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
Room 242
Fri 15 Dec, 6:15 a.m. PST
We will facilitate interdisciplinary discussions to identify gaps and opportunities for AI in the drug discovery and development pipeline.
Chat is not available.
Timezone: America/Los_Angeles
Schedule
|
Fri 6:15 a.m. - 6:25 a.m.
|
Opening Remarks
(
Presentation
)
>
SlidesLive Video |
Chong Liu 🔗 |
|
Fri 6:25 a.m. - 7:05 a.m.
|
Roundtable Discussion
(
Discussion
)
>
SlidesLive Video |
🔗 |
|
Fri 7:05 a.m. - 7:40 a.m.
|
Invited Talk 1 - Wengong Jin (MIT) - DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 7:40 a.m. - 8:00 a.m.
|
2 Oral Presentations
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 8:00 a.m. - 8:30 a.m.
|
Coffee Break
|
🔗 |
|
Fri 8:30 a.m. - 9:05 a.m.
|
Invited Talk 2 - Marinka Zitnik (Harvard) - Foundation Models for Molecular Drug Design and Clinical Drug Development
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 9:05 a.m. - 9:40 a.m.
|
2 Oral Presentations
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 9:25 a.m. - 10:00 a.m.
|
Invited Talk 3 - Haoda Fu (Eli Lilly) - LLM Is Not All You Need. Generative AI on Smooth Manifolds
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 10:00 a.m. - 11:20 a.m.
|
Lunch Break
|
🔗 |
|
Fri 11:20 a.m. - 12:25 p.m.
|
Poster Session
(
Poster
)
>
|
🔗 |
|
Fri 12:25 p.m. - 1:00 p.m.
|
Invited Talk 4 - Michael Bronstein (Oxford) - Harnessing geometry for molecular design
(
Presentation
)
>
SlidesLive Video |
Michael Bronstein 🔗 |
|
Fri 1:00 p.m. - 1:30 p.m.
|
Coffee Break
|
🔗 |
|
Fri 1:30 p.m. - 2:05 p.m.
|
Invited Talk 5 - Jian Tang (MILA) - Diffusion Models for Molecular Structure Prediction
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 2:05 p.m. - 2:40 p.m.
|
Invited Talk 6 - Iya Khalil (Merck) - Decoding Biology with AI and High-Throughput Biology
(
Presentation
)
>
SlidesLive Video |
🔗 |
|
Fri 2:40 p.m. - 3:10 p.m.
|
Award Ceremony
(
Presentation
)
>
SlidesLive Video |
Lucian Chan · Denis Tarasov 🔗 |
|
Fri 3:10 p.m. - 3:20 p.m.
|
Concluding Remarks
(
Presentation
)
>
SlidesLive Video |
Chong Liu 🔗 |
|
-
|
Removing Biases from Molecular Representations via Information Maximization ( Poster ) > link | Chenyu Wang · Sharut Gupta · Caroline Uhler · Tommi Jaakkola 🔗 |
|
-
|
MolSiam: Simple Siamese Self-supervised Representation Learning for Small Molecules ( Poster ) > link | Joshua Yao-Yu Lin 🔗 |
|
-
|
Multitask-Guided Self-Supervised Tabular Learning for Patient-Specific Survival Prediction ( Poster ) > link | You Wu · Omid Bazgir · Yongju Lee · Tommaso Biancalani · James Lu · Ehsan Hajiramezanali 🔗 |
|
-
|
Do chemical language models provide a better compound representation? ( Poster ) > link | Mirko Torrisi · Saeid Asadollahi · Antonio De la Vega de Leon · Kai Wang · Wilbert Copeland 🔗 |
|
-
|
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning ( Poster ) > link | Xiangzhe Kong · Wenbing Huang · Yang Liu 🔗 |
|
-
|
Inpainting Protein Sequence and Structure with ProtFill ( Poster ) > link | Elizaveta Kozlova · Arthur Valentin · Daniel Nakhaee-Zadeh Gutierrez 🔗 |
|
-
|
$\textit{In vitro}$ validated antibody design against multiple therapeutic antigens using generative inverse folding ( Poster ) > link | Amir Shanehsazzadeh 🔗 |
|
-
|
TopoPool: An Adaptive Graph Pooling Layer for Extracting Molecular and Protein Substructures ( Poster ) > link | Mattson Thieme · Majdi Hassan · Chetan Rupakheti · Kedar Thiagarajan · Abhishek Pandey · Han Liu 🔗 |
|
-
|
Offline RL for generative design of protein binders ( Poster ) > link | Denis Tarasov · Ulrich Armel Mbou Sob · Miguel Arbesú · Nima Siboni · Sebastien Boyer · Andries Smit · Oliver Bent · Arnu Pretorius · Marcin Skwark 🔗 |
|
-
|
Online Learning of Optimal Prescriptions under Bandit Feedback with Unknown Contexts ( Poster ) > link | Hongju Park · Mohamad Kazem Shirani Faradonbeh 🔗 |
|
-
|
Hit Expansion Driven By Machine Learning ( Poster ) > link | Jin Xu · Steven Kearnes · JW Feng 🔗 |
|
-
|
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design ( Poster ) > link | Kieran Didi · Francisco Vargas · Simon Mathis · Vincent Dutordoir · Emile Mathieu · Urszula Julia Komorowska · Pietro Lió 🔗 |
|
-
|
Automating reward function configuration for drug design ( Poster ) > link | Temitope Ajileye · Paul Gainer · Marius Urbonas · Douglas Pires 🔗 |
|
-
|
DGFN: Double Generative Flow Networks ( Poster ) > link | Elaine Lau · Nikhil Murali Vemgal · Doina Precup · Emmanuel Bengio 🔗 |
|
-
|
Target Conditioned GFlowNet for Drug Design ( Poster ) > link | Tony Shen · Mohit Pandey · Martin Ester 🔗 |
|
-
|
Towards a more inductive world for drug repurposing approaches ( Poster ) > link |
11 presentersJesus 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 |
|
-
|
Sample-efficient Antibody Design through Protein Language Model for Risk-aware Batch Bayesian Optimization ( Poster ) > link | Yanzheng Wang · Tianyu Shi 🔗 |
|
-
|
De novo design of antibody heavy chains with SE(3) diffusion ( Poster ) > link | Frédéric Dreyer · Daniel Cutting · David Errington · Charlotte Deane 🔗 |
|
-
|
Identifying regularization schemes that make the feature attributions faithful ( Poster ) > link | 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 ( Poster ) > link | Yanjing Li · Hannan Xu · Haiteng Zhao · Hongyu Guo · Shengchao Liu 🔗 |
|
-
|
Leap: molecular synthesisability scoring with intermediates ( Poster ) > link | Antonia Calvi · Théophile Gaudin · Dominik Miketa · Dominique Sydow · Liam Wilbraham 🔗 |
|
-
|
PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling ( Poster ) > link | Seonghwan Seo · Woo Youn Kim 🔗 |
|
-
|
Model-free selective inference and its applications to drug discovery ( Poster ) > link | Ying Jin · Emmanuel Candes 🔗 |
|
-
|
AlphaFold Meets Flow Matching for Generating Protein Ensembles ( Poster ) > link | Bowen Jing · Bonnie Berger · Tommi Jaakkola 🔗 |
|
-
|
RetroBridge: Modeling Retrosynthesis with Markov Bridges ( Poster ) > link | Ilia Igashov · Arne Schneuing · Marwin Segler · Michael Bronstein · Bruno Correia 🔗 |
|
-
|
Ab-DeepGA: A generative modeling framework leveraging deep learning for antibody affinity tuning ( Poster ) > link | 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 ( Poster ) > link | Tung Nguyen · Sudhanshu Agrawal · Aditya Grover 🔗 |
|
-
|
On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data? ( Poster ) > link | Arushi Gandhi 🔗 |
|
-
|
Machine Learning Guided AQFEP: A Fast & Efficient Absolute Free Energy Perturbation Solution for Virtual Screening ( Poster ) > link | 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 ( Poster ) > link | Seojin Kim · Jaehyun Nam · Sihyun Yu · Younghoon Shin · Jinwoo Shin 🔗 |
|
-
|
PiNUI: A Dataset of Protein-Protein Interactions for Machine Learning ( Poster ) > link | Geoffroy Dubourg-Felonneau · Eyal Akiva · Daniel Wesego · Ranjani Varadan 🔗 |
|
-
|
Protein Language Model-Powered 3-Dimensional Ligand Binding Site Prediction from Protein Sequence ( Poster ) > link | Shuo Zhang · Lei Xie 🔗 |
|
-
|
All You Need is LOVE: Large Optimized Vector Embeddings Network for Drug Repurposing ( Poster ) > link | Sina Akbarian · Sepehr Asgarian · Jouhyun Jeon 🔗 |
|
-
|
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses ( Poster ) > link | 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 ( Poster ) > link | 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 ( Poster ) > link | Julien Martinelli · Yasmine Nahal · Duong Lê · Ola Engkvist · Samuel Kaski 🔗 |
|
-
|
CryoSTAR: Cryo-EM Heterogeneous Reconstruction of Atomic Models with Structural Regularization ( Poster ) > link | Yi Zhou · Yilai Li · Jing Yuan · Fei YE · Quanquan Gu 🔗 |
|
-
|
TrustAffinity: accurate, reliable and scalable out-of-distribution protein-ligand binding affinity prediction using trustworthy deep learning ( Poster ) > link | Amitesh Badkul · Li Xie · Shuo Zhang · Lei Xie 🔗 |
|
-
|
Scalable Normalizing Flows Enable Boltzmann Generators for Macromolecules ( Poster ) > link | Joseph Kim · David Bloore · Karan Kapoor · Jun Feng · Ming-Hong Hao · Mengdi Wang 🔗 |
|
-
|
Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation ( Poster ) > link | Divya Nori · Simon Mathis · Amir Shanehsazzadeh 🔗 |
|
-
|
CongFu: Conditional Graph Fusion for Drug Synergy Prediction ( Poster ) > link | Oleksii Tsepa · Bohdan Naida · Anna Goldenberg · Bo Wang 🔗 |
|
-
|
The neural scaling laws for phenotypic drug discovery ( Poster ) > link | 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 ( Poster ) > link | Florian Sestak · Lisa Schneckenreiter · Sepp Hochreiter · Andreas Mayr · Günter Klambauer 🔗 |
|
-
|
SALSA: Semantically-Aware Latent Space Autoencoder ( Poster ) > link | Kathryn E. Kirchoff · Travis Maxfield · Alexander Tropsha · Shawn Gomez 🔗 |
|
-
|
Gotta be SAFE: A New Framework for Molecular Design ( Poster ) > link | Emmanuel Noutahi · Cristian Gabellini · Michael Craig · Jonathan Siu Chi Lim · Prudencio Tossou 🔗 |
|
-
|
MoleculeGPT: Instruction Following Large Language Models for Molecular Property Prediction ( Poster ) > link | Weitong ZHANG · Xiaoyun Wang · Weili Nie · Joe Eaton · Brad Rees · Quanquan Gu 🔗 |
|
-
|
Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions ( Poster ) > link | Lucian Chan · Marcel Verdonk · Carl Poelking 🔗 |
|
-
|
FragXsiteDTI: an interpretable transformer-based model for drug-target interaction prediction ( Poster ) > link | Ali Khodabandeh Yalabadi · Mehdi Yazdani-Jahromi · Niloofar Yousefi · Aida Tayebi · Sina Abdidizaji · OZLEM GARIBAY 🔗 |
|
-
|
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization ( Poster ) > link | Jiahao Qiu · Hui Yuan · Jinghong Zhang · Wentao Chen · Huazheng Wang · Mengdi Wang 🔗 |
|
-
|
GraphPrint: Extracting Features from 3D Protein Structure for Drug Target Affinity Prediction ( Poster ) > link | Amritpal Singh 🔗 |
|
-
|
Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening ( Poster ) > link | Zhonglin Cao · Simone Sciabola · Ye Wang 🔗 |
|
-
|
Role of Structural and Conformational Diversity for Machine Learning Potentials ( Poster ) > link | Nikhil Shenoy · Prudencio Tossou · Emmanuel Noutahi · Hadrien Mary · Dominique Beaini · Jiarui Ding 🔗 |
|
-
|
DrugImprover: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization ( Poster ) > link | 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 ( Poster ) > link | Zachary Rollins · Talal Widatalla · Andrew Waight · Alan Cheng · Essam Metwally 🔗 |
|
-
|
DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility ( Poster ) > link | Michael Plainer · Marcella Toth · Simon Dobers · Hannes Stärk · Gabriele Corso · Céline Marquet · Regina Barzilay 🔗 |
|
-
|
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design ( Poster ) > link | Chuanrui Wang · Bozitao Zhong · Zuobai Zhang · Narendra Chaudhary · Sanchit Misra · Jian Tang 🔗 |
|
-
|
Protein Language Models Enable Accurate Cryptic Ligand Binding Pocket Prediction ( Poster ) > link | David Bloore · Joseph Kim · Karan Kapoor · Eric Chen · Kaifu Gao · Mengdi Wang · Ming-Hong Hao 🔗 |
|
-
|
Explaining Drug Repositioning: A Case-Based Reasoning Graph Neural Network Approach ( Poster ) > link | Adriana Carolina Gonzalez Cavazos 🔗 |
|
-
|
Graph Neural Bayesian Optimization for Virtual Screening ( Poster ) > link | Miles Wang-Henderson · Bartu Soyuer · Parnian Kassraie · Andreas Krause · Ilija Bogunovic 🔗 |
|
-
|
Synthon Embeddings for Modeling DNA Encoded Libraries ( Poster ) > link | Benson Chen · Mohammad Sultan · Theofanis Karaletsos 🔗 |
|
-
|
Learning Scalar Fields for Molecular Docking with Fast Fourier Transforms ( Poster ) > link | Bowen Jing · Tommi Jaakkola · Bonnie Berger 🔗 |
|
-
|
$\textit{In vitro}$ validated antibody design against multiple therapeutic antigens using generative inverse folding ( Oral ) > link | Amir Shanehsazzadeh 🔗 |
|
-
|
Offline RL for generative design of protein binders
(
Oral
)
>
link
SlidesLive Video |
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 ( Oral ) > link | Kieran Didi · Francisco Vargas · Simon Mathis · Vincent Dutordoir · Emile Mathieu · Urszula Julia Komorowska · Pietro Lió 🔗 |
|
-
|
Towards a more inductive world for drug repurposing approaches ( Oral ) > link |
11 presentersJesus 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 |
|
-
|
Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions
(
Oral
)
>
link
SlidesLive Video |
Lucian Chan · Marcel Verdonk · Carl Poelking 🔗 |
|
-
|
DrugImprover: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization
(
Oral
)
>
link
SlidesLive Video |
Xuefeng Liu · Songhao Jiang · Archit Vasan · Alexander Brace · Ozan Gokdemir · Thomas Brettin · Fangfang Xia · Ian Foster · Rick Stevens 🔗 |