Supervised Learning apporach for DNA classification - Deep Learning

Using Frequency matrix of Chaos Game Representation (FCGR) as input.

GOAL Classify hCoV19 DNA sequences in a supervised fashion.

Input: DNA sequence Output: Clade of the sequence

Name		Name	Last commit message	Last commit date
Latest commit History 34 Commits
.dvc		.dvc
.vscode		.vscode
__pycache__		__pycache__
supervised_dna		supervised_dna
tests		tests
.dvcignore		.dvcignore
.gitignore		.gitignore
01-undersample_sequences.py		01-undersample_sequences.py
02-extract_sequences.py		02-extract_sequences.py
03-generate_fcgr.py		03-generate_fcgr.py
04-train_val_test_split.py		04-train_val_test_split.py
05-train_model.py		05-train_model.py
06-test_model.py		06-test_model.py
07-saliency_maps.py		07-saliency_maps.py
08-avg_per_clade.py		08-avg_per_clade.py
Average-per-clade.ipynb		Average-per-clade.ipynb
Characterization-of-clades.ipynb		Characterization-of-clades.ipynb
Paper-analysis.ipynb		Paper-analysis.ipynb
README.md		README.md
Untitled.ipynb		Untitled.ipynb
checkpoints.dvc		checkpoints.dvc
datasets.json.dvc		datasets.json.dvc
evaluation_on_outer_data.ipynb		evaluation_on_outer_data.ipynb
extract_sequences_comparison.py		extract_sequences_comparison.py
nexclade-comparison.ipynb		nexclade-comparison.ipynb
npy-files-server.json.dvc		npy-files-server.json.dvc
parameters.py		parameters.py
poetry.lock		poetry.lock
pyproject.toml		pyproject.toml
reference_array.py		reference_array.py
results_nextclade_comparison.csv		results_nextclade_comparison.csv
run_experiment.sh		run_experiment.sh
streamlit_app.py		streamlit_app.py
summary_labels.csv.dvc		summary_labels.csv.dvc
train-colab.ipynb		train-colab.ipynb
upsetoplot.ipynb		upsetoplot.ipynb

Provide feedback