BiomixQA Dataset

Overview

BiomixQA is a curated biomedical question-answering dataset comprising two distinct components:

1. Multiple Choice Questions (MCQ)
2. True/False Questions

This dataset has been utilized to validate the Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) framework across different Large Language Models (LLMs). The diverse nature of questions in this dataset, spanning multiple choice and true/false formats, along with its coverage of various biomedical concepts, makes it particularly suitable for assessing the performance of KG-RAG framework.

Hence, this dataset is designed to support research and development in biomedical natural language processing, knowledge graph reasoning, and question-answering systems.

Dataset Components

1. Multiple Choice Questions (MCQ)

• File: mcq_biomix.csv
• Size: 306 questions
• Format: Each question has five choices with a single correct answer

2. True/False Questions

• File: true_false_biomix.csv
• Size: 311 questions
• Format: Binary (True/False) questions

Potential Uses

1. Evaluating biomedical question-answering systems
2. Testing natural language processing models in the biomedical domain
3. Assessing retrieval capabilities of various RAG (Retrieval-Augmented Generation) frameworks
4. Supporting research in biomedical ontologies and knowledge graphs

Performance Analysis

We conducted a comprehensive analysis of the performance of three Large Language Models (LLMs) - Llama-2-13b, GPT-3.5-Turbo (0613), and GPT-4 - on the BiomixQA dataset. We compared their performance using both a standard prompt-based approach (zero-shot) and our novel Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) framework.

Performance Summary

Table 1: Performance (accuracy) of LLMs on BiomixQA datasets using prompt-based (zero-shot) and KG-RAG approaches (For more details, refer this paper)

Model	True/False Dataset		MCQ Dataset
	Prompt-based	KG-RAG	Prompt-based	KG-RAG
Llama-2-13b	0.89 ± 0.02	0.94 ± 0.01	0.31 ± 0.03	0.53 ± 0.03
GPT-3.5-Turbo (0613)	0.87 ± 0.02	0.95 ± 0.01	0.63 ± 0.03	0.79 ± 0.02
GPT-4	0.90 ± 0.02	0.95 ± 0.01	0.68 ± 0.03	0.74 ± 0.03

Key Observations

1. Consistent Performance Enhancement: We observed a consistent performance enhancement for all LLM models when using the KG-RAG framework on both True/False and MCQ datasets.

2. Significant Improvement for Llama-2: The KG-RAG framework significantly elevated the performance of Llama-2-13b, particularly on the more challenging MCQ dataset. We observed an impressive 71% increase in accuracy, from 0.31 ± 0.03 to 0.53 ± 0.03.

3. GPT-4 vs GPT-3.5-Turbo on MCQ: Intriguingly, we observed a small but statistically significant drop in the performance of the GPT-4 model (0.74 ± 0.03) compared to the GPT-3.5-Turbo model (0.79 ± 0.02) on the MCQ dataset when using the KG-RAG framework. This difference was not observed in the prompt-based approach.

   • Statistical significance: T-test, p-value < 0.0001, t-statistic = -47.7, N = 1000

4. True/False Dataset Performance: All models showed high performance on the True/False dataset, with the KG-RAG approach yielding slightly better results across all models.

Source Data

1. SPOKE: A large scale biomedical knowledge graph that consists of ~40 million biomedical concepts and ~140 million biologically meaningful relationships (Morris et al. 2023).
2. DisGeNET: Consolidates data about genes and genetic variants linked to human diseases from curated repositories, the GWAS catalog, animal models, and scientific literature (Piñero et al. 2016).
3. MONDO: Provides information about the ontological classification of Disease entities in the Open Biomedical Ontologies (OBO) format (Vasilevsky et al. 2022).
4. SemMedDB: Contains semantic predications extracted from PubMed citations (Kilicoglu et al. 2012).
5. Monarch Initiative: A platform for disease-gene association data (Mungall et al. 2017).
6. ROBOKOP: A knowledge graph-based system for biomedical data integration and analysis (Bizon et al. 2019).

Citation

If you use this dataset in your research, please cite the following paper:

@article{soman2024biomedical,
  title={Biomedical knowledge graph-optimized prompt generation for large language models},
  author={Soman, Karthik and Rose, Peter W and Morris, John H and Akbas, Rabia E and Smith, Brett and Peetoom, Braian and Villouta-Reyes, Catalina and Cerono, Gabriel and Shi, Yongmei and Rizk-Jackson, Angela and others},
  journal={Bioinformatics},
  volume={40},
  number={9},
  pages={btae560},
  year={2024},
  publisher={Oxford University Press}
}