precalculate graph and successor relationship for more efficient call-time performance

Author: sfluegel05

chebai/result/analyse_sem.py

@@ -135,6 +135,8 @@ def get_chebi_graph(data_module, label_names):
         chebi_graph = data_module._extract_class_hierarchy(
             os.path.join(data_module.raw_dir, "chebi.obo")
         )
+        if label_names is None:
+            return chebi_graph
         return chebi_graph.subgraph([int(n) for n in label_names])
     print(
         f"Failed to retrieve ChEBI graph, {os.path.join(data_module.raw_dir, 'chebi.obo')} not found"
@@ -190,32 +192,38 @@ class PredictionSmoother:
     """Removes implication and disjointness violations from predictions"""
 
     def __init__(self, dataset, label_names=None, disjoint_files=None):
-        if label_names:
-            self.label_names = label_names
-        else:
-            self.label_names = get_label_names(dataset)
-        self.chebi_graph = get_chebi_graph(dataset, self.label_names)
+        self.chebi_graph = get_chebi_graph(dataset, None)
+        self.set_label_names(label_names)
         self.disjoint_groups = get_disjoint_groups(disjoint_files)
 
+    def set_label_names(self, label_names):
+        if label_names is not None:
+            self.label_names = [int(label) for label in label_names]
+            chebi_subgraph = self.chebi_graph.subgraph(self.label_names)
+            self.label_successors = torch.zeros(
+                (len(self.label_names), len(self.label_names)), dtype=torch.bool
+            )
+            for i, label in enumerate(self.label_names):
+                self.label_successors[i, i] = 1
+                for p in chebi_subgraph.successors(label):
+                    if p in self.label_names:
+                        self.label_successors[i, self.label_names.index(p)] = 1
+            self.label_successors = self.label_successors.unsqueeze(0)
+
     def __call__(self, preds):
         preds_sum_orig = torch.sum(preds)
-        for i, label in enumerate(self.label_names):
-            succs = [
-                self.label_names.index(str(p))
-                for p in self.chebi_graph.successors(int(label))
-            ] + [i]
-            if len(succs) > 0:
-                preds[:, i] = torch.max(preds[:, succs], dim=1).values
+        # step 1: apply implications: for each class, set prediction to max of itself and all successors
+        preds = preds.unsqueeze(1)
+        preds_masked_succ = torch.where(self.label_successors, preds, 0)
+        preds = preds_masked_succ.max(dim=2).values
         if torch.sum(preds) != preds_sum_orig:
             print(f"Preds change (step 1): {torch.sum(preds) - preds_sum_orig}")
         preds_sum_orig = torch.sum(preds)
         # step 2: eliminate disjointness violations: for group of disjoint classes, set all except max to 0.49 (if it is not already lower)
         preds_bounded = torch.min(preds, torch.ones_like(preds) * 0.49)
         for disj_group in self.disjoint_groups:
             disj_group = [
-                self.label_names.index(str(g))
-                for g in disj_group
-                if g in self.label_names
+                self.label_names.index(g) for g in disj_group if g in self.label_names
             ]
             if len(disj_group) > 1:
                 old_preds = preds[:, disj_group]
@@ -232,26 +240,17 @@ def __call__(self, preds):
                     print(
                         f"disjointness group {[self.label_names[d] for d in disj_group]} changed {samples_changed} samples"
                     )
+        if torch.sum(preds) != preds_sum_orig:
+            print(f"Preds change (step 2): {torch.sum(preds) - preds_sum_orig}")
         preds_sum_orig = torch.sum(preds)
         # step 3: disjointness violation removal may have caused new implication inconsistencies -> set each prediction to min of predecessors
-        for i, label in enumerate(self.label_names):
-            predecessors = [i] + [
-                self.label_names.index(str(p))
-                for p in self.chebi_graph.predecessors(int(label))
-            ]
-            lowest_predecessors = torch.min(preds[:, predecessors], dim=1)
-            preds[:, i] = lowest_predecessors.values
-            for idx_idx, idx in enumerate(lowest_predecessors.indices):
-                if idx > 0:
-                    print(
-                        f"class {label}: changed prediction of sample {idx_idx} to value of class "
-                        f"{self.label_names[predecessors[idx]]} ({preds[idx_idx, i].item():.2f})"
-                    )
-            if torch.sum(preds) != preds_sum_orig:
-                print(
-                    f"Preds change (step 3) for {label}: {torch.sum(preds) - preds_sum_orig}"
-                )
-                preds_sum_orig = torch.sum(preds)
+        preds = preds.unsqueeze(1)
+        preds_masked_predec = torch.where(
+            torch.transpose(self.label_successors, 1, 2), preds, 1
+        )
+        preds = preds_masked_predec.min(dim=2).values
+        if torch.sum(preds) != preds_sum_orig:
+            print(f"Preds change (step 3): {torch.sum(preds) - preds_sum_orig}")
         return preds
 
 

setup.py

@@ -12,6 +12,8 @@
     license="",
     author="MGlauer",
     author_email="martin.glauer@ovgu.de",
+    maintainer="sfluegel05",
+    maintainer_email="simon.fluegel@uni-osnabrueck.de",
     description="",
     zip_safe=False,
     python_requires=">=3.9, <3.13",