MEnet

MEnet is a neural-net based deconvolution method for methylation data. MEnet can be used only for humans so far.

Installation

Without Docker

Install pytorch. https://pytorch.org/get-started/locally/
git clone this repo.
python setup.py install
If you use the --input_type bismark option, you need to install bedtools locally.

with Docker

docker build -t menet:latest .

Example usage

docker run --rm -it -v $PWD:/menet menet:latest MEnet predict -i Minion_STR1_Fr6.bis.cov.gz -m 657.pickle

Prediction

usage: MEnet predict [-h] -i input -m model
                     [--input_type {auto,bismark,table,array}] [-o output_dir]
                     [--bedtools BEDTOOLS]

optional arguments:
  -h, --help            show this help message and exit
  -i input, --input input
                        input
  -m model, --model model
                        Traind model (pickle file).
  --input_type {auto,bismark,table,array}
                        input type. (default : auto)
  -o output_dir, --output_dir output_dir
                        output directory
  --bedtools BEDTOOLS   Full path to bedtools.

example

MEnet predict --input Minion_STR1_Fr6.bis.cov.gz --model ../train/210228_optuna_CV/best_model.pickle --input_type bismark  -o Minion_STR1_Fr6

Output

cell_proportion_MajorGroup.csv and cell_proportion_MinorGroup.csv are infered cell proportions for Major categories and Minor categories.

Tissue,Minion_STR1_Fr6
Adipocytes,0.00017756927380603907
AdrenalGland,1.738096416975436e-05
Neuron,0.0006150502083486212
Skin,0.00013093999620681127
Muscle,1.2423588317326314e-05
Cardiovascular,9.538600816076434e-05
...

heatmap

barplot

log

MEnet.*.log contains MEnet version and execution date.

Training an original model(advanced usage)

Users can define and train models. Before training, users need to create the reference matrix, categories, and input yaml. Details are on the directory create_ref.

usage: MEnet train [-h] [--device DEVICE] input_yaml

positional arguments:
  input_yaml       input yaml file.

optional arguments:
  -h, --help       show this help message and exit
  --device DEVICE  device for pytorch. (ex. cpu, cuda)

input_yaml (example)

reference: test/train/ref_MinorGroup_1000bp_500regions_0.5diff.210228.csv
integrated: test/train/210228_integrated_1000bp.csv.gz
pickle: test/train/210228_df.pickle
ref_table: test/train/210228_ref_ordered.csv
category: test/train/210228_categories.csv
output_dir: test/train/210228_optuna_CV
study_name: 210228_optuna_CV
storage: sqlite:///MEnet.optuna.db
n_splits: 5
fill: mean
n_epochs: 200000
patience: 500
n_trials: 10
train_noise: 0.01
seed: 0
batch_size: 200

SQLite cannot be used for training by multi clients. If using GCP, install PyMySQL by pip install PyMySQL, create a db,

mysql --host=IP --user=root --password  -e "CREATE DATABASE IF NOT EXISTS MEnet"

and specify storage like,

storage: mysql+pymysql://root:PASS@IP/MEnet

example

MEnet train test/train/210228_optuna_CV.yaml

By just runnning MEnet train in other terminals, user can train a model in parallel. Optuna dashboard is useful for monitoring the reusult. https://github.com/optuna/optuna-dashboard

optuna-dashboard sqlite:///MEnet.optuna.db

For developers

conda env create --file conda_env.yaml

conda activate menet_dev

install

python setup.py develop

run

python cli.py

ex.

python cli.py train --help

export the environment

conda env export > conda_env.yaml

Contact

Yoshiaki Yasumizu (yyasumizu@ifrec.osaka-u.ac.jp)

Licence

This software is freely available for academic users. Usage for commercial purposes is not allowed. Please refer to the LICENCE page.

yyoshiaki/MEnet