Upload README.md with huggingface_hub

README.md

@@ -0,0 +1,113 @@
+---
+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