Workshop
Generative and Experimental Perspectives for Biomolecular Design
Chenghao Liu · Jarrid Rector-Brooks · Jason Yim · Soojung Yang · Sidney Lisanza · Francesca-Zhoufan Li · Pranam Chatterjee · Tommi Jaakkola · Regina Barzilay · David Baker · Frances Arnold · Yoshua Bengio
Halle A 2
Sat 11 May, midnight PDT
Biomolecular design, through artificial engineering of proteins, ligands, and nucleic acids, holds immense promise in addressing pressing medical, industrial, and environmental challenges. While generative machine learning has shown significant potential in this area, a palpable disconnect exists with experimental biology: many ML research efforts prioritize static benchmark performance, potentially sidelining impactful biological applications. This workshop seeks to bridge this gap by bringing computationalists and experimentalists together, catalyzing a deeper interdisciplinary discourse. Together, we will explore the strengths and challenges of generative ML in biology, experimental integration of generative ML, and pinpoint biological problems ready for ML. To attract high-quality and diverse research, we partnered with Cell Systems for a special collection, and we created dedicated tracks for in-silico ML research and hybrid ML-experimental biology research. Our lineup features renowned scientists as speakers and emerging leaders as panelists, encapsulating a spectrum from high-throughput experimentation and computational biology to generative ML. With a diverse organizing team and backed by industry sponsors, we dedicate the workshop to pushing the boundaries of ML's role in biology.
Schedule
Fri 11:50 p.m. - 12:00 a.m.
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Opening remarks
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Sat 12:00 a.m. - 12:30 a.m.
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Bruno Correia
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SlidesLive Video |
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Sat 12:30 a.m. - 1:00 a.m.
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Andreea Gane
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Talk
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SlidesLive Video |
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Sat 1:00 a.m. - 1:15 a.m.
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Intermission
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Sat 1:15 a.m. - 1:25 a.m.
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PROflow: An iterative refinement model for PROTAC-induced structure prediction
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Oral
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SlidesLive Video |
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Sat 1:25 a.m. - 1:35 a.m.
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A New Ultra-High-Throughput Assay for Measuring Protein Fitness
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Oral
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SlidesLive Video |
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Sat 1:35 a.m. - 1:45 a.m.
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Towards Generative RNA Design With Tertiary Interaactions
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Oral
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SlidesLive Video |
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Sat 1:45 a.m. - 2:00 a.m.
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AI Safety Institute
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Talk
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SlidesLive Video |
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Sat 2:00 a.m. - 3:00 a.m.
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Poster session 1
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Sat 3:00 a.m. - 4:00 a.m.
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On-site Lunch (catering provided)
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Sat 4:00 a.m. - 4:30 a.m.
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Alex Rives
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SlidesLive Video |
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Sat 4:30 a.m. - 4:45 a.m.
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Intermission
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Sat 4:45 a.m. - 5:30 a.m.
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Panel discussion
SlidesLive Video |
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Sat 5:30 a.m. - 6:00 a.m.
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Debora Marks
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Talk
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Sat 6:00 a.m. - 6:10 a.m.
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Antibody Design with Constrained Bayesian Optimization
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Oral
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SlidesLive Video |
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Sat 6:10 a.m. - 6:20 a.m.
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Generative Active Learning for the Search of Small-molecule Protein Binders
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Oral
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SlidesLive Video |
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Sat 6:20 a.m. - 6:25 a.m.
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The Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design
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Oral
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SlidesLive Video |
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Sat 6:30 a.m. - 6:45 a.m.
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Sponsor presentations
SlidesLive Video |
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Sat 6:45 a.m. - 7:45 a.m.
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Poster session 2
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Posters
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Sat 7:45 a.m. - 8:00 a.m.
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Closing remarks
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Closing
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SlidesLive Video |
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Few-Shot prediction of the experimental functional measurements for proteins with single point mutations ( Poster ) > link | Michael Bikman · Rachel Kolodny · Margarita Osadchy 🔗 |
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Accurate predictions of enzymatic biochemistry as an enabler for generation of de-novo sequences ( Poster ) > link | Raman Samusevich · Petr Kouba · Roman Bushuiev · Anton Bushuiev · Josef Sivic · Tomas Pluskal 🔗 |
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Epitope-specific antibody design using diffusion models on the latent space of ESM embeddings ( Poster ) > link | Tomer Cohen · Dina Schneidman 🔗 |
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The Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design ( Oral ) > link | Chase Armer · Henning Redestig · Erika DeBenedictis · Hassan Kane · Dana Cortade · Peter Kelly · Adil Yusuf · TJ Brunette 🔗 |
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Towards Generative RNA Design with Tertiary Interactions ( Oral ) > link | Sharat Patil · Frederic Runge · Jörg Franke · Frank Hutter 🔗 |
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PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling ( Poster ) > link | Tianlai Chen · Sarah Pertsemlidis · Pranam Chatterjee 🔗 |
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DiffTopo: Fold exploration using coarse grained protein topology representations ( Poster ) > link | Yangyang Miao · Bruno Correia 🔗 |
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DiffPaSS – Differentiable and scalable pairing of biological sequences using soft scores ( Poster ) > link | Umberto Lupo · Damiano Sgarbossa · Martina Milighetti · Anne-Florence Bitbol 🔗 |
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Accelerating the Generation of Molecular Conformations with Progressive Distillation of Equivariant Latent Diffusion Models ( Poster ) > link | Romain Lacombe · Neal Vaidya 🔗 |
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Re-evaluating Retrosynthesis Algorithms with Syntheseus ( Poster ) > link | Krzysztof Maziarz · Austin Tripp · Guoqing Liu · Megan Stanley · Shufang Xie · Piotr Gaiński · Philipp Seidl · Marwin Segler 🔗 |
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SynFlowNet: Towards Molecule Design with Guaranteed Synthesis Pathways ( Poster ) > link | Miruna Cretu · Charles Harris · Julien Roy · Emmanuel Bengio · Pietro Lio 🔗 |
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PROTEIN FITNESS LANDSCAPE NAVIGATION IS BOOSTED VIA INCORPORATING EVOLUTIONARY INFORMATION INTO MACHINE LEARNING MODELS ( Poster ) > link | Mehrsa Mardikoraem · Daniel Woldring 🔗 |
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Contrastive RNA Representation Learning Through Maximizing Mutual Information Between Splice Isoforms ( Poster ) > link | Philip Fradkin · Ruian Shi · Keren Isaev · Caitlin Harrigan · Quaid Morris · BO WANG · Brendan Frey · Leo J Lee 🔗 |
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A proteome-scale masked language model for fast protein-protein interaction prediction ( Poster ) > link | Cyril Malbranke · Anne-Florence Bitbol 🔗 |
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Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders ( Poster ) > link | Allan Costa · Ilan Mitnikov · Mario Geiger · MANVITHA PONNAPATI · Tess Smidt · JOSEPH JACOBSON 🔗 |
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Fine-tuning Pocket-conditioned 3D Molecule Generation via Reinforcement Learning ( Poster ) > link | Daeseok Lee · Yongjun Cho 🔗 |
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Green fluorescent protein engineering with a biophysics-based protein language model ( Poster ) > link | Sam Gelman · Bryce Johnson · Chase Freschlin · Sameer D'Costa · Anthony Gitter · Philip Romero 🔗 |
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Programmable Protein Stabilization with Language Model-Derived Peptide Guides ( Poster ) > link | Lauren Hong · Tianzheng Ye · Tian Wang · Divya Srijay · Lin Zhao · Sophia Vincoff · Tianlai Chen · Matthew DeLisa · Pranam Chatterjee 🔗 |
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Protein language models are biased by unequal sequence sampling across the tree of life ( Poster ) > link | Frances Ding · Jacob Steinhardt 🔗 |
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How well do generative protein models generate? ( Poster ) > link | Han Spinner · Aaron Kollasch · Debora Marks 🔗 |
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Generative Active Learning for the Search of Small-molecule Protein Binders ( Oral ) > link |
34 presentersMaksym Korablyov · Chenghao Liu · Moksh Jain · Almer van der Sloot · Eric Jolicoeur · Andrei Nica · Emmanuel Bengio · Kostiantyn Lapchevskyi · Daniel St-Cyr · Doris Schuetz · Victor Butoi · Jarrid Rector-Brooks · Simon Blackburn · Leo Feng · Hadi Nekoei · Vijaya Sai Krishna Gottipati · Priyesh Vijayan · Prateek Gupta · Ladislav Rampášek · Sasikanth Avancha · Pierre-Luc Bacon · William Hamilton · Brooks Paige · Sanchit Misra · Stanislaw Jastrzebski · Bharat Kaul · Doina Precup · José Miguel Hernández Lobato · Marwin Segler · Michael Bronstein · Edward Ruediger · Anne Marinier · Mike Tyers · Yoshua Bengio |
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Demystify the Secret Function in Protein Sequence via Conditional Diffusion Models ( Poster ) > link | Yaoyao Xu · Xuxi Chen · Tong Wang · Huan He · Tianlong Chen · Manolis Kellis 🔗 |
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Development of A Molecular Exchange Mechanism-based Biomolecular Neural Network ( Poster ) > link | Muhtasim Ishmum Khan · Moshiur Rahman · Md. Shahriar Karim 🔗 |
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$\textit{In vitro}$ VALIDATED ANTIBODY DESIGN AGAINST MULTIPLE THERAPEUTIC ANTIGENS USING GENERATIVE INVERSE FOLDING ( Poster ) > link | Amir Shanehsazzadeh 🔗 |
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Equivariant Pretrained Transformer for Unified Geometric Learning on Multi-Domain 3D Molecules ( Poster ) > link | Rui Jiao · Xiangzhe Kong · Ziyang Yu · Wenbing Huang · Yang Liu 🔗 |
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A High-Throughput Human Display Screen to Identify Target-Specific Binder Proteins via Chimeric Antigen Receptors ( Poster ) > link | Lin Zhao · Aditya Mohan · Anoop Patel · Pranam Chatterjee 🔗 |
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PPI-Llama2: De Novo Generation of Binding Proteins Conditioned On Target Sequence Alone ( Poster ) > link | Yinuo Zhang · Phil He · Ashley Hsu · Sophia Vincoff · Pranam Chatterjee 🔗 |
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Active learning to discover pairwise genetic interactions via representation learning ( Poster ) > link | Moksh Jain · Alisandra Denton · Shawn Whitfield · Aniket Rajiv Didolkar · Berton Earnshaw · Jason Hartford 🔗 |
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Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design ( Poster ) > link | Andrew Campbell · Jason Yim · Regina Barzilay · Tom Rainforth · Tommi Jaakkola 🔗 |
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Diverse Hits in de Novo Molecule Design: A Diversity-based Comparison of Goal-directed Generators ( Poster ) > link | Philipp Renz · Sohvi Luukkonen · Günter Klambauer 🔗 |
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Evolution-Inspired Loss Functions for Protein Representation Learning ( Poster ) > link | Chengyue Gong · Adam Klivans · James Loy · Tianlong Chen · Qiang Liu · Daniel Diaz 🔗 |
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Unveiling the Entangled Landscape of Artificial Knotted Proteins ( Poster ) > link | Eva Klimentová · Petr Simecek 🔗 |
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On Recovering Higher-order Interactions from Protein Language Models ( Poster ) > link | Darin Tsui · Amirali Aghazadeh 🔗 |
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A New Ultra-High-Throughput Assay for Measuring Protein Fitness ( Oral ) > link | Vikram Sundar · Boqiang Tu · Lindsey Guan · Kevin Esvelt 🔗 |
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CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes ( Oral ) > link | Peter Mikhael · Itamar Chinn · Regina Barzilay 🔗 |
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GeoDirDock: Guiding Docking Along Geodesic Paths ( Poster ) > link | Raúl Miñán · Javier Sáenz · Alvaro Ciudad Serrano · Alexis Molina 🔗 |
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Dirichlet Flow Matching with Applications to DNA Sequence Design ( Poster ) > link | Hannes Stärk · Bowen Jing · Chenyu Wang · Gabriele Corso · Bonnie Berger · Regina Barzilay · Tommi Jaakkola 🔗 |
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Revealing data leakage in protein interaction benchmarks ( Poster ) > link | Anton Bushuiev · Roman Bushuiev · Jiri Sedlar · Tomas Pluskal · Jiri Damborsky · Stanislav Mazurenko · Josef Sivic 🔗 |
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Evaluating predictive patterns of antigen specific B cells by single cell transcriptome and antibody repertoire sequencing ( Poster ) > link | Lena Erlach · Raphael Kuhn · Andreas Agrafiotis · Danielle Shlesinger · Alexander Yermanos · Sai Reddy 🔗 |
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Structure-Informed Protein Language Model ( Poster ) > link | Zuobai Zhang · Jiarui Lu · Vijil Chenthamarakshan · Aurelie Lozano · Payel Das · Jian Tang 🔗 |
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Future-proof vaccine design with a generative model of antibody cross-reactivity ( Poster ) > link | Sarah Gurev · Noor Youssef · Hannah Pierce-Hoffman · Debora Marks 🔗 |
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Generative Humanization for Therapeutic Antibodies ( Poster ) > link | Cade Gordon · Aniruddh Raghu · Peyton Greenside · Hunter Elliott 🔗 |
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F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching ( Poster ) > link | Shaoning Li · Yusong Wang · Mingyu Li · Bin Shao · Nanning Zheng · Zhang Jian · Jian Tang 🔗 |
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Multi-objective generative AI for designing novel brain-targeting small molecules ( Poster ) > link | Ayush Noori · Iñaki Arango · William Byrd · Nada Amin 🔗 |
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Equivariant amortized inference of poses for cryo-EM ( Poster ) > link | Larissa de Ruijter · Gabriele Cesa 🔗 |
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Towards Structure-based Drug Design with Protein Flexibility ( Poster ) > link | Arne Schneuing · Ilia Igashov · Thomas Castiglione · Michael Bronstein · Bruno Correia 🔗 |
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Antibody Design with Constrained Bayesian Optimization ( Oral ) > link | Yimeng Zeng · Hunter Elliott · Phillip Maffettone · Peyton Greenside · Osbert Bastani · Jacob Gardner 🔗 |
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DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements ( Poster ) > link | Simon Senan 🔗 |
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RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets ( Poster ) > link | Piotr Gaiński · Michał Koziarski · Krzysztof Maziarz · Marwin Segler · Jacek Tabor · Marek Śmieja 🔗 |
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AceGen: A TorchRL-based toolkit for reinforcement learning in generative chemistry ( Poster ) > link |
13 presentersAlbert Bou · Morgan Thomas · Sebastian Dittert · Carles Ramírez · Maciej Majewski · Ye Wang · Shivam Patel · Gary Tresadern · Mazen Ahmad · Vincent Moens · Woody Sherman · simone sciabola · Gianni De Fabritiis |
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Low N, High N Protein Engineering ( Poster ) > link | Gabriel Abrahams · Carlos Outeiral · Harrison Steel · Charlotte Deane 🔗 |
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How to Go With the Flow: an Analysis of Flow Matching Molecular Docking Performance With Priors of Varying Information Content ( Poster ) > link | Dina A. Sharon · Yining Huang · Motolani Oyewole · Sammy Mustafa 🔗 |
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Preference optimization of protein language models as a multi-objective binder design paradigm ( Poster ) > link | Pouria Mistani · Venkatesh Mysore 🔗 |
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AI-accelerated biocatalyst engineering by rapid microfluidic sequence-function mapping ( Poster ) > link |
15 presentersMaximilian Gantz · Simon Mathis · Friederike E.H. Nintzel · Paul Zurek · Tanja Knaus · Elie Patel · Daniel Boros · Friedrich-Maximilian Weberling · Elliot J. Medcalf · Jacob Moss · Michael Herger · Tomasz Kaminski · Francesco Mutti · Pietro Lio · Florian Hollfelder |
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p-IgGen: A Paired Antibody Generative Language Model ( Poster ) > link | Oliver Turnbull · Dino Oglic · Charlotte Deane 🔗 |
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Diffusion Generative Models for Molecule Optimization ( Poster ) > link | Xiaochuan Zha · xinyangao · Wenxue Hui · Zonghua Luo 🔗 |
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Protein binding affinity prediction under multiple substitutions applying eGNNs on residue and atomic graphs combined with language model information: eGRAL ( Poster ) > link | Arturo Fiorellini-Bernardis · Sebastien Boyer · Christoph Brunken · Bakary Diallo · Karim Beguir · Nicolas Carranza · Oliver Bent 🔗 |
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Graph-Based Forward Synthesis Prediction of Biocatalyzed Reactions ( Poster ) > link | Peter Mikhael · Itamar Chinn · Regina Barzilay 🔗 |
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CLASSIC: A platform for high throughput mapping of genetic design spaces in mammalian cells and ML guided prediction of gene circuit behavior ( Poster ) > link | Kshitij Rai · Ronan O'Connell · Pankaj Mehta · Ankit B Patel · Caleb Bashor 🔗 |
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Evolution Guided Generative Flow Networks ( Poster ) > link | Zarif Ikram · Ling Pan · Dianbo Liu 🔗 |
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Improved motif-scaffolding with SE(3) flow matching ( Poster ) > link |
12 presentersJason Yim · Andrew Campbell · Emile Mathieu · Andrew Y. K. Foong · Michael Gastegger · Jose Jimenez-Luna · Sarah Lewis · Victor Garcia Satorras · Bas Veeling · Frank Noe · Regina Barzilay · Tommi Jaakkola |
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PROflow: An iterative refinement model for PROTAC-induced structure prediction ( Oral ) > link | Bo Qiang · Wenxian Shi · Yuxuan Song · Menghua (Rachel) Wu 🔗 |
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Model-based reinforcement learning for protein backbone design ( Poster ) > link | Frédéric Renard · Cyprien Courtot · Alfredo Reichlin · Oliver Bent 🔗 |
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COMPUTATIONAL DESIGN OF NOVEL AMPAR AND NMDAR PEPTIDE MODULATORS. ( Poster ) > link | Khondamir Rustamov · Kamila Nebesnaya · Artyom Baev 🔗 |
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Physics-informed geometric regularization of heterogeneous reconstructions in cryo-EM ( Poster ) > link | Victor Prins · Willem Diepeveen · Erik Bekkers · Ozan Öktem 🔗 |
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RNAFlow: RNA Structure & Sequence Co-Design via Inverse Folding-Based Flow Matching ( Poster ) > link | Divya Nori · Wengong Jin 🔗 |
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Antibody sequence optimization with gradient-guided discrete walk-jump sampling ( Poster ) > link | Zarif Ikram · Dianbo Liu · M Saifur Rahman 🔗 |
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Machine learning of force fields towards molecular dynamics simulations of proteins at DFT accuracy ( Poster ) > link | Christoph Brunken · Sebastien Boyer · Mustafa Omar · Bakary Diallo · Karim Beguir · Nicolas Carranza · Oliver Bent 🔗 |
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Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations ( Poster ) > link | Jiarui Lu · Zuobai Zhang · Bozitao Zhong · Chence Shi · Jian Tang 🔗 |
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Pairing interacting protein sequences using masked language modeling ( Poster ) > link | Damiano Sgarbossa · Umberto Lupo · Anne-Florence Bitbol 🔗 |
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EvoSBDD: Latent Evolution for Accurate and Efficient Structure-Based Drug Design ( Poster ) > link | Danny Reidenbach 🔗 |
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Towards DNA-Encoded Library Generation with GFlowNets ( Poster ) > link | Michał Koziarski · Mohammed Abukalam · Vedant Shah · Louis Vaillancourt · Doris Schuetz · Moksh Jain · Almer van der Sloot · Mathieu Bourgey · Anne Marinier · Yoshua Bengio 🔗 |
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DyMol: Dynamic Many-Objective Molecular Optimization with Objective Decomposition and Progressive Optimization ( Poster ) > link | Dong-Hee Shin · Young-Han Son · Deok-Joong Lee · JiWung Han · Tae-Eui Kam 🔗 |
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3D Inverse Design of RNA using Deep Learning ( Poster ) > link | Christian Choe · Gina EL Nesr · Ana Espeleta · Rhiju Das · Possu Huang 🔗 |
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RNA-Protein Interaction Classification via Sequence Embeddings ( Poster ) > link | Dominika Matus · Frederic Runge · Jörg Franke · Lars Gerne · Michael Uhl · Frank Hutter · Rolf Backofen 🔗 |
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Lucy Colwell
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