Sep 15–18, 2025 | Eldorado Hotel & Spa, Santa Fe, NM, United States
Scientific Organizers:
David R. Kelley and Jean Fan

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Scientific Organizers: David R. Kelley and Jean Fan
David R. Kelley
Jean Fan
***Meeting program subject to change.
Available Formats: = In Person = On DemandMonday, September 15, 2025
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Tuesday, September 16, 2025
Machine Learning Methods for Live-Cell Imaging Cell Behavioral Analyses
Tissue Reassembly with Generative AI
Learning Multiscale Cellular Organization and Interactions
Self-Supervised and Unsupervised Learning for 2D Visualization of Scientific Datasets
Equitable Machine Learning in Healthcare
Deep Learning and Nanopore Technology Reveal Single-Molecule Insights Into DNA, RNA, and Protein Modifications
Mapping the Mechanistic Impact of Genetic Variation with Interpretable Deep Learning
Dissecting Cellular Plasticity in Glioblastoma via Deep Learning of Single-Cell Gene Regulatory Networks
Allele-Specific Expression Prediction from Personal Genome Sequences Using Fine-Tuned Enformer Models
Detecting and Avoiding Homology-Based Data Leakage in Genome-Trained Sequence Models
Synergistic Control of Gene Expression by 5’ UTR and Synonymous Codon Variants
Fast and Interpretable Motif Discovery from Attribution Maps via Fourier-Based Clustering
Decoding the Sequence Basis of Pol II Elongation with Deep Learning
Predicting Gene Expression from DNA Sequence
Single-Cell Multiomic Inference of Gene Regulatory Networks
Machine Learning for Single Cell and Regulatory Genomics in Cancer
Short Talk: Deep Learning Prediction of The Chromatin Response to Transcription Factor Dosage from DNA Sequence
Short Talk: Secondary Structures as Key Regulators of Transcription at CpG island Promoters
Wednesday, September 17, 2025
Machine Learning for Spatial Omics Data Integration
Unlocking the Power of Spatial Omics with AI
Multimodal, Generative, and Agentic AI for Pathology
Modeling Cell Fate Transition in Space and Time with Graph Neural Networks
Short Talk: A Machine Learning Approach to Soft Segmentation and Manifold Unrolling of Visium HD Data
Short Talk: Robust Self-Supervised Machine Learning for Single Cell Embeddings and Annotations
Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology
Cell Segmentation Foundation Models
Short Talk: Deep Learning-Driven Profiling of Biomolecular Condensate Images Reveals Mesoscale Structure-Molecular Function Relationships
Short Talk: Spatially-Restricted Circuits Between CXCL9+ Macrophages and T Cells Drive Acute Cellular Rejection in Lung Transplant Patients
Short Talk: A Multi-Modal Resource for Integrating Histopathology with Multi-Omics Data in R/Bioconductor
Short Talk: A Virtual Machine for Multimodal Spatial Omics
Thursday, September 18, 2025
Learning the Combinatorial Code of Epigenetic Reprogramming
Bioengineering Cells to Produce Biofuels and Renewable Biomaterials
We Are Not All the Same: Early Insights into Human Diversity from Single Cell and spatial Omics
UniGeneX Creates a Universal Gene Expression Single-Cell Atlas and Uncovers Key Transitional Pathological Cell States
Short Talk: Decoding Microglial State Dynamics via CRISPR Perturbations and Multi-Modal Generative Single-Cell Modeling
Short Talk: Uncovering Dynamic Regulatory Circuits Underlying Bifurcating Human B Cell States
Scalable Inference of Biophysical Models from Multi-Omics Data
FateNet: an Integration of Dynamical Systems and Deep Learning for Cell Fate Prediction
Sliding Window INteraction Grammar (SWING): A Generalized Interaction Language Model for Peptide and Protein Interactions
Harnessing Coupled Protein Language Model and Geometric Deep Learning for Protein Interaction Prediction on Dynamically Sampled Surfaces
AutoScreen: an AI Scientist System for Target Discovery in Functional Genomics
Learning the Language of Somatic Mutations: A Large Language Model Approach to Precision Oncology
Reconstructing Signaling Histories of Single Cells Via Perturbation Screens and Transfer Learning
Large-scale Proteomics for AI/ML Applications: Insights from Quantifying 1,000 Proteins In 20,000 Samples
Protein Language Models: Strengths and Limitations
Generative AI for Protein Sequence Design
Short Talk: Protein Codes Promote Selective Subcellular Compartmentalization
Short Talk: Machine Learning the Binding Affinities of Protein–Peptide Interactions in Cell Signaling
Remote Presentation: Protein Design using Deep Learning
Friday, September 19, 2025
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