Change re config to match format described in notion notebook and add option to process on document level

mobie.py

@@ -53,6 +53,7 @@ _URLs = {
 
 
 def simplify_dict(d, remove_attribute=True):
+    """Simplify nested dictionary by removing unnecessary keys"""
     if isinstance(d, dict):
         new_dict = {}
         for k, v in d.items():
@@ -123,7 +124,7 @@ class Mobie(datasets.GeneratorBasedBuilder):
             "time",
             "trigger",
         ]
-        concept_mentions = [
+        entity_mentions = [
             {
                 "id": datasets.Value("string"),
                 "text": datasets.Value("string"),
@@ -158,44 +159,31 @@ class Mobie(datasets.GeneratorBasedBuilder):
                 {
                     "id": datasets.Value("string"),
                     "text": datasets.Value("string"),
-                    "concept_mentions": concept_mentions
+                    "entity_mentions": entity_mentions
                 }
             )
         elif self.config.name == "re":
             features = datasets.Features(
                 {
                     "id": datasets.Value("string"),
-                    "text": datasets.Value("string"),
-                    "concept_mentions": concept_mentions,
-                    "relation_mentions": [
-                        {
-                            "id": datasets.Value("string"),
-                            "trigger": {
-                                "id": datasets.Value("string"),
-                                "text": datasets.Value("string"),
-                                "start": datasets.Value("int32"),
-                                "end": datasets.Value("int32")
-                            },
-                            "argument": {
-                                "id": datasets.Value("string"),
-                                "text": datasets.Value("string"),
-                                "start": datasets.Value("int32"),
-                                "end": datasets.Value("int32")
-                            },
-                            "type": datasets.features.ClassLabel(
-                                names=[
-                                    "no_arg", "location", "delay", "direction", "start_loc", "end_loc",
-                                    "start_date", "end_date", "cause", "jam_length", "route"
-                                ]
-                            ),
-                            "event_type": datasets.features.ClassLabel(
-                                names=[
-                                    "O", "Accident", "CanceledRoute", "CanceledStop", "Delay", "Obstruction",
-                                    "RailReplacementService", "TrafficJam"
-                                ]
-                            )
-                        }
-                    ]
+                    "tokens": datasets.Sequence(datasets.Value("string")),
+                    "entities": datasets.Sequence([datasets.Value("int32")]),
+                    "entity_roles": datasets.Sequence(datasets.features.ClassLabel(
+                        names=[
+                            "no_arg", "trigger", "location", "delay", "direction", "start_loc", "end_loc",
+                            "start_date", "end_date", "cause", "jam_length", "route"
+                        ]
+                    )),
+                    "entity_types": datasets.Sequence(datasets.features.ClassLabel(
+                        names=labels
+                    )),
+                    "event_type": datasets.features.ClassLabel(
+                        names=[
+                            "O", "Accident", "CanceledRoute", "CanceledStop", "Delay", "Obstruction",
+                            "RailReplacementService", "TrafficJam"
+                        ]
+                    ),
+                    "entity_ids": datasets.Sequence(datasets.Value("string"))
                 }
             )
         elif self.config.name == "ee":
@@ -204,7 +192,7 @@ class Mobie(datasets.GeneratorBasedBuilder):
                 {
                     "id": datasets.Value("string"),
                     "text": datasets.Value("string"),
-                    "entity_mentions": concept_mentions,
+                    "entity_mentions": entity_mentions,
                     "event_mentions": [
                         {
                             "id": datasets.Value("string"),
@@ -284,7 +272,7 @@ class Mobie(datasets.GeneratorBasedBuilder):
             ),
         ]
 
-    def _generate_examples(self, filepath, split):
+    def _generate_examples(self, filepath, split, sentence_level=False):
         """Yields examples."""
 
         if self.config.name == "ner":
@@ -307,11 +295,8 @@ class Mobie(datasets.GeneratorBasedBuilder):
 
             for doc in decode_stacked(raw):
                 text = doc["text"]["string"]
-
-                # entity_starts = []
-                # for m in doc["conceptMentions"]["array"]:
-                #     entity_starts.append(m["span"]["start"])
-                for s in doc["sentences"]["array"]:
+                iterable = doc["sentences"]["array"] if sentence_level else [doc]
+                for s in iterable:
                     toks = []
                     lbls = []
                     sid = s["id"]
@@ -331,16 +316,17 @@ class Mobie(datasets.GeneratorBasedBuilder):
                     doc = json.loads(line)
                     doc = simplify_dict(doc)
                     text = doc["text"]
-                    for sentence in doc["sentences"]:
+                    iterable = doc["sentences"] if sentence_level else [doc]
+                    for sentence in iterable:
                         sentence_id = sentence["id"]
-                        sentence_start = sentence["span"]["start"]
+                        sentence_start = sentence["span"]["start"] if "span" in sentence else 0
                         mobie_cms = sentence["conceptMentions"]
-                        concept_mentions = []
+                        entity_mentions = []
                         for cm in mobie_cms:
                             cm_start = cm["span"]["start"]
                             cm_end = cm["span"]["end"]
                             cm_text = text[cm_start:cm_end]
-                            concept_mentions.append({
+                            entity_mentions.append({
                                 "id": cm["id"],
                                 "text": cm_text,
                                 "start": cm_start - sentence_start,
@@ -354,58 +340,72 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                 ] if "refids" in cm and cm["refids"] else []
                             })
                         if self.config.name == "el":
+                            # TODO use osm_id as entity id?
                             yield sentence_id, {
                                 "id": sentence_id,
                                 "text": text,
-                                "concept_mentions": concept_mentions
+                                "entity_mentions": entity_mentions
                             }
                         elif self.config.name == "re":
                             mobie_rms = sentence["relationMentions"]
                             if not mobie_rms:
                                 continue
-                            relation_mentions = []
-                            for rm in mobie_rms:
-                                # Find trigger in rm["args"]
-                                trigger = None
-                                for arg in rm["args"]:
-                                    if arg["role"] == "trigger":
-                                        trigger = arg
+                            tokens = [text[token["span"]["start"]:token["span"]["end"]] for token in sentence["tokens"]]
+                            entities = []
+                            entity_types = []
+                            entity_ids = []
+                            for cm in mobie_cms:
+                                # Find token offsets for entity mentions
+                                start = -1
+                                end = -1
+                                for idx, token in enumerate(sentence["tokens"]):
+                                    if token["span"]["start"] == cm["span"]["start"]:
+                                        start = idx
+                                    if token["span"]["end"] == cm["span"]["end"]:
+                                        end = idx
+                                assert start != -1 and end != -1, f"Could not find token offsets for {cm['id']}"
+                                entities.append([start, end])
+                                entity_types.append(cm["type"])
+                                found_osm_id = False
+                                for refid in cm["refids"]:
+                                    if refid["key"] == "osm_id":
+                                        entity_ids.append(refid["value"])
+                                        found_osm_id = True
                                         break
-                                if trigger is None:
-                                    continue
-                                trigger_start = trigger["conceptMention"]["span"]["start"]
-                                trigger_end = trigger["conceptMention"]["span"]["end"]
-                                trigger_text = text[trigger_start:trigger_end]
+                                if not found_osm_id:
+                                    entity_ids.append("NIL")
+                            for rm in mobie_rms:
+                                entity_roles = ["no_arg"] * len(entities)
                                 for arg in rm["args"]:
-                                    if arg["role"] == "trigger":
-                                        continue
-                                    argument_start = arg["conceptMention"]["span"]["start"]
-                                    argument_end = arg["conceptMention"]["span"]["end"]
-                                    argument_text = text[argument_start:argument_end]
-                                    relation_mentions.append({
-                                        "id": f"{sentence_id}-{example_idx}",
-                                        "trigger": {
-                                            "id": trigger["conceptMention"]["id"],
-                                            "text": trigger_text,
-                                            "start": trigger_start - sentence_start,
-                                            "end": trigger_end - sentence_start
-                                        },
-                                        "argument": {
-                                            "id": arg["conceptMention"]["id"],
-                                            "text": argument_text,
-                                            "start": argument_start - sentence_start,
-                                            "end": argument_end - sentence_start
-                                        },
-                                        "type": arg["role"],
-                                        "event_type": rm["name"]
-                                    })
-                                    yield f"{sentence_id}_{example_idx}", {
-                                        "id": f"{sentence_id}_{example_idx}",
-                                        "text": text,
-                                        "concept_mentions": concept_mentions,
-                                        "relation_mentions": relation_mentions
-                                    }
-                                    example_idx += 1
+                                    entity_role = arg["role"]
+                                    # Matching via ids does not work, need to match via position
+                                    # Find token offsets for entity mentions
+                                    start = -1
+                                    end = -1
+                                    cm = arg["conceptMention"]
+                                    for idx, token in enumerate(sentence["tokens"]):
+                                        if token["span"]["start"] == cm["span"]["start"]:
+                                            start = idx
+                                        if token["span"]["end"] == cm["span"]["end"]:
+                                            end = idx
+                                    assert start != -1 and end != -1, f"Could not find token offsets for {cm['id']}"
+                                    entity_idx = -1
+                                    for idx, entity in enumerate(entities):
+                                        if entity == [start, end]:
+                                            entity_idx = idx
+                                            break
+                                    assert entity_idx != -1, f"Could not find entity for {cm['id']}"
+                                    entity_roles[entity_idx] = entity_role
+                                yield f"{sentence_id}_{example_idx}", {
+                                    "id": f"{sentence_id}_{example_idx}",
+                                    "tokens": tokens,
+                                    "entities": entities,
+                                    "entity_roles": entity_roles,
+                                    "entity_types": entity_types,
+                                    "event_type": rm["name"],
+                                    "entity_ids": entity_ids
+                                }
+                                example_idx += 1
                         elif self.config.name == "ee":
                             mobie_rms = sentence["relationMentions"]
                             if not mobie_rms:
@@ -452,7 +452,7 @@ class Mobie(datasets.GeneratorBasedBuilder):
                             yield sentence_id, {
                                 "id": sentence_id,
                                 "text": text,
-                                "entity_mentions": concept_mentions,
+                                "entity_mentions": entity_mentions,
                                 "event_mentions": event_mentions
                             }
                         else: