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