from __future__ import print_function import json import numpy as np from networkx.readwrite import json_graph from argparse import ArgumentParser def get_class_labels(ids): subjs = ["CU", "DA", "DR", "NI", "GU", "IA"] class_map = {} for i, code in enumerate(subjs): with open("/dfs/scratch0/scisurv/clean/{}.tsv".format(code)) as fp: fp.readline() for line in fp: class_map[int(line.split()[0])] = i classes = [class_map[i] for i in ids] return classes 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 dummy = DummyClassifier() dummy.fit(train_embeds, train_labels) log = 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 citation 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.") 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 + "/isi-G.json"))) 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]] test_labels = get_class_labels(test_ids) train_labels = get_class_labels(train_ids) if data_dir == "feat": print("Using only features..") feats = np.load(dataset_dir + "/isi-feats.npy") feat_id_map = json.load(open(dataset_dir + "/isi-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..") run_regression(train_feats, train_labels, test_feats, test_labels) elif "n2v" in data_dir: print("Using n2v vectors.") base_embeds = np.load(data_dir + "/val.npy") base_id_map = {} with open(data_dir + "/val.txt") as fp: for i, line in enumerate(fp): base_id_map[int(line.strip())] = i tuned_embeds = np.load(data_dir + "/val-test.npy") tuned_id_map = {} with open(data_dir + "/val-test.txt") as fp: for i, line in enumerate(fp): tuned_id_map[int(line.strip())] = i train_embeds = base_embeds[[base_id_map[id] for id in train_ids]] test_embeds = tuned_embeds[[tuned_id_map[id] for id in test_ids]] print("Running regression..") run_regression(train_embeds, train_labels, test_embeds, test_labels) # loading feats feats = np.load(dataset_dir + "/isi-feats.npy") feat_id_map = json.load(open(dataset_dir + "/isi-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]] train_embeds = np.hstack([train_feats, train_embeds]) test_embeds = np.hstack([test_feats, test_embeds]) from sklearn.preprocessing import StandardScaler scaler = StandardScaler() scaler.fit(train_embeds) train_embeds = scaler.transform(train_embeds) test_embeds = scaler.transform(test_embeds) print("Running regression with feats..") run_regression(train_embeds, train_labels, test_embeds, 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)