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Workshop

Machine Learning for Genomics Explorations (MLGenX)

Ehsan Hajiramezanali ⋅ Aviv Regev ⋅ Arman Hasanzadeh ⋅ Mengdi Wang ⋅ Fabian Theis ⋅ Sara Mostafavi ⋅ Tommaso Biancalani

Abstract

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Schedule

Timezone: America/Los_Angeles
6:00 PM
Opening Remark
Edward De Brouwer
6:15 PM
Test-Time View Selection for Multi-Modal Decision Making
Eeshaan Jain ⋅ Johann Wenckstern
7:00 PM
Coffee Break
8:05 PM
LangPert: LLM-Driven Contextual Synthesis for Unseen Perturbation Prediction
Kaspar Märtens ⋅ Marc Boubnovski Martell
8:30 PM
Lunch Break
10:00 PM
Invited Talk II - Jure Leskovec
Jure Leskovec
10:45 PM
Panel Discussion - AI Agents in Biology and Drug Discovery
Gabriele Scalia ⋅ Limsoon Wong ⋅ Aya Ismail ⋅ Daniel Burkhardt ⋅ Jan-Christian Huetter
12:00 AM
Coffee Break
2:25 AM
Closing Remarks
Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond
Dai Shi ⋅ Kuan Yan ⋅ Lequan Lin ⋅ Yue Zeng ⋅ Ting Zhang ⋅ Jialing Zhang ⋅ Matsypura Dmytro ⋅ Mark Gillies ⋅ Ling Zhu ⋅ Junbin Gao
Detecting cell level transcriptomic changes of Perturb-seq using Contrastive Fine-tuning of Single-Cell Foundation Models
Millie (Wenmin) Zhao ⋅ Ana Solaguren-Beascoa Negre ⋅ Grant Neilson ⋅ Regina Reynolds ⋅ Louwai Muhammed ⋅ Liisi Laaniste ⋅ Sera Aylin Cakiroglu
Learning Representations of Instruments for Partial Identification of Treatment Effects
Jonas Schweisthal ⋅ Dennis Frauen ⋅ Maresa Schröder ⋅ Konstantin Hess ⋅ Niki Kilbertus ⋅ Stefan Feuerriegel
Capturing functional context of genetic pathways through hyperedge disentanglement
Yoonho Lee ⋅ Junseok Lee ⋅ Sangwoo Seo ⋅ Sungwon Kim ⋅ Yeongmin Kim ⋅ Chanyoung Park
GENATATOR: de novo Gene Annotation With DNA Language Model
Aleksei Shmelev ⋅ Artem Shadskiy ⋅ Yuri Kuratov ⋅ Mikhail Burtsev ⋅ Olga Kardymon ⋅ Veniamin Fishman
When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes
Marina Popova ⋅ Iaroslav Chelombitko ⋅ Aleksey Komissarov
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
Yijia Xiao ⋅ Edward Sun ⋅ Yiqiao Jin ⋅ Qifan Wang ⋅ Wei Wang
Sampling Protein Language Models for Functional Protein Design
Jeremie Theddy Darmawan ⋅ Yarin Gal ⋅ Pascal Notin
ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings
Abhishek Sharma ⋅ Lin Yang ⋅ Cory McLean ⋅ Justin Cosentino ⋅ Farhad Hormozdiari
Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics
Yuning You ⋅ Zitong Jerry Wang ⋅ Kevin Fleisher ⋅ Rex Liu ⋅ Matt Thomson
ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation
Yuxuan Song ⋅ Zhe Zhang ⋅ Yu Pei ⋅ Jingjing Gong ⋅ Mingxuan Wang ⋅ Hao Zhou ⋅ Jingjing Liu ⋅ Wei-Ying Ma
Large Language Models for Zero-shot Inference of Causal Structures in Biology
Izzy Newsham ⋅ Luka Kovacevic ⋅ Richard Moulange ⋅ Nan Rosemary Ke ⋅ Sach Mukherjee
Supervised Contrastive Block Disentanglement
Taro Makino ⋅ Ji Won Park ⋅ Natasa Tagasovska ⋅ TAKAMASA KUDO ⋅ Paula Coelho ⋅ Heming Yao ⋅ Jan-Christian Huetter ⋅ Ana Leote ⋅ Burkhard Hoeckendorf ⋅ Stephen Ra ⋅ David Richmond ⋅ Kyunghyun Cho ⋅ Aviv Regev ⋅ Romain Lopez
LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs – Evaluation through Synthetic Data Generation
Tejumade Afonja ⋅ Ivaxi Sheth ⋅ Ruta Binkyte ⋅ Waqar Hanif ⋅ Shubhi Ambast ⋅ Charles Kaumbutha ⋅ Matthias Becker ⋅ Mario Fritz
Talk2Biomodels and Talk2KnowledgeGraph: AI agent-based application for prediction of patient biomarkers and reasoning over biomedical knowledge graphs
Gurdeep Singh ⋅ Lilija Wehling ⋅ Ahmad Wisnu Mulyadi ⋅ Rakesh Sreenath ⋅ Thomas Klabunde ⋅ Tommaso Andreani ⋅ Douglas McCloskey
Test-Time View Selection for Multi-Modal Decision Making
Eeshaan Jain ⋅ Johann Wenckstern ⋅ Benedikt von Querfurth ⋅ Charlotte Bunne
Uncertainty-aware genomic deep learning with knowledge distillation
Jessica Zhou ⋅ Kaeli Rizzo ⋅ Ziqi Tang ⋅ Peter Koo
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
Namkyeong Lee ⋅ Edward De Brouwer ⋅ Ehsan Hajiramezanali ⋅ Tommaso Biancalani ⋅ Chanyoung Park ⋅ Gabriele Scalia
EFFICIENT FINE-TUNING OF SINGLE-CELL FOUNDATION MODELS ENABLES ZERO-SHOT MOLECULAR PERTURBATION PREDICTION
Sepideh Maleki ⋅ Jan-Christian Huetter ⋅ David Richmond ⋅ Kangway Chuang ⋅ Gabriele Scalia ⋅ Tommaso Biancalani
LangPert: LLM-Driven Contextual Synthesis for Unseen Perturbation Prediction
Kaspar Märtens ⋅ Marc Boubnovski Martell ⋅ Cesar Prada-Medina ⋅ Rory Donovan-Maiye
Multiplexed DNA Assembly from Oligo-pools
Shaozhong Zou ⋅ zhien wu ⋅ Chunfu Xu
AI-Powered Virtual Tissues from Spatial Proteomics for Clinical Diagnostics and Biomedical Discovery
Johann Wenckstern ⋅ Eeshaan Jain ⋅ Kiril Vasilev ⋅ Matteo Pariset ⋅ Andreas Wicki ⋅ Gabriele Gut ⋅ Charlotte Bunne
A data-driven recommendation framework for genomic discovery
Ying Yang ⋅ Zhaoying Pan ⋅ Jinge Ma ⋅ Daniel Klionsky
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
Keyue Qiu ⋅ Yuxuan Song ⋅ Zhehuan Fan ⋅ Peidong Liu ⋅ Zhe Zhang ⋅ Mingyue Zheng ⋅ Hao Zhou ⋅ Wei-Ying Ma
Structure-based metabolite function prediction using graph neural networks
Tancredi Cogne ⋅ Mariam Ait Oumelloul ⋅ Ali Saadat ⋅ Janna Hastings ⋅ Jacques Fellay
Leveraging GPT Continual Fine-Tuning for Improved RNA Editing Site Prediction
Zohar Rosenwasser-Maymon ⋅ Erez Levanon ⋅ Michael Levitt ⋅ Gal Oren
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Monireh Safari ⋅ Pablo Millan Arias ⋅ Scott C Lowe ⋅ Lila Kari ⋅ Angel Chang ⋅ Graham W Taylor
Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization
Dongmin Bang ⋅ Inyoung Sung ⋅ Yinhua Piao ⋅ Sangseon Lee ⋅ Sun Kim
RNAGym: Benchmarks for RNA Fitness and Structure Prediction
Rohit Arora ⋅ Murphy Angelo ⋅ Christian Choe ⋅ Aaron Kollasch ⋅ Fiona Qu ⋅ Courtney Shearer ⋅ Ruben Weitzman ⋅ Artem Gazizov ⋅ Sarah Gurev ⋅ Erik Xie ⋅ Debora Marks ⋅ Pascal Notin
PIONEER: a virtual platform for iterative improvement of genomic deep learning
Alessandro Crnjar ⋅ John Desmarais ⋅ Justin Kinney ⋅ Peter Koo
NOLAN: SELF-SUPERVISED FRAMEWORK FOR MAPPING CONTINUOUS TISSUE ORGANIZATION
Artemii Bakulin ⋅ Nathan LEVY ⋅ Can Ergen ⋅ Jonas Maaskola ⋅ Nir Yosef
Curly Flow Matching for Learning Non-gradient Field Dynamics
Katarina Petrović ⋅ Lazar Atanackovic ⋅ Kacper Kapusniak ⋅ Michael Bronstein ⋅ Joey Bose ⋅ Alexander Tong
A Scalable LLM Framework for Therapeutic Biomarker Discovery: Grounding Q/A Generation in Knowledge Graphs and Literature
Marc Boubnovski Martell ⋅ Kaspar Märtens ⋅ Lawrence Phillips ⋅ Daniel Keitley ⋅ Maria Dermit ⋅ Julien Fauqueur
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
Carl Edwards ⋅ Ziqing Lu ⋅ Ehsan Hajiramezanali ⋅ Tommaso Biancalani ⋅ Heng Ji ⋅ Gabriele Scalia
HybriDNA: A Hybird Transformer-Mamba2 Long-Range DNA Language Model
Mingqian Ma ⋅ Guoqing Liu ⋅ Chuan Cao ⋅ Pan Deng ⋅ Tri Dao ⋅ Albert Gu ⋅ Peiran Jin ⋅ Zhao Yang ⋅ Yingce Xia ⋅ Renqian Luo ⋅ Pipi Hu ⋅ Zun Wang ⋅ Yuan-Jyue Chen ⋅ Haiguang Liu ⋅ Tao Qin
Relaxed Equivariance via Multitask Learning
Ahmed Elhag ⋅ T. Konstantin Rusch ⋅ Francesco Di Giovanni ⋅ Michael Bronstein
Integrating Protein Language Model and Active Learning for Few-Shot Viral Variant Detection
Marian Huot ⋅ Dianzhuo Wang ⋅ Jiacheng Liu ⋅ Eugene Shakhnovich
Decision Tree Induction with Dynamic Feature Generation: A Framework for Interpretable DNA Sequence Analysis
Nicolas Huynh ⋅ Krzysztof Kacprzyk ⋅ Ryan Sheridan ⋅ David Bentley ⋅ Mihaela van der Schaar
Uncovering BioLOGICAL Motifs and Syntax via Sufficient and Necessary Explanations
Beepul Bharti ⋅ Gabriele Scalia ⋅ Tommaso Biancalani ⋅ Alex M Tseng
InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
Tianyu Cui ⋅ Song-Jun Xu ⋅ Artem Moskalev ⋅ Shuwei Li ⋅ Tommaso Mansi ⋅ Mangal Prakash ⋅ Rui Liao
Gene Set Function Discovery with LLM-Based Agents and Knowledge Retrieval
Daniela Pinto Veizaga ⋅ Aécio Santos ⋅ Juliana Freire ⋅ Wenke Liu ⋅ Sarah Keegan ⋅ David Fenyo
Reference-free cell-type annotation with LLM agents
Yidi Huang ⋅ Ivan Cohen ⋅ Van Truong ⋅ Pedram Bayat ⋅ Sameer Bhatti ⋅ Luca Paruzzo ⋅ Mark Painter ⋅ Shirong Zheng ⋅ Derek Oldridge ⋅ Joost Wagenaar ⋅ Allison Greenplate ⋅ Dokyoon Kim
MutEmbed: Self-Supervised Learning of Biological Latent Embeddings from Cancer Mutational Profiles
Aakansha Narain ⋅ Wu Andy ⋅ Hannan Wong ⋅ Vedant Sandhu ⋅ Jason J. Pitt
Searching for Phenotypic Needles in Genomic Haystacks: DNA Language Models for Sex Prediction
Alla Chepurova ⋅ Yuri Kuratov ⋅ Polina Belokopytova ⋅ Mikhail Burtsev ⋅ Veniamin Fishman
stDiffusion: A Diffusion Based Model for Generative Spatial Transcriptomics
Sumeer Khan ⋅ Xabier de Morentin ⋅ Vincenzo Lagani ⋅ Robert Lehmann ⋅ Narsis Kiani ⋅ David Gomez-Cabrero ⋅ Jesper Tegnér
Enhancing Downstream Analysis in Genome Sequencing: Species Classification While Basecalling
Riselda Kodra ⋅ Hadjer Benmeziane ⋅ Irem Boybat ⋅ William A Simon
Pathway-Attentive GAN for Interpretable Biomolecular Design
Azmine Toushik Wasi ⋅ Mahfuz Ahmed Anik
HARMONY: A Multi-Representation Framework for RNA Property Prediction
Junjie Xu ⋅ Artem Moskalev ⋅ Tommaso Mansi ⋅ Mangal Prakash ⋅ Rui Liao
SPELL: Spatial Prompting with Chain-of-Thought for Zero-Shot Learning in Spatial Transcriptomics
Sumeer Khan ⋅ Xabier Martinez de Morentin ⋅ Vincenzo Lagani ⋅ Robert Lehmann ⋅ Abdel Rahman Alsabbagh ⋅ Mahmoud Zahran ⋅ Narsis Kiani ⋅ David Gomez-Cabrero ⋅ Jesper Tegnér
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction
Yoshitaka Inoue ⋅ Tianci Song ⋅ Xinling Wang ⋅ Augustin Luna ⋅ Tianfan Fu
Benchmarking Fine-Tuned RNA Language Models for Branch Point Prediction
Pablo Ruiz ⋅ Ali Saadat ⋅ Timothy Tran ⋅ Oliver Smedt ⋅ Peng Zhang ⋅ Jacques Fellay
Multi-modal single-cell foundation models via dynamic token adaptation
Millie (Wenmin) Zhao ⋅ Ana Solaguren-Beascoa Negre ⋅ Grant Neilson ⋅ Louwai Muhammed ⋅ Liisi Laaniste ⋅ Sera Aylin Cakiroglu
Interpretable single-cell perturbations from decoder gradients
Andreas Bjerregaard ⋅ Vivek Das ⋅ Anders Krogh
Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics
Matthew Wood ⋅ Mathieu Klop ⋅ Maxime Allard
BirdieDNA: Reward-Based Pre-Training for Genomic Sequence Modeling
Samuel Blouir ⋅ Defne Circi ⋅ Asher Moldwin ⋅ Amarda Shehu
2DE: a probabilistic method for differential expression across niches in spatial transcriptomics data
Nathan LEVY ⋅ Florian Ingelfinger ⋅ Artemii Bakulin ⋅ Giacomo Cinnirella ⋅ Pierre Boyeau ⋅ Can Ergen ⋅ Nir Yosef
Interpretable prediction of DNA replication origins in S. cerevisiae using attention-based motif discovery
Zohreh Piroozeh ⋅ Ildem Akerman ⋅ Stefan Kesselheim ⋅ Olga Kalinina ⋅ Alina Bazarova
Gradient-Based Gene Selection for scRNA-seq Foundation Models
Farhan khodaee ⋅ Rohola Zandie ⋅ Pakaphol Thadawasin ⋅ Elazer Edelman