Using convolution neural networks (CNN) for better understanding of human genome

This repository is a part of my master's project called "Identification of chromatin regions active in human brain using neural networks".

Versions

• Python 3.6
• pandas 1.0.1
• numpy 1.18.1
• pytorch 1.3.1

Example dataset

Example of trained network is in /data/custom40 directory.

Calculating integrated gradients

To calculate integrads based on example model and set of sequences just run:

python3 calculate_integrads.py \
        --model custom40_last.model \
        --seq extreme_custom40_train_1.fasta \
        --baseline CHOSEN-BASELINE

CHOSEN-BASELINE depends on what baseline you want to use for calculating integrated gradients (see: https://arxiv.org/abs/1703.01365 for details of the method), select one of the options:

• zeros - use zeros array as baseline
• fixed - use the same set of random sequences as the baseline for each sequence
• random - use different random set of sequences as the baseline for each sequence
• test-balanced-8-3_baseline.npy - use pre-calculated balanced baseline (each 3 nucleotides in the given position occur exactly once across all 64. baseline sequences)

As the output new directory called integrads_NETWORK_SEQUENCES_BASELINE_TRIALS-STEPS is created (integrads_custom40_extreme-custom40-train-1_CHOSEN-BASELINE_10-50 if the default data was used). Inside there are result files:

• integrads_all.npy - numpy array with calculated gradients
• params.txt - file with parameters of the analysis

Plotting seqlogos

To plot seqlogos based on the calculated integrads run:

python3 plot_seqlogo.py \
integrads_custom40_extreme-custom40-train-1_CHOSEN-BASELINE_10-50/integrads_all.npy \
--global_ylim \
--one \
--clip NUM

Options global_ylim, one and clip are optional:

• global_ylim - set the same y axis range for all sequences from the given array
• one - plot only one nucleotide in one position (the one from the original sequence)
• clip - subset of nucleotides to plot: +-NUM from the middle of the sequences, by default NUM=100

As the output new directory with plots is created.