ICLR 2025 Past GenomicsHealthcare & 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 10, 2025, 23:59 AoE (UTC−12) SEED 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.
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2DE: a probabilistic method for differential expression across niches in spatial transcriptomics data
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A data-driven recommendation framework for genomic discovery
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A Scalable LLM Framework for Therapeutic Biomarker Discovery: Grounding Q/A Generation in Knowledge Graphs and Literature
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A Topologically Guided Machine Learning Framework for Enhanced Fine-Mapping in Whole-Genome Bacterial Studies
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AI AGENT FOR DATA-DRIVEN HYPOTHESIS EXPLORATION IN SINGLE-CELL TRANSCRIPTOMICS
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AI-Powered Virtual Tissues from Spatial Proteomics for Clinical Diagnostics and Biomedical Discovery
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Aligning Molecules and Fragments in a Shared Embedding Space for RL-Based Molecule Generation
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Benchmarking Fine-Tuned RNA Language Models for Intronic Branch Point Prediction
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BEYOND SEQUENCE-ONLY MODELS: LEVERAGING STRUCTURAL CONSTRAINTS FOR ANTIBIOTIC RESISTANCE PREDICTION IN SPARSE GENOMIC DATASETS
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Beyond the Factual vs. Hallucinatory Dichotomy: A Refined Taxonomy for LLM Medical Response Categorization
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BirdieDNA: Reward-Based Pre-Training for Genomic Sequence Modeling
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Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics
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Capturing functional context of genetic pathways through hyperedge disentanglement
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CellMemory: Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer
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COLOR: A COMPOSITIONAL LINEAR OPERATION BASED REPRESENTATION OF PROTEIN SEQUENCES FOR IDENTIFICATION OF MONOMER CONTRIBUTIONS TO PROPERTIES
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Curly Flow Matching for Learning Non-gradient Field Dynamics
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Decision Tree Induction with Dynamic Feature Generation: A Framework for Interpretable DNA Sequence Analysis
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Detecting cell level transcriptomic changes of Perturb-seq using Contrastive Fine-tuning of Single-Cell Foundation Models
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DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction
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ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings
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EFFICIENT FINE-TUNING OF SINGLE-CELL FOUNDATION MODELS ENABLES ZERO-SHOT MOLECULAR PERTURBATION PREDICTION
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Enhancing DNA Foundation Models to Address Masking Inefficiencies
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Enhancing Downstream Analysis in Genome Sequencing: Species Classification While Basecalling
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Enhancing E. coli Genomic Analysis with Retrieval-Augmented Generation
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ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation's Functional Effect
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Exploring the potential of genetic variation and zygosity in DNA language models
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FACA-GEN: Investigating Bias and Generalization in Active Learning for Genomics AI
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Featurization of single cell trajectories through kernel mean embedding of optimal transport maps
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Flexible Models of Functional Annotations to Variant Effects using Accelerated Linear Algebra
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GENATATOR: de novo Gene Annotation With DNA Language Model
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Gene Set Function Discovery with LLM-Based Agents and Knowledge Retrieval
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Gradient-Based Gene Selection for Multimodal scRNA-seq Foundation Models
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Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond
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GraphPINE: Graph importance propagation for interpretable drug response prediction
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HARMONY: A Multi-Representation Framework for RNA Property Prediction
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Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics
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Hierarchical Assembly of Long DNA Libraries from Short Oligonucleotide Pools
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HybriDNA: A Hybird Transformer-Mamba2 Long-Range DNA Language Model
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InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
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Integrating Protein Language Model and Active Learning for Few-Shot Viral Variant Detection
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Interpretable prediction of DNA replication origins in S. cerevisiae using attention-based motif discovery
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Knockoff Statistics-Driven Interpretable Deep Learning Models for Uncovering Potential Biomarkers for COVID-19 Severity Prediction
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LangPert: LLM-Driven Contextual Synthesis for Unseen Perturbation Prediction
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Large Language Models for Zero-shot Inference of Causal Structures in Biology
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Learning Non-Equilibrium Signaling Dynamics in Single-Cell Perturbation Dynamics
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Learning Representations of Instruments for Partial Identification of Treatment Effects
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Leveraging GPT Continual Fine-Tuning for Improved RNA Editing Site Prediction
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LIMEADE: Local Interpretable Manifold Explanations for Dimension Evaluations
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LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs – Evaluation through Synthetic Data Generation
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LoFTPat: Low-Rank Subspace Optimization for Parameter-Efficient Fine-Tuning of Genomic Language Models in Pathogenicity Identification
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MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
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Multi-modal single-cell foundation models via dynamic token adaptation
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Multi-omic Causal Discovery using Genotypes and Gene Expression
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MutEmbed: Self-Supervised Learning of Biological Latent Embeddings from Cancer Mutational Profiles
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NOLAN: SELF-SUPERVISED FRAMEWORK FOR MAPPING CONTINUOUS TISSUE ORGANIZATION
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Pathway-Attentive GAN for Interpretable Biomolecular Design
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Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
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PIONEER: a virtual platform for iterative improvement of genomic deep learning
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Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization
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PREDICTING TIME-VARYING METABOLIC DYNAMICS USING STRUCTURED NEURAL ODE PROCESSES
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PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
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ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding
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RAG-Enhanced Collaborative LLM Agents for Drug Discovery
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RAG-ESM: Improving pretrained protein language models via sequence retrieval
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Reference-free cell-type annotation with LLM agents
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Relaxed Equivariance via Multitask Learning
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RNAGym: Benchmarks for RNA Fitness and Structure Prediction
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Sampling Protein Language Models for Functional Protein Design
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Searching for Phenotypic Needles in Genomic Haystacks: DNA Language Models for Sex Prediction
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ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation
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SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model
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SpaceDX: A Bayesian test for localized differential expression in population-level spatial transcriptomics datasets
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Spatially-Informed Sampling Enables Accurate Prediction of Large-Scale Mutational Effects
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SPELL: Spatial Prompting with Chain-of-Thought for Zero-Shot Learning in Spatial Transcriptomics
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stDiffusion: A Diffusion Based Model for Generative Spatial Transcriptomics
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Structure-based metabolite function prediction using graph neural networks
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Supervised Contrastive Block Disentanglement
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Talk2Biomodels and Talk2KnowledgeGraph: AI agent-based application for prediction of patient biomarkers and reasoning over biomedical knowledge graphs
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Test-Time View Selection for Multi-Modal Decision Making
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To trap or not to trap--analyzing the trade-offs in diffusion transport models
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Transferring Preclinical Drug Response to Patient via Tumor Heterogeneity-Aware Alignment and Perturbation Modeling
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Uncertainty-aware genomic deep learning with knowledge distillation
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Uncovering BioLOGICAL Motifs and Syntax via Sufficient and Necessary Explanations
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WASSERSTEIN CYCLEGAN FOR SINGLE-CELL RNA- SEQ DATA GENERATION USING CROSS-MODALITY TRANSLATION
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What do single-cell models already know about perturbations?
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When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes