mlsanityData to 7 Oct 2026

Thought Graph: Generating Thought Process for Biological Reasoning

arXiv 2403.07144 ↗First posted 11 Mar 2024cs.CLcited by 10

On the map: LLM reasoning → Clinical and biomedical applications

Abstract (arXiv)

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine.

Key facts. Cited by 10 papers in the map (data through 7 Oct 2026). Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning. Builds on 9 of its 12 references that are in the map. First posted on arXiv 11 Mar 2024.

Builds on

9 of 12 references.

References · 9

  1. 2022Chain-of-Thought Prompting Elicits Reasoning in Large Language Modelscited by 12,302
  2. 2022Self-Consistency Improves Chain of Thought Reasoning in Language Modelscited by 5,601
  3. 2023Tree of Thoughts: Deliberate Problem Solving with Large Language Modelscited by 3,155
  4. 2022Least-to-Most Prompting Enables Complex Reasoning in Large Language Modelscited by 1,397
  5. 2023Graph of Thoughts: Solving Elaborate Problems with Large Language Modelscited by 873
  6. 2020Self-Alignment Pretraining for Biomedical Entity Representationscited by 233
  7. 2023Can Knowledge Graphs Reduce Hallucinations in LLMs? : A Surveycited by 92
  8. 2023MindMap: Knowledge Graph Prompting Sparks Graph of Thoughts in Large Language Modelscited by 73
  9. 2023Evaluation of large language models for discovery of gene set functioncited by 13

Built on by

Cited by year

Citing papers per year: 2024: 3; 2025: 7.

10 papers.

  1. 2025A Survey of Graph Retrieval-Augmented Generation for Customized Large Language Modelscited by 85
  2. 2025Graphs Meet AI Agents: Taxonomy, Progress, and Future Opportunitiescited by 23
  3. 2025Graph-Augmented Large Language Model Agents: Current Progress and Future Prospectscited by 14
  4. 2025Contextualizing biological perturbation experiments through languagecited by 10
  5. 2024Time Matters: Examine Temporal Effects on Biomedical Language Modelscited by 7
  6. 2025Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applicationscited by 5
  7. 2024Examining Imbalance Effects on Performance and Demographic Fairness of Clinical Language Modelscited by 4
  8. 2025Incorporating Spatial Information into Goal-Conditioned Hierarchical Reinforcement Learning via Graph Representationscited by 3
  9. 2024BrainMAP: Learning Multiple Activation Pathways in Brain Networkscited by 2
  10. 2025Knowledge-Augmented Long-CoT Generation for Complex Biomolecular Reasoningcited by 2

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. 2026When Do Biological Reasoning Models Use Their Biological Inputs?
  3. 2025BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning
  4. 2026BioPhys-Bridge: A Benchmark for Interdisciplinary Scientific Reasoning in Physics-Grounded Biological Research
  5. 2025Biomedical Hypothesis Explainability with Graph-Based Context Retrieval
  6. 2025BioHopR: A Benchmark for Multi-Hop, Multi-Answer Reasoning in Biomedical Domain
  7. 2023Beyond Chain-of-Thought, Effective Graph-of-Thought Reasoning in Language Models
  8. 2026LLMBDC: Language Model for Biological Domains Oriented Clustering of Gene Ontology