mlsanityData to 14 Oct 2026

Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis

arXiv 2509.10575 ↗First posted 11 Sep 2025q-bio.GN cs.AIcited by 2

On the map: LLM reasoning → Clinical and biomedical applications

Abstract (arXiv)

The gene set analysis (GSA) is a foundational approach for uncovering the molecular functions associated with a group of genes. Recently, LLM-powered methods have emerged to annotate gene sets with biological functions together with coherent explanatory insights. However, existing studies primarily focus on proprietary models, which have been shown to outperform their open-source counterparts despite concerns over cost and data privacy. Furthermore, no research has investigated the application of advanced reasoning strategies to the GSA task. To address this gap, we introduce Gene-R1, a data-augmented learning framework that equips lightweight and open-source LLMs with step-by-step reasoning capabilities tailored to GSA. Experiments on 1,508 in-distribution gene sets demonstrate that Gene-R1 achieves substantial performance gains, matching commercial LLMs. On 106 out-of-distribution gene sets, Gene-R1 performs comparably to both commercial and large-scale LLMs, exhibiting robust generalizability across diverse gene sources.

Key facts. Cited by 2 papers in the map (data through 14 Oct 2026). Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning. Builds on 18 of its 39 references that are in the map. First posted on arXiv 11 Sep 2025.

Builds on

18 of 39 references.

Closest ancestors · 1

Same direction, newest first

  1. 2025Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with Reinforcement Learning3 Jun

Other references · 17

  1. 2023LLaMA: Open and Efficient Foundation Language Modelscited by 14,132
  2. 2024DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Modelscited by 9,379
  3. 2019Sentence-BERT: Sentence Embeddings using Siamese BERT-Networkscited by 9,170
  4. 2023AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversationcited by 1,988
  5. 2023MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Datacited by 286
  6. 2024ReFT: Reasoning with Reinforced Fine-Tuningcited by 239
  7. 2020Self-Alignment Pretraining for Biomedical Entity Representationscited by 237
  8. 2023MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrievalcited by 185
  9. 2023GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Informationcited by 117
  10. 2023Clinical Camel: An Open Expert-Level Medical Language Model with Dialogue-Based Knowledge Encodingcited by 71
  11. 2024UltraMedical: Building Specialized Generalists in Biomedicinecited by 67
  12. 2025Injecting Domain-Specific Knowledge into Large Language Models: A Comprehensive Surveycited by 51
5 more
  1. 2024Online DPO: Online Direct Preference Optimization with Fast-Slow Chasingcited by 39
  2. 2023Evaluation of large language models for discovery of gene set functioncited by 14
  3. 2023Gene Set Summarization using Large Language Modelscited by 12
  4. 2024Re2LLM: Reflective Reinforcement Large Language Model for Session-based Recommendationcited by 8
  5. 2024Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicinecited by 7

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2026: 2.

2 papers.

  1. 2026How Post-Training Shapes Biological Reasoning Modelscited by 1
  2. 2026SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotationcited by 0

Similar, not cited

Close in wording, no citation either way

  1. 2026SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding
  2. 2026Tool-Augmented On-Policy Distillation for LLM Domain Adaptation in Sequence-Based Omics Tasks
  3. 2024Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research
  4. 2026GenoMorph: Pathway-Grounded Genomic Disease Reasoning via Adaptive Latent Computation
  5. 2026Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction
  6. 2024Long-range gene expression prediction with token alignment of large language model
  7. 2024GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis
  8. 2024LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs -- Evaluation through Synthetic Data Generation