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fix(medcat): CU-869bvptgq Relcat infer output for v2 #303

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Merged
mart-r merged 6 commits into from
Jan 21, 2026
Merged

fix(medcat): CU-869bvptgq Relcat infer output for v2 #303

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97f6f2a
CU-869bvptgq: Simplify relations output somewhat
mart-r Jan 21, 2026
a890663
CU-869bvptgq: Add relation both entity start and end char positions
mart-r Jan 21, 2026
53d80f0
CU-869bvptgq: Add entity start / end positions to rel-cat
mart-r Jan 21, 2026
d8cb9cc
CU-869bvptgq: Add relevant changes to relation datasets
mart-r Jan 21, 2026
91aa3f9
CU-869bvptgq: Minor linting change
mart-r Jan 21, 2026
8de5ac1
CU-869bvptgq: Fix minor linting issue
mart-r Jan 21, 2026
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29 changes: 15 additions & 14 deletions medcat-v2/medcat/components/addons/relation_extraction/rel_cat.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,9 @@ def __init__(self, base_tokenizer: BaseTokenizer,
def _init_data_paths(self):
doc_cls = self.base_tokenizer.get_doc_class()
doc_cls.register_addon_path('relations', def_val=[], force=True)
entity_cls = self.base_tokenizer.get_entity_class()
entity_cls.register_addon_path('start', def_val=None, force=True)
entity_cls.register_addon_path('end', def_val=None, force=True)

def save(self, save_path: str = "./") -> None:
self.component.save(save_path=save_path)
Expand Down Expand Up @@ -833,27 +836,23 @@ def pipe(self, stream: Iterable[MutableDocument], *args, **kwargs

relations: list = doc.get_addon_data( # type: ignore
"relations")
out_rels = predict_rel_dataset.dataset[
"output_relations"][rel_idx]
relations.append(
{
"relation": rc_cnf.general.idx2labels[
predicted_label_id],
"label_id": predicted_label_id,
"ent1_text": predict_rel_dataset.dataset[
"output_relations"][rel_idx][
2],
"ent2_text": predict_rel_dataset.dataset[
"output_relations"][rel_idx][
3],
"ent1_text": out_rels[2],
"ent2_text": out_rels[3],
"confidence": float("{:.3f}".format(
confidence[0])),
"start_ent_pos": "",
"end_ent_pos": "",
"start_entity_id":
predict_rel_dataset.dataset[
"output_relations"][rel_idx][8],
"end_entity_id":
predict_rel_dataset.dataset[
"output_relations"][rel_idx][9]
"start_ent1_char_pos": out_rels[18],
"end_ent1_char_pos": out_rels[19],
"start_ent2_char_pos": out_rels[20],
"end_ent2_char_pos": out_rels[21],
"start_entity_id": out_rels[8],
"end_entity_id": out_rels[9],
})
pbar.update(len(token_ids))
pbar.close()
Expand Down Expand Up @@ -901,6 +900,8 @@ def predict_text_with_anns(self, text: str, annotations: list[dict]
entity = base_tokenizer.create_entity(
doc, min(tkn_idx), max(tkn_idx) + 1, label=ann["value"])
entity.cui = ann["cui"]
entity.set_addon_data('start', ann['strat'])
entity.set_addon_data('end', ann['end'])
doc.ner_ents.append(entity)

doc = self(doc)
Expand Down
54 changes: 28 additions & 26 deletions medcat-v2/medcat/components/addons/relation_extraction/rel_dataset.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -246,6 +246,9 @@ def _create_relation_validation(self,
ent2_token: Union[str, MutableEntity] = tmp_doc_text[
ent2_start_char_pos: ent2_end_char_pos]

annotation_token_text = self.tokenizer.hf_tokenizers.convert_ids_to_tokens(
self.config.general.annotation_schema_tag_ids)

if (abs(ent2_start_char_pos - ent1_start_char_pos
) <= self.config.general.window_size and
ent1_token != ent2_token):
Expand Down Expand Up @@ -281,24 +284,20 @@ def _create_relation_validation(self,

if is_spacy_doc or is_mct_export:
tmp_doc_text = text
_pre_e1 = tmp_doc_text[0: (ent1_start_char_pos)]
_e1_s2 = (
tmp_doc_text[ent1_end_char_pos: ent2_start_char_pos - 1])
_e2_end = tmp_doc_text[ent2_end_char_pos + 1: text_length]
ent2_token_end_pos = (ent2_token_end_pos + 2)

annotation_token_text = (
self.tokenizer.hf_tokenizers.convert_ids_to_tokens(
self.config.general.annotation_schema_tag_ids))
s1, e1, s2, e2 = annotation_token_text

tmp_doc_text = (
str(_pre_e1) + " " +
annotation_token_text[0] + " " +
str(ent1_token) + " " +
annotation_token_text[1] + " " + str(_e1_s2) + " " +
annotation_token_text[2] + " " + str(ent2_token) + " " +
annotation_token_text[3] + " " + str(_e2_end)
)
tmp_doc_text[:ent2_end_char_pos] +
e2 + tmp_doc_text[ent2_end_char_pos:])
tmp_doc_text = (
tmp_doc_text[:ent2_start_char_pos] +
s2 + tmp_doc_text[ent2_start_char_pos:])
tmp_doc_text = (
tmp_doc_text[:ent1_end_char_pos] +
e1 + tmp_doc_text[ent1_end_char_pos:])
tmp_doc_text = (
tmp_doc_text[:ent1_start_char_pos] +
s1 + tmp_doc_text[ent1_start_char_pos:])

ann_tag_token_len = len(annotation_token_text[0])

Expand All @@ -309,11 +308,10 @@ def _create_relation_validation(self,

_right_context_start_end_pos = ( # 8 for spces
right_context_end_char_pos + (ann_tag_token_len * 4) + 8)
right_context_end_char_pos = (
len(tmp_doc_text) + 1 if
right_context_end_char_pos >= len(tmp_doc_text) or
_right_context_start_end_pos >= len(tmp_doc_text)
else _right_context_start_end_pos)
right_context_end_char_pos = len(tmp_doc_text) if (
right_context_end_char_pos >= len(tmp_doc_text)
or _right_context_start_end_pos >= len(tmp_doc_text)
) else _right_context_start_end_pos

# reassign the new text with added tags
text_length = len(tmp_doc_text)
Expand Down Expand Up @@ -363,16 +361,20 @@ def _create_relation_validation(self,
ent2_token_start_pos += ent1_token_start_pos

ent1_ent2_new_start = (ent1_token_start_pos, ent2_token_start_pos)
en1_start, en1_end = window_tokenizer_data[
"offset_mapping"][ent1_token_start_pos]
en2_start, en2_end = window_tokenizer_data[
"offset_mapping"][ent2_token_start_pos]
os_map = window_tokenizer_data["offset_mapping"]
s1_start, s1_end = os_map[ent1_token_start_pos]
e1_start, e1_end = os_map[_ent1_token_end_pos]

s2_start, s2_end = os_map[ent2_token_start_pos]
e2_start, e2_end = os_map[_ent2_token_end_pos]

return [window_tokenizer_data["input_ids"], ent1_ent2_new_start,
ent1_token, ent2_token, "UNK",
self.config.model.padding_idx,
None, None, None, None, None, None, doc_id, "",
en1_start, en1_end, en2_start, en2_end]
s1_start, e1_end, s2_start, e2_end,
ent1_start_char_pos, ent1_end_char_pos,
ent2_start_char_pos, ent2_end_char_pos]
return []

def _get_token_type_and_start_end(
Expand Down
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