dna-ssl-augmentations

Code for the paper:

DNA augmentations for semi-supervised learning in genomic sequence classification

This repository contains implementations of biologically motivated DNA sequence augmentations and the experimental framework used to evaluate them in semi-supervised learning (SSL) settings on genomic sequence classification tasks.

Features

This repository currently supports:

• biologically motivated DNA sequence augmentations
• semi-supervised learning with FixMatch
• semi-supervised learning with FlexMatch
• experiments on:
  • AMR
  • Oncovirus

Implemented augmentations

Implemented DNA sequence augmentations include:

• reverse complement
• codon back-translation
• nucleotide masking/substitution (NN)
• high-rate mutation
• length-preserving insertion/deletion (InDel)
• combined InDel + NN

Repository structure

dna-ssl-augmentations/
├── src/
│   ├── augmentations.py
│   ├── common.py
│   ├── fixmatch_core.py
│   ├── flexmatch_core.py
│   ├── run_amr_fixmatch.py
│   ├── run_amr_flexmatch.py
│   ├── run_oncovirus_fixmatch.py
│   └── run_oncovirus_flexmatch.py
├── data/
│   ├── amr/
│   └── oncovirus/
├── outputs/
├── requirements.txt
└── README.md


## Installation

Clone the repository and install dependencies:

```bash
git clone https://github.com/EESI/dna-ssl-augmentations.git
cd dna-ssl-augmentations
pip install -r requirements.txt

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Datasets

This repository does not redistribute the datasets.

Please download or prepare the datasets yourself and place them in the following locations.

AMR

Expected files:

data/amr/train_6classes.csv
data/amr/val_6classes.csv
data/amr/test_6classes.csv

Oncovirus

Expected files:

data/oncovirus/train.csv
data/oncovirus/val.csv
data/oncovirus/test.csv

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Expected CSV format

Each CSV file should contain at least the following columns:

sequence,label

If your sequence column is named DNA Sequence, it will be automatically renamed internally.

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Running experiments

AMR + FixMatch

python src/run_amr_fixmatch.py

AMR + FlexMatch

python src/run_amr_flexmatch.py

Oncovirus + FixMatch

python src/run_oncovirus_fixmatch.py

Oncovirus + FlexMatch

python src/run_oncovirus_flexmatch.py