AI in Molecular Biology (G2)
September 15-18, 2025  | Eldorado Hotel & Spa, Santa Fe, NM, United States
David R. Kelley and Jean Fan
Scholarship Deadline: Jun. 4, 2025 | Abstract Deadline: Aug. 22, 2025 | Early Registration Deadline: Jul. 18, 2025
* Session Chair † Invited but not yet accepted | Program current as of August 23, 2025 4 AM | For the most up-to-date details, visit https://www.keystonesymposia.org
Monday, September 15, 2025
4:00–8:00 PM Registration Concourse
6:00–8:00 PM Welcome Mixer Cava Santa Fe
Tuesday, September 16, 2025
7:00–8:00 AM Breakfast Anasazi Ballroom
7:30–8:00 AM Poster Setup Anasazi Ballroom
7:30–5:00 PM Poster Viewing Anasazi Ballroom
8:00–9:00 AM Welcome and Keynote Address Eldorado Ballroom
  * Jean Fan, Johns Hopkins University
  
  Barbara Engelhardt, Stanford University School of Medicine and Gladstone Institutes
Machine Learning Methods for Live-Cell Imaging Cell Behavioral Analyses		  
9:00–11:30 AM Extracting Interpretable Insights from Biological AI Eldorado Ballroom
  * Jean Fan, Johns Hopkins University
Session Chair		  
  Maria Brbic, EPFL
Generative AI for Unlocking the Complexity of Cells		  
  Jian Ma, Carnegie Mellon University
Learning Multiscale Cellular Organization and Interactions		  
  Dmitry Kobak, Tübingen University
Self-Supervised and Unsupervised Learning for 2D Visualization of Scientific Datasets		  
  Emma Pierson, University of California, Berkeley
Equitable Machine Learning in Healthcare		  
9:30–9:50 AM Coffee Break Concourse
11:30–12:30 PM Lunch Anasazi Ballroom
12:00–2:30 PM Poster Session 1 Anasazi Ballroom
2:30–4:30 PM Symposia Spotlight 1: Late-breaking research presentations selected from abstract submissions Eldorado Ballroom
  * Jian Ma, Carnegie Mellon University
Session Chair		  
  Miten Jain, Northeastern University
Deep Learning and Nanopore Technology Reveal Single-Molecule Insights Into DNA, RNA, and Protein Modifications		  
  Evan Seitz, Cold Spring Harbor Laboratory
Mapping the Mechanistic Impact of Genetic Variation with Interpretable Deep Learning		  
  Manu Saraswat, German Cancer Research Centre
Dissecting Cellular Plasticity in Glioblastoma via Deep Learning of Single-Cell Gene Regulatory Networks		  
  Ryan Keivanfar, UC Berkeley + UCSF Gladstone Institutes
Allele-Specific Expression Prediction from Personal Genome Sequences Using Fine-Tuned Enformer Models		  
  Abdul Muntakim Rafi, University of British Columbia
Detecting and Avoiding Homology-Based Data Leakage in Genome-Trained Sequence Models		  
  Alexander S Garruss, Stowers Institute for Medical Research
Synergistic Control of Gene Expression by 5’ UTR and Synonymous Codon Variants		  
  Ofir Yaish, Ben-Gurion University of the Negev
Fast and Interpretable Motif Discovery from Attribution Maps via Fourier-Based Clustering		  
  Yijie Kang, Stony Brook University; Cold Spring Harbor Laboratory
Decoding the Sequence Basis of Pol II Elongation with Deep Learning		  
4:30–5:00 PM Coffee Available Concourse
5:00–7:00 PM Parsing and Annotating the Noncoding Genome Eldorado Ballroom
  * Stein Aerts, Katholieke Universiteit Leuven
Session Chair		  
  David R. Kelley, Calico Life Sciences
Predicting Gene Expression from DNA Sequence		  
  Stein Aerts, Katholieke Universiteit Leuven
Modeling and Design of Genomic Enhancers in the Context of Whole Organisms		  
  Christina S. Leslie, Memorial Sloan-Kettering Cancer Center
Machine Learning for Single Cell and Regulatory Genomics in Cancer		  
  Sahin Naqvi, Boston Children's Hospital
Short Talk: Deep Learning Prediction of The Chromatin Response to Transcription Factor Dosage from DNA Sequence		  
  McKayla Ford, University of Rochester
Short Talk: Secondary Structures as Key Regulators of Transcription at CpG island Promoters		  
7:00–8:00 PM On Own for Dinner
Wednesday, September 17, 2025
7:00–8:00 AM Breakfast Anasazi Ballroom
8:00–11:00 AM Mapping Cellular Interactions in Tissues with Spatial Imaging and Genomics Eldorado Ballroom
  * Joshua Welch, University of Michigan
Session Chair		  
  Jean Fan, Johns Hopkins University
Machine Learning for Spatial Omics Data Integration		  
  Mingyao Li, University of Pennsylvania School of Medicine
Unlocking the Power of Spatial Omics with AI		  
  Faisal Mahmood, Brigham and Women's Hospital
Multimodal, Generative, and Agentic AI for Pathology		  
  Joshua Welch, University of Michigan
Modeling Cell Fate Transition in Space and Time with Graph Neural Networks		  
  Juanru Guo, Washington University in St. Louis School of Medicine
Short Talk: A Machine Learning Approach to Soft Segmentation and Manifold Unrolling of Visium HD Data		  
  Christine Y Yeh, Stanford University
Short Talk: Robust Self-Supervised Machine Learning for Single Cell Embeddings and Annotations		  
9:00–9:20 AM Coffee Break Concourse
11:00–1:00 PM Poster Setup Anasazi Ballroom
11:00–1:30 PM On Own for Lunch
1:00–10:00 PM Poster Viewing Anasazi Ballroom
1:45–2:45 PM Career Roundtable Eldorado Ballroom
3:00–4:30 PM Panel Discussion: Challenges and Opportunities for Innovation and Responsibility in AI-Driven Biology with Academic and Industry Leaders Eldorado Ballroom
  * Jean Fan, Johns Hopkins University
Moderator		  
  Shyam Prabhakar, Agency for Science, Technology and Research (A*STAR)
Panelist		  
  Mona Singh, Princeton University
Panelist		  
  Jacob Kimmel, NewLimit
Panelist		  
4:30–5:00 PM Coffee Available Concourse
5:00–7:00 PM Learning a Language of Cellular Morphology from Imaging Eldorado Ballroom
  * David Van Valen, Caltech
Session Chair		  
  Berton Earnshaw, Recursion Pharmaceuticals
Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology		  
  David Van Valen, Caltech
Cell Segmentation Foundation Models		  
  Anita Donlic, Princeton University
Short Talk: Deep Learning-Driven Profiling of Biomolecular Condensate Images Reveals Mesoscale Structure-Molecular Function Relationships		  
  Lucy Luo, Northwestern University
Short Talk: Spatially-Restricted Circuits Between CXCL9+ Macrophages and T Cells Drive Acute Cellular Rejection in Lung Transplant Patients		  
  Sehyun Oh, The City University of New York
Short Talk: A Multi-Modal Resource for Integrating Histopathology with Multi-Omics Data in R/Bioconductor		  
  Wei Li, University of Pennsylvania
Short Talk: A Virtual Machine for Multimodal Spatial Omics		  
7:00–8:00 PM Social Hour with Dinner Anasazi Ballroom
7:30–10:00 PM Poster Session 2 Anasazi Ballroom
Thursday, September 18, 2025
7:00–8:00 AM Breakfast Anasazi Ballroom
8:00–11:00 AM Toward an Integration of AI and Systems Biology Eldorado Ballroom
  * Angela R Wu, Hong Kong University of Science and Technology
Session Chair		  
  Jacob Kimmel, NewLimit
Learning the Combinatorial Code of Epigenetic Reprogramming		  
  Hector Garcia Martin, Lawrence Berkeley National Laboratory
Bioengineering Cells to Produce Biofuels and Renewable Biomaterials		  
  Shyam Prabhakar, Agency for Science, Technology and Research (A*STAR)
We Are Not All the Same: Early Insights into Human Diversity from Single Cell and spatial Omics		  
  Angela R Wu, Hong Kong University of Science and Technology
UniGeneX Creates a Universal Gene Expression Single-Cell Atlas and Uncovers Key Transitional Pathological Cell States		  
  Reet Mishra, UC Berkeley-UCSF
Short Talk: Decoding Microglial State Dynamics via CRISPR Perturbations and Multi-Modal Generative Single-Cell Modeling		  
  Akanksha Sachan, University of Pittsburgh
Short Talk: Uncovering Dynamic Regulatory Circuits Underlying Bifurcating Human B Cell States		  
9:00–9:20 AM Coffee Break Concourse
11:00–12:00 PM Panel Discussion: Complementarity of Industry and Academia Eldorado Ballroom
  * David R. Kelley, Calico Life Sciences
Moderator		  
  Jean Fan, Johns Hopkins University
Panelist		  
  Hector Garcia Martin, Lawrence Berkeley National Laboratory
Panelist		  
  Barbara Engelhardt, Stanford University School of Medicine and Gladstone Institutes
Panelist		  
  Berton Earnshaw, Recursion Pharmaceuticals
Panelist		  
11:00–2:30 PM On Own for Lunch
2:30–4:30 PM Symposia Spotlight 2: Late-breaking research presentations selected from abstract submissions Eldorado Ballroom
  * Christina S. Leslie, Memorial Sloan-Kettering Cancer Center
Session Chair		  
  Suryanarayana Maddu, Simons Foundation
Scalable Inference of Biophysical Models from Multi-Omics Data		  
  Mehrshad Sadria, Altos Labs
FateNet: an Integration of Dynamical Systems and Deep Learning for Cell Fate Prediction		  
  Jishnu Das, University of Pittsburgh
Sliding Window INteraction Grammar (SWING): A Generalized Interaction Language Model for Peptide and Protein Interactions		  
  Adela Habib, Los Alamos National Laboratory
Harnessing Coupled Protein Language Model and Geometric Deep Learning for Protein Interaction Prediction on Dynamically Sampled Surfaces		  
  Yuanhao Qu, Stanford University
AutoScreen: an AI Scientist System for Target Discovery in Functional Genomics		  
  John-William Sidhom, Weill Cornell Mediine
Learning the Language of Somatic Mutations: A Large Language Model Approach to Precision Oncology		  
  Nicholas Hutchins, Massachusetts Institute of Technology
Reconstructing Signaling Histories of Single Cells Via Perturbation Screens and Transfer Learning		  
  Nathaniel Robichaud, Nomic Bio
Large-scale Proteomics for AI/ML Applications: Insights from Quantifying 1,000 Proteins In 20,000 Samples		  
4:30–5:00 PM Coffee Available Concourse
5:00–5:45 PM Closing Keynote Address Eldorado Ballroom
  * David R. Kelley, Calico Life Sciences
Session Chair		  
  David Baker, University of Washington
Remote Presentation: Protein Design using Deep Learning		  
5:45–7:15 PM Analyzing and Harnessing Proteins Eldorado Ballroom
  * David R. Kelley, Calico Life Sciences
Session Chair		  
  Ava Amini, Microsoft Research
Remote Presentation: Generative AI for Protein Sequence Design		  
  Mona Singh, Princeton University
Protein Language Models: Strengths and Limitations		  
  Henry R Kilgore, Whitehead Institute for Biomedical Research
Short Talk: Protein Codes Promote Selective Subcellular Compartmentalization		  
  Julia Rogers, Columbia University
Short Talk: Machine Learning the Binding Affinities of Protein–Peptide Interactions in Cell Signaling		  
7:15–7:30 PM Meeting Wrap-Up: Outcomes and Future Directions (Organizers) Eldorado Ballroom
7:30–8:30 PM Social Hour with Dinner Anasazi Ballroom
8:00–9:00 PM Entertainment Eldorado Ballroom
8:00–9:00 PM Cash Bar Anasazi Ballroom
Friday, September 19, 2025
12:00–11:59 PM Departure