55
66def _config_str_to_dict (input_str ):
77 # e.g.
8- # input_str = "precision_recall_pair_threshold : 0.92 ,f_score_param: 0.5"
9- # result_dict = {'precision_recall_pair_threshold ': 0.92 , 'f_score_param': 0.5}
8+ # input_str = "precision_recall_pair_thresholds : 0.86;0.88;0.90;0.92;0.94 ,f_score_param: 0.5"
9+ # result_dict = {'precision_recall_pair_thresholds ': [0.86;0.88;0.90;0.92;0.94] , 'f_score_param': 0.5}
1010
1111
1212 # Split the string into key-value pairs
@@ -24,12 +24,15 @@ def _config_str_to_dict(input_str):
2424 value = value .strip ()
2525 # Convert the value to float if possible
2626 try :
27- value = float (value )
27+ if key == "precision_recall_pair_thresholds" :
28+ # Split the value by semicolons and convert each to float
29+ value = [float (v .strip ()) for v in value .split (';' )]
30+ else :
31+ value = float (value )
2832 except ValueError :
2933 pass # Keep the value as a string if it cannot be converted
3034 # Add the key-value pair to the dictionary
3135 result_dict [key ] = value
32-
3336 return result_dict
3437
3538
@@ -70,7 +73,7 @@ def read_ground_truth_pairs(ground_truth_file):
7073 print (f"Ignoring invalid line: { line .strip ()} )
7174 return pairs
7275
73- def compute_precision_recall (node_to_clusters , pairs , threshold ):
76+ def compute_precision_recall (node_to_clusters , pairs , thresholds , f_score_param ):
7477 """
7578 Computes precision and recall based on the clusters and ground truth pairs.
7679 Handles overlapping clusters where a node can belong to multiple clusters.
@@ -83,66 +86,74 @@ def compute_precision_recall(node_to_clusters, pairs, threshold):
8386 FP = 0 # False Positive
8487 FN = 0 # False Negative
8588
86- for node1 , node2 , weight in pairs :
87- # Determine if the pair is positive or negative
88- is_positive = weight > threshold
89-
90- # Determine if the nodes are in the same cluster (overlapping clusters)
91- if node1 in node_to_clusters and node2 in node_to_clusters :
92- clusters1 = node_to_clusters [node1 ]
93- clusters2 = node_to_clusters [node2 ]
94- in_same_cluster = bool (clusters1 & clusters2 ) # Check for non-empty intersection
95- else :
96- logging .warning ("skipping nodes %s, %s" , node1 , node2 )
97- # Nodes not found in clusters; skip this pair
98- continue
99-
100- if is_positive :
101- if in_same_cluster :
102- TP += 1
103- else :
104- FN += 1
105- else :
106- if not in_same_cluster :
107- TN += 1
108- else :
109- FP += 1
110-
111- # Calculate precision and recall
112- precision = TP / (TP + FP ) if (TP + FP ) > 0 else 0
113- recall = TP / (TP + FN ) if (TP + FN ) > 0 else 0
114-
115- return precision , recall , TP , FP , TN , FN
89+ precisions = {}
90+ recalls = {}
91+ f_scores = {}
92+
93+ for threshold in thresholds :
94+ for node1 , node2 , weight in pairs :
95+ # Determine if the pair is positive or negative
96+ is_positive = weight > threshold
97+
98+ # Determine if the nodes are in the same cluster (overlapping clusters)
99+ if node1 in node_to_clusters and node2 in node_to_clusters :
100+ clusters1 = node_to_clusters [node1 ]
101+ clusters2 = node_to_clusters [node2 ]
102+ in_same_cluster = bool (clusters1 & clusters2 ) # Check for non-empty intersection
103+ else :
104+ logging .warning ("skipping nodes %s, %s" , node1 , node2 )
105+ # Nodes not found in clusters; skip this pair
106+ continue
107+
108+ if is_positive :
109+ if in_same_cluster :
110+ TP += 1
111+ else :
112+ FN += 1
113+ else :
114+ if not in_same_cluster :
115+ TN += 1
116+ else :
117+ FP += 1
118+
119+ # Calculate precision and recall
120+ precision = TP / (TP + FP ) if (TP + FP ) > 0 else 0
121+ recall = TP / (TP + FN ) if (TP + FN ) > 0 else 0
122+ f_score = 0
123+ if precision != 0 and recall != 0 :
124+ f_score = (1 + f_score_param * f_score_param ) * precision * recall / ((f_score_param * f_score_param * precision ) + recall )
125+
126+ precisions [threshold ] = precision
127+ recalls [threshold ] = recall
128+ f_scores [threshold ] = f_score
129+
130+ return precisions , recalls , f_scores
116131
117132
118133def compute_precision_recall_pair (in_clustering , input_communities , out_statistics , stats_config , stats_dict ):
119134 """
120135 Compute pair precision and recall, and record result into stats_dict
121136 """
122137 stats_config = _config_str_to_dict (stats_config )
123- precision_recall_pair_threshold = stats_config ["precision_recall_pair_threshold " ]
138+ precision_recall_pair_thresholds = stats_config ["precision_recall_pair_thresholds " ]
124139 f_score_param = stats_config .get ("f_score_param" , 1 )
125140 print ()
126141 print ("clustering file" , in_clustering )
127142 print ("community file" , input_communities )
128143 print ("stats file" , out_statistics )
129- print ("parameters, " , precision_recall_pair_threshold , f_score_param )
144+ print ("parameters, " , precision_recall_pair_thresholds , f_score_param )
130145
131146 # Read clusters and ground truth pairs
132147 clusters = read_clusters (in_clustering )
133148 pairs = read_ground_truth_pairs (input_communities )
134149
135150 # Compute precision and recall
136- precision , recall , TP , FP , TN , FN = compute_precision_recall (clusters , pairs , precision_recall_pair_threshold )
137-
138- f_score = 0
139- if precision != 0 and recall != 0 :
140- f_score = (1 + f_score_param * f_score_param ) * precision * recall / ((f_score_param * f_score_param * precision ) + recall )
151+ precisions , recalls , f_scores = compute_precision_recall (clusters , pairs , precision_recall_pair_thresholds , f_score_param )
141152
142- stats_dict ["fScore_mean" ] = f_score
143- stats_dict ["communityPrecision_mean" ] = precision
144- stats_dict ["communityRecall_mean" ] = recall
145- stats_dict ["PrecisionRecallPairThreshold " ] = precision_recall_pair_threshold
153+ stats_dict ["fScore_mean" ] = f_scores
154+ stats_dict ["communityPrecision_mean" ] = precisions
155+ stats_dict ["communityRecall_mean" ] = recalls
156+ stats_dict ["PrecisionRecallPairThresholds " ] = precision_recall_pair_thresholds
146157 stats_dict ["fScoreParam" ] = f_score_param
147158
148159 with open (out_statistics , 'w' , encoding = 'utf-8' ) as f :
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