Add dataset documentation

README.md

@@ -1,27 +1,100 @@
 ---
-dataset_info:
-  features:
-  - name: chromosome
-    dtype: string
-  - name: start
-    dtype: int64
-  - name: end
-    dtype: int64
-  - name: sequence
-    dtype: string
-  - name: strand
-    dtype: string
-  - name: n_content
-    dtype: float64
-  splits:
-  - name: train
-    num_bytes: 16428486
-    num_examples: 1000
-  download_size: 5672422
-  dataset_size: 16428486
-configs:
-- config_name: default
-  data_files:
-  - split: train
-    path: data/train-*
+license: cc-by-4.0
+task_categories:
+- text-generation
+- token-classification
+language:
+- en
+tags:
+- genomics
+- dna
+- grch38
+- human-genome
+- evo2
+- sparse-autoencoder
+size_categories:
+- 100K<n<1M
 ---
+
+# Human GRCh38 Genome Segments
+
+## Dataset Description
+
+This dataset contains 16,384 base pair segments from the human reference genome (GRCh38) prepared for Sparse Autoencoder (SAE) training with the Evo2 model. The segments are extracted using a sliding window approach with 75% overlap.
+
+## Dataset Details
+
+- **Total segments**: 718,648
+- **Segment size**: 16,384 base pairs
+- **Stride**: 4,096 base pairs (75% overlap)
+- **Source genome**: GRCh38.primary_assembly (GENCODE Release 41)
+- **Chromosomes**: chr1-22, chrX, chrY, plus alternative/random contigs
+- **Filtering**: Segments with >10% N-content removed
+
+## Data Structure
+
+Each segment contains:
+- `chromosome`: Chromosome identifier
+- `start`: Start position (0-based)
+- `end`: End position (exclusive)
+- `sequence`: DNA sequence (16,384 bp)
+- `strand`: Strand orientation (always "+")
+- `n_content`: Fraction of N bases (ambiguous nucleotides)
+
+## Usage
+
+```python
+from datasets import load_dataset
+
+# Load the dataset
+dataset = load_dataset("harari/human_grch38_segment")
+
+# Access a segment
+segment = dataset['train'][0]
+print(f"Chromosome: {segment['chromosome']}")
+print(f"Position: {segment['start']}-{segment['end']}")
+print(f"Sequence length: {len(segment['sequence'])}")
+```
+
+## Intended Use
+
+This dataset is designed for:
+- Training Sparse Autoencoders on genomic sequences
+- Analyzing DNA sequence patterns with foundation models
+- Genomic representation learning
+- Evo2 model feature extraction and interpretation
+
+## Citation
+
+If you use this dataset, please cite the original GRCh38 reference genome and GENCODE annotations:
+
+```
+@article{grch38,
+  title={The reference genome sequence of the human genome},
+  journal={Nature},
+  year={2013}
+}
+
+@article{gencode,
+  title={GENCODE: the reference human genome annotation},
+  journal={Genome Research},
+  year={2012}
+}
+```
+
+## Data Source
+
+- Reference genome: GENCODE GRCh38.p13 Release 41
+- URL: https://www.gencodegenes.org/human/release_41.html
+- Processing: Sliding window chunking with N-content filtering
+
+## Preprocessing
+
+1. Downloaded GRCh38.primary_assembly.genome.fa.gz
+2. Extracted 16,384 bp segments with 4,096 bp stride
+3. Filtered segments with >10% N-content
+4. Added genomic coordinates and metadata
+
+## License
+
+This dataset is released under CC-BY-4.0 license, consistent with the GENCODE data usage terms.