SiNE embeddings

Author: NoeCecillon

SiNE/graph.py

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+import networkx as nx
+import numpy as np
+import csv
+
+# From https://github.com/CompNet/SignedCentrality
+
+class Vocabulary(object):
+    def __init__(self, graph):
+        self._id2node = {}
+        self._node2id = {}
+        self._curr_id = 1
+        for node in graph.nodes():
+            if node not in self._node2id:
+                self._curr_id += 1
+                self._node2id[node] = self._curr_id
+                self._id2node[self._curr_id] = node
+
+    def id2node(self, id):
+        return self._id2node[id]
+
+    def node2id(self, node):
+        return self._node2id[node]
+
+    def augment(self, graph):
+        for node in graph.nodes():
+            if node not in self._node2id:
+                self._curr_id += 1
+                self._node2id[node] = self._curr_id
+                self._id2node[self._curr_id] = node
+
+    def __len__(self):
+        return self._curr_id
+
+
+class Graph(object):
+    def __init__(self, positive_graph, negative_graph):
+        self.positive_graph = positive_graph
+        self.negative_graph = negative_graph
+        self.vocab = Vocabulary(positive_graph)
+        self.vocab.augment(negative_graph)
+
+    def get_positive_edges(self):
+        return self.positive_graph.edges()
+
+    def get_negative_edges(self):
+        return self.negative_graph.edges()
+
+    def __len__(self):
+        return len(self.vocab)
+        #return max(len(self.positive_graph), len(self.negative_graph))
+
+    def get_triplets(self, p0=True, ids=True):
+        triplets = []
+        for xi in self.positive_graph.nodes():
+            for xj in self.positive_graph[xi]:
+                if xj in self.negative_graph:
+                    for xk in self.negative_graph[xj]:
+                        a, b, c = xi, xj, xk
+                        if ids:
+                            a = self.vocab.node2id(xi)
+                            b = self.vocab.node2id(xj)
+                            c = self.vocab.node2id(xk)
+                        triplets.append([a, b, c])
+                elif p0:
+                    a, b = xi, xj
+                    c = 0
+                    if ids:
+                        a = self.vocab.node2id(xi)
+                        b = self.vocab.node2id(xj)
+                    triplets.append([a, b, c])
+        triplets = np.array(triplets)
+        return triplets
+
+    @staticmethod
+    def read_from_file(filepath, delimiter=',', directed=False):
+        positive_graph = nx.DiGraph() if directed else nx.Graph()
+        negative_graph = nx.DiGraph() if directed else nx.Graph()
+        file = open(filepath)
+        #skip header line
+        next(file)
+        for line in file:
+            line = line.strip()
+            #print(line)
+            u, v, w = line.split(delimiter)
+            w = float(w)
+            if w > 0:
+                positive_graph.add_edge(u, v, weight=w)
+            if w < 0:
+                negative_graph.add_edge(u, v, weight=w)
+        file.close()
+        graph = Graph(positive_graph, negative_graph)
+        return graph
+
+
+
+
+
+
+

SiNE/learn_SiNE_emb.py

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+from SiNEmaster.graph import *
+from SiNEmaster.stemmodels import SiNE, fit_sine_model as fit_model
+import pickle
+
+#pickled list of labels
+labels_path = "labels.pickle"
+graphs_path = "data/CCS"
+
+embeddings = []
+labels = []
+with open(labels_path, "rb") as f:
+	lb = pickle.load(f)
+
+
+for i in range(2545):
+	try:
+		graph = Graph.read_from_file("%s/%s.csv" %(graphs_path, i), delimiter=',', directed=True)
+		if len(graph.get_positive_edges()) + len(graph.get_negative_edges()) > 1:
+
+			model = fit_model(
+						num_nodes=len(graph),
+						dims_arr=[32, 32],
+						triples=graph.get_triplets(),
+						triples0=None,
+						delta=1.0,
+						delta0=0.5,
+						batch_size=300,
+						batch_size0=300,
+						epochs=30,
+						lr=0.01,
+						lam=0.0001,
+						lr_decay=0.0,
+						p=2,
+						print_loss=False,
+						p0=False,
+					)
+
+			embedding = model.get_x()
+			embedding = embedding.detach().numpy().tolist()[0]
+			embeddings.append(embedding)
+			labels.append(lb[i])
+			print (i)
+	except:
+		print ("error")
+
+with open("out/SiNE/sine_embeddings.pkl", "wb") as f:
+	pickle.dump(embeddings, f)

SiNE/model.py

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+import torch
+import torch.nn as nn
+from torch.nn.parameter import Parameter
+from torch.autograd import Variable
+import numpy as np
+import torch.optim as optim
+
+# From https://github.com/CompNet/SignedCentrality
+
+def hadamard(x, y):
+    return x * y
+
+
+def average(x, y):
+    return (x + y)/2.0
+
+
+def l1(x, y):
+    return np.abs(x - y)
+
+
+def l2(x, y):
+    return np.power(x - y, 2)
+
+
+def concat(x, y):
+    return np.concatenate((x, y), axis=1)
+
+
+FEATURE_FUNCS = {
+    'l1': l1,
+    'l2': l2,
+    'concat': concat,
+    'average': average,
+    'hadamard': hadamard
+}
+
+
+class SiNE(nn.Module):
+    def __init__(self, num_nodes, dim1, dim2):
+        super(SiNE, self).__init__()
+        self.tanh = nn.Tanh()
+        self.embeddings = nn.Embedding(num_nodes + 1, dim1)
+        self.layer11 = nn.Linear(dim1, dim2, bias=False)
+        self.layer12 = nn.Linear(dim1, dim2, bias=False)
+        self.bias1 = Parameter(torch.zeros(1))
+        self.layer2 = nn.Linear(dim2, 1, bias=False)
+        self.bias2 = Parameter(torch.zeros(1))
+        self.register_parameter('bias1', self.bias1)
+        self.register_parameter('bias2', self.bias2)
+
+    def forward(self, xi, xj, xk, delta):
+        i_emb = self.embeddings(xi)
+        j_emb = self.embeddings(xj)
+        k_emb = self.embeddings(xk)
+
+        z11 = self.tanh(self.layer11(i_emb) + self.layer12(j_emb) + self.bias1)
+        z12 = self.tanh(self.layer11(i_emb) + self.layer12(k_emb) + self.bias1)
+
+        f_pos = self.tanh(self.layer2(z11) + self.bias2)
+        f_neg = self.tanh(self.layer2(z12) + self.bias2)
+
+        zeros = Variable(torch.zeros(1))
+
+        loss = torch.max(zeros, f_pos + delta - f_neg)
+        loss = torch.sum(loss)
+
+        return loss
+
+    def _regularizer(self, x):
+        zeros = torch.zeros_like(x)
+        normed = torch.norm(x - zeros, p=2)
+        term = torch.pow(normed, 2)
+        # print('The parameter of ', x)
+        # print('Yields ',term)
+        return term
+
+    def regularize_weights(self):
+        loss = 0
+        for parameter in self.parameters():
+            loss += self._regularizer(parameter)
+        return loss
+
+    def get_embedding(self, x):
+        x = Variable(torch.LongTensor([x]))
+        emb = self.embeddings(x)
+        emb = emb.data.numpy()[0]
+        return emb
+
+    def get_edge_feature(self, x, y, operation='hadamard'):
+        func = FEATURE_FUNCS[operation]
+        x = self.get_embedding(x)
+        y = self.get_embedding(y)
+        return func(x, y)
+
+
+
+
+def tensorfy_col(x, col_idx):
+    col = x[:,col_idx]
+    col = torch.LongTensor(col)
+    col = Variable(col)
+    return col
+
+
+def get_training_batch(triples, batch_size):
+    nrows = triples.shape[0]
+    rows = np.random.choice(nrows, batch_size, replace=False)
+    choosen = triples[rows,:]
+    xi = tensorfy_col(choosen, 0)
+    xj = tensorfy_col(choosen, 1)
+    xk = tensorfy_col(choosen, 2)
+    return xi, xj, xk
+
+
+def fit_model(sine, triplets, delta, batch_size, epochs, alpha,
+                lr=0.4, weight_decay=0.0, print_loss=True):
+    optimizer = optim.Adagrad(sine.parameters(), lr=lr, weight_decay=weight_decay)
+    for epoch in range(epochs):
+        sine.zero_grad()
+        xi, xj, xk = get_training_batch(triplets, batch_size)
+        loss = sine(xi, xj, xk, delta)
+        # print(loss)
+        regularizer_loss = alpha * sine.regularize_weights()
+        # print(regularizer_loss)
+        loss += regularizer_loss
+        loss.backward()
+        optimizer.step()
+        if print_loss:
+            print('Loss at epoch ', epoch + 1, ' is ', loss.data[0])
+    return sine
+
+
+

SiNE/stemgraph.py

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+import networkx as nx
+import numpy as np
+
+# From https://github.com/CompNet/SignedCentrality
+
+def get_empty_graph(directed=True):
+    if directed:
+        return nx.DiGraph()
+    return nx.Graph()
+
+def from_edgelist_array_to_graph(X, y, directed=True):
+    positive_graph = get_empty_graph(directed)
+    negative_graph = get_empty_graph(directed)
+
+    for edge, label in zip(X, y):
+        u, v = edge
+        if label == 0:
+            negative_graph.add_edge(u, v)
+        else:
+            positive_graph.add_edge(u, v)
+    return positive_graph, negative_graph
+
+
+def get_triples(positive_graph, negative_graph, p0=True):
+    triples = []
+    triples0 = []
+    for u, v in positive_graph.edges():
+        if v in negative_graph:
+            v_neigbors = negative_graph[v]
+            for w in v_neigbors:
+                triple = (u, v, w)
+                triples.append(triple)
+        elif p0:
+            triple0 = (u, v, 0)
+            triples0.append(triple0)
+    triples = np.array(triples)
+    triples0 = np.array(triples0)
+    if p0:
+        return triples, triples0
+    return triples
+
+