import os from datetime import datetime import argparse os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVICES"] = "-1" import pandas as pd import numpy as np from tqdm import tqdm import networkx as nx import stellargraph as sg from stellargraph.mapper import PaddedGraphGenerator from stellargraph.layer import DeepGraphCNN from sklearn.model_selection import train_test_split from sklearn.preprocessing import LabelBinarizer from sklearn.metrics import accuracy_score from tensorflow.keras.callbacks import Callback, ModelCheckpoint from tensorflow.keras import Model from tensorflow.keras.optimizers import Adam from tensorflow.keras.layers import Dense, Conv1D, MaxPool1D, Dropout, Flatten from tensorflow.keras.losses import binary_crossentropy, categorical_crossentropy import wandb def load_graphs_to_stellargraph(graph_uris, graphs_dir): uri_to_sg_graph = {} for uri in tqdm(graph_uris): file_path = os.path.join(graphs_dir, uri.lstrip('http://kglids.org/resource/kaggle/') + '.tsv') df_spo = pd.read_csv(file_path, delimiter='\t').astype(str) node_embeddings = pd.read_pickle(file_path.replace('.tsv', '.pickle')) g = nx.DiGraph() df_spo.apply(lambda x: g.add_edge(x['s'], x['o'], type=x['p']), axis=1) for node in g.nodes(): g.nodes[node]['features'] = node_embeddings[node]['transE'] # ['complEx'] # TODO: complEx or transE? g = sg.StellarDiGraph.from_networkx(g, edge_type_attr='type', node_features='features') uri_to_sg_graph[uri] = g return uri_to_sg_graph def train_and_evaluate_classification_model(train_graphs, val_graphs, test_graphs, train_labels, val_labels, test_labels, epochs=100, batch_size=50, sysname='KGLiDS'): gen = PaddedGraphGenerator(graphs=train_graphs + val_graphs + test_graphs) k = wandb.config.k # the number of rows for the output tensor layer_sizes = [wandb.config.gcn_layer_size] * (wandb.config.gcn_layers - 1) + [1] # last layer is of size 1. activations = ["tanh"] * wandb.config.gcn_layers dgcnn_model = DeepGraphCNN( layer_sizes=layer_sizes, activations=activations, k=k, bias=False, generator=gen, ) x_inp, x_out = dgcnn_model.in_out_tensors() x_out = Conv1D(filters=16, kernel_size=sum(layer_sizes), strides=sum(layer_sizes))(x_out) x_out = MaxPool1D(pool_size=2)(x_out) x_out = Conv1D(filters=32, kernel_size=5, strides=1)(x_out) x_out = Flatten()(x_out) x_out = Dense(units=wandb.config.fc_size, activation="relu")(x_out) # 128 x_out = Dropout(rate=wandb.config.dropout)(x_out) predictions = Dense(units=1, activation="sigmoid")(x_out) model = Model(inputs=x_inp, outputs=predictions) model.compile(optimizer=Adam(learning_rate=wandb.config.lr), loss=binary_crossentropy, metrics=["acc"]) train_gen = gen.flow( graphs=train_graphs, targets=train_labels, batch_size=batch_size, symmetric_normalization=False, ) val_gen = gen.flow( graphs=val_graphs, targets=val_labels, batch_size=1, symmetric_normalization=False, ) test_gen = gen.flow( graphs=test_graphs, targets=test_labels, batch_size=1, symmetric_normalization=False, ) checkpoint = ModelCheckpoint(f'tmp/{task}_{sysname}.h5', verbose=False, monitor='val_acc', save_weights_only=True, save_best_only=True, mode='max') # fit history = model.fit(train_gen, epochs=epochs, verbose=1, validation_data=val_gen, shuffle=True, callbacks=[checkpoint]) # , callbacks=[Metrics(model, test_graphs, test_labels)]) for i in range(len(history.history['loss'])): wandb.log({"Epoch": i + 1, f"{sysname} Train Loss": history.history['loss'][i], f"{sysname} Train Acc": history.history['acc'][i], f"{sysname} Valid Loss": history.history['val_loss'][i], f"{sysname} Valid Acc": history.history['val_acc'][i]}) model.load_weights(f'tmp/{task}_{sysname}.h5') # best model test_predictions = model.predict(test_gen) test_accuracy = accuracy_score(test_labels, test_predictions.round()) print(f"{sysname} Test Accuracy:", round(test_accuracy, 4)) best_epoch = np.argmax(history.history['val_acc']) wandb.log({f"{sysname} Best Train Acc": history.history['acc'][best_epoch], f"{sysname} Best Valid Acc": history.history['val_acc'][best_epoch], f"{sysname} Test Acc": round(test_accuracy, 4)}) sg.utils.plot_history(history) parser = argparse.ArgumentParser() parser.add_argument('--epochs', type=int, default=30) parser.add_argument('--dropout', type=float, default=0.25) parser.add_argument('--lr', type=float, default=0.0001) parser.add_argument('--gcn_layers', type=int, default=3) parser.add_argument('--gcn_layer_size', type=int, default=32) parser.add_argument('--k', type=int, default=35) parser.add_argument('--fc_size', type=int, default=32) args = parser.parse_args() wandb.init(project="task2-classical-vs-deep", config={'epochs': args.epochs, 'dropout': args.dropout, 'lr': args.lr, 'gcn_layers': args.gcn_layers, 'gcn_layer_size': args.gcn_layer_size, 'k': args.k, 'fc_size': args.fc_size}) task = 'task2' # get graph names and classes uris_labels = pd.read_csv(f'{task}_uris_labels.csv') uris_labels = uris_labels[uris_labels['uri'].apply( lambda x: os.path.exists(f'{task}_kglids_graphs/' + x.lstrip('http://kglids.org/resource/kaggle/') + '.tsv'))] uris_labels = uris_labels[uris_labels['uri'].apply( lambda x: os.path.exists(f'{task}_kglids_graphs/' + x.lstrip('http://kglids.org/resource/kaggle/') + '.pickle'))] uris_labels = uris_labels[uris_labels['uri'].apply( lambda x: os.path.exists(f'{task}_graph4code_graphs/' + x.lstrip('http://kglids.org/resource/kaggle/') + '.tsv'))] uris_labels = uris_labels[uris_labels['uri'].apply(lambda x: os.path.exists( f'{task}_graph4code_graphs/' + x.lstrip('http://kglids.org/resource/kaggle/') + '.pickle'))] uris_labels['label'] = uris_labels['label'].astype('category').cat.codes pips = uris_labels['uri'].tolist() labels = uris_labels['label'].tolist() print(len(pips), 'Pipelines') print(uris_labels.label.value_counts()) train_names, test_names, train_labels, test_labels = train_test_split(pips, labels, train_size=0.8, stratify=labels, random_state=3) val_names, test_names, val_labels, test_labels = train_test_split(test_names, test_labels, train_size=0.5, stratify=test_labels, random_state=3) kglids_stellargraph = load_graphs_to_stellargraph(pips, f'{task}_kglids_graphs') d0 = datetime.now() train_and_evaluate_classification_model(train_graphs=[kglids_stellargraph[i] for i in train_names], val_graphs = [kglids_stellargraph[i] for i in val_names], test_graphs=[kglids_stellargraph[i] for i in test_names], train_labels=train_labels, val_labels=val_labels, test_labels=test_labels, epochs=wandb.config.epochs, batch_size=50, sysname='KGLiDS') d1 = datetime.now() kglids_stellargraph=None graph4code_stellargraph = load_graphs_to_stellargraph(pips, f'{task}_graph4code_graphs') d2 = datetime.now() train_and_evaluate_classification_model(train_graphs=[graph4code_stellargraph[i] for i in train_names], val_graphs=[graph4code_stellargraph[i] for i in val_names], test_graphs=[graph4code_stellargraph[i] for i in test_names], train_labels=train_labels, val_labels=val_labels, test_labels=test_labels, epochs=wandb.config.epochs, batch_size=5, sysname='GraphGen4Code') d3 = datetime.now() print('KGLiDS Time:', d1 - d0) print('GraphGen4Code Time:', d3 - d2)