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

NeurIPS 2025 Workshop @ San Diego, California, USA

San Diego Convention Center Upper Level Room 28A-E

Saturday, December 6, 2025

Workshop Schedule

All times listed are in Pacific Standard Time (PST, UTC-8, San Diego Local Time).

Time Event
8:30 - 8:35 Opening Remarks
8:35 - 9:30 Roundtable Discussion
9:30 - 10:00 Invited Talk 1 - Linda Goodman
10:15 - 10:45 Invited Talk 2 - Arvind Ramanathan
10:45 - 11:15 Invited Talk 3 - Eric P. Xing
11:15 - 11:45 Invited Talk 4 - Alex Zhavoronkov
11:45 - 12:05 2 Paper Award Talks
12:05 - 1:00 Lunch Break
1:00 - 2:10 Poster Session
2:10 - 2:40 Invited Talk 5 - Mengdi Wang
2:40 - 3:00 2 Oral Talks
3:00 - 3:30 Coffee Break
3:30 - 3:50 4 Spotlight Talks
3:50 - 4:20 Invited Talk 6 - Jinbo Xu
4:20 - 4:30 Concluding Remarks

Oral Presentation Schedule

  • [11:45 – 11:55] Best Student Paper Award: Constrained Molecular Generation with Discrete Diffusion for Drug Discovery
    Michael Cardei, Jacob K Christopher, Bhavya Kailkhura, Thomas Hartvigsen, Ferdinando Fioretto

  • [11:55 – 12:05] Best Paper Award: PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA
    Alice Del Vecchio, Chantriolnt-Andreas Kapourani, Abdullah M Athar, Agnieszka Dobrowolska, Andrew Anighoro, Benjamin Tenmann, Lindsay Edwards, Cristian Regep

  • [2:40 – 2:50] Oral Talk: rbio1 - training scientific reasoning LLMs with biological world models as soft verifiers
    Ana-Maria Istrate, fausto milletari, Fabrizio Castrotorres, Jakub M. Tomczak, Michaela Torkar, Donghui Li, Theofanis Karaletsos

  • [2:50 – 3:00] Oral Talk: FocusMR: An Attention-Based Single-Cell Mendelian Randomization Framework to Map Cellular Contexts at Candidate Genes
    Martin Meinel, Jan P. Engelmann, Michael Patrick Menden, Theofanis Karaletsos, Francesco Paolo Casale

  • [3:30 – 3:35] Spotlight Talk: OligoGym: Curated Datasets and Benchmarks for Oligonucleotide Drug Discovery
    Rachapun Rotrattanadumrong, Carlo De Donno

  • [3:35 – 3:40] Spotlight Talk: Probing Functional Plasticity in Peptide–Protein Interaction with Minimal Data
    Pouriya Bayat, Spencer Perkins, Sebastian Clancy, Sahil Swapnesh Patel, Richard Fei Yin, Krištof Bozovičar, Idorenyin IWE, Serena Singh, Sepehr Bayat, Vivian White, Matthew Xie, Sean Palter, Mohammad Simchi, Ilan Yaniv Zeisler, Keith Pardee

  • [3:40 – 3:45] Spotlight Talk: 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 et al.

  • [3:45 – 3:50] Spotlight Talk: 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

Accepted Papers

  • DiffDAG: Diffusion DAG Models for modeling Gene Perturbations (Poster)
    Shiv Shankar
  • FocusMR: An Attention-Based Single-Cell Mendelian Randomization Framework to Map Cellular Contexts at Candidate Genes (Oral)
    Martin Meinel, Jan P. Engelmann, Michael Patrick Menden, Theofanis Karaletsos, Francesco Paolo Casale
  • Predicting cellular responses to perturbation across diverse contexts with State (Spotlight)
    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 et al.
  • Mol-SGCL: Molecular Substructure-Guided Contrastive Learning for Out-of-Distribution Generalization (Poster)
    Andrew Zhou, Yasha Ektefaie, Maha Farhat
  • Gene42: Long-Range Genomic Foundation Model With Dense Attention (Poster)
    Kirill Vishniakov, Boulbaba Ben Amor, Engin Tekin, Nancy A. ElNaker, Karthik Viswanathan, Aleksandr Medvedev, Aahan Singh, Maryam Nadeem, Mohammad Amaan Sayeed, Praveenkumar Kanithi, Tiago Magalhaes, Natalia Vassilieva, Dwarikanath Mahapatra, Marco AF Pimentel, Shadab Khan
  • Chem42∗: a Family of chemical Language Models for Target-aware Ligand Generation (Poster)
    Maryam Nadeem, Aahan Singh, Engin Tekin, Nancy A. ElNaker, Mohammad Amaan Sayeed, Natalia Vassilieva, Boulbaba Ben Amor
  • Prot42 : a Novel Family of Protein Language Models for Target-aware Protein Binder Generation (Poster)
    Mohammad Amaan Sayeed, Engin Tekin, Maryam Nadeem, Nance A. Elnaker, Aahan Singh, Natalia Vassilieva, Boulbaba Ben Amor
  • Probing Functional Plasticity in Peptide–Protein Interaction with Minimal Data (Spotlight)
    Pouriya Bayat, Spencer Perkins, Sebastian Clancy, Sahil Swapnesh Patel, Richard Fei Yin, Krištof Bozovičar, Idorenyin IWE, Serena Singh, Sepehr Bayat, Vivian White, Matthew Xie, Sean Palter, Mohammad Simchi, Ilan Yaniv Zeisler, Keith Pardee
  • PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA (Oral)
    Alice Del Vecchio, Chantriolnt-Andreas Kapourani, Abdullah M Athar, Agnieszka Dobrowolska, Andrew Anighoro, Benjamin Tenmann, Lindsay Edwards, Cristian Regep
  • OligoGym: Curated Datasets and Benchmarks for Oligonucleotide Drug Discovery (Spotlight)
    Rachapun Rotrattanadumrong, Carlo De Donno