ICLR 2025PastGenomicsHealthcare & biology
Workshop on Machine Learning for Genomics Explorations
MLGenX
Unverified seed entry. Some fields are estimates — confirm everything on the official website before planning a submission.
- Submission deadline
- Feb 11, 2025, 11:59 UTCSEED estimate of the historical deadline — verify
- Workshop day
- Apr 27, 2025
- Submission portal
- OpenReview
- Notes
- SEED DATA — name/website from the OpenReview venue record; dates estimated — verify.
Accepted papers (86)
Fetched from OpenReview (v2) on 2026-06-10.
2DE: a probabilistic method for differential expression across niches in spatial transcriptomics data
A data-driven recommendation framework for genomic discovery
A Scalable LLM Framework for Therapeutic Biomarker Discovery: Grounding Q/A Generation in Knowledge Graphs and Literature
A Topologically Guided Machine Learning Framework for Enhanced Fine-Mapping in Whole-Genome Bacterial Studies
AI AGENT FOR DATA-DRIVEN HYPOTHESIS EXPLORATION IN SINGLE-CELL TRANSCRIPTOMICS
AI-Powered Virtual Tissues from Spatial Proteomics for Clinical Diagnostics and Biomedical Discovery
Aligning Molecules and Fragments in a Shared Embedding Space for RL-Based Molecule Generation
Benchmarking Fine-Tuned RNA Language Models for Intronic Branch Point Prediction
BEYOND SEQUENCE-ONLY MODELS: LEVERAGING STRUCTURAL CONSTRAINTS FOR ANTIBIOTIC RESISTANCE PREDICTION IN SPARSE GENOMIC DATASETS
Beyond the Factual vs. Hallucinatory Dichotomy: A Refined Taxonomy for LLM Medical Response Categorization
BirdieDNA: Reward-Based Pre-Training for Genomic Sequence Modeling
Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics
Capturing functional context of genetic pathways through hyperedge disentanglement
CellMemory: Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer
COLOR: A COMPOSITIONAL LINEAR OPERATION BASED REPRESENTATION OF PROTEIN SEQUENCES FOR IDENTIFICATION OF MONOMER CONTRIBUTIONS TO PROPERTIES
Curly Flow Matching for Learning Non-gradient Field Dynamics
Decision Tree Induction with Dynamic Feature Generation: A Framework for Interpretable DNA Sequence Analysis
Detecting cell level transcriptomic changes of Perturb-seq using Contrastive Fine-tuning of Single-Cell Foundation Models
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction
ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings
EFFICIENT FINE-TUNING OF SINGLE-CELL FOUNDATION MODELS ENABLES ZERO-SHOT MOLECULAR PERTURBATION PREDICTION
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Enhancing Downstream Analysis in Genome Sequencing: Species Classification While Basecalling
Enhancing E. coli Genomic Analysis with Retrieval-Augmented Generation
ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation's Functional Effect
Exploring the potential of genetic variation and zygosity in DNA language models
FACA-GEN: Investigating Bias and Generalization in Active Learning for Genomics AI
Featurization of single cell trajectories through kernel mean embedding of optimal transport maps
Flexible Models of Functional Annotations to Variant Effects using Accelerated Linear Algebra
GENATATOR: de novo Gene Annotation With DNA Language Model
Gene Set Function Discovery with LLM-Based Agents and Knowledge Retrieval
Gradient-Based Gene Selection for Multimodal scRNA-seq Foundation Models
Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond
GraphPINE: Graph importance propagation for interpretable drug response prediction
HARMONY: A Multi-Representation Framework for RNA Property Prediction
Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics
Hierarchical Assembly of Long DNA Libraries from Short Oligonucleotide Pools
HybriDNA: A Hybird Transformer-Mamba2 Long-Range DNA Language Model
InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
Integrating Protein Language Model and Active Learning for Few-Shot Viral Variant Detection
Interpretable prediction of DNA replication origins in S. cerevisiae using attention-based motif discovery
Knockoff Statistics-Driven Interpretable Deep Learning Models for Uncovering Potential Biomarkers for COVID-19 Severity Prediction
LangPert: LLM-Driven Contextual Synthesis for Unseen Perturbation Prediction
Large Language Models for Zero-shot Inference of Causal Structures in Biology
Learning Non-Equilibrium Signaling Dynamics in Single-Cell Perturbation Dynamics
Learning Representations of Instruments for Partial Identification of Treatment Effects
Leveraging GPT Continual Fine-Tuning for Improved RNA Editing Site Prediction
LIMEADE: Local Interpretable Manifold Explanations for Dimension Evaluations
LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs – Evaluation through Synthetic Data Generation
LoFTPat: Low-Rank Subspace Optimization for Parameter-Efficient Fine-Tuning of Genomic Language Models in Pathogenicity Identification
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
Multi-modal single-cell foundation models via dynamic token adaptation
Multi-omic Causal Discovery using Genotypes and Gene Expression
MutEmbed: Self-Supervised Learning of Biological Latent Embeddings from Cancer Mutational Profiles
NOLAN: SELF-SUPERVISED FRAMEWORK FOR MAPPING CONTINUOUS TISSUE ORGANIZATION
Pathway-Attentive GAN for Interpretable Biomolecular Design
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
PIONEER: a virtual platform for iterative improvement of genomic deep learning
Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization
PREDICTING TIME-VARYING METABOLIC DYNAMICS USING STRUCTURED NEURAL ODE PROCESSES
PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
RAG-ESM: Improving pretrained protein language models via sequence retrieval
Reference-free cell-type annotation with LLM agents
Relaxed Equivariance via Multitask Learning
RNAGym: Benchmarks for RNA Fitness and Structure Prediction
Sampling Protein Language Models for Functional Protein Design
Searching for Phenotypic Needles in Genomic Haystacks: DNA Language Models for Sex Prediction
ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation
SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model
SpaceDX: A Bayesian test for localized differential expression in population-level spatial transcriptomics datasets
Spatially-Informed Sampling Enables Accurate Prediction of Large-Scale Mutational Effects
SPELL: Spatial Prompting with Chain-of-Thought for Zero-Shot Learning in Spatial Transcriptomics
stDiffusion: A Diffusion Based Model for Generative Spatial Transcriptomics
Structure-based metabolite function prediction using graph neural networks
Supervised Contrastive Block Disentanglement
Talk2Biomodels and Talk2KnowledgeGraph: AI agent-based application for prediction of patient biomarkers and reasoning over biomedical knowledge graphs
Test-Time View Selection for Multi-Modal Decision Making
To trap or not to trap--analyzing the trade-offs in diffusion transport models
Transferring Preclinical Drug Response to Patient via Tumor Heterogeneity-Aware Alignment and Perturbation Modeling
Uncertainty-aware genomic deep learning with knowledge distillation
Uncovering BioLOGICAL Motifs and Syntax via Sufficient and Necessary Explanations
WASSERSTEIN CYCLEGAN FOR SINGLE-CELL RNA- SEQ DATA GENERATION USING CROSS-MODALITY TRANSLATION
What do single-cell models already know about perturbations?
When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes