. - Bonnie T. Chao; Andrew T. Sage; Micheal C. McInnis; Jun Ma 016; Micah Grubert Van Iderstine; Xuanzi Zhou; Jerome Valero; Marcelo Cypel; Mingyao Liu; Bo Wang 044; Shaf Keshavjee (npj Digit. Medicine, 2024)

Current opinions on large cellular models. - Minsheng Hao; Lei Wei; Fan Yang 081; Jianhua Yao 001; Christina V. Theodoris; Bo Wang 044; Xin Li; Ge Yang 002; Xuegong Zhang (Quant. Biol., 2024)

MorphoDiff: Cellular Morphology Painting with Diffusion Models. - Zeinab Navidi; Jun Ma 016; Esteban Miglietta; Le Liu; Anne E. Carpenter; Beth A. Cimini; Benjamin Haibe-Kains; Bo Wang 044 (ICLR, 2025)

Transformers and genome language models. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (Nat. Mac. Intell., 2025)

Moving towards genome-wide data integration for patient stratification with Integrate Any Omics. - Shihao Ma; Andy G. X. Zeng; Benjamin Haibe-Kains; Anna Goldenberg; John E. Dick; Bo Wang 044 (Nat. Mac. Intell., 2025)

FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Russell Greiner; Hannes Rost (Trans. Mach. Learn. Res., 2025)

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model. - Adibvafa Fallahpour; Andrew Magnuson; Purav Gupta; Shihao Ma; Jack Naimer; Arnav Shah; Haonan Duan 002; Omar Ibrahim; Hani Goodarzi; Chris J. Maddison; Bo Wang 044 (CoRR, 2025)

Facial Foundational Model Advances Early Warning of Coronary Artery Disease from Live Videos with DigitalShadow. - Juexiao Zhou; Zhongyi Han; Mankun Xin; Xingwei He 007; Guotao Wang; Jiaoyan Song; Gongning Luo; Wenjia He; Xintong Li; Yuetan Chu; Juanwen Chen; Bo Wang 044; et al. (CoRR, 2025)

Towards Applying Large Language Models to Complement Single-Cell Foundation Models. - Steven Palayew; Bo Wang 044; Gary D. Bader (CoRR, 2025)

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop. - Elizabeth Fahsbender; Alma Andersson; Jeremy Ash; Polina Binder; Daniel Burkhardt; Benjamin Chang 009; Georg K. Gerber; Anthony Gitter; Patrick Godau; Ankit Gupta; Genevieve Haliburton; Siyu He; et al. (CoRR, 2025)