upload hubscripts/bio_sim_verb_hub.py to hub from bigbio repo

bio_sim_verb.py

@@ -0,0 +1,169 @@
+# coding=utf-8
+# Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+This repository contains the evaluation datasets for the paper Bio-SimVerb and
+Bio-SimLex: Wide-coverage Evaluation Sets of Word Similarity in Biomedicine by
+Billy Chiu, Sampo Pyysalo and Anna Korhonen.
+"""
+
+import csv
+from typing import Dict, List, Tuple
+
+import datasets
+
+from .bigbiohub import pairs_features
+from .bigbiohub import BigBioConfig
+from .bigbiohub import Tasks
+
+# TODO: Add BibTeX citation
+_LANGUAGES = ['English']
+_PUBMED = True
+_LOCAL = False
+_CITATION = """\
+@article{article,
+  title        = {
+    Bio-SimVerb and Bio-SimLex: Wide-coverage evaluation sets of word
+    similarity in biomedicine
+  },
+  author       = {Chiu, Billy and Pyysalo, Sampo and Vulić, Ivan and Korhonen, Anna},
+  year         = 2018,
+  month        = {02},
+  journal      = {BMC Bioinformatics},
+  volume       = 19,
+  pages        = {},
+  doi          = {10.1186/s12859-018-2039-z}
+}
+"""
+
+_DATASETNAME = "bio_sim_verb"
+_DISPLAYNAME = "Bio-SimVerb"
+
+_DESCRIPTION = """
+This repository contains the evaluation datasets for the paper Bio-SimVerb and \
+Bio-SimLex: Wide-coverage Evaluation Sets of Word Similarity in Biomedicine by \
+Billy Chiu, Sampo Pyysalo and Anna Korhonen.
+"""
+
+_HOMEPAGE = "https://github.com/cambridgeltl/bio-simverb"
+
+_LICENSE = 'License information unavailable'
+
+_URLS = {
+    _DATASETNAME: "https://raw.githubusercontent.com/cambridgeltl/bio-simverb/master/wvlib/word-similarities/bio-simverb/Bio-SimVerb.txt",
+}
+
+_SUPPORTED_TASKS = [Tasks.SEMANTIC_SIMILARITY]
+
+_SOURCE_VERSION = "1.0.0"
+_BIGBIO_VERSION = "1.0.0"
+
+
+# TODO: Name the dataset class to match the script name using CamelCase instead of snake_case
+#  Append "Dataset" to the class name: BioASQ --> BioasqDataset
+class BioSimVerb(datasets.GeneratorBasedBuilder):
+    """Evaluation of word similarity in biomedical texts."""
+
+    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
+    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
+
+    BUILDER_CONFIGS = [
+        BigBioConfig(
+            name="bio_sim_verb_source",
+            version=SOURCE_VERSION,
+            description="bio_sim_verb source schema",
+            schema="source",
+            subset_id="bio_sim_verb",
+        ),
+        BigBioConfig(
+            name="bio_sim_verb_bigbio_pairs",
+            version=BIGBIO_VERSION,
+            description="bio_sim_verb BigBio schema",
+            schema="bigbio_pairs",
+            subset_id="bio_sim_verb",
+        ),
+    ]
+
+    DEFAULT_CONFIG_NAME = "bio_sim_verb_source"
+
+    def _info(self) -> datasets.DatasetInfo:
+
+        if self.config.schema == "source":
+            features = datasets.Features(
+                {
+                    "text_1": datasets.Value("string"),
+                    "text_2": datasets.Value("string"),
+                    "label": datasets.Value("float32"),
+                }
+            )
+
+        # Using in pairs schema
+        elif self.config.schema == "bigbio_pairs":
+            features = pairs_features
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage=_HOMEPAGE,
+            license=str(_LICENSE),
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
+        """Returns SplitGenerators."""
+
+        urls = _URLS[_DATASETNAME]
+        data_dir = dl_manager.download_and_extract(urls)
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN,
+                # Whatever you put in gen_kwargs will be passed to _generate_examples
+                gen_kwargs={"filepath": data_dir, "split": "train"},
+            )
+        ]
+
+    def _generate_examples(self, filepath, split: str) -> Tuple[int, Dict]:
+        """Yields examples as (key, example) tuples."""
+
+        with open(filepath, encoding="utf-8") as csv_file:
+            csv_reader = csv.reader(
+                csv_file,
+                quotechar='"',
+                delimiter="\t",
+                quoting=csv.QUOTE_ALL,
+                skipinitialspace=True,
+            )
+
+            if self.config.schema == "source":
+                for id_, row in enumerate(csv_reader):
+                    text_1, text_2, label = row
+                    yield id_, {
+                        "text_1": text_1,
+                        "text_2": text_2,
+                        "label": float(label),
+                    }
+
+            elif self.config.schema == "bigbio_pairs":
+                uid = 0
+                for id_, row in enumerate(csv_reader):
+                    uid += 1
+                    text_1, text_2, label = row
+                    yield id_, {
+                        "id": str(uid),
+                        "document_id": "NULL",
+                        "text_1": text_1,
+                        "text_2": text_2,
+                        "label": str(label),
+                    }