# openpomResource

**Repository Path**: tom_ud/openpom-resource

## Basic Information

- **Project Name**: openpomResource
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-04-10
- **Last Updated**: 2024-04-10

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Open Principal Odor Map
Replication of the Principal Odor Map paper by Brian K. Lee et al. (2023) \[1\].
The model is implemented such that it integrates with [DeepChem](https://github.com/deepchem/deepchem ).

## Benchmarks
| Model    | Data      | Type  | ROC-AUC Score |
| :------------: |   :---:       |   :---:       | :--------: |
| [MPNNPOMModel](https://github.com/ARY2260/openpom/blob/74e964eb5b1086badcb3e3ba47df3528259d7000/openpom/models/mpnn_pom.py)        |  [curated_GS_LF_merged_4983.csv](https://github.com/ARY2260/openpom/blob/74e964eb5b1086badcb3e3ba47df3528259d7000/openpom/data/curated_datasets/curated_GS_LF_merged_4983.csv)       | 5-Fold CV with ensemble of 10 models per fold   | 0.8872

## Installation (Python 3.9 and above)
### PyPI based installation
1. ```bash
   pip install openpom
   ```

**openpom** requires [cuda verion of dgl libraries](https://www.dgl.ai/pages/start.html)<br>
For cuda 11.7, steps below can be followed:

2. ```bash
   pip install  dgl -f https://data.dgl.ai/wheels/cu117/repo.html
   ```
3. ```bash
   pip install  dglgo -f https://data.dgl.ai/wheels-test/repo.html
   ```

Note: If you are using Amazon Linux 2 based OS on EC2 instance, use:
```bash
pip install  dgl==1.1.2 -f https://data.dgl.ai/wheels/cu117/repo.html
```

### Github fork based installation
1. Fork the [OpenPOM](https://github.com/ARY2260/openpom) repository
and clone the forked repository

```bash
git clone https://github.com/YOUR-USERNAME/openpom.git
cd openpom
```

2. Setup conda environment
```bash
conda create -n open_pom python=3.9
conda activate open_pom
```

3. Install openpom

```bash
pip install .
```

or (for developing)
```bash
python setup.py develop
```
4. Install DGL cuda libs
```bash
pip install  dgl -f https://data.dgl.ai/wheels/cu117/repo.html

pip install  dglgo -f https://data.dgl.ai/wheels-test/repo.html
```

## Getting started
Example notebooks for model training and finetuning are available [here](https://github.com/ARY2260/openpom/tree/main/examples).

## Contributors:
**Aryan Amit Barsainyan**, National Institute of Technology Karnataka, India: code, data cleaning, model development<br/>
**Ritesh Kumar**, CSIR-CSIO, Chandigarh, India: data cleaning, hyperparameter optimisation<br/>
**Pinaki Saha**, University of Hertfordshire, UK: discussions and feedback<br/>
**Michael Schmuker**, University of Hertfordshire, UK: conceptualisation, project lead<br/>

## References:
\[1\] A Principal Odor Map Unifies Diverse Tasks in Human Olfactory Perception.<br/>

Brian K. Lee, Emily J. Mayhew, Benjamin Sanchez-Lengeling, Jennifer N. Wei, Wesley W. Qian, Kelsie A. Little, Matthew Andres, Britney B. Nguyen, Theresa Moloy, Jacob Yasonik, Jane K. Parker, Richard C. Gerkin, Joel D. Mainland, Alexander B. Wiltschko<br/>

Science381,999-1006(2023).DOI: [10.1126/science.ade4401](https://doi.org/10.1126/science.ade4401) <br/>
bioRxiv 2022.09.01.504602; doi: [https://doi.org/10.1101/2022.09.01.504602](https://doi.org/10.1101/2022.09.01.504602)