Source code for pygod.models.scan

# -*- coding: utf-8 -*-
""" Structural Clustering Algorithm for Networks
# Author: Kay Liu <>
# License: BSD 2 clause

import math
import torch
import warnings
from torch import nn
import networkx as nx
from pygod.metrics import *
import torch.nn.functional as F
from torch_geometric.utils import to_dense_adj
from sklearn.utils.validation import check_is_fitted

from . import BaseDetector
from ..utils import validate_device

[docs]class SCAN(BaseDetector): """ SCAN (Structural Clustering Algorithm for Networks) is a clustering algorithm, which only takes the graph structure without the node features as the input. Note: This model will output detected clusters instead of "outliers" descibed in the original paper. See :cite:`xu2007scan` for details. Parameters ---------- eps : float, optional Neighborhood threshold. Default: ``.5``. mu : int, optional Minimal size of clusters. Default: ``2``. contamination : float, optional Valid in (0., 0.5). The proportion of outliers in the data set. Used when fitting to define the threshold on the decision function. Default: ``0.1``. verbose : bool Verbosity mode. Turn on to print out log information. Default: ``False``. Examples -------- >>> from pygod.models import SCAN >>> model = SCAN() >>> # PyG graph data object >>> prediction = model.predict(None) """ def __init__(self, eps=.5, mu=2, contamination=0.1, verbose=False): super(SCAN, self).__init__(contamination=contamination) # model param self.eps = eps = mu # other param self.verbose = verbose self.model = None
[docs] def fit(self, G, y_true=None): """ Fit detector with input data. Parameters ---------- G : The input data. y_true : numpy.ndarray, optional The optional outlier ground truth labels used to monitor the training progress. They are not used to optimize the unsupervised model. Default: ``None``. Returns ------- self : object Fitted estimator. """ decision_scores = np.zeros(G.num_nodes) G = self.process_graph(G) c = 0 clusters = {} nomembers = [] for n in G.nodes(): if self.hasLabel(clusters, n): continue else: N = self.neighborhood(G, n) if len(N) > c = c + 1 Q = self.neighborhood(G, n) clusters[c] = [] # append core vertex itself clusters[c].append(n) while len(Q) != 0: w = Q.pop(0) R = self.neighborhood(G, w) # include current vertex itself R.append(w) for s in R: if not (self.hasLabel(clusters, s)) or \ s in nomembers: clusters[c].append(s) if not (self.hasLabel(clusters, s)): Q.append(s) else: nomembers.append(n) for k, v in clusters.items(): decision_scores[v] = 1 if self.verbose and y_true is not None: auc = eval_roc_auc(y_true, decision_scores) print("AUC {:.4f}".format(auc)) self.decision_scores_ = decision_scores self._process_decision_scores() return self
[docs] def similarity(self, G, v, u): v_set = set(G.neighbors(v)) u_set = set(G.neighbors(u)) inter = v_set.intersection(u_set) if inter == 0: return 0 # need to account for vertex itself, add 2(1 for each vertex) sim = (len(inter) + 2) / ( math.sqrt((len(v_set) + 1) * (len(u_set) + 1))) return sim
[docs] def neighborhood(self, G, v): eps_neighbors = [] v_list = G.neighbors(v) for u in v_list: if (self.similarity(G, u, v)) > self.eps: eps_neighbors.append(u) return eps_neighbors
[docs] def hasLabel(self, cliques, vertex): for k, v in cliques.items(): if vertex in v: return True return False
[docs] def sameClusters(self, G, clusters, u): n = G.neighbors(u) b = [] i = 0 while i < len(n): for k, v in clusters.items(): if n[i] in v: if k in b: continue else: b.append(k) i = i + 1 if len(b) > 1: return False return True
[docs] def decision_function(self, G): """ Predict raw anomaly score using the fitted detector. Outliers are assigned with larger anomaly scores. Parameters ---------- G : PyTorch Geometric Data instance ( The input data. Returns ------- outlier_scores : numpy.ndarray The anomaly score of shape :math:`N`. """ check_is_fitted(self, ['model']) if G is not None: warnings.warn('The model is transductive only. ' 'Training data is used to predict') outlier_scores = self.decision_scores_ return outlier_scores
[docs] def process_graph(self, G): """ Process the raw PyG data object into a tuple of sub data objects needed for the model. Parameters ---------- G : PyTorch Geometric Data instance ( The input data. Returns ------- G : networkx.classes.graph.Graph NetworkX Graph """ G = nx.from_edgelist(G.edge_index.T.tolist()) return G