deepSnapPred.py

import copy
from sklearn.metrics import roc_auc_score
from utilities import plot_roc, plot_prc
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from matplotlib import pyplot as plt
import heterograph_construction
from datetime import datetime
from deepsnap.dataset import GraphDataset
from deepsnap.batch import Batch
from deepsnap.hetero_gnn import (
    HeteroSAGEConv,
    HeteroConv,
    forward_op
)

#DeepSnap has some deprecated functions and throws a warning.
import warnings
warnings.filterwarnings("ignore")

edges = [('phenotype', 'dis_dru_the', 'drug')]
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')

# ---------------------------
# FUNCTIONS
# ---------------------------
def generate_convs_link_pred_layers(hete, conv, hidden_size):
    convs1 = {}
    convs2 = {}
    for message_type in hete.message_types:
        n_type = message_type[0]
        s_type = message_type[2]
       
        # Attention: This should be changed to n_feat_dim = hete.num_node_features(n_type) and s_feat_dim = hete.num_node_features(s_type)
        # If features are not an identity matrix.
        n_feat_dim = hete.num_node_features(n_type)
        s_feat_dim = hete.num_node_features(s_type)

        convs1[message_type] = conv(n_feat_dim, hidden_size, s_feat_dim)
        convs2[message_type] = conv(hidden_size, hidden_size)
    return [convs1, convs2]

class HeteroGNN(torch.nn.Module):
    def __init__(self, convs, hetero, hidden_size, dropout):
        super(HeteroGNN, self).__init__()

        self.convs1 = HeteroConv(convs[0])  # Wrap the heterogeneous GNN layers
        self.convs2 = HeteroConv(convs[1])
         
        self.bns1 = nn.ModuleDict()
        self.bns2 = nn.ModuleDict()
        
        self.dropout1 = nn.ModuleDict()
        
        self.relus1 = nn.ModuleDict()
        
        self.loss_fn = torch.nn.BCEWithLogitsLoss()
        
        
        for node_type in hetero.node_types:
            self.bns1[node_type] = nn.BatchNorm1d(hidden_size)
            self.bns2[node_type] = nn.BatchNorm1d(hidden_size)
            
            self.dropout1[node_type] = nn.Dropout(p=dropout)
            
            self.relus1[node_type] = nn.LeakyReLU()
            
            
    def getEmbeddings(self, data, training = True):
        x = data.node_feature
        edge_index = data.edge_index
        edge_weight = data.edge_feature
        keys = [key for key in edge_weight]
        for key in keys:
            newKey = key[1]
            edge_weight[newKey] = edge_weight[key]
            del edge_weight[key]

        x = self.convs1(x, edge_index, edge_weight)
        x = forward_op(x, self.bns1)
        x = forward_op(x, self.relus1)
        
        x = forward_op(x, self.dropout1)
        x = self.convs2(x, edge_index, edge_weight)
        x = forward_op(x, self.bns2)
       
        return x
      
    def forward(self, data):
        x = self.getEmbeddings(data)

        pred = {}
        pred2 = {}
        for message_type in edges:
            nodes_first = None
            nodes_second = None
            if message_type == ('phenotype', 'dis_dru_the', 'drug'):
                nodes_first = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][0, :].long())
                nodes_second = torch.index_select(x['drug'], 0, data.edge_label_index[message_type][1, :].long())

            elif message_type == ('drug', 'dru_dis_the', 'phenotype'):
                nodes_first = torch.index_select(x['drug'], 0, data.edge_label_index[message_type][0, :].long())
                nodes_second = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][1, :].long())
                
            elif message_type == ('phenotype', 'dse_sym', 'phenotype'):
                nodes_first = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][0, :].long())
                nodes_second = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][1, :].long())
                
            elif message_type == ('phenotype', 'sym_dse', 'phenotype'):
                nodes_first = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][0, :].long())
                nodes_second = torch.index_select(x['phenotype'], 0, data.edge_label_index[message_type][1, :].long())
                
            pred[message_type] = torch.sigmoid(torch.sum(nodes_first * nodes_second, dim=-1))
       
        return pred
     
    def predict_all(self, data):
        x = self.getEmbeddings(data)
        
        pred = {}
        for message_type in edges:
            nodes_first = None
            nodes_second = None
            if message_type == ('phenotype', 'dis_dru_the', 'drug'):
                nodes_first = x['phenotype']
                nodes_second = x['drug']
                    
            for i, elem in enumerate(nodes_first):
                pred[message_type, i] = torch.sigmoid(torch.sum(elem * nodes_second, dim=-1))
        return pred
        
    def predict_all_type(self, data, type, id):
        x = self.getEmbeddings(data)

        pred = {}
        for message_type in edges:
            nodes_first = None
            nodes_second = None
            if message_type == ('phenotype', 'dis_dru_the', 'drug') and type == 'phenotype':
                nodes_first = x['phenotype'][id].unsqueeze(0)
                nodes_second = x['drug']

            elif message_type == ('phenotype', 'dis_dru_the', 'drug') and type == 'drug':
                nodes_first = x['phenotype']
                nodes_second = x['drug'][id].unsqueeze(0)

            elif message_type == ('phenotype', 'dse_sym', 'phenotype'):
                nodes_first = x['phenotype']
                nodes_second = x['phenotype']

            for i, elem in enumerate(nodes_first):
                pred[message_type, i] = torch.sigmoid(torch.sum(elem * nodes_second, dim=-1))
        return pred
        
    def pred(self, data, eid):
        x = self.getEmbeddings(data, False)
        heads = x['phenotype']
        tails = x['drug']
        pred = []
        for head, tail in zip(eid[0], eid[1]):
            pred.append(torch.sigmoid(torch.sum(heads[head] * tails[tail], dim=-1)))
        return pred

    def loss(self, pred, y):
        loss = 0
        for key in pred:
            loss += self.loss_fn(pred[key], y[key].type(pred[key].dtype))
        return loss


def train(model, dataloaders, optimizer, epochs):
    min_value = 1
    best_model = model
    t_accu = []
    v_accu = []
    e_accu = []
    lossL = []
    lossLV = []
    criterion = torch.nn.BCEWithLogitsLoss()
    for epoch in range(1, epochs + 1):
        for batch in dataloaders['train']:
            batch.to(device)
            model.train()
            
            optimizer.zero_grad()
            
            pred = model(batch)
                        
            loss = model.loss(pred, batch.edge_label)

            if epoch == epochs:
                loss.backward()
            else:
                loss.backward(retain_graph=True)
            optimizer.step()

            accs = test(model, dataloaders)

            #log = '     Epoch: {:03d}, Loss: {:.4f}, Train: {:.4f}, Val: {:.4f}, Test: {:.4f}'
            #print(log.format(epoch, loss.item(), accs['train'], accs['val'], accs['test']))
            
            t_accu.append(accs['train'])
            v_accu.append(accs['val'])
            e_accu.append(accs['test'])
            
            lossL.append(loss.cpu().detach().numpy())
            lossLV.append(accs['valLoss'].cpu().detach().numpy())

            if min_value > lossLV[-1] and epoch >= epochs - 200:
                min_value = lossLV[-1]
                best_model = copy.deepcopy(model)
                best_it = epoch
                
            torch.cuda.empty_cache()
            
    log = 'Best: Iteration {:d} Train: {:.4f}, Val: {:.4f}, Test: {:.4f}'
    accs = test(best_model, dataloaders)
    print(log.format(best_it, accs['train'], accs['val'], accs['test']))
     
    plt.plot(lossL)
    plt.plot(lossLV)
    plt.plot(best_it,min_value,'k+', linewidth=100)
    plt.title('Loss Evolution')
    plt.legend(['Train', 'Validation','Best Model'])
    plt.ylabel('Loss')
    plt.xlabel('Iteration')
    plt.xticks(range(0, epochs+1, int(epochs/10)))
    plt.yticks((0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85))
    plt.savefig('plots/behor/metrics/loss.svg', format='svg', dpi=1200)
    plt.clf()
    
    return t_accu, v_accu, e_accu, best_model


def test(model, dataloaders):
    model.eval()
    accs = {}
    for mode, dataloader in dataloaders.items():
        acc = 0
        num = 0
        for batch in dataloader:
            batch.to(device)
            pred = model(batch)
            loss = model.loss(pred, batch.edge_label)
            for key in pred:
                pred = pred[key].flatten().cpu().detach().numpy()
                label = batch.edge_label[key].flatten().cpu().numpy()
             
                acc += roc_auc_score(label, pred)
                num += 1

        accs[mode] = acc / num
        accs[mode+'Loss'] = loss
    return accs


def test2(model, test_loader):
    true_labels = []
    keys = []
    pure_pred_labels = []
    for batch in test_loader:
        batch.to(device)
        pred = model(batch)
        for key in pred:
            p = pred[key].cpu().detach().numpy()
            pure_pred_labels.append(p)
            true_labels.append(batch.edge_label[key].cpu().detach().numpy())
            keys.append(key)
    return pure_pred_labels, true_labels, keys


def main(epochs, hidden_dim, lr, weight_decay, dropout):
    constructor = heterograph_construction.DISNETConstructor(device='cuda')
    hetero, _ = constructor.DISNETHeterographDeepSnap(full=False, withoutRepoDB=True)

    edge_train_mode = 'disjoint'
    print('edge train mode: {}'.format(edge_train_mode))
    dataset = GraphDataset(
        [hetero],
        task='link_pred',
        edge_train_mode=edge_train_mode,
        edge_message_ratio=0.8,
        edge_negative_sampling_ratio=1
    )

    dataset_train, dataset_val, dataset_test = dataset.split(
        transductive=True, split_ratio=[0.8, 0.1, 0.1], shuffle=True
    )

    train_loader = DataLoader(
        dataset_train, collate_fn=Batch.collate(), batch_size=1
    )
    val_loader = DataLoader(
        dataset_val, collate_fn=Batch.collate(), batch_size=1
    )
    test_loader = DataLoader(
        dataset_test, collate_fn=Batch.collate(), batch_size=1
    )
    dataloaders = {
        'train': train_loader, 'val': val_loader, 'test': test_loader
    }

    convs = generate_convs_link_pred_layers(hetero, HeteroSAGEConv, hidden_dim)
    model = HeteroGNN(convs, hetero, hidden_dim, dropout).to(device)
    optimizer = torch.optim.Adam(
        model.parameters(), lr=lr, weight_decay=weight_decay)

    print("Started training at", datetime.now().strftime("%H:%M:%S"))
    _, _, _, model = train(model, dataloaders, optimizer, epochs)
    print("Finished training at", datetime.now().strftime("%H:%M:%S"))

    torch.save(model.state_dict(), "models/behor")

    # Testing
    model.eval()

    print("Started testing at", datetime.now().strftime("%H:%M:%S"))
    pure_pred_labels, true_labels, keys = test2(model, test_loader)
    print("Finished testing at", datetime.now().strftime("%H:%M:%S"))

    labels = [item for sublist in true_labels for item in sublist]
    pure_predictions = [item for sublist in pure_pred_labels for item in sublist]
    
    plot_roc(labels, pure_predictions, keys[0], "behor/")
    plot_prc(torch.tensor(labels), pure_predictions, keys[0], "behor/")
    return model


if __name__ == '__main__':
    main(2752, 107, 0.0008317, 0.006314, 0.8)