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Workshop Mon, Apr 27, 2026 • 5:00 AM – 1:00 PM PDT 203 C

Learning Meaningful Representations of Life (LMRL) Workshop @ ICLR 2026

Kristina Ulicna ⋅ Rebecca Boiarsky ⋅ Till Richter ⋅ Soo-Jeong Kim ⋅ Lazar Atanackovic ⋅ Jason Hartford ⋅ Romain Lopez ⋅ Thouis Jones
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Abstract

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Schedule

Timezone: America/Los_Angeles
5:00 AM
Opening remarks
Kristina Ulicna
5:10 AM
Keynote #1 + Q&A
Alexander Tong
5:45 AM
Spotlights #1
Kevin Michalewicz ⋅ Hugh Yeh ⋅ Jiarui Li ⋅ Jay Shenoy ⋅ Julien Duquesne
7:35 AM
Panel Discussion
Daniel Burkhardt ⋅ Kristina Ulicna
8:50 AM
Lunch Break
10:00 AM
Keynote #3 + Q&A
10:35 AM
Oral #1
Ivan Svatko
10:48 AM
Oral #2
Alon Hacohen
12:00 PM
Oral #3
Yifan Xu
12:13 PM
Oral #4
Janani Durairaj
12:25 PM
Keynote #4 + Q&A
Tommaso Biancalani
1:00 PM
Closing Remarks
Kristina Ulicna
Wasserstein Motifs: Non-deterministic Alignment of Ecological Networks
Yifan Xu ⋅ Carlos Taveras ⋅ Lydia Beaudrot ⋅ Cesar A Uribe
Exploring Perturbation Effects on Transcriptional Dynamics with ContrastiveBiVI
Ashenafee Mandefro ⋅ Ethan Weinberger ⋅ Addie Woicik ⋅ Tal Ashuach
Physics-Constrained Correlation-Aware Attention for Collective Cell Dynamics
Dmitriy Stanislavchuk-Abovsky ⋅ Andrei Zakharov ⋅ Ilya Makarov
A Transcriptomic Benchmark for Foundation Models in Immunology and Inflammation Drug Development
Karim Kanbi ⋅ Yannis Cattan ⋅ Pierre Marschall ⋅ Matthew Corney ⋅ Aziz Fouché ⋅ Vincent Bouget ⋅ Julien Duquesne
TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
Hanqun Cao ⋅ Aastha Pal ⋅ Sophia Tang ⋅ Yinuo Zhang ⋅ Jingjie Zhang ⋅ Pheng-Ann Heng ⋅ Pranam Chatterjee
Antibody design with steerable discrete diffusion
Hugh Yeh ⋅ Niksa Praljak ⋅ Zhijie Chen ⋅ Thomas Walsh ⋅ Juan Mendoza ⋅ Jun Huang ⋅ Andrew Ferguson
Converting diffusions to flows accelerates sampling and suggests over-conditioning of co-folding models on sequence
Nele Quast ⋅ Niklas Abraham ⋅ Aaron Schöne ⋅ Fergus Imrie ⋅ Matthew Raybould ⋅ Yee Whye Teh ⋅ Charlotte Deane
ALPHASURF: ON-THE-FLY SURFACE COMPUTATIONS FOR PROTEIN REPRESENTATION LEARNING
Victor Gertner ⋅ Frédéric Cazals ⋅ Vincent Mallet
Learning image representation for limited cryo-EM data
Radosław Kuczbański ⋅ Wojciech Kozłowski ⋅ Lukas Frey ⋅ Konrad Karanowski ⋅ Mateusz Grzesiuk ⋅ Andrzej Rzepiela ⋅ Maciej Zieba
Tracing Pharmacological Knowledge in Large Language Models
Basil Khwaja ⋅ Dylan Chen ⋅ Guntas Toor ⋅ Anastasiya Kuznetsova
mRNABench: A curated benchmark for mature mRNA property and function prediction
Ruian Shi ⋅ Taykhoom Dalal ⋅ Philip Fradkin ⋅ Divya Koyyalagunta ⋅ Simran Chhabria ⋅ Andrew Jung ⋅ Cyrus Tam ⋅ Defne Ceyhan ⋅ Jessica Lin ⋅ Kaitlin Laverty ⋅ Ilyes Baali ⋅ BO WANG ⋅ Quaid Morris
Agentic orchestration of drug discovery ML tools under partial observability
Sara Masarone ⋅ Katie Victoria Beckwith ⋅ Matthew Mason ⋅ Thomas Clelford ⋅ Layla Hosseini-Gerami
Entropy, Disagreement, and the Limits of Foundation Models in Genomics
Maxime Rochkoulets ⋅ Lovro Vrček ⋅ Mile Sikic
Interpretable AI Reasoning for the Identification of Vibrational Spectroscopic Markers of Acetaminophen Impurities
Kaio dos Santos Soares ⋅ Ludmilla da Silva Augusto ⋅ Roner da Costa ⋅ Eveline Bezerra
Generative Modeling of Protein Conformational Ensembles With Cryo-EM Density Map Diffusion
Jay Shenoy ⋅ Axel Levy ⋅ Miro Astore ⋅ FREDERIC POITEVIN ⋅ Sonya Hanson ⋅ Gordon Wetzstein
TCR-EML: Explainable Model Layers for TCR-pMHC Prediction
Jiarui Li ⋅ Zixiang Yin ⋅ Zhengming Ding ⋅ Samuel Landry ⋅ Ramgopal Mettu
A Hierarchical Surface Graph Framework for Protein–Protein Binding Affinity Prediction
Sharmi Banerjee ⋅ Mostafa Karimi ⋅ Sukanya Sasmal ⋅ Jonah Noh ⋅ Pete Bowry ⋅ Tommi Jaakkola ⋅ Bella Dubrov ⋅ Shang Shang
AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance
Tong Chen ⋅ Yinuo Zhang ⋅ Sophia Vincoff ⋅ Pranam Chatterjee
On the role of drug representations for single-cell perturbation modeling
Marco Pegoraro ⋅ Sanketh Vedula ⋅ Lion Halika ⋅ Michael Danziger ⋅ Alexander Bronstein ⋅ Michal Rosen-Zvi
Learning Joint Morpho-Molecular Tissue Representations with a Multimodal Transformer
Adriano Martinelli ⋅ Bernd Illing ⋅ Isinsu Katircioglu ⋅ Alice Driessen ⋅ Fei Tang ⋅ Robert Berke ⋅ Raphael Gottardo ⋅ Marianna Rapsomaniki
PepRePs: Peptide-Retargeted Phosphatases via Generative Language Models
Lauren Hong ⋅ Tai-Chen Ho ⋅ Yi-Shiuan Tseng ⋅ Sophia Vincoff ⋅ Tong Chen ⋅ Po-Han Chen ⋅ Pranam Chatterjee
Intermediate Layers Encode Optimal Biological Representations in Single-Cell Foundation Models
Vincenzo Civale ⋅ Roberto Semeraro ⋅ Andrew Bagdanov ⋅ Alberto Magi
What information is preserved in latent cell embeddings? A Benchmark for Single-Cell Reconstruction
Xiaotong Fu ⋅ Dominik Klein ⋅ Alessandro Palma ⋅ Egor Antipov ⋅ Alejandro Tejada Lapuerta ⋅ Fabian Theis
Rewriting protein alphabets with language models
Lorenzo Pantolini ⋅ Gabriel Studer ⋅ Laura Engist ⋅ Ieva Pudžiuvelytė ⋅ Florian Pommerening ⋅ Andrew Waterhouse ⋅ Stefan Bienert ⋅ Gerardo Tauriello ⋅ Martin Steinegger ⋅ Torsten Schwede ⋅ Janani Durairaj
A Comprehensive Benchmark of Batch Integration Methods for Spatial Transcriptomics Using a Large-Scale Cancer Atlas
Liam Ludington ⋅ Xavier Sécheresse ⋅ Khalil Ouardini ⋅ Regis Loeb ⋅ vincent cabeli ⋅ Omar Darwiche Domingues ⋅ Arthur Pignet
Generating a Novel Dataset for Mechanisms of Drug-Induced Toxicity using LLM-supported tools
Sara Masarone ⋅ Alex Beeson ⋅ Katie Victoria Beckwith ⋅ Matthew Mason ⋅ Thomas Clelford ⋅ Arran Willmott ⋅ Giovanni Montana ⋅ Layla Hosseini-Gerami
EVA-RNA: A Scaling Cross-Species Transcriptomic Foundation Models for Immunology & Inflammation
Aziz Fouché ⋅ Yannis Cattan ⋅ Charlotte Claye ⋅ Matthew Corney ⋅ Pierre Marschall ⋅ Karim Kanbi ⋅ Julien Duquesne
Multimodal Manifold Learning for Clonally Constrained Trajectory Inference
Irene Bonafonte Pardàs ⋅ Myriam Lizotte ⋅ Guy Wolf ⋅ Benjamin Schubert
JUST ADD STRUCTURE: PROTEIN LANGUAGE MODELS COMBINED WITH STRUCTURAL EQUIVARIANCE EXCEL AT PROTEIN TASKS
Qurat ul ain Qurat ul ain ⋅ Charlotte Deane ⋅ Yee Whye Teh ⋅ Carlos Outeiral ⋅ Matteo Cagiada
Enigma: An Efficient Model for Deciphering Regulatory Genomics
Andrew Jung ⋅ Alice Gao ⋅ Vivian Chu ⋅ Leo J Lee ⋅ Brendan Frey
Beyond Motif Localization: Probing Rule-Level Signals in Synthetic Genomic Grammars
Lakshmanan Ramu ⋅ Rafael Peres Da Silva ⋅ Niranjan Nagarajan
Learning Continuous Morphological Trajectories via Latent Principal Curves
Sebastian Magana ⋅ Wenjun Zhao ⋅ Khanh Dao Duc
From Words to Amino Acids: Does the Curse of Depth Persist?
Aleena Siji ⋅ Amir Mohammad Karimi Mamaghan ⋅ Ferdinand Kapl ⋅ Tobias Höppe ⋅ Emmanouil Angelis ⋅ Andrea Dittadi ⋅ Maurice Brenner ⋅ Michael Heinzinger ⋅ Karl H. Johansson ⋅ Kaitlin Maile ⋅ Johannes von Oswald ⋅ Stefan Bauer
Mechanistic Interpretability of Antibody Language Models Using SAEs
Rebonto Haque ⋅ Oliver Turnbull ⋅ Anisha Parsan ⋅ Nithin Parsan ⋅ John J. Yang ⋅ Charlotte Deane
Learning Dynamic Protein Representations at Scale with Distograms
Nicolas Portal ⋅ Wissam Karroucha ⋅ Vincent Mallet ⋅ Massimiliano Bonomi
Efficient Cell Painting Image Representation Learning via Cross-Well Aligned Masked Siamese Network
PIN-JUI HUANG ⋅ Yu-Hsuan Liao ⋅ Soo Heon Kim ⋅ Noseong Park ⋅ Park Bae ⋅ Dongmyung Shin
Deep Learning for BioImaging: What Are We Learning?
Ivan Svatko ⋅ Maxime Sanchez ⋅ Ihab Bendidi ⋅ Gilles Cottrell ⋅ Auguste Genovesio
From Static to Dynamic: Inferring Protein Dynamics from Structure and Language Embeddings
Arthur Monnier ⋅ Pengkang Guo ⋅ Bruno Correia ⋅ Pierre Vandergheynst
Hiding in Plain Sight: Visible Gene Correlations Undermine Single-Cell Representations
Alon Hacohen ⋅ Joseph Bingham ⋅ Binyamin Perets ⋅ Dvir Aran
Reading TEA leaves for de novo protein design
Lorenzo Pantolini ⋅ Janani Durairaj
On The Robustness of scRNA-seq Foundation Models for Plants Under Cross-Domain Experimental Shift
Manuel Fernández Burda ⋅ Rodrigo Bonazzola ⋅ Georgina Stegmayer ⋅ Enzo Ferrante ⋅ Diego Milone
Incorporating contextual information into KGWAS for interpretable GWAS discovery
Cheng Jiang ⋅ Brady Ryan ⋅ Megan Crow ⋅ Kipper Fletez-Brant ⋅ Kashish Doshi ⋅ Sandra Melo ⋅ Kexin Huang ⋅ Burkhard Hoeckendorf ⋅ Heming Yao ⋅ David Richmond
Higher-order grammar representations for molecular generation and learning
Yiming Huang ⋅ Yujie Zeng ⋅ Vijay Prakash Dwivedi ⋅ Simone Foti ⋅ Jianmin Wang ⋅ Jure Leskovec ⋅ Tolga Birdal
Protein generation with embedding learning for motif diversification
Kevin Michalewicz ⋅ Chen Jin ⋅ Philip Teare ⋅ Tom Diethe ⋅ Mauricio Barahona ⋅ Barbara Bravi ⋅ Asher Mullokandov
Graph Set Transformer: Learning Graph Representations with Set Context
Daniel Probst ⋅ Jose Eduardo Escrig Molina
How Far Can LLMs Go On Cognitive Health Prediction? A Study On EMA Data
Sambit Mukherjee ⋅ Anthony Fu ⋅ Kai Zhao ⋅ Yang Ren ⋅ Dezhi Wu ⋅ Chih-Hsiang Yang
Geometric Fragility in Alzheimer's Disease: Probing the Loss of Hippocampal Hierarchical Abstraction via Contrastive Point Cloud Modeling
Yiquan Wang ⋅ Yuhan Chang ⋅ Jialin Zhang ⋅ Minnuo Cai ⋅ Jiayao Yan ⋅ Hongtian Zhao ⋅ Alzheimer's Initiative
pCoMole: Pareto-Constrained Molecule Editing with Discrete Flows
Tong Chen ⋅ Maximilian Holsman ⋅ Lin Zhao ⋅ Yinuo Zhang ⋅ Pranam Chatterjee
Towards Cross-Sample Alignment for Multi-Modal Representation Learning in Spatial Transcriptomics
Justina Dai ⋅ Kalin Nonchev ⋅ Viktor Koelzer ⋅ Gunnar Ratsch
Hierarchical Multi-Scale Modeling of Absolute Binding Affinity in Protein Complexes
Dongyun Kim ⋅ Soorin Yim ⋅ Sungjoon Park ⋅ Kiwoong Yoo ⋅ Kyungwook Lee ⋅ Doyeong Hwang ⋅ Soonyoung Lee ⋅ Jongseong Jang ⋅ Kiyoung Kim
scJEPA: Dual-Space Self-Supervised Learning for Single-Cell Representations
Yuyao Zhai ⋅ WEIXU WANG ⋅ Till Richter ⋅ Fabian Theis