biomedical-qa-system
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Scientific Fields
Repository
Basic Info
- Host: GitHub
- Owner: DebjyotiRay
- Language: Python
- Default Branch: main
- Size: 17 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Biomedical QA System with PubMed Citation Integration
A biomedical question answering system that provides answers with relevant scientific citations from PubMed.
Features
- Answer biomedical questions with LLM-powered responses
- Automatically retrieve relevant PubMed citations to support answers
- Entity-based query optimization for improved citation relevance
- Fallback to OpenAI GPT models when needed
Quick Start
Install dependencies:
bash pip install -r requirements.txtSet up your API keys in a
.envfile:OPENAI_API_KEY=your_openai_api_key NCBI_API_KEY=your_ncbi_api_keyRun in interactive mode:
bash python main.py --interactiveOr ask a single question:
bash python main.py --question "What genes are associated with Parkinson's disease?"
System Components
- QA Handler: Coordinates the question answering process
- Citations Module: Retrieves relevant scientific publications from PubMed
- Model Module: Manages language model interaction and fallback mechanisms
- Entity Extraction: Identifies biomedical entities for better search results
Documentation
See the docs directory for:
- System architecture diagram
- Training guide for fine-tuning models
Testing
Run the test script to verify the system is working properly:
bash
python biomed_qa_system_final/test_direct_fallback_live.py
Configuration
The system can be customized through the config.json file, including:
- PubMed citation parameters
- Model selection and configuration
- Fallback model settings
Owner
- Login: DebjyotiRay
- Kind: user
- Repositories: 1
- Profile: https://github.com/DebjyotiRay
Citation (citations.log)
GitHub Events
Total
- Member event: 1
- Push event: 2
- Create event: 5
Last Year
- Member event: 1
- Push event: 2
- Create event: 5
Dependencies
- matplotlib >=3.6.0
- networkx >=3.0.0
- numpy >=1.22.0
- openai >=1.0.0
- pandas >=1.5.0
- peft >=0.4.0
- pytest >=7.0.0
- python-dotenv >=1.0.0
- python-json-logger >=2.0.0
- requests >=2.30.0
- torch >=2.0.0
- transformers >=4.30.0
- pdnet 0.1.0