Upload 45 files

BindingDB_filtered/data.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:724dc1c93b1cc7c98f8662be27c900852f8e274ce4c6ae6df95ef02adf6689c1
-size 19595981
+oid sha256:d0f8691a96876f09766e574c5600df55f0d0b1c11cfd1705faf841d924f89f20
+size 19595446

BindingDB_filtered/train/dataset_info.json

@@ -7,11 +7,11 @@
   "description": "",
   "download_checksums": {
     "/Users/aryopg/Documents/school/BALM-benchmark/./BindingDB_filtered/data.csv": {
-      "num_bytes": 19595981,
+      "num_bytes": 19595446,
       "checksum": null
     }
   },
-  "download_size": 19595981,
+  "download_size": 19595446,
   "features": {
     "Index": {
       "dtype": "int64",
@@ -40,7 +40,7 @@
   },
   "homepage": "",
   "license": "",
-  "size_in_bytes": 39163103,
+  "size_in_bytes": 39162568,
   "splits": {
     "train": {
       "name": "train",

BindingDB_filtered/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "765430ff6f250851",
+  "_fingerprint": "8ea2da55f109634f",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

CATS/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "e87f6abd6563cfbd",
+  "_fingerprint": "bd2c73d46dafe08b",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

HIF2A/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "04deae323b874de9",
+  "_fingerprint": "9132f6afd5525c48",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

HSP90/train/data-00000-of-00001.arrow

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:da662972b79300eecfa5b1c9ceff65a001d858909f7df9d8975cf3d99276bf58
-size 143944
+oid sha256:78a809fc0efe6069c6d0e4b256f53fc2dd6b7e581353b81997860380483e3fca
+size 157408

HSP90/train/dataset_info.json

@@ -3,41 +3,45 @@
   "citation": "",
   "config_name": "default",
   "dataset_name": "csv",
-  "dataset_size": 143051,
+  "dataset_size": 156354,
   "description": "",
   "download_checksums": {
     "/Users/aryopg/Documents/school/BALM-benchmark/./HSP90/data.csv": {
-      "num_bytes": 140081,
+      "num_bytes": 156282,
       "checksum": null
     }
   },
-  "download_size": 140081,
+  "download_size": 156282,
   "features": {
     "Index": {
-      "dtype": "int64",
-      "_type": "Value"
-    },
-    "Y": {
-      "dtype": "int64",
+      "dtype": "string",
       "_type": "Value"
     },
     "Drug": {
       "dtype": "string",
       "_type": "Value"
     },
+    "IC50 (nM)": {
+      "dtype": "float64",
+      "_type": "Value"
+    },
     "Target": {
       "dtype": "string",
       "_type": "Value"
+    },
+    "Y": {
+      "dtype": "float64",
+      "_type": "Value"
     }
   },
   "homepage": "",
   "license": "",
-  "size_in_bytes": 283132,
+  "size_in_bytes": 312636,
   "splits": {
     "train": {
       "name": "train",
-      "num_bytes": 143051,
-      "num_examples": 180,
+      "num_bytes": 156354,
+      "num_examples": 192,
       "dataset_name": "csv"
     }
   },

HSP90/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "53daa23b5802002b",
+  "_fingerprint": "c934a957821bca66",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

LeakyPDB/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "0f32f1188fc7aa86",
+  "_fingerprint": "3a1d36a9999cc374",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

MCL1/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "56afff6d8815d904",
+  "_fingerprint": "7b70c098fb3d71e3",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

Mpro/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "6bc4bc41f892d666",
+  "_fingerprint": "5dde51d52f7a4c07",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

README.md

@@ -1,152 +1,205 @@
----
-dataset_info:
-- config_name: bindingdb_filtered
-  features:
-  - name: Index
-    dtype: string
-  - name: Drug_ID
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: Target_ID
-    dtype: string
-  - name: Target
-    dtype: string
-  - name: 'Y'
-    dtype: float32
-  splits:
-  - name: train
-    num_examples: 24700
-- config_name: CATS
-  features:
-  - name: Index
-    dtype: string
-  - name: Compound ID
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: IC50
-    dtype: float32
-  - name: Target
-    dtype: string
-  - name: 'Y'
-    dtype: float32
-  splits:
-  - name: train
-    num_examples: 136
-- config_name: HSP9
-  features:
-  - name: Index
-    dtype: string
-  - name: 'Y'
-    dtype: float32
-  - name: Drug
-    dtype: string
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 180
-- config_name: leakypdb
-  features:
-  - name: Index
-    dtype: string
-  - name: header
-    dtype: string
-  - name: smiles
-    dtype: string
-  - name: category
-    dtype: string
-  - name: seq
-    dtype: string
-  - name: resolution
-    dtype: float32
-  - name: date
-    dtype: string
-  - name: type
-    dtype: string
-  - name: new_split
-    dtype: string
-  - name: CL1
-    dtype: bool
-  - name: CL2
-    dtype: bool
-  - name: CL3
-    dtype: bool
-  - name: remove_for_balancing_val
-    dtype: bool
-  - name: kd/ki
-    dtype: string
-  - name: value
-    dtype: float32
-  - name: covalent
-    dtype: bool
-  splits:
-  - name: train
-    num_examples: 19443
-- config_name: Mpro
-  features:
-  - name: Index
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: 'Y'
-    dtype: float32
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 2749
-configs:
-- config_name: bindingdb_filtered
-  data_files:
-  - split: train
-    path: bindingdb_filtered/train/data-*
-- config_name: CATS
-  data_files:
-  - split: train
-    path: CATS/train/data-*
-- config_name: HSP9
-  data_files:
-  - split: train
-    path: HSP9/train/data-*
-- config_name: leakypdb
-  data_files:
-  - split: train
-    path: leakypdb/train/data-*
-- config_name: Mpro
-  data_files:
-  - split: train
-    path: Mpro/train/data-*
-license: cc-by-4.0
-pretty_name: BALM-Benchmark
-tags:
-- chemistry
-- biology
-size_categories:
-- 10K<n<100K
----
-
-# Dataset Card for BALM-Benchmark
-
-<!-- Provide a quick summary of the dataset. -->
-
-## Dataset Details
-
-### Dataset Description
-
-## Citation
-
-<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
-
-**BibTeX:**
-
-```
-
-```
-
-## Dataset Card Contact
-
-- Rohan Gorantla (rohan.gorantla@ed.ac.uk)
-- Aryo Pradipta Gema (aryo.gema@ed.ac.uk)
-- Antonia Mey (antonia.mey@ed.ac.uk)
+---
+dataset_info:
+- config_name: BindingDB_filtered
+  features:
+  - name: Index 
+    dtype: string
+  - name: Drug_ID
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: Target_ID
+    dtype: string
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 24700
+- config_name: CATS
+  features:
+  - name: Index 
+    dtype: string
+  - name: Compound ID
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: IC50
+    dtype: float32
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 136
+- config_name: HIF2A
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 37
+- config_name: HSP90
+  features:
+  - name: Index
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: IC50 (nM)
+    dtype: float32
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 192
+- config_name: LeakyPDB
+  features:
+  - name: Index 
+    dtype: string
+  - name: header
+    dtype: string
+  - name: smiles
+    dtype: string
+  - name: category
+    dtype: string
+  - name: seq
+    dtype: string
+  - name: resolution
+    dtype: float32
+  - name: date
+    dtype: string
+  - name: type
+    dtype: string
+  - name: new_split
+    dtype: string
+  - name: CL1
+    dtype: bool
+  - name: CL2
+    dtype: bool
+  - name: CL3
+    dtype: bool
+  - name: remove_for_balancing_val
+    dtype: bool
+  - name: kd/ki
+    dtype: string
+  - name: value
+    dtype: float32
+  - name: covalent
+    dtype: bool
+  splits:
+  - name: train
+    num_examples: 19443
+- config_name: MCL1
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 25
+- config_name: Mpro
+  features:
+  - name: Index 
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 2749
+- config_name: SYK
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 44
+configs:
+- config_name: BindingDB_filtered
+  data_files:
+  - split: train
+    path: BindingDB_filtered/train/data-*
+- config_name: CATS
+  data_files:
+  - split: train
+    path: CATS/train/data-*
+- config_name: HIF2A
+  data_files:
+  - split: train
+    path: HIF2A/train/data-*
+- config_name: HSP90
+  data_files:
+  - split: train
+    path: HSP90/train/data-*
+- config_name: LeakyPDB
+  data_files:
+  - split: train
+    path: LeakyPDB/train/data-*
+- config_name: MCL1
+  data_files:
+  - split: train
+    path: MCL1/train/data-*
+- config_name: Mpro
+  data_files:
+  - split: train
+    path: Mpro/train/data-*
+- config_name: SYK
+  data_files:
+  - split: train
+    path: SYK/train/data-*
+license: cc-by-4.0
+pretty_name: BALM-Benchmark
+tags:
+  - chemistry
+  - biology
+size_categories:
+  - 10K<n<100K
+---
+
+# Dataset Card for BALM-Benchmark
+
+<!-- Provide a quick summary of the dataset. -->
+
+## Dataset Details
+
+### Dataset Description
+
+## Citation
+
+<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
+
+**BibTeX:**
+
+```
+
+```
+
+## Dataset Card Contact
+
+- Rohan Gorantla (rohan.gorantla@ed.ac.uk)
+- Aryo Pradipta Gema (aryo.gema@ed.ac.uk)
+- Antonia Mey ()

SYK/train/state.json

@@ -4,7 +4,7 @@
       "filename": "data-00000-of-00001.arrow"
     }
   ],
-  "_fingerprint": "bfdea1926fb3b980",
+  "_fingerprint": "3699086d45fd9258",
   "_format_columns": null,
   "_format_kwargs": {},
   "_format_type": null,

convert_csv_to_hf_dataset.py

@@ -22,8 +22,8 @@ def main():
         # Add Index column, make sure it's the left most column
         if "Index" not in df.columns:
             df["Index"] = df.index
-            df = df[["Index"] + [col for col in df.columns if col != "Index"]]
-            df.to_csv(filepath, index=False)
+        df = df[["Index"] + [col for col in df.columns if col != "Index"]]
+        df.to_csv(filepath, index=False)
 
         dataset = load_dataset("csv", data_files=filepath, delimiter=",")
         print(dataset)