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Workshop Mon, Apr 27, 2026 • 5:00 AM – 1:00 PM PDT 101 D

Machine Learning for Genomics Explorations (MLGenX)

Ehsan Hajiramezanali ⋅ Wei Qiu ⋅ Arman Hasanzadeh ⋅ Tommaso Biancalani ⋅ Mihaela van der Schaar ⋅ Fabian Theis ⋅ Aviv Regev
Project Page

Abstract

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Schedule

Timezone: America/Los_Angeles
5:00 AM
Opening Remark
Sepideh Maleki
6:00 AM
Coffee Break
7:30 AM
Lunch Break
9:45 AM
Panel Discussion - AI Agents in Biology and Drug Discovery
Nick Myerberg ⋅ Claudia Iriondo ⋅ Patrick Schwab ⋅ Sara-Jane Dunn ⋅ Gabriele Corso
1:15 PM
Closing Remarks
Hugues Van Assel
SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
Lawrence Phillips ⋅ Marc Boubnovski Martell ⋅ Aditya Misra ⋅ Josefa Stoisser ⋅ Cesar Prada-Medina ⋅ Rory Donovan-Maiye ⋅ Kaspar Märtens
DELBERT: Fingerprint Language Modeling For Generalizable Hit Discovery in DNA-Encoded Libraries
Arman Seyed-Ahmadi ⋅ Bing Hu ⋅ Armin Geraili ⋅ ⋅ Helen Chen ⋅ Shana Kelley ⋅ BO WANG
STAGE: A Foundation Model for Spatial Transcriptomics Analysis via Graph Embeddings with Hierarchical Prototypes
Zhengchao Luo ⋅ Peiting Shi ⋅ Qichen Sun ⋅ Li Yongge ⋅ Han Wen ⋅ Jinzhuo Wang
DREAM-DNA: Controlled Design via Reasoning and Matched-flows for DNA
Weimin Wu ⋅ JIUNHAU CHEN ⋅ Xuefeng Song ⋅ Jerry Yao-Chieh Hu ⋅ Han Liu
RAPTORGraph: Graph-Based Pathway Modeling for Causal Discovery in Single-Cell Perturbations
Yeremia Adhisantoso ⋅ Stephanie Kristin Schröder ⋅ Maximilian Greß ⋅ Mikel Hernaez ⋅ Jan Voges
Nexus: A Multi-Scale Simulator for Biological Control and Causal Discovery
Amogh Singh ⋅ Patrick Schwab ⋅ Kim Branson ⋅ Pietro Lio ⋅ Arash Mehrjou
Learning Adaptive Perturbation-Conditioned Contexts for Robust Transcriptional Response Prediction
Yinhua Piao ⋅ Hyomin Kim ⋅ Seonghwan Kim ⋅ Yunhak Oh ⋅ Junhyeok Jeon ⋅ Sang-Yeon Hwang ⋅ Jaechang Lim ⋅ Woo Youn Kim ⋅ Chanyoung Park ⋅ Sungsoo Ahn
Enigma: An Efficient Model for Deciphering Regulatory Genomics
Andrew Jung ⋅ Alice Gao ⋅ Vivian Chu ⋅ Leo J Lee ⋅ Brendan Frey
Adversarial Genomic Sequences Could Evade Biosecurity Screening
Jeyashree Krishnan ⋅ Ajay Mandyam Rangarajan ⋅ Andrea Loehr ⋅ Jason Hoelscher-Obermaier
MapPFN: Learning Causal Perturbation Maps in Context
Marvin Sextro ⋅ Weronika Kłos ⋅ Gabriel Dernbach
GenePT Revisited: Do Better Text Embeddings Make Better Gene Embeddings?
Jonathan Hedley ⋅ Philip Torr ⋅ Kaspar Märtens
SIMULTANEOUS LEARNING FROM BULK AND SINGLE-CELL EXPRESSION DATA WITH PERCEIVER-BASED MODELS
Rafal Powalski ⋅ Albert Roethel ⋅ Joanna Krawczyk ⋅ Przemysław Pietrzak ⋅ Łukasz Smoliński ⋅ Maciej Sypetkowski ⋅ Paweł Biernat ⋅ Dariusz Plewczyński ⋅ Tomasz Jetka
CAUSALPERT: GROUNDING LLM HYPOTHESES IN REGULATORY NETWORKS FOR GENE PERTURBATION PREDICTION
Marc Boubnovski Martell ⋅ Josefa Stoisser ⋅ Lawrence Phillips ⋅ Aditya Misra ⋅ Robert Kitchen ⋅ Jesper Ferkinghoff-Borg ⋅ Jialin Yu ⋅ Philip Torr ⋅ Kaspar Märtens
Reinforcement Learning for Black-Box Objectives in Logit-Based Protein Hallucination
Jacob Pettit ⋅ Steven Magana-Zook ⋅ Mikel Landajuela Larma
Modern Gene Finders: ab initio gene discovery benchmark with DNA language models
Aleksei Shmelev ⋅ Artem Shadskiy ⋅ Yuri Kuratov ⋅ Mikhail Burtsev ⋅ Olga Kardymon ⋅ Veniamin Fishman
A CONVERSATIONAL MULTI-AGENT AI FRAMEWORK FOR INTEGRATED MULTI-OMICS ANALYSIS AND BIOMEDICAL DISCOVERY
Pankaj Rajdeo ⋅ Shunya Asanuma ⋅ Michal Kouril ⋅ Peixin Lu ⋅ Jichao Chen ⋅ Aman Chadha ⋅ Surya Prasath ⋅ Bruce Aronow ⋅ Nathan Salomonis
PerturBERT: Learning Gene Co-Variation Embeddings from Perturbation Signatures
Artur Szałata ⋅ Russell Littman ⋅ Zoe Piran ⋅ Fabian Theis ⋅ David Richmond ⋅ Jan-Christian Huetter ⋅ Alexander Wu
Investigation of Scaling Laws for Encoder-Decoder Protein Language Models
Mufan Qiu ⋅ Sharmi Banerjee ⋅ Athanasios Nikolakopoulos ⋅ Gherman Uritskiy ⋅ HAMID MOHAMADI ⋅ Huda Khayrallah ⋅ Jonah Noh ⋅ Jiachen Li ⋅ Mostafa Karimi ⋅ Tianlong Chen ⋅ Bella Dubrov ⋅ Shang Shang
Learning Perturbation Effects Through Contrastive Alignment of Transcriptomics and Textual Embeddings
Tianyu Liu ⋅ Artur Szałata ⋅ Wenxin Long ⋅ Fabian Theis ⋅ Lingzhou Xue ⋅ Hongyu Zhao
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
Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models
Alena Aspidova ⋅ Yuri Kuratov ⋅ Artem Shadskiy ⋅ Mikhail Burtsev ⋅ Veniamin Fishman
Beyond Mean Shifts: Predicting Distributional Responses to Unseen Genetic Perturbations
Kalyan Ramakrishnan ⋅ Jonathan Hedley ⋅ Sisi Qu ⋅ Puneet Dokania ⋅ Philip Torr ⋅ Cesar Prada-Medina ⋅ Julien Fauqueur ⋅ Kaspar Märtens
Agentic Orchestration of Drug Discovery ML Tools Under Partial Observability
Sara Masarone ⋅ Katie Victoria Beckwith ⋅ Matthew Mason ⋅ Thomas Clelford ⋅ Arran Willmott ⋅ Layla Hosseini-Gerami
Genomic Next-Token Predictors are In-Context Learners
Nathan Breslow ⋅ Aayush Mishra ⋅ Mahler Revsine ⋅ Michael Schatz ⋅ Anqi Liu ⋅ Daniel Khashabi
Joint Variable Selection in Proteomics Survival Models
Jakub Bajzik ⋅ Al Depope ⋅ Yasaman Zolfimoselo ⋅ Alexander Sharipov ⋅ Holger Klein ⋅ Marco Mondelli ⋅ Matthew Robinson
BIO-Distiller: Boosting Supervised Baselines by Distilling Biological Foundation Models
Mohan Vamsi Nallapareddy ⋅ Maria Boulougouri ⋅ Pierre Vandergheynst ⋅ Francesco Craighero
GREmLN: A Cellular Graph Structure Aware Transcriptomics Foundation Model
Mingxuan Zhang ⋅ Vinay Swamy ⋅ Rowan Cassius ⋅ Léo Dupire ⋅ Charilaos Kanatsoulis ⋅ Evan Paull ⋅ Mohammed AlQuraishi ⋅ THEOFANIS KARALETSOS ⋅ Andrea Califano
From Edge Detection to Regulatory Logic Discovery: Residual Set Models for Exact Regulator Recovery in Gene Regulatory Networks
Siddhi Kanta Mishra ⋅ Maryam Rahimimovassagh ⋅ Niloofar Yousefi ⋅ Ivan Garibay
From k-mers to Genomic Foundation Models: Benchmarking COX1 Taxonomy under Extreme Class Imbalance
Luis Valenzuela ⋅ Sebastian Aguilera ⋅ Luis Martí ⋅ Nayat Sánchez-Pi
DNACHUNKER: Learnable Tokenization for DNA Language Models
Taewon Kim ⋅ Jihwan Shin ⋅ Hyomin Kim ⋅ Youngmok Jung ⋅ Jonghoon Lee ⋅ Won-Chul Lee ⋅ Insu Han ⋅ Sungsoo Ahn
PANGENSA: A graph-constrained machine learning framework for identifying antibiotic resistance determinants in bacterial pangenomes
Tamsin James ⋅ Jordan Meadows ⋅ Andreas Karwath ⋅ Nicole Wheeler ⋅ Peter Tino
DC-W2S: Dual-Consensus Weak-to-Strong Training for Reliable Process Reward Modeling in Biological Reasoning
Chi-Min Chan ⋅ Ehsan Hajiramezanali ⋅ Xiner Li ⋅ Edward De Brouwer ⋅ Carl Edwards ⋅ Wei Xue ⋅ Sirui Han ⋅ Yike Guo ⋅ Gabriele Scalia
Taking The Easy Way Out: When Single-Cell Foundation Models Learn Shortcuts Instead of Biology
Alon Hacohen ⋅ Joseph Bingham ⋅ Binyamin Perets ⋅ Dvir Aran
Generating and decoding methylated DNA with a Human Epigenetic Foundation Model
Pouya Niki ⋅ Christoforos Nalmpantis ⋅ Javkhlan-Ochir Ganbat ⋅ Donal Byrne ⋅ Husam Babikir ⋅ Anjeet Jhutty ⋅ Andrey Karailiev ⋅ Pooja Kathail ⋅ Luca Giacomoni ⋅ Francisco M Martín-Zamora ⋅ Netanel Loyfer ⋅ Khaled Saab ⋅ Hannah Madan ⋅ Jonathan Wan ⋅ Ravi Solanki
Discrete Diffusion for Single-Cell Gene Expression Modeling
Sanjukta Bhattacharya ⋅ Christian Gensbigler ⋅ Shaamil Karim Shaw Alem ⋅ Jon Lees
LENS: LLM-based Enrichment of Nested Subclusters
Alisha Saboowala ⋅ ⋅ Yogesh Pandit ⋅ David Richmond ⋅ Jan-Christian Huetter ⋅ Avtar Singh ⋅ Vladimir Ermakov
Beyond single-axis designs: multi-objective optimization for complex perturbation atlases
Zihe Zheng ⋅ Soroor Hediyeh-zadeh ⋅ Jenni Liu ⋅ Fabian Theis
LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses
Betty Xiong ⋅ Jan-Christian Huetter ⋅ Gabriele Scalia ⋅ Tommaso Biancalani ⋅ Sepideh Maleki
Rethinking Perturbation Prediction Baselines
Junwei Sun ⋅ Ouyang Zhu ⋅ Yiqun Chen
SQUINT: Spatial Quantization for Understanding and IN-painting Tissues
Arpit Merchant ⋅ Sebastian Birk ⋅ Amirhossein Vahidi ⋅ Daniyal Jafree ⋅ lloyd steele ⋅ April Foster ⋅ Vijaya Baskar ⋅ Muzlifah Haniffa ⋅ Mohammad Lotfollahi
Structure-aware graph learning predicts RNA editability across tissues and species
Zohar Rosenwasser-Maymon ⋅ Michael Levitt ⋅ Erez Levanon ⋅ Gal Oren
Exploring Perturbation Effects on Transcriptional Dynamics with ContrastiveBiVI
Ashenafee Mandefro ⋅ Ethan Weinberger ⋅ Addie Woicik ⋅ Tal Ashuach
Conditional Monte Carlo Tree Diffusion for Designing Cell-Type-Specific and Biologically Faithful Regulatory DNA
Animesh Awasthi ⋅ Raphael Bednarsky ⋅ Moritz Schaefer ⋅ Christoph Bock
Ancestry Inference with GNNs on IBD Graphs for Genetically Similar Populations
Aleksei Shmelev ⋅ Nikita Chervov ⋅ Dmitriy Glyzin ⋅ Valery Ilinsky ⋅ Alexander Rakitko ⋅ Vladimir Shchur
Single-Cell Concept Bottleneck Generative Models for Interpretable and Controllable Cellular Editing
Alma Andersson ⋅ Aya Ismail ⋅ Edward De Brouwer ⋅ Doron Haviv ⋅ Tommaso Biancalani ⋅ Kyunghyun Cho ⋅ Gabriele Scalia ⋅ Aicha BenTaieb ⋅ Hector Corrada Bravo