Create README.md

README.md

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+---
+license: apache-2.0
+---
+
+## Dataset Overview
+
+The dataset consists of five tasks for cross-species modeling plant genomes at single-nucleotide resolution in plants. These tasks are:
+
+1. **Translation Initiation Site (TIS) Prediction**
+2. **Translation Termination Site (TTS) Prediction**
+3. **Splice Donor Site Prediction**
+4. **Splice Acceptor Site Prediction**
+5. **Evolutionary Conservation Prediction**
+
+### Tasks 1-4: Site Predictions
+- **Training Dataset**: Generated from Arabidopsis chromosomes 1-4
+- **Validation Dataset**: Generated from Arabidopsis chromosome 5
+- **Testing Datasets**: Compiled from rice, sorghum, and maize
+
+### Task 5: Evolutionary Conservation Prediction
+- **Training Dataset**: Generated from sorghum chromosomes 1-9
+- **Validation Dataset**: Generated from sorghum chromosome 10
+- **Testing Datasets**: Compiled in maize
+
+This datasets facilitate robust cross-species nucleotide annotation.
+
+## Dataset sizes
+
+#### TIS, TTS, Donor, Acceptor
+|                         | TIS                          | TTS                          | Donor                         | Acceptor                      |
+|-------------------------|------------------------------|------------------------------|-------------------------------|-------------------------------|
+|                         | # of positives | # of negative | # of positives | # of negative | # of positives | # of negative | # of positives | # of negative |
+| Training on Arabidopsis chromosome 1-4 | 24,711         | 173,880        | 25,112         | 220,452        | 96,752          | 483,268        | 97,224          | 536,179        |
+| Validation on Arabidopsis chromosome 5 | 7,311          | 50,514         | 7,461          | 64,365         | 29,377          | 140,536        | 29,567          | 155,397        |
+| Rice test   | 2,974          | 1,400,115      | 2,974          | 3,718,029      | 21,963          | 3,764,549      | 21,963          | 4,151,774      |
+| Sorghum test | 3,214          | 3,937,719      | 3,214          | 10,445,530     | 24,801          | 10,821,941     | 24,801          | 12,640,573     |
+| Maize test  | 3,098          | 11,265,574     | 3,098          | 29,535,973     | 24,399          | 34,516,038     | 24,399          | 40,025,899     |
+
+#### Evolutionary conservation
+|             | # of positives | # of negative |
+|-------------|----------------|---------------|
+| Train       | 429,043        | 429,043       |
+| Validation  | 19,030         | 19,030        |
+| Test        | 947,769        | 976,230       |
+
+## How to use
+```
+from datasets import load_dataset
+import pandas as pd
+repo_id = 'kuleshov-group/cross-species-single-nucleotide-annotation'
+tis = load_dataset(repo_id, data_files={'train': 'TIS/train.tsv', 'valid': 'TIS/valid.tsv', 'test_rice':'TIS/test_rice.tsv', 'test_sorghum':'TIS/test_sorghum.tsv', 'test_maize':'TIS/test_maize.tsv'})
+tis_train = tis['train']
+# convert to pandas dataframe
+tis_train_df = tis_train.to_pandas()
+```