Workshop
Machine Learning for Drug Discovery (MLDD)
Pascal Notin · Stefan Bauer · Andrew Jesson · Yarin Gal · Patrick Schwab · Debora Marks · Sonali Parbhoo · Ece Ozkan · Clare Lyle · Ashkan Soleymani · Júlia Domingo · Arash Mehrjou · Melanie Fernandez Pradier · Anna Bauer-Mehren · Max Shen
Fri 29 Apr, 6 a.m. PDT
We are at a pivotal moment in healthcare characterized by unprecedented scientific and technological progress in recent years together with the promise of personalized medicine to radically transform the way we provide care to patients. However, drug discovery has become an increasingly challenging endeavour: not only has the success rate of developing new therapeutics been historically low, but this rate has been steadily declining. The average cost to bring a new drug to market is now estimated at 2.6 billion – 140% higher than a decade earlier. Machine learning-based approaches present a unique opportunity to address this challenge. While there has been growing interest and pioneering work in the machine learning (ML) community over the past decade, the specific challenges posed by drug discovery are largely unknown by the broader community. We would like to organize a workshop on ‘Machine Learning for Drug Discovery’ (MLDD) at ICLR 2022 with the ambition to federate the community interested in this application domain where i) ML can have a significant positive impact for the benefit of all and ii) the application domain can drive ML method development through novel problem settings, benchmarks and testing grounds at the intersection of many subfields ranging representation, active and reinforcement learning to causality and treatment effects.
Schedule
Fri 6:00 a.m. - 6:10 a.m.
|
Opening remarks
(
Intro
)
>
|
🔗 |
Fri 6:10 a.m. - 6:50 a.m.
|
Keynote - Regina Barzilay
(
Keynote
)
>
|
🔗 |
Fri 6:50 a.m. - 7:10 a.m.
|
Invited Talk - Miguel Hernandez-Lobato
(
Invited Talk
)
>
|
🔗 |
Fri 7:10 a.m. - 7:30 a.m.
|
Invited Talk - Ole Winther
(
Invited Talk
)
>
|
🔗 |
Fri 7:30 a.m. - 7:50 a.m.
|
Spotlight Presentations (Part 1)
(
Spotlight Presentations
)
>
|
🔗 |
Fri 7:30 a.m. - 7:35 a.m.
|
Deep sharpening of topological features for de novo protein design
(
Spotlight
)
>
link
SlidesLive Video |
Zander Harteveld · Joshua Southern · Michaël Defferrard · Andreas Loukas · Pierre Vandergheynst · Micheal Bronstein · Bruno Correia 🔗 |
Fri 7:35 a.m. - 7:40 a.m.
|
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction
(
Spotlight
)
>
link
SlidesLive Video |
Hannes Stärk · Octavian Ganea · Lagnajit Pattanaik · Regina Barzilay · Tommi Jaakkola 🔗 |
Fri 7:40 a.m. - 7:45 a.m.
|
Predicting single-cell perturbation responses for unseen drugs
(
Spotlight
)
>
link
SlidesLive Video |
Leon Hetzel · Simon Boehm · Niki Kilbertus · Stephan Günnemann · Mohammad Lotfollahi · Fabian Theis 🔗 |
Fri 7:45 a.m. - 7:50 a.m.
|
GRPE: Relative Positional Encoding for Graph Transformer
(
Spotlight
)
>
link
SlidesLive Video |
Wonpyo Park · Woong-Gi Chang · Donggeon Lee · Juntae Kim · seung-won hwang 🔗 |
Fri 7:50 a.m. - 8:00 a.m.
|
Break
|
🔗 |
Fri 8:00 a.m. - 8:40 a.m.
|
Keynote - Aviv Regev
(
Keynote
)
>
SlidesLive Video |
🔗 |
Fri 8:40 a.m. - 9:00 a.m.
|
Invited Talk - Connor Coley
(
Invited Talk
)
>
|
🔗 |
Fri 9:00 a.m. - 9:45 a.m.
|
Poster Session (Part 1) ( Poster Session ) > link | 🔗 |
Fri 9:45 a.m. - 10:30 a.m.
|
Lunch Break
|
🔗 |
Fri 10:30 a.m. - 11:10 a.m.
|
Keynote - Daphne Koller
(
Keynote
)
>
|
🔗 |
Fri 11:10 a.m. - 11:30 a.m.
|
Invited Talk - John Chodera
(
Invited Talk
)
>
|
🔗 |
Fri 11:30 a.m. - 11:50 a.m.
|
Invited Talk - Mohammed AlQuraishi
(
Invited Talk
)
>
|
🔗 |
Fri 11:50 a.m. - 12:30 p.m.
|
Keynote - Yoshua Bengio
(
Keynote
)
>
|
🔗 |
Fri 12:30 p.m. - 12:40 p.m.
|
Break
|
🔗 |
Fri 12:40 p.m. - 1:00 p.m.
|
Spotlight Presentations (Part 2)
(
Spotlight Presentations
)
>
|
🔗 |
Fri 12:40 p.m. - 12:45 p.m.
|
SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching
(
Spotlight
)
>
link
SlidesLive Video |
Scott Gigante · Varsha Raghavan · Amanda Robinson · Rob Barton · Adeeb Rahman · Drausin Wulsin · Jacques Banchereau · Noam Solomon · Luis Voloch · Fabian Theis 🔗 |
Fri 12:45 p.m. - 12:50 p.m.
|
Physics-informed deep neural network for rigid-body protein docking
(
Spotlight
)
>
link
SlidesLive Video |
Freyr Sverrisson · Jean Feydy · Joshua Southern · Michael Bronstein · Bruno Correia 🔗 |
Fri 12:50 p.m. - 12:55 p.m.
|
Multi-Segment Preserving Sampling for Deep Manifold Sampler
(
Spotlight
)
>
link
SlidesLive Video |
Dan Berenberg · Jae Hyeon Lee · Simon Kelow · Ji Park · Andrew Watkins · Richard Bonneau · Vladimir Gligorijevic · Stephen Ra · Kyunghyun Cho 🔗 |
Fri 12:55 p.m. - 1:00 p.m.
|
Regression Transformer: Concurrent Conditional Generation and Regression by Blending Numerical and Textual Tokens
(
Spotlight
)
>
link
SlidesLive Video |
Jannis Born · Matteo Manica 🔗 |
Fri 1:00 p.m. - 1:40 p.m.
|
GeneDisco Challenge
(
Discussion
)
>
|
🔗 |
Fri 1:40 p.m. - 2:25 p.m.
|
Poster Session (Part 2) ( Poster Session ) > link | 🔗 |
Fri 2:25 p.m. - 2:30 p.m.
|
Closing remarks
(
Intro
)
>
|
🔗 |
-
|
Auto-regressive WaveNet Variational Autoencoders for Alignment-free Generative Protein Design and Fitness Prediction ( Poster ) > link | Niksa Praljak · Andrew Ferguson 🔗 |
-
|
Learning multi-scale functional representations of proteins from single-cell microscopy data ( Poster ) > link | Anastasia Razdaibiedina · Alexander Brechalov 🔗 |
-
|
Variational Interpretable Deep Canonical Correlation Analysis ( Poster ) > link | Lin Qiu · Lynn Lin · Vernon Chinchilli 🔗 |
-
|
Graph Anisotropic Diffusion for Molecules ( Poster ) > link | Ahmed Elhag · Gabriele Corso · Hannes Stärk · Michael Bronstein 🔗 |
-
|
SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching ( Poster ) > link | Scott Gigante · Varsha Raghavan · Amanda Robinson · Rob Barton · Adeeb Rahman · Drausin Wulsin · Jacques Banchereau · Noam Solomon · Luis Voloch · Fabian Theis 🔗 |
-
|
Evaluating Generalization in GFlowNets for Molecule Design ( Poster ) > link | Andrei Nica · Moksh Jain · Emmanuel Bengio · Cheng-Hao Liu · Maksym Korablyov · Michael Bronstein · Yoshua Bengio 🔗 |
-
|
Data-Driven Optimization for Protein Design: Workflows, Algorithms and Metrics ( Poster ) > link | Sathvik Kolli · Amy Lu · Xinyang Geng · Aviral Kumar · Sergey Levine 🔗 |
-
|
Fragment-based ligand generation guided by geometric deep learning on protein-ligand structures ( Poster ) > link | Alexander Powers · Helen Yu · Patricia Suriana · Ron Dror 🔗 |
-
|
Decoding Surface Fingerprints for Protein-Ligand Interactions ( Poster ) > link | Ilia Igashov · Arian Jamasb · Ahmed Sadek · Freyr Sverrisson · Arne Schneuing · Tom Blundell · Pietro Lio · Michael Bronstein · Bruno Correia 🔗 |
-
|
Torsional Diffusion for Molecular Conformer Generation
(
Poster
)
>
link
SlidesLive Video |
Bowen Jing · Gabriele Corso · Regina Barzilay · Tommi Jaakkola 🔗 |
-
|
Machine Learning to Hunt for Phage Proteins to Catch Klebsiella ( Poster ) > link | George Wright · Fayyaz ul Amir Minhas · Slawomir Michniewski · Eleanor Jameson 🔗 |
-
|
Physics-informed deep neural network for rigid-body protein docking ( Poster ) > link | Freyr Sverrisson · Jean Feydy · Joshua Southern · Michael Bronstein · Bruno Correia 🔗 |
-
|
High-Content Similarity-Based Virtual Screening Using a Distance Aware Transformer Model ( Poster ) > link | Manuel Sellner · Amr Mahmoud · Markus Lill 🔗 |
-
|
De novo design of protein target specific scaffold-based Inhibitors via Reinforcement Learning ( Poster ) > link | Andrew McNaughton · Carter Knutson · Mridula Bontha · Jenna Pope · Neeraj Kumar 🔗 |
-
|
Partial Product Aware Machine Learning on DNA-Encoded Libraries ( Poster ) > link | Polina Binder · Meghan Lawler · LaShadric Grady · Neil Carlson · Svetlana Belyanskaya · Joe Franklin · Nicolas Tilmans · Henri Palacci 🔗 |
-
|
DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction ( Poster ) > link | Rıza Özçelik · Alperen Bağ · Berk Atıl · Arzucan Özgür · Elif Ozkirimli 🔗 |
-
|
Improving the assessment of deep learning models in the context of drug-target interaction prediction ( Poster ) > link | Mirko Torrisi · Antonio De la Vega de Leon · Guillermo Climent · Remco Loos · Alejandro Panjkovich 🔗 |
-
|
Deep Learning Model for Flexible and Efficient Protein-Ligand Docking ( Poster ) > link | Matthew Masters · Amr Mahmoud · Yao Wei · Markus Lill 🔗 |
-
|
Predicting single-cell perturbation responses for unseen drugs
(
Poster
)
>
link
SlidesLive Video |
Leon Hetzel · Simon Boehm · Niki Kilbertus · Stephan Günnemann · Mohammad Lotfollahi · Fabian Theis 🔗 |
-
|
Contrastive learning of image- and structure-based representations in drug discovery ( Poster ) > link | Ana Sanchez-Fernandez · Elisabeth Rumetshofer · Sepp Hochreiter · Günter Klambauer 🔗 |
-
|
The Rosenbluth sampling Calculation of Hydrophobic-Polar Model
(
Poster
)
>
link
SlidesLive Video |
Marcin Wierzbinski · Alessandro Crimi 🔗 |
-
|
GRPE: Relative Positional Encoding for Graph Transformer ( Poster ) > link | Wonpyo Park · Woong-Gi Chang · Donggeon Lee · Juntae Kim · seung-won hwang 🔗 |
-
|
Multi-Segment Preserving Sampling for Deep Manifold Sampler
(
Poster
)
>
link
SlidesLive Video |
Dan Berenberg · Jae Hyeon Lee · Simon Kelow · Ji Park · Andrew Watkins · Richard Bonneau · Vladimir Gligorijevic · Stephen Ra · Kyunghyun Cho 🔗 |
-
|
MetaDTA: Meta-learning-based drug-target binding affinity prediction ( Poster ) > link | Eunjoo Lee · Jiho Yoo · Huisun Lee · Seunghoon Hong 🔗 |
-
|
An evaluation framework for the objective functions of de novo drug design benchmarks ( Poster ) > link | Austin Tripp · Wenlin Chen · José Miguel Hernández Lobato 🔗 |
-
|
PREDICTION OF MOLECULAR FIELD POINTS USING SE(3)-TRANSFORMER MODEL ( Poster ) > link | Florian Hinz · Amr Mahmoud · Markus Lill 🔗 |
-
|
Convolutions are competitive with transformers for protein sequence pretraining ( Poster ) > link | Kevin K Yang · Alex Lu · Nicolo Fusi 🔗 |
-
|
Glolloc: Mixture of Global and Local Experts for Molecular Activity Prediction
(
Poster
)
>
link
SlidesLive Video |
Héléna A. Gaspar · Matthew Seddon 🔗 |
-
|
Benchmarking Uncertainty Quantification for Protein Engineering ( Poster ) > link | Kevin P Greenman · Ava Soleimany · Kevin K Yang 🔗 |
-
|
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction ( Poster ) > link | Hannes Stärk · Octavian Ganea · Lagnajit Pattanaik · Regina Barzilay · Tommi Jaakkola 🔗 |
-
|
ChemSpacE: Toward Steerable and Interpretable Chemical Space Exploration ( Poster ) > link | Yuanqi Du · Xian Liu · Shengchao Liu · Jieyu Zhang · Bolei Zhou 🔗 |
-
|
Deep sharpening of topological features for de novo protein design
(
Poster
)
>
link
SlidesLive Video |
Zander Harteveld · Joshua Southern · Michaël Defferrard · Andreas Loukas · Pierre Vandergheynst · Micheal Bronstein · Bruno Correia 🔗 |
-
|
Isolating salient variations of interest in single-cell transcriptomic data with contrastiveVI ( Poster ) > link | Ethan Weinberger · Chris Lin · Su-In Lee 🔗 |
-
|
Regression Transformer: Concurrent Conditional Generation and Regression by Blending Numerical and Textual Tokens ( Poster ) > link | Jannis Born · Matteo Manica 🔗 |