Gary D. Bader

Full Professor, Computer Science, University of Toronto

Joined

September 2019

Names

Gary D. Bader (Preferred)

Gary Bader

Gary D Bader

Emails

****@utoronto.ca (Confirmed)

Personal Links

Career & Education History

Full Professor

Computer Science, University of Toronto (utoronto.ca)

2006 – Present

Advisors, Relations & Conflicts

No relations added

Expertise

natural language processing

single cell genomics

computational biology

1998 – Present

Publications

Bridging Gene Expression and Text: LLMs Can Complement Single-Cell Foundation Models
Steven Palayew, BO WANG, Gary D. Bader
- Submitted to ICLR 2026
- Readers: Everyone
scMPT: towards applying large language models to complement single-cell foundation models
Steven Palayew, BO WANG, Gary D. Bader
- ICLR 2025 Conference Withdrawn Submission
- Readers: Everyone
Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval
John Michael Giorgi, Luca Soldaini, BO WANG, Gary D. Bader, Kyle Lo, Lucy Lu Wang, Arman Cohan
- EMNLP 2023 Findings
- Readers: Everyone
Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning
Ronald Xie, Kuan Pang, Sai W Chung, Catia Perciani, Sonya MacParland, BO WANG, Gary Bader
- NeurIPS 2023 poster
- Readers: Everyone
A sequence-to-sequence approach for document-level relation extraction
John M. Giorgi, Gary D. Bader, Bo Wang
- 2022 (modified: 03 Nov 2022)
- BioNLP@ACL 2022
- Readers: Everyone
A sequence-to-sequence approach for document-level relation extraction
John M. Giorgi, Gary D. Bader, Bo Wang
- 2022 (modified: 03 Nov 2022)
- CoRR 2022
- Readers: Everyone
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks
Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein
- 2021 (modified: 03 Nov 2022)
- Briefings Bioinform. 2021
- Readers: Everyone
DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations
John M. Giorgi, Osvald Nitski, Bo Wang, Gary D. Bader
- 2021 (modified: 03 Nov 2022)
- ACL/IJCNLP (1) 2021
- Readers: Everyone
A flexible search system for high-accuracy identification of biological entities and molecules
Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader
- 2021 (modified: 03 Nov 2022)
- J. Open Source Softw. 2021
- Readers: Everyone
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
Igor V. Rodchenkov, Ozgun Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami et al. (5 additional authors not shown)
- 2020 (modified: 03 Nov 2022)
- Nucleic Acids Res. 2020
- Readers: Everyone

View all 66 publications

Co-Authors

View all 492 co-authors