Fix doc with faulty spans and add more information to example

README.md

@@ -21,6 +21,387 @@ paperswithcode_id: mobie
 pretty_name: MobIE
 tags:
 - structure-prediction
+dataset_info:
+- config_name: ee
+  features:
+  - name: id
+    dtype: string
+  - name: text
+    dtype: string
+  - name: entity_mentions
+    list:
+    - name: id
+      dtype: string
+    - name: text
+      dtype: string
+    - name: start
+      dtype: int32
+    - name: end
+      dtype: int32
+    - name: type
+      dtype:
+        class_label:
+          names:
+            '0': date
+            '1': disaster-type
+            '2': distance
+            '3': duration
+            '4': event-cause
+            '5': location
+            '6': location-city
+            '7': location-route
+            '8': location-stop
+            '9': location-street
+            '10': money
+            '11': number
+            '12': organization
+            '13': organization-company
+            '14': org-position
+            '15': percent
+            '16': person
+            '17': set
+            '18': time
+            '19': trigger
+    - name: refids
+      list:
+      - name: key
+        dtype: string
+      - name: value
+        dtype: string
+  - name: event_mentions
+    list:
+    - name: id
+      dtype: string
+    - name: trigger
+      struct:
+      - name: id
+        dtype: string
+      - name: text
+        dtype: string
+      - name: start
+        dtype: int32
+      - name: end
+        dtype: int32
+    - name: arguments
+      list:
+      - name: id
+        dtype: string
+      - name: text
+        dtype: string
+      - name: start
+        dtype: int32
+      - name: end
+        dtype: int32
+      - name: role
+        dtype:
+          class_label:
+            names:
+              '0': no_arg
+              '1': location
+              '2': delay
+              '3': direction
+              '4': start_loc
+              '5': end_loc
+              '6': start_date
+              '7': end_date
+              '8': cause
+              '9': jam_length
+              '10': route
+      - name: type
+        dtype:
+          class_label:
+            names:
+              '0': date
+              '1': disaster-type
+              '2': distance
+              '3': duration
+              '4': event-cause
+              '5': location
+              '6': location-city
+              '7': location-route
+              '8': location-stop
+              '9': location-street
+              '10': money
+              '11': number
+              '12': organization
+              '13': organization-company
+              '14': org-position
+              '15': percent
+              '16': person
+              '17': set
+              '18': time
+              '19': trigger
+    - name: event_type
+      dtype:
+        class_label:
+          names:
+            '0': O
+            '1': Accident
+            '2': CanceledRoute
+            '3': CanceledStop
+            '4': Delay
+            '5': Obstruction
+            '6': RailReplacementService
+            '7': TrafficJam
+  - name: tokens
+    sequence: string
+  - name: pos_tags
+    sequence: string
+  - name: lemma
+    sequence: string
+  - name: ner_tags
+    sequence:
+      class_label:
+        names:
+          '0': O
+          '1': B-date
+          '2': B-disaster-type
+          '3': B-distance
+          '4': B-duration
+          '5': B-event-cause
+          '6': B-location
+          '7': B-location-city
+          '8': B-location-route
+          '9': B-location-stop
+          '10': B-location-street
+          '11': B-money
+          '12': B-number
+          '13': B-organization
+          '14': B-organization-company
+          '15': B-org-position
+          '16': B-percent
+          '17': B-person
+          '18': B-set
+          '19': B-time
+          '20': B-trigger
+          '21': I-date
+          '22': I-disaster-type
+          '23': I-distance
+          '24': I-duration
+          '25': I-event-cause
+          '26': I-location
+          '27': I-location-city
+          '28': I-location-route
+          '29': I-location-stop
+          '30': I-location-street
+          '31': I-money
+          '32': I-number
+          '33': I-organization
+          '34': I-organization-company
+          '35': I-org-position
+          '36': I-percent
+          '37': I-person
+          '38': I-set
+          '39': I-time
+          '40': I-trigger
+  splits:
+  - name: train
+    num_bytes: 2023843
+    num_examples: 788
+  - name: test
+    num_bytes: 1232888
+    num_examples: 484
+  - name: validation
+    num_bytes: 395053
+    num_examples: 152
+  download_size: 8190212
+  dataset_size: 3651784
+- config_name: el
+  features:
+  - name: id
+    dtype: string
+  - name: text
+    dtype: string
+  - name: entity_mentions
+    list:
+    - name: id
+      dtype: string
+    - name: text
+      dtype: string
+    - name: start
+      dtype: int32
+    - name: end
+      dtype: int32
+    - name: type
+      dtype:
+        class_label:
+          names:
+            '0': date
+            '1': disaster-type
+            '2': distance
+            '3': duration
+            '4': event-cause
+            '5': location
+            '6': location-city
+            '7': location-route
+            '8': location-stop
+            '9': location-street
+            '10': money
+            '11': number
+            '12': organization
+            '13': organization-company
+            '14': org-position
+            '15': percent
+            '16': person
+            '17': set
+            '18': time
+            '19': trigger
+    - name: refids
+      list:
+      - name: key
+        dtype: string
+      - name: value
+        dtype: string
+  splits:
+  - name: train
+    num_bytes: 1345663
+    num_examples: 2115
+  - name: test
+    num_bytes: 503058
+    num_examples: 623
+  - name: validation
+    num_bytes: 298974
+    num_examples: 494
+  download_size: 8190212
+  dataset_size: 2147695
+- config_name: ner
+  features:
+  - name: id
+    dtype: string
+  - name: tokens
+    sequence: string
+  - name: ner_tags
+    sequence:
+      class_label:
+        names:
+          '0': O
+          '1': B-date
+          '2': B-disaster-type
+          '3': B-distance
+          '4': B-duration
+          '5': B-event-cause
+          '6': B-location
+          '7': B-location-city
+          '8': B-location-route
+          '9': B-location-stop
+          '10': B-location-street
+          '11': B-money
+          '12': B-number
+          '13': B-organization
+          '14': B-organization-company
+          '15': B-org-position
+          '16': B-percent
+          '17': B-person
+          '18': B-set
+          '19': B-time
+          '20': B-trigger
+          '21': I-date
+          '22': I-disaster-type
+          '23': I-distance
+          '24': I-duration
+          '25': I-event-cause
+          '26': I-location
+          '27': I-location-city
+          '28': I-location-route
+          '29': I-location-stop
+          '30': I-location-street
+          '31': I-money
+          '32': I-number
+          '33': I-organization
+          '34': I-organization-company
+          '35': I-org-position
+          '36': I-percent
+          '37': I-person
+          '38': I-set
+          '39': I-time
+          '40': I-trigger
+  splits:
+  - name: train
+    num_bytes: 1112606
+    num_examples: 2115
+  - name: test
+    num_bytes: 354244
+    num_examples: 623
+  - name: validation
+    num_bytes: 251031
+    num_examples: 494
+  download_size: 8190212
+  dataset_size: 1717881
+- config_name: re
+  features:
+  - name: id
+    dtype: string
+  - name: tokens
+    sequence: string
+  - name: entities
+    sequence:
+      list: int32
+  - name: entity_roles
+    sequence:
+      class_label:
+        names:
+          '0': no_arg
+          '1': trigger
+          '2': location
+          '3': delay
+          '4': direction
+          '5': start_loc
+          '6': end_loc
+          '7': start_date
+          '8': end_date
+          '9': cause
+          '10': jam_length
+          '11': route
+  - name: entity_types
+    sequence:
+      class_label:
+        names:
+          '0': date
+          '1': disaster-type
+          '2': distance
+          '3': duration
+          '4': event-cause
+          '5': location
+          '6': location-city
+          '7': location-route
+          '8': location-stop
+          '9': location-street
+          '10': money
+          '11': number
+          '12': organization
+          '13': organization-company
+          '14': org-position
+          '15': percent
+          '16': person
+          '17': set
+          '18': time
+          '19': trigger
+  - name: event_type
+    dtype:
+      class_label:
+        names:
+          '0': O
+          '1': Accident
+          '2': CanceledRoute
+          '3': CanceledStop
+          '4': Delay
+          '5': Obstruction
+          '6': RailReplacementService
+          '7': TrafficJam
+  - name: entity_ids
+    sequence: string
+  splits:
+  - name: train
+    num_bytes: 1048457
+    num_examples: 1199
+  - name: test
+    num_bytes: 501336
+    num_examples: 609
+  - name: validation
+    num_bytes: 179001
+    num_examples: 228
+  download_size: 8190212
+  dataset_size: 1728794
 ---
 
 # Dataset Card for "MobIE"

mobie.py

@@ -77,6 +77,62 @@ def simplify_dict(d, remove_attribute=True):
         return d
 
 
+def find_concept_mention_token_offsets(sentence, concept_mention):
+    arg_char_start = concept_mention["span"]["start"]
+    arg_char_end = concept_mention["span"]["end"]
+    arg_start = -1
+    arg_end = -1
+    for idx, token in enumerate(sentence["tokens"]):
+        if token["span"]["start"] == arg_char_start:
+            arg_start = idx
+        if token["span"]["end"] == arg_char_end:
+            arg_end = idx+1
+    assert arg_start != -1 and arg_end != -1, f"Could not find token offsets for {concept_mention['id']}"
+    return arg_start, arg_end
+
+
+def fix_doc(doc):
+    """Fix document with faulty spans. REMOVE IF FIXED IN DATASET!"""
+    if doc["id"] == "1111185208647274501":
+        offset = 0
+        # Fix token spans
+        tokens = doc["tokens"]["array"]
+        for idx, token in enumerate(tokens):
+            if idx == 6:
+                offset += 1
+            token["span"]["start"] -= offset
+            if idx == 3:
+                offset += 1
+            token["span"]["end"] -= offset
+        # Fix concept mentions and relation mentions
+        offset = 0
+        concept_mentions = doc["conceptMentions"]["array"]
+        for idx, cm in enumerate(concept_mentions):
+            if idx == 1 or idx == 2:
+                offset += 1
+            cm["span"]["start"] -= offset
+            cm["span"]["end"] -= offset
+        rm = doc["relationMentions"]["array"][0]
+        rm["span"]["start"] -= 1
+        rm["span"]["end"] -= 2
+        rm["args"]["array"][0]["conceptMention"]["span"]["start"] -= 1
+        rm["args"]["array"][0]["conceptMention"]["span"]["end"] -= 1
+        rm["args"]["array"][1]["conceptMention"]["span"]["start"] -= 2
+        rm["args"]["array"][1]["conceptMention"]["span"]["end"] -= 2
+
+        doc["tokens"]["array"] = tokens
+        doc["sentences"]["array"][0]["span"]["end"] -= 2
+        doc["sentences"]["array"][0]["tokens"]["array"] = tokens[:20]
+        doc["sentences"]["array"][0]["conceptMentions"]["array"] = concept_mentions[:-1]
+        doc["sentences"]["array"][0]["relationMentions"]["array"] = [rm]
+        doc["sentences"]["array"][1]["span"]["start"] -= 2
+        doc["sentences"]["array"][1]["span"]["end"] -= 2
+        doc["sentences"]["array"][1]["tokens"]["array"] = tokens[20:]
+        doc["sentences"]["array"][1]["conceptMentions"]["array"] = [concept_mentions[-1]]
+        print("Fixed spans")
+    return doc
+
+
 class Mobie(datasets.GeneratorBasedBuilder):
     """MobIE is a German-language dataset which is human-annotated with 20 coarse- and fine-grained entity types and entity linking information for geographically linkable entities"""
 
@@ -139,17 +195,16 @@ class Mobie(datasets.GeneratorBasedBuilder):
                 ]
             }
         ]
+        prefixes = ["B", "I"]
+        ner_tags = ["O"] + [f"{prefix}-{label}" for prefix in prefixes for label in labels]
         if self.config.name == "ner":
-            prefixes = ["B", "I"]
-
-            names = ["O"] + [f"{prefix}-{label}" for prefix in prefixes for label in labels]
             features = datasets.Features(
                 {
                     "id": datasets.Value("string"),
                     "tokens": datasets.Sequence(datasets.Value("string")),
                     "ner_tags": datasets.Sequence(
                         datasets.features.ClassLabel(
-                            names=names
+                            names=ner_tags
                         )
                     ),
                 }
@@ -224,7 +279,11 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                 ]
                             ),
                         }
-                    ]
+                    ],
+                    "tokens": datasets.Sequence(datasets.Value("string")),
+                    "pos_tags": datasets.Sequence(datasets.Value("string")),
+                    "lemma": datasets.Sequence(datasets.Value("string")),
+                    "ner_tags": datasets.Sequence(datasets.features.ClassLabel(names=ner_tags))
                 }
             )
         else:
@@ -294,6 +353,8 @@ class Mobie(datasets.GeneratorBasedBuilder):
                 raw = f.read()
 
             for doc in decode_stacked(raw):
+                if doc["id"] == "1111185208647274501":
+                    doc = fix_doc(doc)
                 text = doc["text"]["string"]
                 iterable = doc["sentences"]["array"] if sentence_level else [doc]
                 for s in iterable:
@@ -314,6 +375,8 @@ class Mobie(datasets.GeneratorBasedBuilder):
             with open(filepath, encoding="utf-8") as f:
                 for line in f:
                     doc = json.loads(line)
+                    if doc["id"] == "1111185208647274501":
+                        doc = fix_doc(doc)
                     doc = simplify_dict(doc)
                     text = doc["text"]
                     iterable = doc["sentences"] if sentence_level else [doc]
@@ -323,15 +386,24 @@ class Mobie(datasets.GeneratorBasedBuilder):
                         mobie_cms = sentence["conceptMentions"]
                         entity_mentions = []
                         for cm in mobie_cms:
-                            cm_start = cm["span"]["start"]
-                            cm_end = cm["span"]["end"]
-                            cm_text = text[cm_start:cm_end]
+                            char_start = cm["span"]["start"]
+                            char_end = cm["span"]["end"]
+                            # Find token offsets for entity mentions
+                            start, end = find_concept_mention_token_offsets(sentence, cm)
+                            cm_text = text[char_start:char_end]
+                            entity_id = "NIL"
+                            for refid in cm["refids"]:
+                                if refid["key"] == "osm_id":
+                                    entity_id = refid["value"]
+                                    break
                             entity_mentions.append({
-                                "id": cm["id"],
                                 "text": cm_text,
-                                "start": cm_start - sentence_start,
-                                "end": cm_end - sentence_start,
+                                "start": start,
+                                "end": end,
+                                "char_start": char_start - sentence_start,
+                                "char_end": char_end - sentence_start,
                                 "type": cm["type"],
+                                "entity_id": entity_id,
                                 "refids": [
                                     {
                                         "key": refid["key"], 
@@ -339,56 +411,41 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                     } for refid in cm["refids"]
                                 ] if "refids" in cm and cm["refids"] else []
                             })
+                        tokens = []
+                        lemmas = []
+                        ner_tags = []
+                        pos_tags = []
+                        for token in sentence["tokens"]:
+                            token_text = text[token["span"]["start"]:token["span"]["end"]]
+                            tokens.append(token_text)
+                            lemmas.append(token["lemma"])
+                            ner_tags.append(token["ner"])
+                            pos_tags.append(token["posTag"])
                         if self.config.name == "el":
-                            # TODO use osm_id as entity id?
                             yield sentence_id, {
                                 "id": sentence_id,
                                 "text": text,
+                                "tokens": tokens,
                                 "entity_mentions": entity_mentions
                             }
                         elif self.config.name == "re":
                             mobie_rms = sentence["relationMentions"]
                             if not mobie_rms:
                                 continue
-                            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])
+                            for cm in entity_mentions:
+                                entities.append([cm["start"], cm["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 not found_osm_id:
-                                    entity_ids.append("NIL")
+                                entity_ids.append(cm["entity_id"])
                             for rm in mobie_rms:
                                 entity_roles = ["no_arg"] * len(entities)
                                 for arg in rm["args"]:
                                     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
+                                    # Matching via ids does not work, need to match via positions
                                     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']}"
+                                    start, end = find_concept_mention_token_offsets(sentence, cm)
                                     entity_idx = -1
                                     for idx, entity in enumerate(entities):
                                         if entity == [start, end]:
@@ -420,21 +477,32 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                         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]
+                                trigger_char_start = trigger["conceptMention"]["span"]["start"]
+                                trigger_char_end = trigger["conceptMention"]["span"]["end"]
+                                trigger_start, trigger_end = find_concept_mention_token_offsets(sentence, trigger["conceptMention"])
+                                trigger_text = text[trigger_char_start:trigger_char_end]
                                 args = []
                                 for arg in rm["args"]:
                                     if arg["role"] == "trigger":
                                         continue
-                                    arg_start = arg["conceptMention"]["span"]["start"]
-                                    arg_end = arg["conceptMention"]["span"]["end"]
-                                    arg_text = text[arg_start:arg_end]
+                                    arg_char_start = arg["conceptMention"]["span"]["start"]
+                                    arg_char_end = arg["conceptMention"]["span"]["end"]
+                                    arg_start = -1
+                                    arg_end = -1
+                                    for idx, token in enumerate(sentence["tokens"]):
+                                        if token["span"]["start"] == arg_char_start:
+                                            arg_start = idx
+                                        if token["span"]["end"] == arg_char_end:
+                                            arg_end = idx+1
+                                    assert arg_start != -1 and arg_end != -1, f"Could not find token offsets for {arg['conceptMention']['id']}"
+                                    arg_text = text[arg_char_start:arg_char_end]
                                     args.append({
                                         "id": arg["conceptMention"]["id"],
                                         "text": arg_text,
-                                        "start": arg_start - sentence_start,
-                                        "end": arg_end - sentence_start,
+                                        "start": arg_start,
+                                        "end": arg_end,
+                                        "char_start": arg_char_start - sentence_start,
+                                        "char_end": arg_char_end - sentence_start,
                                         "role": arg["role"],
                                         "type": arg["conceptMention"]["type"]
                                     })
@@ -443,8 +511,10 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                     "trigger": {
                                         "id": trigger["conceptMention"]["id"],
                                         "text": trigger_text,
-                                        "start": trigger_start - sentence_start,
-                                        "end": trigger_end - sentence_start
+                                        "start": trigger_start,
+                                        "end": trigger_end,
+                                        "char_start": trigger_char_start - sentence_start,
+                                        "char_end": trigger_char_end - sentence_start
                                     },
                                     "arguments": args,
                                     "event_type": rm["name"]
@@ -453,7 +523,11 @@ class Mobie(datasets.GeneratorBasedBuilder):
                                 "id": sentence_id,
                                 "text": text,
                                 "entity_mentions": entity_mentions,
-                                "event_mentions": event_mentions
+                                "event_mentions": event_mentions,
+                                "tokens": tokens,
+                                "pos_tags": pos_tags,
+                                "lemma": lemmas,
+                                "ner_tags": ner_tags
                             }
                         else:
                             raise ValueError("Invalid configuration name")