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---
license: apache-2.0
task_categories:
- question-answering
- text-generation
language:
- zh
- en
tags:
- microbiology
- medical
- qa
- infectious-diseases
- pathogens
size_categories:
- 100K<n<1M
---
# 🦠 Microbiology QA Complete Dataset v2.1
The most comprehensive microbiology question-answering dataset, combining LLM-generated content, real clinical reports, and filtered open-source medical data.
## 📊 Dataset Statistics
| Split | Samples |
|-------|---------|
| Train | 278,073 |
| Validation | 15,448 |
| Test | 15,450 |
| **Total** | **308,971** |
## 📚 Data Sources
### 1. LLM Textbook QA (15,487 samples)
High-quality QA pairs extracted by Qwen-Plus from authoritative textbooks:
- Sanford Guide to Antimicrobial Therapy: 3,350
- Manual of Clinical Microbiology (Vol.1 & 2): 7,665
- Harrison's Principles of Infectious Diseases: 4,472
### 2. CSV Report Analysis QA (22,842 samples) ✨ Enhanced
From 9,990 real microbiology metagenomic reports:
- Species identification & abundance analysis
- Pathogen detection & clinical significance
- Microbiome diversity assessment
- **Enhancement**: Deduplicated 1,183 entries + Question diversification (5 variants per high-frequency question via Qwen-Plus)
### 3. Filtered Open-source Medical Data (270,642 samples)
Filtered from 546K+ open-source medical QA using 272 microbiology keywords:
| Source | Samples | Language | Content |
|--------|---------|----------|---------|
| PubMedQA | 187,403 | English | Biomedical research QA |
| MedMCQA | 49,226 | English | Medical multiple choice |
| CMtMedQA | 27,377 | Chinese | Doctor-patient dialogues |
| MedQA | 6,637 | English | USMLE-style questions |
## 📝 Data Format
```json
{
"instruction": "Is reflective functioning associated with clinical symptoms?",
"input": "Mentalization is the capacity to understand behavior...",
"output": "These findings indicate that RF is associated with...",
"source": "pubmedqa/train_pqa_unlabeled.jsonl",
"category": "pubmed_qa",
"matched_keywords": ["uti"],
"data_source": "opensource"
}
```
## 🎯 Topic Coverage
- **Pathogens**: Bacteria, viruses, fungi, parasites
- **Infections**: Pneumonia, sepsis, UTI, etc.
- **Antimicrobials**: Antibiotics, antivirals, antifungals
- **Resistance**: MRSA, VRE, CRE, ESBL
- **Diagnostics**: Culture, PCR, mNGS, mass spectrometry
- **Microbiome**: Gut flora, dysbiosis
## 📦 Usage
```python
from datasets import load_dataset
dataset = load_dataset("xingqiang/microbiology-qa-complete")
print(f"Training samples: {len(dataset['train']):,}")
# Output: Training samples: 278,073
# Filter by data source
llm_data = dataset['train'].filter(lambda x: x['data_source'] == 'llm_textbook')
opensource_data = dataset['train'].filter(lambda x: x['data_source'] == 'opensource')
```
## 🔄 v2.1 Updates
- CSV data deduplication: Removed 1,183 duplicate QA pairs
- Question diversification: Generated 5 expression variants for high-frequency questions
- Reduced question reuse rate for better training diversity
## 🔗 Related Datasets
- [microbiology-llm-qa](https://huggingface.co/datasets/xingqiang/microbiology-llm-qa) - Pure LLM-generated (39K)
- [microbiology-qa-v1](https://huggingface.co/datasets/xingqiang/microbiology-qa-v1) - Earlier version (226K)
## 📅 Version Info
- **Version**: 2.1 (Enhanced)
- **Date**: December 2024
- **Project**: [DeepMicroPath](https://github.com/chenxingqiang/DeepMicroPath)
## 📜 License
Apache 2.0
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