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README.md

@@ -3,7 +3,6 @@ license: apache-2.0
 task_categories:
   - text-classification
   - token-classification
-  - text-generation
 language:
   - en
 tags:
@@ -12,177 +11,63 @@ tags:
   - kluyveromyces-marxianus
   - biobert
   - functional-genomics
-  - pangenome
   - yeast
-  - gut-microbiome
-  - nlp
-  - transformers
 size_categories:
   - 10K<n<100K
 ---
 
-# Kluyveromyces marxianus Genomics - Chunked Dataset for BioBERT
-
-<div align="center">
-  <img src="https://img.shields.io/badge/BioBERT-Optimized-green" alt="BioBERT Optimized"/>
-  <img src="https://img.shields.io/badge/Chunk_Size-512_tokens-blue" alt="512 tokens"/>
-  <img src="https://img.shields.io/badge/Model-BiOMistral--7B-orange" alt="BiOMistral-7B"/>
-  <img src="https://img.shields.io/badge/License-Apache_2.0-yellow" alt="Apache 2.0"/>
-</div>
-
-## 📋 Overview
-
-This dataset contains **semantically-optimized chunks** of scientific literature and genomic data related to *Kluyveromyces marxianus*, specifically prepared for **BioBERT-Large v1.1 fine-tuning**. The data was processed using **BiOMistral-7B** to ensure:
-
-- ✅ Deep semantic coherence
-- ✅ Optimal chunk size (512 tokens for BioBERT)
-- ✅ Preservation of genomic entity relationships
-- ✅ Quality scoring and filtering
-
-## 🎯 Research Context
-
-**PhD Thesis:** *Functional Genomics of Robust Linear Yeasts (Kluyveromyces marxianus) using BioBERT and Pangenome Methodology for Identifying Key Survival Genes in Severe Gut Conditions*
-
-This dataset supports research into:
-- Gene survival mechanisms in extreme gut environments
-- Metabolic pathway adaptations
-- Stress response systems in yeast
-- Comparative pangenomics
-
-## 📊 Dataset Statistics
-
-| Metric | Value |
-|--------|-------|
-| **Total Chunks** | TBD |
-| **High-Quality Chunks** | TBD |
-| **Average Token Count** | ~512 |
-| **Semantic Coherence** | TBD |
-| **Processing Date** | 2025-10-31 |
-
-## 🧬 Data Structure
-
-Each chunk contains:
-
-```json
-{
-  "chunk_id": "unique_identifier",
-  "text": "chunk_content",
-  "token_count": 512,
-  "semantic_coherence": 0.85,
-  "information_density": 0.72,
-  "quality_score": 0.785,
-  "entities": {
-    "genes": ["ABC1", "XYZ2"],
-    "proteins": [...],
-    "pathways": [...],
-    "conditions": [...]
-  },
-  "biobert_ready": true,
-  "source_document": {...}
-}
-```
+# 🧬 Kluyveromyces marxianus - BioBERT-Optimized Chunks
 
-## 📁 Files
+**PhD Research Dataset**: Functional Genomics of Robust Linear Yeasts
 
-- `chunks_complete.json` - All processed chunks with full metadata
-- `chunks_high_quality.json` - Premium chunks (quality ≥ 0.7)
-- `chunks.jsonl` - Streaming-friendly format
-- `chunks.csv` - Simplified tabular format
-- `processing_statistics.json` - Numerical summaries
-- `chunk_analysis.png` - Statistical visualizations
-- `interactive_analysis.html` - Interactive exploration dashboard
+## Overview
 
-## 🚀 Usage
+Semantically-optimized 512-token chunks for BioBERT fine-tuning, processed with BiOMistral-7B.
 
-### Loading the Dataset
+## Dataset Info
 
-```python
-from datasets import load_dataset
+- **Processing Date**: 2025-10-31
+- **Target Model**: BioBERT-Large v1.1
+- **Chunk Size**: 512 tokens (optimal)
+- **Source**: [Milad96/Kluyveromyces-marxianus](https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus)
 
-# Load complete dataset
-dataset = load_dataset("Milad96/Kluyveromyces-marxianus-chunks")
+## Features
 
-# Load high-quality chunks only
-import json
-with open('chunks_high_quality.json', 'r') as f:
-    hq_chunks = json.load(f)
-```
+- Deep semantic coherence analysis
+- Automatic genomic entity extraction
+- Quality scoring and filtering
+- BioBERT-ready format
 
-### BioBERT Fine-tuning Example
+## Usage
 
 ```python
-from transformers import BertTokenizer, BertForSequenceClassification
-from transformers import Trainer, TrainingArguments
-
-# Load BioBERT
-model = BertForSequenceClassification.from_pretrained(
-    "dmis-lab/biobert-large-cased-v1.1-squad",
-    num_labels=YOUR_NUM_CLASSES
-)
-
-tokenizer = BertTokenizer.from_pretrained(
-    "dmis-lab/biobert-large-cased-v1.1-squad"
-)
+from datasets import load_dataset
+import json
 
-# Chunks are already optimized for 512 tokens!
-# Direct use without additional preprocessing
+# Load high-quality chunks
+with open('chunks_high_quality.json', 'r') as f:
+    chunks = json.load(f)
+
+# Each chunk has:
+# - text: optimized content
+# - token_count: ~512
+# - semantic_coherence: 0-1
+# - quality_score: 0-1
+# - entities: {genes, proteins, pathways}
 ```
 
-## 🔬 Processing Pipeline
-
-1. **BiOMistral-7B Loading**: 4-bit quantized for efficiency
-2. **Semantic Analysis**: Deep understanding of genomic context
-3. **Intelligent Chunking**: Boundary detection at semantic breaks
-4. **Entity Extraction**: Automatic identification of genes, proteins, pathways
-5. **Quality Scoring**: Multi-factor assessment (coherence + density)
-6. **BioBERT Optimization**: 512-token target with special token support
-
-## 📈 Quality Metrics
-
-### Semantic Coherence (0-1)
-Measures thematic consistency within chunks using BiOMistral embeddings.
-
-### Information Density (0-1)
-Ratio of unique to total words, indicating vocabulary diversity.
-
-### Quality Score (0-1)
-Combined metric: `(Coherence + Density) / 2`
-
-## 🎓 Citation
-
-If you use this dataset in your research, please cite:
+## Citation
 
 ```bibtex
 @dataset{kmx_chunks_2024,
   author = {Milad96},
-  title = {Kluyveromyces marxianus Genomics - Chunked Dataset for BioBERT},
+  title = {Kluyveromyces marxianus BioBERT Chunks},
   year = {2024},
   publisher = {HuggingFace},
   url = {https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus-chunks}
 }
 ```
 
-## 📜 License
-
-This dataset is released under the Apache 2.0 License.
-
-## 🤝 Source Data
-
-Original dataset: [Milad96/Kluyveromyces-marxianus](https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus)
-
-## 🔗 Related Resources
-
-- [BioBERT Models](https://huggingface.co/dmis-lab)
-- [BiOMistral-7B](https://huggingface.co/BioMistral/BioMistral-7B)
-- [Pangenome Analysis Tools](https://github.com/pangenome)
-
-## 📧 Contact
-
-For questions or collaborations, please open an issue in this repository.
-
----
+## License
 
-**Generated by:** BiOMistral Quantum Chunking System  
-**Processing Model:** BiOMistral-7B (4-bit quantized)  
-**Target Application:** BioBERT-Large v1.1 Fine-tuning  
-**Date:** 2025-10-31 20:09:08
+Apache 2.0