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Workshop Sat, Dec 6, 2025 • 8:00 AM – 5:00 PM PST

AI Virtual Cells and Instruments: A New Era in Drug Discovery and Development

Quanquan Gu ⋅ Michelle Li ⋅ Xuefeng Liu ⋅ Chong Liu ⋅ Abhishek Pandey ⋅ Ji Won Park ⋅ Nataša Tagasovska ⋅ Marinka Zitnik
Project Page [ OpenReview] 

Abstract

Video

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Schedule

Timezone: America/Los_Angeles
8:30 AM
Opening Remarks
9:30 AM
Invited Talk 1
Linda Goodman
10:00 AM
Invited Talk 2
Eric Xing
10:30 AM
Invited Talk 3
Arvind Ramanathan
11:00 AM
Invited Talk 4
Alex Zhavoronkov
11:50 AM
Lunch Break
1:00 PM
Poster Session
2:10 PM
Invited Talk 5
Mengdi Wang
2:40 PM
2 Oral Talks
3:00 PM
Coffee Break
3:50 PM
Invited Talk 6
Jinbo Xu
GRASP: Graph Reasoning Agents for Systems Pharmacology with Human-in-the-Loop
Omid Bazgir ⋅ Mohammad Jafarnejad ⋅ Vineeth Manthapuri ⋅ Ilia Rattsev
Perturbation-aware representation learning for in vivo genetic screens
Florian Hugi ⋅ Tanmay Tanna ⋅ Randall Platt ⋅ Gunnar Rätsch
SigSpace: an LLM-based agent for drug response signature interpretation
Rohit Khurana ⋅ Ishita Mangla ⋅ Giovanni Palla ⋅ Siddhant Sanghi ⋅ Daniele Merico
Gene42: Long-Range Genomic Foundation Model With Dense Attention
Kirill Vishniakov ⋅ Boulbaba Ben Amor ⋅ Engin Tekin ⋅ Nance Elnaker ⋅ Karthik Viswanathan ⋅ Aleksandr Medvedev ⋅ Aahan Singh ⋅ Maryam Nadeem ⋅ Mohammad Amaan Sayeed ⋅ Praveenkumar Kanithi ⋅ Tiago Magalhaes ⋅ Natalia Vassilieva ⋅ Dwarikanath Mahapatra ⋅ Marco Pimentel ⋅ Shadab Khan
Early Prediction of Overall Survival in Oncology Trials Using Tumor Dynamic Neural-ODE
Gengbo Liu ⋅ Victor Poon ⋅ Omid Bazgir ⋅ Phyllis Chan ⋅ Kenta Yoshida ⋅ Chanu Pascal
Chem42∗: a Family of chemical Language Models for Target-aware Ligand Generation
Maryam Nadeem ⋅ Aahan Singh ⋅ Engin Tekin ⋅ Nance Elnaker ⋅ Mohammad Amaan Sayeed ⋅ Natalia Vassilieva ⋅ Boulbaba Ben Amor
Label-free biochemical imaging of neural organoids via deep learning-enhanced Raman microspectroscopy
Dimitar Georgiev ⋅ Ruoxiao Xie ⋅ Daniel Reumann ⋅ Xiaoyu Zhao ⋅ Álvaro Fernández-Galiana ⋅ Mauricio Barahona ⋅ Molly Stevens
Refine Drugs, Don’t Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery
Benno Kaech ⋅ Luis Wyss ⋅ Karsten Borgwardt ⋅ Gianvito Grasso
Monte Carlo Tree Diffusion with Multiple Experts for Protein Design
Xuefeng Liu ⋅ Mingxuan Cao ⋅ Songhao Jiang ⋅ Xiao Luo ⋅ Xiaotian Duan ⋅ Mengdi Wang ⋅ Tobin Sosnick ⋅ Jinbo Xu ⋅ Rick Stevens
PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA
Alice Del Vecchio ⋅ Chantriolnt-Andreas Kapourani ⋅ Abdullah Athar ⋅ Agnieszka Dobrowolska ⋅ Andrew Anighoro ⋅ Benjamin Tenmann ⋅ Lindsay Edwards ⋅ Cristian Regep
Why Pool When You Can Flow? Active Learning with GFlowNets
Renfei Zhang ⋅ Mohit Pandey ⋅ Artem Cherkasov ⋅ Martin Ester
rbio1 - training scientific reasoning LLMs with biological world models as soft verifiers
Ana-Maria Istrate ⋅ Fausto Milletari ⋅ Fabrizio Castrotorres ⋅ Jakub Tomczak ⋅ Michaela Torkar ⋅ Donghui Li ⋅ Theofanis Karaletsos
HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields
Sudarshan Babu ⋅ Phillip Lo ⋅ Xiao Zhang ⋅ Aadi Srivastava ⋅ Ali Davariashtiyani ⋅ Jason Perera ⋅ Michael Maire ⋅ Aly A. Khan
BEACON: Bayesian Contrastive Learning for Single-Cell Gene Regulatory Inference
Yunwei Zhao ⋅ Ankit Bhardwaj ⋅ Lakshminarayanan Subramanian
LLM-Integrated Representative Path Selection for Context-Aware Drug Repurposing on Biomedical Knowledge Graphs
HAERIN SONG ⋅ Dongmin Bang ⋅ Bonil Koo ⋅ Sun Kim ⋅ Sangseon Lee
Virtual Cells as Causal World Models: A Perspective on Evaluation
Tiffany Callahan ⋅ Zane Beckwith ⋅ Thomas Merth ⋅ Constantijn van der Poel ⋅ Adam Lewis ⋅ Pablo Lemos
Constrained Molecular Generation with Discrete Diffusion for Drug Discovery
Michael Cardei ⋅ Jacob K Christopher ⋅ Bhavya Kailkhura ⋅ Tom Hartvigsen ⋅ Ferdinando Fioretto
Patient-level prediction from single-cell data using attention-based multiple instance learning with regulatory priors
Kristin Tsui ⋅ Kameron Rodrigues ⋅ Xianghao Zhan ⋅ Yiyun Chen ⋅ Kelvin Mo ⋅ Crystal Mackall ⋅ David Miklos ⋅ Olivier Gevaert ⋅ Zinaida Good
FocusMR: An Attention-Based Single-Cell Mendelian Randomization Framework to Map Cellular Contexts at Candidate Genes
Martin Meinel ⋅ Jan Engelmann ⋅ Michael Menden ⋅ Theofanis Karaletsos ⋅ Francesco Paolo Casale
MoAgent: A Hypothesis-Driven Multi-Agent Framework for Drug Mechanism of Action Discovery
Jun Hyeong Kim ⋅ Seokhyun Moon ⋅ SEONGHWAN KIM ⋅ Junhyeok Jeon ⋅ Taein Kim ⋅ Jisu Seo ⋅ Songmi Kim ⋅ Woo Youn Kim
Cross-Species Graph Neural Network for Translating Animal Disease Resistance to Human Drug Targets
Deek Guruge ⋅ Michelle Li ⋅ Natalie DeForest ⋅ Phil McNamara ⋅ Manashvi Borad ⋅ Linda Goodman
Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning
Patricia Suriana ⋅ Joshua Rackers ⋅ Ewa Nowara ⋅ Pedro O. Pinheiro ⋅ Vishnu Sresht ⋅ John Nicoludis
LLMs as Virtual Instruments for Drug Formulation
Michael Craig ⋅ Gary Tom ⋅ Pauric Bannigan ⋅ Christine Allen ⋅ Riley Hickman
FragmentGPT: A Unified GPT Model for Fragment Growing, Linking, and Merging in Molecular Design
Xuefeng Liu ⋅ Songhao Jiang ⋅ Qinan Huang ⋅ Tinson xu ⋅ Ian Foster ⋅ Mengdi Wang ⋅ Hening Lin ⋅ Rick Stevens
Predicting cellular responses to perturbation across diverse contexts with State
Abhinav Adduri ⋅ Dhruv Gautam ⋅ Beatrice Bevilacqua ⋅ Alishba Imran ⋅ Rohan Shah ⋅ Mohsen Naghipourfar ⋅ Noam Teyssier ⋅ Rajesh Ilango ⋅ Sanjay Nagaraj ⋅ Chiara Ricci-Tam ⋅ Chris Carpenter ⋅ Vishvak Subramanyam ⋅ Aidan Winters ⋅ Mingze Dong ⋅ Sravya Tirukkovalur ⋅ Jeremy Sullivan ⋅ Brian Plosky ⋅ Basak Eraslan ⋅ Nick Youngblut ⋅ Jure Leskovec ⋅ Luke Gilbert ⋅ Silvana Konermann ⋅ Patrick Hsu ⋅ Alexander Dobin ⋅ Dave Burke ⋅ Hani Goodarzi ⋅ Yusuf Roohani
A Scalable Latent Diffusion Model for Single-Cell Gene Expression Data
Giovanni Palla ⋅ Sudarshan Babu ⋅ Payam Dibaeinia ⋅ Donghui Li ⋅ Aly A. Khan ⋅ Theofanis Karaletsos ⋅ Jakub Tomczak
Improving Classification of Cell Types in Acute Myeloid Leukemia with Self-guided Masking Technique
Amirreza Naziri ⋅ Arash Asgari ⋅ Eleftherios Sachlos ⋅ Aijun An ⋅ Laleh Seyyed-Kalantari
Domain Knowledge Infused Conditional Generative Models for Accelerating Drug Discovery
Bing Hu ⋅ Jong-Hoon Park ⋅ Anita Layton ⋅ Young-Rae Cho ⋅ Sun Sun ⋅ Helen Chen
Probing Functional Plasticity in Peptide–Protein Interaction with Minimal Data
Pouriya Bayat ⋅ Spencer Perkins ⋅ Sebastian Clancy ⋅ Sahil Patel ⋅ Richard Yin ⋅ Krištof Bozovičar ⋅ Idorenyin IWE ⋅ Serena Singh ⋅ Sepehr Bayat ⋅ Vivian White ⋅ Matthew Xie ⋅ Sean Palter ⋅ Mohammad Simchi ⋅ Ilan Zeisler ⋅ Keith Pardee
Prot42 : a Novel Family of Protein Language Models for Target-aware Protein Binder Generation
Mohammad Amaan Sayeed ⋅ Engin Tekin ⋅ Maryam Nadeem ⋅ Nance Elnaker ⋅ Aahan Singh ⋅ Natalia Vassilieva ⋅ Boulbaba Ben Amor
Context-aware geometric deep learning for RNA sequence design
Parth Bibekar ⋅ Lucien Krapp ⋅ Matteo Dal Peraro
D-Flow: Multi-modality Flow Matching for D-peptide Design
Fang Wu ⋅ Shuting Jin ⋅ Robert Tang ⋅ Junlin Xu ⋅ James Zou ⋅ Mark Gerstein
High-Throughput Protein Perturbation Screens with AI-Designed Degraders
Lin Zhao ⋅ Aastha Pal ⋅ Tong Chen ⋅ Pranam Chatterjee
Learning from B Cell Evolution: Adaptive Multi-Expert Diffusion for Antibody Design via Online Optimization
Peng Qiu ⋅ Hanqi Feng ⋅ Yiran Tao ⋅ Mengchun Zhang ⋅ You Fan ⋅ Jingtao Xu ⋅ Barnabas Poczos