Data file and loading script

.gitattributes

@@ -53,3 +53,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
+biovdb_1000.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,3 @@
+# biovdb
+
+Test set of ~1000 samples from GEO.

biovdb_1000.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dc6c493ff7eca194d8c9d9f4c221bb81d5e8478bf94d9fb5f3b7f830e75ed8ea
+size 452384517

biovdb_1000.py

@@ -0,0 +1,50 @@
+import pandas as pd
+import datasets
+
+CSV_PATH = "./biovdb_1000.csv"
+
+CITATION = """
+"""
+
+class CustomDataset(datasets.GeneratorBasedBuilder):
+    VERSION = datasets.Version("1.0.0")
+    BUILDER_CONFIGS = []
+
+    def _info(self):
+        return datasets.DatasetInfo(
+            description="Test set of ~1000 samples from GEO",
+            citation=CITATION,
+            homepage="",
+        )
+    
+    def _split_generators(self, dl_manager):
+        data = pd.read_csv(CSV_PATH)
+        unique_series_ids = data['series_id'].unique()
+
+        for series_id in unique_series_ids:
+            self.BUILDER_CONFIGS.append(
+                datasets.BuilderConfig(
+                    name=str(series_id),
+                    version=datasets.Version("1.0.0"),
+                    description=f"Dataset for series_id {series_id}"
+                )
+            )
+        
+        return [
+            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={
+                "data": data[data['series_id'] == self.config.name]
+            }),
+        ]
+
+    def _generate_examples(self, data):
+        metadata_columns = data.columns[:40]
+        expression_columns = data.columns[40:]
+
+        for idx, row in data.iterrows():
+            yield idx, {
+                "data": row[expression_columns].values.tolist(),
+                "metadata": row[metadata_columns].to_dict()
+            }
+
+if __name__ == '__main__':
+    ds = datasets.load_dataset("./biovdb_1000.py", "GSE52", split='train')