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DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution

We provide the PyTorch implementations for both predicting and training procedures.

Summary

DeepHiC is a deep learning model developed for boosting the resolution of Hi-C data. It is based on Generative Adversarial Network. It takes low-resolution data as conditional inputs for Generator Net in GAN and outputs the enhanced Hi-C matrices.

We trained DeepHiC for 300 epochs on chromosome 1-14 in the GM12878 cell line from Rao's HiC and evaluated on remaining data including other two cell lines' data (IMR90, K562).

Heatmap of

The framework of DeepHiC. With 10kb high-resolution data as the ground truth, DeepHiC predicts enhanced outputs from low-resolution Hi-C data (1/10 - 1/100 randomly downsampled reads). The structure similarity index (SSIM) between enhanced outputs and real 10-kb high-resolution data achieves 0.8 (1% reads) to 0.9 (4% reads) on average.

Dependency

DeepHiC is written in Python3 with PyTorch framework. It demands Python version 3.6+

Other python packages used in this repo (version numbers are recommanded):

  • pytorch 1.1.0 (www.pytorch.org)
  • torchvision 0.3.0
  • numpy 1.16.4
  • scipy 1.3.0
  • pandas 0.24.2
  • scikit-learn 0.21.2
  • matplotlib 3.1.0
  • tqdm 4.32.2
  • visdom 0.1.8.8

Note: 1. visdom must be runned in background 2. GPU acceleration is strongly recommended.

Data Preparation

1. Raw data

We used Rao's HiC data from GEO. Take the data in GM12878 cell line as example.

The string variable root_dir defined in all_parser.py determines the directory storing all raw and processed data.

Here we unzip Hi-C data into /data/RaoHiC/raw/GM12878. root_dir could be customized according to the folder path you store data. But raw data must be putted in $root_dir/raw/[cell_line_name]

2. Processed data

We also uploaded the processed data for training our model, and the processed data in GM12878 replicate which could be predicted directly. Just move the data folder to $root_dir/data.

Usage

1. Data Preprocessing

Taking the GM12878 cell line data for example. Raw data is stored in directory: $root_dir/raw/GM12878

  1. Reading raw data and storing Hi-C matrices as np.ndarrays in .npz format.
python data_aread.py -c GM12878

Note: We only provide the script for parsing Rao's data. If you are using different types of Hi-C data, please replace them with yours.

Note: currently, we also provided a script for convert HiC-Pro output to our input in ./scripts/hicpro2deephic.py. the chrN_10kb.npz files for one cell line data should be putted in $root_dir/mat/[cell_line_name]

Note: except for Hi-C matrices, we also stored the index of bins whose sum greater than zero for each chromosome, a.k.a variable compact in the same .npz file

  1. Randomly downsampling to 1/16 reads.
python data_downsample.py -hr 10kb -lr 40kb -r 16 -c GM12878
  • -hr: the resolution of high-resolution data
  • -lr: the low-resolution (just for convenience) for downsampled data, e.g. I named 1/16 downsampled data as chrN_40kb.npz
  • -r : the downsampling factor
  • -c : cell_line_name of data
  1. Generating trainable/predictable data
python data_generate.py -hr 10kb -lr 40kb -s train -chunk 40 -stride 40 -bound 201 -scale 1 -c GM12878
  • -hr: the high-resolution data we used for train
  • -lr: the low-coverage (downsampled) data we used for training input
  • -s : specifying dataset: train/test/human/mouse
  • -chunk: chunk size for each small samples
  • -stride: should be same with -chunk
  • -bound: upper bound of genomic distance, e.g. 201 means 200 x 10kb
  • -scale: whether to pooling input matrices, current version is no, it should be 1 in default.
  • -c : cell_line_name of data

2. Traning or Predicting

  1. For training purpose
python train.py
  1. For predicting purpose
python data_predict.py -lr 40kb -ckpt save/a_suitable_parameter_file.pytorch -c GM12878
  • -lr: the low-coverage (downsampled) data we used for input
  • -ckpt : trained parameters
  • -c : cell_line_name of data