amartyacsb / mla-gnn

MLA-GNN

This repository is an official PyTorch implementation of the paper **"Multi-Level Attention Graph Neural Network Based on Co-expression Gene Modules for Disease Diagnosis and Prognosis" submitted to Bioinformatics 2021.

Installation

Dependencies

Python 3.6
PyTorch >= 1.5.0
torch_geometric
numpy
pandas
scipy
sklearn
opencv
random

Data Description

For the glioma dataset, 15-fold cross validation is conducted to evaluate the model performance. For each train-test split, we compute the adjacency matrix by performing the WGCNA algorithm on the training set. The input features and adjacency matrix are saved at: ./example_data/...

The data structure is:

./example_data

    ├── input_features_labels                
        ├── split1_train_320d_features_labels.csv
        ├── split1_test_320d_features_labels.csv
        ├── ...
        ├── ...
        ├── split15_train_320d_features_labels.csv
        ├── split15_test_320d_features_labels.csv
        
    ├── input_adjacency_matrix
        ├── split1_adjacency_matrix.csv
        ├── split2_adjacency_matrix.csv
        ├── ...
        ├── ...
        ├── split15_adjacency_matrix.csv

• For each train or test set, the RNAseq features and labels (for survival prediction and histological grading) are contained in the "xxx_xxx_320d_features_labels.csv" in the following format:

  0	1	2	3	...	321	322	323
  TCGA-06-0141	-0.751162972	-1.72656962	0.876216622	...	1	313	2
  TCGA-06-0187	-0.751162972	-1.72656962	2.305385481	...	1	828	2
  ...	...	...	...	...	...	...
  TCGA-S9-A7R3	-0.751162972	0.57918313	-0.55295223	...	0	3013	0

  ** Each row represents the features and labels of one patient.

  ** Since we used the preprocessed data from the Pathomic fusion paper, the features are 320d, containing 80d CNV features (1-80 columns) and 240d RNAseq features (81-320 columns). In our work, we only used the RNAseq data, so we extracted the 81-320 columns from this file as input features.

  ** The last three columns represent the labels. The 321-th column indicates whether a patient is censored, the 322-th column denotes the survival time, while the last column shows the ground-truth class for the histological grading task (0, 1, 2 denotes grade II, III, IV, respectively).

• For each train-test split, the adjacency matrix is computed based on the training set and saved in the following format:

  V83	V84	V85	...	V321	V322
  1	0.001676229	3.07E-06	...	5.30E-07	5.89E-09
  0.001676229	1	1.93E-07	...	3.33E-10	1.69E-07
  3.07E-06	1.93E-07	1	...	1.98E-09	0.000125699
  ...	...	...	...	...	...
  5.89E-09	1.69E-07	0.000125699	...	1.04E-06	1

  ** The shape of the adjacency matrix is 240*240.

  ** Each element E_i, j represents the correlation between the i-th and j-th genes.

Output files

• After training the MLA-GNN model, the model will be save at: "./pretrained_models/".

• The pretrained files are named as '/split' + str(k) + '' + opt.task + '' + str(opt.lin_input_dim) + 'd_' + opt.which_layer + '_' +str(opt.num_epochs) +'epochs.pt'. As an example, the model for the grading task trained with all three level features is saved as "split1_grad_720d_all_50epochs.pt".

• After training, the model will also output the feature importance computed by the FGS mechanism, showing the contribution of each gene to the prediction task.

• The model prediction is saved in the .pkl format, including the following information: risk_pred_all, survtime_all, censor_all, probs_all, gt_all.

Usage

Step1: gene co-expression network computation.

run WGCNA_gbmlgg.R

** The adjacency matrix computed by the WGCNA algorithm should be saved in the folder "./example_data".

Step2: Model inference.

### The users should parse different arguments to change the experiment settings and evaluate different models.
python3 test_cv.py

Step3: Model interpretation.

### You can compute the feature importance with the FGS mechanism with the following script.
python3 gradients_to_feature_importance.py

Scripts

test_cv.py: Load the well-trained model from the folder “/pretrained_models/…” and test the performance on the testing set of the 15 splits.

test_model.py: the definitions for "test".

model_GAT.py: the definitions for the network optimizer and the GAT network, which can be selected as 720d model(GAT_features = layer1+layer2+layer3) or 240d (either use the layer1, or layer2, or layer3 as the GAT features) model.

model_GAT_v4.py: Optimized implementation of the GAT layer, we employed the “GATconv” function encapsulated in the pytorch Geometric package, which is optimized to save computational cost.

utils.py: contains data_loader and other functions (cindex, cox_loss, …).

options.py: Contains all the options for the argparser.

WGCNA_gbmlgg.R: compute the adjacency matrix using WGCNA method.

gradients_to_feature_importance.py: combine the gradients produced by different splits, and obtain the feature importance according to the proposed FGS mechanism.

Disclaimer

This tool is for research purpose and not approved for clinical use.

This is not an official Tencent product.

Copyright

This tool is developed in Tencent AI Lab.

The copyright holder for this project is Tencent AI Lab.

All rights reserved.