use sequence tagging formulation of dataset

blurb.py

@@ -44,7 +44,6 @@ import re
 import pandas
 import datasets
 
-#from .bigbiohub import kb_features
 from .bigbiohub import BigBioConfig
 from .bigbiohub import Tasks
 
@@ -165,7 +164,7 @@ _DESCRIPTION = {
 
 _HOMEPAGE = "https://microsoft.github.io/BLURB/tasks.html"
 
-_LICENSE = "MIXED"  # Licenses.GPL_3p0
+_LICENSE = "MIXED"
 
 
 _URLs = {
@@ -202,8 +201,7 @@ _BIGBIO_VERSION = "1.0.0"
 
 
 class BlurbDataset(datasets.GeneratorBasedBuilder):
-    """Source splits for BLURB data (train/val/test) for easy access.
-    """
+    """Source splits for BLURB data (train/val/test) for easy access."""
 
     DEFAULT_CONFIG_NAME = "bc5chem"
     SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
@@ -253,12 +251,12 @@ class BlurbDataset(datasets.GeneratorBasedBuilder):
             {
                 "id": datasets.Value("string"),
                 "tokens": datasets.Sequence(datasets.Value("string")),
-                "word_idx": datasets.Value("int32"),
                 "type": datasets.Value("string"),
-                "tags": datasets.Sequence(
+                "ner_tags": datasets.Sequence(
                     datasets.features.ClassLabel(
                         names=[
                             "O",
+                            "B",
                             "I",
                         ]
                     )
@@ -314,7 +312,7 @@ class BlurbDataset(datasets.GeneratorBasedBuilder):
                 if line.strip() == "":
                     toks, tags = zip(*tagged)
                     # transform tags
-                    tags = [t[0] if t[0] in ["I", "O"] else "I" for t in tags]
+                    tags = tags = [t[0] for t in tags]
                     yield (toks, tags)
                     tagged = []
                     continue
@@ -341,16 +339,11 @@ class BlurbDataset(datasets.GeneratorBasedBuilder):
 
             uid = 0
             for item in self._load_iob(filepath):
-                if len(item) != 2:
-                    print("ERROR", len(item), item, split)
-                    continue
                 toks, tags = item
-                for word_idx in range(len(toks)):
-                    yield uid, {
-                        "id": uid,
-                        "tokens": toks,
-                        "type": ner_types[self.config.name],
-                        "tags": tags,
-                        "word_idx": word_idx,
-                    }
-                    uid += 1
+                yield uid, {
+                    "id": uid,
+                    "tokens": toks,
+                    "type": ner_types[self.config.name],
+                    "ner_tags": tags,
+                }
+                uid += 1