from __future__ import print_function import json import numpy as np from networkx.readwrite import json_graph from argparse import ArgumentParser def run_regression(train_embeds, train_labels, test_embeds, test_labels): np.random.seed(1) from sklearn.linear_model import SGDClassifier from sklearn.dummy import DummyClassifier from sklearn.metrics import f1_score from sklearn.multioutput import MultiOutputClassifier dummy = MultiOutputClassifier(DummyClassifier()) dummy.fit(train_embeds, train_labels) log = MultiOutputClassifier(SGDClassifier(loss="log"), n_jobs=10) log.fit(train_embeds, train_labels) print("F1 score", f1_score(test_labels, log.predict(test_embeds), average="micro")) print("Random baseline F1 score", f1_score(test_labels, dummy.predict(test_embeds), average="micro")) if __name__ == '__main__': parser = ArgumentParser("Run evaluation on PPI data.") parser.add_argument("dataset_dir", help="Path to directory containing the dataset.") parser.add_argument("data_dir", help="Path to directory containing the learned node embeddings. Set to 'feat' for raw features.") parser.add_argument("setting", help="Either val or test.") args = parser.parse_args() dataset_dir = args.dataset_dir data_dir = args.data_dir setting = args.setting print("Loading data...") G = json_graph.node_link_graph(json.load(open(dataset_dir + "/ppi-G.json"))) labels = json.load(open("/dfs/scratch0/graphnet/ppi/ppi-class_map.json")) labels = {int(i):l for i, l in labels.iteritems()} train_ids = [n for n in G.nodes() if not G.node[n]['val'] and not G.node[n]['test']] test_ids = [n for n in G.nodes() if G.node[n][setting]] train_labels = np.array([labels[i] for i in train_ids]) test_labels = np.array([labels[i] for i in test_ids]) print("running", data_dir) if data_dir == "feat": print("Using only features..") feats = np.load(dataset_dir + "/ppi-feats.npy") ## Logistic gets thrown off by big counts, so log transform num comments and score feats[:,0] = np.log(feats[:,0]+1.0) feats[:,1] = np.log(feats[:,1]-min(np.min(feats[:,1]), -1)) feat_id_map = json.load(open("/dfs/scratch0/graphnet/ppi/ppi-id_map.json")) feat_id_map = {int(id):val for id,val in feat_id_map.iteritems()} train_feats = feats[[feat_id_map[id] for id in train_ids]] test_feats = feats[[feat_id_map[id] for id in test_ids]] print("Running regression..") from sklearn.preprocessing import StandardScaler scaler = StandardScaler() scaler.fit(train_feats) train_feats = scaler.transform(train_feats) test_feats = scaler.transform(test_feats) run_regression(train_feats, train_labels, test_feats, test_labels) else: embeds = np.load(data_dir + "/val.npy") id_map = {} with open(data_dir + "/val.txt") as fp: for i, line in enumerate(fp): id_map[int(line.strip())] = i train_embeds = embeds[[id_map[id] for id in train_ids]] test_embeds = embeds[[id_map[id] for id in test_ids]] print("Running regression..") run_regression(train_embeds, train_labels, test_embeds, test_labels)