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Workshop

New Frontiers of AI for Drug Discovery and Development

Animashree Anandkumar ⋅ Ilija Bogunovic ⋅ Ti-chiun Chang ⋅ Quanquan Gu ⋅ Jure Leskovec ⋅ Michelle Li ⋅ Chong Liu ⋅ Nataša Tagasovska ⋅ Mengdi Wang ⋅ Wei Wang
Project Page

Abstract

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Schedule

Timezone: America/Los_Angeles
6:15 AM
Opening Remarks
Chong Liu
8:00 AM
Coffee Break
10:00 AM
Lunch Break
11:20 AM
Poster Session
1:00 PM
Coffee Break
2:40 PM
Award Ceremony
Lucian Chan ⋅ Denis Tarasov
3:10 PM
Concluding Remarks
Chong Liu
Removing Biases from Molecular Representations via Information Maximization
Chenyu Wang ⋅ Sharut Gupta ⋅ Caroline Uhler ⋅ Tommi Jaakkola
Multitask-Guided Self-Supervised Tabular Learning for Patient-Specific Survival Prediction
You Wu ⋅ Omid Bazgir ⋅ Yongju Lee ⋅ Tommaso Biancalani ⋅ James Lu ⋅ Ehsan Hajiramezanali
Do chemical language models provide a better compound representation?
Mirko Torrisi ⋅ Saeid Asadollahi ⋅ Antonio De la Vega de Leon ⋅ Kai Wang ⋅ Wilbert Copeland
Inpainting Protein Sequence and Structure with ProtFill
Elizaveta Kozlova ⋅ Arthur Valentin ⋅ Daniel Nakhaee-Zadeh Gutierrez
TopoPool: An Adaptive Graph Pooling Layer for Extracting Molecular and Protein Substructures
Mattson Thieme ⋅ Majdi Hassan ⋅ Chetan Rupakheti ⋅ Kedar Thiagarajan ⋅ Abhishek Pandey ⋅ Han Liu
Offline RL for generative design of protein binders
Denis Tarasov ⋅ Ulrich Armel Mbou Sob ⋅ Miguel Arbesú ⋅ Nima Siboni ⋅ Sebastien Boyer ⋅ Andries Smit ⋅ Oliver Bent ⋅ Arnu Pretorius ⋅ Marcin Skwark
Hit Expansion Driven By Machine Learning
Jin Xu ⋅ Steven Kearnes ⋅ JW Feng
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
Kieran Didi ⋅ Francisco Vargas ⋅ Simon Mathis ⋅ Vincent Dutordoir ⋅ Emile Mathieu ⋅ Urszula Julia Komorowska ⋅ Pietro Lió
Automating reward function configuration for drug design
Temitope Ajileye ⋅ Paul Gainer ⋅ Marius Urbonas ⋅ Douglas Pires
DGFN: Double Generative Flow Networks
Elaine Lau ⋅ Nikhil Murali Vemgal ⋅ Doina Precup ⋅ Emmanuel Bengio
Target Conditioned GFlowNet for Drug Design
Tony Shen ⋅ Mohit Pandey ⋅ Martin Ester
Towards a more inductive world for drug repurposing approaches
Jesus de la Fuente Cedeño ⋅ Guillermo Serrano ⋅ Uxia Veleiro ⋅ Mikel Casals ⋅ Laura Vera ⋅ Marija Pizurica ⋅ Antonio Pineda-Lucena ⋅ Idoia Ochoa ⋅ Silve Vicent ⋅ Olivier Gevaert ⋅ Mikel Hernaez
De novo design of antibody heavy chains with SE(3) diffusion
Frédéric Dreyer ⋅ Daniel Cutting ⋅ David Errington ⋅ Charlotte Deane
Identifying regularization schemes that make the feature attributions faithful
Julius Adebayo ⋅ Samuel Stanton ⋅ Simon Kelow ⋅ Michael Maser ⋅ Richard Bonneau ⋅ Vladimir Gligorijevic ⋅ Kyunghyun Cho ⋅ Stephen Ra ⋅ Nathan Frey
ChatPathway: Conversational Large Language Models for Biology Pathway Detection
Yanjing Li ⋅ Hannan Xu ⋅ Haiteng Zhao ⋅ Hongyu Guo ⋅ Shengchao Liu
Leap: molecular synthesisability scoring with intermediates
Antonia Calvi ⋅ Théophile Gaudin ⋅ Dominik Miketa ⋅ Dominique Sydow ⋅ Liam Wilbraham
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing ⋅ Bonnie Berger ⋅ Tommi Jaakkola
RetroBridge: Modeling Retrosynthesis with Markov Bridges
Ilia Igashov ⋅ Arne Schneuing ⋅ Marwin Segler ⋅ Michael Bronstein ⋅ Bruno Correia
Ab-DeepGA: A generative modeling framework leveraging deep learning for antibody affinity tuning
BoRam Lee ⋅ Yara Seif ⋅ Kevin Teng ⋅ Xiao Xiao ⋅ Isha Verma ⋅ Ming-Tang Chen ⋅ Alan Cheng
ExPT: Scaling Foundation Models for Experimental Design via Synthetic Pretraining
Tung Nguyen ⋅ Sudhanshu Agrawal ⋅ Aditya Grover
Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening
Jordan Crivelli-Decker ⋅ Zane Beckwith ⋅ Gary Tom ⋅ Ly Le ⋅ Sheenam Khuttan ⋅ Romelia Salomon-Ferrer ⋅ Jackson Beall ⋅ Andrea Bortolato
Data-Efficient Molecular Generation with Hierarchical Textual Inversion
Seojin Kim ⋅ Jaehyun Nam ⋅ Sihyun Yu ⋅ Younghoon Shin ⋅ Jinwoo Shin
PiNUI: A Dataset of Protein-Protein Interactions for Machine Learning
Geoffroy Dubourg-Felonneau ⋅ Eyal Akiva ⋅ Daniel Wesego ⋅ Ranjani Varadan
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris ⋅ Kieran Didi ⋅ Arian Jamasb ⋅ Chaitanya K. Joshi ⋅ Simon Mathis ⋅ Pietro Lió ⋅ Tom Blundell
Neurosymbolic AI Reveals Biases and Limitations in ML-Driven Drug Discovery
Lauren Nicole DeLong ⋅ Yojana Gadiya ⋅ Jacques Fleuriot ⋅ Daniel Domingo-Fernández
Leveraging expert feedback to align proxy and ground truth rewards in goal-oriented molecular generation
Julien Martinelli ⋅ Yasmine Nahal ⋅ Duong Lê ⋅ Ola Engkvist ⋅ Samuel Kaski
CryoSTAR: Cryo-EM Heterogeneous Reconstruction of Atomic Models with Structural Regularization
Yi Zhou ⋅ Yilai Li ⋅ Jing Yuan ⋅ Fei YE ⋅ Quanquan Gu
Scalable Normalizing Flows Enable Boltzmann Generators for Macromolecules
Joseph Kim ⋅ David Bloore ⋅ Karan Kapoor ⋅ Jun Feng ⋅ Ming-Hong Hao ⋅ Mengdi Wang
CongFu: Conditional Graph Fusion for Drug Synergy Prediction
Oleksii Tsepa ⋅ Bohdan Naida ⋅ Anna Goldenberg ⋅ Bo Wang
The neural scaling laws for phenotypic drug discovery
Drew Linsley ⋅ John Griffin ⋅ Jason Brown ⋅ Adam Roose ⋅ Steven Finkbeiner ⋅ Peter Linsley ⋅ Jeremy Linsley
VN-EGNN: Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
Florian Sestak ⋅ Lisa Schneckenreiter ⋅ Sepp Hochreiter ⋅ Andreas Mayr ⋅ Günter Klambauer
SALSA: Semantically-Aware Latent Space Autoencoder
Kathryn E. Kirchoff ⋅ Travis Maxfield ⋅ Alexander Tropsha ⋅ Shawn Gomez
Gotta be SAFE: A New Framework for Molecular Design
Emmanuel Noutahi ⋅ Cristian Gabellini ⋅ Michael Craig ⋅ Jonathan Siu Chi Lim ⋅ Prudencio Tossou
MoleculeGPT: Instruction Following Large Language Models for Molecular Property Prediction
Weitong ZHANG ⋅ Xiaoyun Wang ⋅ Weili Nie ⋅ Joe Eaton ⋅ Brad Rees ⋅ Quanquan Gu
FragXsiteDTI: an interpretable transformer-based model for drug-target interaction prediction
Ali Khodabandeh Yalabadi ⋅ Mehdi Yazdani-Jahromi ⋅ Niloofar Yousefi ⋅ Aida Tayebi ⋅ Sina Abdidizaji ⋅ OZLEM GARIBAY
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
Jiahao Qiu ⋅ Hui Yuan ⋅ Jinghong Zhang ⋅ Wentao Chen ⋅ Huazheng Wang ⋅ Mengdi Wang
Role of Structural and Conformational Diversity for Machine Learning Potentials
Nikhil Shenoy ⋅ Prudencio Tossou ⋅ Emmanuel Noutahi ⋅ Hadrien Mary ⋅ Dominique Beaini ⋅ Jiarui Ding
DrugImprover: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization
Xuefeng Liu ⋅ Songhao Jiang ⋅ Archit Vasan ⋅ Alexander Brace ⋅ Ozan Gokdemir ⋅ Thomas Brettin ⋅ Fangfang Xia ⋅ Ian Foster ⋅ Rick Stevens
AbLEF: Antibody Language Ensemble Fusion for thermodynamically empowered property predictions
Zachary Rollins ⋅ Talal Widatalla ⋅ Andrew Waight ⋅ Alan Cheng ⋅ Essam Metwally
DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility
Michael Plainer ⋅ Marcella Toth ⋅ Simon Dobers ⋅ Hannes Stärk ⋅ Gabriele Corso ⋅ Céline Marquet ⋅ Regina Barzilay
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
Chuanrui Wang ⋅ Bozitao Zhong ⋅ Zuobai Zhang ⋅ Narendra Chaudhary ⋅ Sanchit Misra ⋅ Jian Tang
Protein Language Models Enable Accurate Cryptic Ligand Binding Pocket Prediction
David Bloore ⋅ Joseph Kim ⋅ Karan Kapoor ⋅ Eric Chen ⋅ Kaifu Gao ⋅ Mengdi Wang ⋅ Ming-Hong Hao
Graph Neural Bayesian Optimization for Virtual Screening
Miles Wang-Henderson ⋅ Bartu Soyuer ⋅ Parnian Kassraie ⋅ Andreas Krause ⋅ Ilija Bogunovic
Synthon Embeddings for Modeling DNA Encoded Libraries
Benson Chen ⋅ Mohammad Sultan ⋅ Theofanis Karaletsos
Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms
Bowen Jing ⋅ Tommi Jaakkola ⋅ Bonnie Berger
Offline RL for generative design of protein binders
Denis Tarasov ⋅ Ulrich Armel Mbou Sob ⋅ Miguel Arbesú ⋅ Nima Siboni ⋅ Sebastien Boyer ⋅ Andries Smit ⋅ Oliver Bent ⋅ Arnu Pretorius ⋅ Marcin Skwark
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
Kieran Didi ⋅ Francisco Vargas ⋅ Simon Mathis ⋅ Vincent Dutordoir ⋅ Emile Mathieu ⋅ Urszula Julia Komorowska ⋅ Pietro Lió
Towards a more inductive world for drug repurposing approaches
Jesus de la Fuente Cedeño ⋅ Guillermo Serrano ⋅ Uxia Veleiro ⋅ Mikel Casals ⋅ Laura Vera ⋅ Marija Pizurica ⋅ Antonio Pineda-Lucena ⋅ Idoia Ochoa ⋅ Silve Vicent ⋅ Olivier Gevaert ⋅ Mikel Hernaez
DrugImprover: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization
Xuefeng Liu ⋅ Songhao Jiang ⋅ Archit Vasan ⋅ Alexander Brace ⋅ Ozan Gokdemir ⋅ Thomas Brettin ⋅ Fangfang Xia ⋅ Ian Foster ⋅ Rick Stevens