---
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()
```