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Similarity.batet_log: fix -0.0 sign
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@dhimmel
dhimmel committed Sep 30, 2021
1 parent 8d1ffde commit 6c2b154
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5 changes: 3 additions & 2 deletions nxontology/ontology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -455,7 +455,7 @@ def intrinsic_ic_sanchez(self) -> float:
# ic_sanchez: Definition 4 / Equation 10 from https://doi.org/10.1016/j.knosys.2010.10.001
all_leaves = self.nxo.leaves
leaves = all_leaves & self.descendants
# replace negative sign with math.abs to avoid returning -0.0.
# replace negative sign with abs to avoid returning -0.0.
return abs(
math.log((len(leaves) / self.n_ancestors + 1) / (len(all_leaves) + 1))
)
Expand Down Expand Up @@ -548,7 +548,8 @@ def batet_log(self) -> float:
"""
if self.batet == 1.0:
return 1.0
return -math.log(1 - self.batet) / math.log(self.n_union_ancestors)
# replace negative sign with abs to avoid returning -0.0.
return abs(math.log(1 - self.batet) / math.log(self.n_union_ancestors))

def results(self, keys: Optional[List[str]] = None) -> Dict[str, Any]:
if keys is None:
Expand Down
120 changes: 60 additions & 60 deletions nxontology/tests/ontology_test_disconnected_sim.tsv
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Original file line number Diff line number Diff line change
@@ -1,99 +1,99 @@
node_0 node_1 node_0_subsumes_1 node_1_subsumes_0 n_common_ancestors n_union_ancestors batet batet_log ic_metric mica resnik resnik_scaled lin jiang jiang_seco
coinage coinage True True 2 2 1 1 intrinsic_ic coinage 1.95 1 1 1 1
coinage coinage True True 2 2 1 1 intrinsic_ic_sanchez coinage 1.2 0.748 1 1 1
coinage conifer False False 0 4 0 -0 intrinsic_ic 0 0 0 0.238 0.178
coinage conifer False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
coinage conifer False False 0 4 0 0 intrinsic_ic 0 0 0 0.238 0.178
coinage conifer False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
coinage metal False True 1 2 0.5 1 intrinsic_ic metal 0.847 0.435 0.607 0.477 0.718
coinage metal False True 1 2 0.5 1 intrinsic_ic_sanchez metal 0.511 0.317 0.596 0.591 0.785
coinage pine False False 0 5 0 -0 intrinsic_ic 0 0 0 0.204 0
coinage pine False False 0 5 0 -0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
coinage pine False False 0 5 0 0 intrinsic_ic 0 0 0 0.204 0
coinage pine False False 0 5 0 0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
coinage precious False False 1 3 0.333 0.369 intrinsic_ic metal 0.847 0.435 0.435 0.313 0.435
coinage precious False False 1 3 0.333 0.369 intrinsic_ic_sanchez metal 0.511 0.317 0.424 0.419 0.569
coinage tree False False 0 3 0 -0 intrinsic_ic 0 0 0 0.264 0.282
coinage tree False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
coinage water False False 0 3 0 -0 intrinsic_ic 0 0 0 0.204 0
coinage water False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
conifer coinage False False 0 4 0 -0 intrinsic_ic 0 0 0 0.238 0.178
conifer coinage False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
coinage tree False False 0 3 0 0 intrinsic_ic 0 0 0 0.264 0.282
coinage tree False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
coinage water False False 0 3 0 0 intrinsic_ic 0 0 0 0.204 0
coinage water False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
conifer coinage False False 0 4 0 0 intrinsic_ic 0 0 0 0.238 0.178
conifer coinage False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
conifer conifer True True 2 2 1 1 intrinsic_ic conifer 1.25 0.644 1 1 1
conifer conifer True True 2 2 1 1 intrinsic_ic_sanchez conifer 1.2 0.748 1 1 1
conifer metal False False 0 3 0 -0 intrinsic_ic 0 0 0 0.323 0.46
conifer metal False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.368 0.467
conifer metal False False 0 3 0 0 intrinsic_ic 0 0 0 0.323 0.46
conifer metal False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.368 0.467
conifer pine True False 2 3 0.667 1 intrinsic_ic conifer 1.25 0.644 0.783 0.591 0.822
conifer pine True False 2 3 0.667 1 intrinsic_ic_sanchez conifer 1.2 0.748 0.953 0.895 0.963
conifer precious False False 0 4 0 -0 intrinsic_ic 0 0 0 0.238 0.178
conifer precious False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
conifer precious False False 0 4 0 0 intrinsic_ic 0 0 0 0.238 0.178
conifer precious False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
conifer tree False True 1 2 0.5 1 intrinsic_ic tree 0.847 0.435 0.807 0.712 0.896
conifer tree False True 1 2 0.5 1 intrinsic_ic_sanchez tree 0.916 0.569 0.864 0.777 0.911
conifer water False False 0 3 0 -0 intrinsic_ic 0 0 0 0.238 0.178
conifer water False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
conifer water False False 0 3 0 0 intrinsic_ic 0 0 0 0.238 0.178
conifer water False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
metal coinage True False 1 2 0.5 1 intrinsic_ic metal 0.847 0.435 0.607 0.477 0.718
metal coinage True False 1 2 0.5 1 intrinsic_ic_sanchez metal 0.511 0.317 0.596 0.591 0.785
metal conifer False False 0 3 0 -0 intrinsic_ic 0 0 0 0.323 0.46
metal conifer False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.368 0.467
metal conifer False False 0 3 0 0 intrinsic_ic 0 0 0 0.323 0.46
metal conifer False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.368 0.467
metal metal True True 1 1 1 1 intrinsic_ic metal 0.847 0.435 1 1 1
metal metal True True 1 1 1 1 intrinsic_ic_sanchez metal 0.511 0.317 1 1 1
metal pine False False 0 4 0 -0 intrinsic_ic 0 0 0 0.264 0.282
metal pine False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
metal pine False False 0 4 0 0 intrinsic_ic 0 0 0 0.264 0.282
metal pine False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
metal precious True False 1 2 0.5 1 intrinsic_ic metal 0.847 0.435 0.607 0.477 0.718
metal precious True False 1 2 0.5 1 intrinsic_ic_sanchez metal 0.511 0.317 0.596 0.591 0.785
metal tree False False 0 2 0 -0 intrinsic_ic 0 0 0 0.371 0.565
metal tree False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
metal water False False 0 2 0 -0 intrinsic_ic 0 0 0 0.264 0.282
metal water False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
pine coinage False False 0 5 0 -0 intrinsic_ic 0 0 0 0.204 0
pine coinage False False 0 5 0 -0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
metal tree False False 0 2 0 0 intrinsic_ic 0 0 0 0.371 0.565
metal tree False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
metal water False False 0 2 0 0 intrinsic_ic 0 0 0 0.264 0.282
metal water False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
pine coinage False False 0 5 0 0 intrinsic_ic 0 0 0 0.204 0
pine coinage False False 0 5 0 0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
pine conifer False True 2 3 0.667 1 intrinsic_ic conifer 1.25 0.644 0.783 0.591 0.822
pine conifer False True 2 3 0.667 1 intrinsic_ic_sanchez conifer 1.2 0.748 0.953 0.895 0.963
pine metal False False 0 4 0 -0 intrinsic_ic 0 0 0 0.264 0.282
pine metal False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
pine metal False False 0 4 0 0 intrinsic_ic 0 0 0 0.264 0.282
pine metal False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
pine pine True True 3 3 1 1 intrinsic_ic pine 1.95 1 1 1 1
pine pine True True 3 3 1 1 intrinsic_ic_sanchez pine 1.32 0.821 1 1 1
pine precious False False 0 5 0 -0 intrinsic_ic 0 0 0 0.204 0
pine precious False False 0 5 0 -0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
pine precious False False 0 5 0 0 intrinsic_ic 0 0 0 0.204 0
pine precious False False 0 5 0 0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
pine tree False True 1 3 0.333 0.369 intrinsic_ic tree 0.847 0.435 0.607 0.477 0.718
pine tree False True 1 3 0.333 0.369 intrinsic_ic_sanchez tree 0.916 0.569 0.819 0.712 0.874
pine water False False 0 4 0 -0 intrinsic_ic 0 0 0 0.204 0
pine water False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.309 0.305
pine water False False 0 4 0 0 intrinsic_ic 0 0 0 0.204 0
pine water False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.309 0.305
precious coinage False False 1 3 0.333 0.369 intrinsic_ic metal 0.847 0.435 0.435 0.313 0.435
precious coinage False False 1 3 0.333 0.369 intrinsic_ic_sanchez metal 0.511 0.317 0.424 0.419 0.569
precious conifer False False 0 4 0 -0 intrinsic_ic 0 0 0 0.238 0.178
precious conifer False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
precious conifer False False 0 4 0 0 intrinsic_ic 0 0 0 0.238 0.178
precious conifer False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.293 0.252
precious metal False True 1 2 0.5 1 intrinsic_ic metal 0.847 0.435 0.607 0.477 0.718
precious metal False True 1 2 0.5 1 intrinsic_ic_sanchez metal 0.511 0.317 0.596 0.591 0.785
precious pine False False 0 5 0 -0 intrinsic_ic 0 0 0 0.204 0
precious pine False False 0 5 0 -0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
precious pine False False 0 5 0 0 intrinsic_ic 0 0 0 0.204 0
precious pine False False 0 5 0 0 intrinsic_ic_sanchez 0 0 0 0.284 0.215
precious precious True True 2 2 1 1 intrinsic_ic precious 1.95 1 1 1 1
precious precious True True 2 2 1 1 intrinsic_ic_sanchez precious 1.2 0.748 1 1 1
precious tree False False 0 3 0 -0 intrinsic_ic 0 0 0 0.264 0.282
precious tree False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
precious water False False 0 3 0 -0 intrinsic_ic 0 0 0 0.204 0
precious water False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
tree coinage False False 0 3 0 -0 intrinsic_ic 0 0 0 0.264 0.282
tree coinage False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
precious tree False False 0 3 0 0 intrinsic_ic 0 0 0 0.264 0.282
precious tree False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
precious water False False 0 3 0 0 intrinsic_ic 0 0 0 0.204 0
precious water False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
tree coinage False False 0 3 0 0 intrinsic_ic 0 0 0 0.264 0.282
tree coinage False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
tree conifer True False 1 2 0.5 1 intrinsic_ic tree 0.847 0.435 0.807 0.712 0.896
tree conifer True False 1 2 0.5 1 intrinsic_ic_sanchez tree 0.916 0.569 0.864 0.777 0.911
tree metal False False 0 2 0 -0 intrinsic_ic 0 0 0 0.371 0.565
tree metal False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
tree metal False False 0 2 0 0 intrinsic_ic 0 0 0 0.371 0.565
tree metal False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
tree pine True False 1 3 0.333 0.369 intrinsic_ic tree 0.847 0.435 0.607 0.477 0.718
tree pine True False 1 3 0.333 0.369 intrinsic_ic_sanchez tree 0.916 0.569 0.819 0.712 0.874
tree precious False False 0 3 0 -0 intrinsic_ic 0 0 0 0.264 0.282
tree precious False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
tree precious False False 0 3 0 0 intrinsic_ic 0 0 0 0.264 0.282
tree precious False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
tree tree True True 1 1 1 1 intrinsic_ic tree 0.847 0.435 1 1 1
tree tree True True 1 1 1 1 intrinsic_ic_sanchez tree 0.916 0.569 1 1 1
tree water False False 0 2 0 -0 intrinsic_ic 0 0 0 0.264 0.282
tree water False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
water coinage False False 0 3 0 -0 intrinsic_ic 0 0 0 0.204 0
water coinage False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water conifer False False 0 3 0 -0 intrinsic_ic 0 0 0 0.238 0.178
water conifer False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water metal False False 0 2 0 -0 intrinsic_ic 0 0 0 0.264 0.282
water metal False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
water pine False False 0 4 0 -0 intrinsic_ic 0 0 0 0.204 0
water pine False False 0 4 0 -0 intrinsic_ic_sanchez 0 0 0 0.309 0.305
water precious False False 0 3 0 -0 intrinsic_ic 0 0 0 0.204 0
water precious False False 0 3 0 -0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water tree False False 0 2 0 -0 intrinsic_ic 0 0 0 0.264 0.282
water tree False False 0 2 0 -0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
tree water False False 0 2 0 0 intrinsic_ic 0 0 0 0.264 0.282
tree water False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
water coinage False False 0 3 0 0 intrinsic_ic 0 0 0 0.204 0
water coinage False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water conifer False False 0 3 0 0 intrinsic_ic 0 0 0 0.238 0.178
water conifer False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water metal False False 0 2 0 0 intrinsic_ic 0 0 0 0.264 0.282
water metal False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.412 0.557
water pine False False 0 4 0 0 intrinsic_ic 0 0 0 0.204 0
water pine False False 0 4 0 0 intrinsic_ic_sanchez 0 0 0 0.309 0.305
water precious False False 0 3 0 0 intrinsic_ic 0 0 0 0.204 0
water precious False False 0 3 0 0 intrinsic_ic_sanchez 0 0 0 0.32 0.341
water tree False False 0 2 0 0 intrinsic_ic 0 0 0 0.264 0.282
water tree False False 0 2 0 0 intrinsic_ic_sanchez 0 0 0 0.353 0.431
water water True True 1 1 1 1 intrinsic_ic water 1.95 1 1 1 1
water water True True 1 1 1 1 intrinsic_ic_sanchez water 0.916 0.569 1 1 1

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