import os import random import numpy as np import matplotlib.pyplot as plt import spektral.datasets as ds import networkx as nx import tensorflow as tf import gradio as gr from tensorflow.keras.callbacks import EarlyStopping from tensorflow.keras.losses import CategoricalCrossentropy from tensorflow.keras.optimizers import Adam from tensorflow.keras import layers from spektral.layers import GCNConv from spektral.layers.convolutional import gcn_conv from spektral.transforms import LayerPreprocess from spektral.transforms import GCNFilter from spektral.data import Dataset from spektral.data import Graph from spektral.data.loaders import SingleLoader tf.config.run_functions_eagerly(True) # Cora (public split) data = ds.citation.Citation("Cora", random_split=False, normalize_x=False) # generate visualisation for the test set G = nx.from_scipy_sparse_matrix(data[0].a) for index, val_mask in enumerate(data.mask_te): if val_mask == 0: G.remove_node(index) default_plot = plt.figure() default_ax = default_plot.add_subplot(111) pos = nx.kamada_kawai_layout(G) nx.draw(G, pos=pos, node_size=30, node_color="grey") plt.title("unlabeled test set") # apply gcn filter to adjacency matrix data.apply(GCNFilter()) def add_fully_connected_layer(model_description, number_of_channels): if len(model_description) >= 20: return model_description else: return model_description[:-1] + [ (str(number_of_channels), "fully connected layer"), model_description[-1], ] def add_gcl_layer(model_description, number_of_channels): if len(model_description) >= 20: return model_description else: return model_description[:-1] + [ (str(number_of_channels), "graph convolutional layer"), model_description[-1], ] def add_dropout_layer(model_description, dropout_rate): if len(model_description) >= 20: return model_description else: return model_description[:-1] + [ (str(dropout_rate), "dropout layer"), model_description[-1], ] def fit_model(model_description, learning_rate, l2_regularization): # set seeds for reproducibility seed_number = 123 os.environ["PYTHONHASHSEED"] = str(seed_number) random.seed(seed_number) np.random.seed(seed_number) tf.random.set_seed(seed_number) l2_reg_value = l2_regularization model_description = model_description[1:-1] class graph_nn(tf.keras.Model): def __init__( self, ): super().__init__() self.list_of_layers = [] for tpl_value_layer in model_description: layer_name = tpl_value_layer[1] layer_value = tpl_value_layer[0] if layer_name == "fully connected layer": self.list_of_layers.append( layers.Dense(int(layer_value), activation="relu") ) elif layer_name == "graph convolutional layer": self.list_of_layers.append( gcn_conv.GCNConv( channels=int(layer_value), activation="relu", kernel_regularizer=tf.keras.regularizers.l2(l2_reg_value), use_bias=True, ) ) elif layer_name == "dropout layer": self.list_of_layers.append(layers.Dropout(float(layer_value))) self.output_layer = layers.Dense(7, activation="softmax") def call(self, inputs): x, a = inputs for index, tpl_value_layer in enumerate(model_description): if tpl_value_layer[1] == ("graph convolutional layer"): x = self.list_of_layers[index]([x, a]) else: x = self.list_of_layers[index](x) x = self.output_layer(x) return x model = graph_nn() model.compile( optimizer=Adam(learning_rate), loss=CategoricalCrossentropy(reduction="sum"), metrics=["accuracy"], ) loader_tr = SingleLoader(data, sample_weights=data.mask_tr) loader_va = SingleLoader(data, sample_weights=data.mask_va) history = model.fit( loader_tr.load(), steps_per_epoch=loader_tr.steps_per_epoch, validation_data=loader_va.load(), validation_steps=loader_va.steps_per_epoch, epochs=2000, verbose=0, callbacks=[ EarlyStopping(patience=30, restore_best_weights=True) ], # , monitor="val_accuracy" ) return plot_loss(history), get_accuracy(model) def get_accuracy(model): loader_te = SingleLoader(data, sample_weights=data.mask_te) preds = model.predict(loader_te.load(), steps=loader_te.steps_per_epoch) ground_truths = data[0].y true_predictions = 0 false_predictions = 0 node_colors = [] for index, val_mask in enumerate(data.mask_te): if val_mask == 0: continue if np.argmax(preds[index]) == np.argmax(ground_truths[index]): true_predictions += 1 node_colors.append("green") else: false_predictions += 1 node_colors.append("red") accuracy = true_predictions / (true_predictions + false_predictions) fig = plt.figure() ax = fig.add_subplot(111) nx.draw(G, pos=pos, node_size=30, node_color=node_colors) plt.title("accuracy on test-set: " + str(accuracy)) return fig def plot_loss(model_history): fig = plt.figure() ax = fig.add_subplot(111) num_epochs = len(model_history.history["loss"]) plt.plot(list(range(num_epochs)), model_history.history["loss"], label="train loss") # 3.57 times more validation instances thann test instances plt.plot( list(range(num_epochs)), np.array(model_history.history["val_loss"]) / 3.57, label="validation loss", ) plt.plot( [num_epochs - 30, num_epochs - 30], [0, max(model_history.history["loss"])], "--", c="black", alpha=0.7, label="early stopping", ) plt.legend(loc="upper right", bbox_to_anchor=(1, 1)) return fig def reset_model(): return ( [ ("_Architecture_: input", "_Legend_:"), ("output", "_Legend_:"), ], default_plot, None, ) demo = gr.Blocks() with demo: gr.Markdown( """ # GNN construction site Welcome to the GNN construction site, where you can build your individual GNN using graph convolutional layers (GCLs) and fully connected layers. The GCLs were implemented using [Spektral](https://github.com/danielegrattarola/spektral/ "https://github.com/danielegrattarola/spektral/"), which builds on the Keras API. ### Data The input dataset is the public split of the Cora dataset ([benchmarks](https://paperswithcode.com/dataset/cora "https://paperswithcode.com/dataset/cora")). Currently, the state of the art [model](https://github.com/chennnM/GCNII "https://github.com/chennnM/GCNII") (doi: 10.48550/arXiv.2007.02133) achieves an accuracy of 0.855 on the test set of this public split. The input data consists of node features and an adjacency matrix. ### How to build 1. Use the sliders to adjust the number of neurons, channels or the dropout rate depending on which layer you want to add 2. Adding layers to your network will update the current model architecture shown in the middle 3. The "train and evaluate model" button will generate two figures after training your model, showing: - The loss during training - The performance on the test set (public split of Cora dataset) 4. Reset your model and try different architectures """ ) with gr.Row(): with gr.Column(): accuracy_plot = gr.Plot(value=default_plot, label="accuracy plot") with gr.Column(): loss_plot = gr.Plot(label="loss plot") with gr.Row(): with gr.Column(): with gr.Row(): number_of_neurons = gr.Slider( minimum=1, maximum=100, step=1, value=32, label="number of neurons for fully connected layer", ) with gr.Row(): number_of_channels = gr.Slider( minimum=1, maximum=100, step=1, value=32, label="number of channels for graph conv. layer", ) with gr.Row(): dropout_rate = gr.Slider( minimum=0, maximum=1, step=0.02, value=0.5, label="dropout rate" ) with gr.Row(): learning_rate = gr.Slider( minimum=0.001, maximum=0.02, step=0.001, value=0.005, label="learning rate", ) l2_regularization = gr.Slider( minimum=0.00005, maximum=0.001, step=0.00005, value=0.00025, label="L2 regularization factor", ) with gr.Column(): with gr.Row(): model_description = gr.Highlightedtext( value=[ ("_Architecture_: input", "_Legend_:"), ("output", "_Legend_:"), ], label="current model", show_legend=True, color_map={ "_Legend_:": "white", "fully connected layer": "blue", "graph convolutional layer": "red", "dropout layer": "yellow", }, ) with gr.Row(): button_add_fully_connected = gr.Button("add fully connected layer") button_add_fully_connected.click( fn=add_fully_connected_layer, inputs=[model_description, number_of_neurons], outputs=model_description, ) with gr.Row(): button_add_fully_connected = gr.Button("add graph convolutional layer") button_add_fully_connected.click( fn=add_gcl_layer, inputs=[model_description, number_of_channels], outputs=model_description, ) with gr.Row(): button_add_fully_connected = gr.Button("add dropout layer") button_add_fully_connected.click( fn=add_dropout_layer, inputs=[model_description, dropout_rate], outputs=model_description, ) with gr.Column(): with gr.Row(): button_fit_model = gr.Button("train and evaluate model") button_fit_model.click( fn=fit_model, inputs=[model_description, learning_rate, l2_regularization], outputs=[loss_plot, accuracy_plot], ) with gr.Row(): button_reset_model = gr.Button("reset model") button_reset_model.click( fn=reset_model, inputs=None, outputs=[model_description, accuracy_plot, loss_plot], ) with gr.Row(): gr.Markdown( """ ### Tips: - training and evaluating might take a moment - hovering over the legend at "current model" will highlight the respective layers - changing the learning rate or L2 regularization factor does not require a model reset """ ) demo.launch()