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