convert to parquet

.gitattributes

@@ -69,3 +69,13 @@ pdbbind-2020-combined.csv filter=lfs diff=lfs merge=lfs -text
 affinity-data-combined.parquet filter=lfs diff=lfs merge=lfs -text
 bindingdb-kd-filtered.csv filter=lfs diff=lfs merge=lfs -text
 davis-filtered.csv filter=lfs diff=lfs merge=lfs -text
+bindingdb-kd.parquet filter=lfs diff=lfs merge=lfs -text
+bindingdb-ki.parquet filter=lfs diff=lfs merge=lfs -text
+davis-filtered.parquet filter=lfs diff=lfs merge=lfs -text
+pdbbind-2020-combined.parquet filter=lfs diff=lfs merge=lfs -text
+pdbbind-2020-refined.parquet filter=lfs diff=lfs merge=lfs -text
+bindingdb-ic50.parquet filter=lfs diff=lfs merge=lfs -text
+davis.parquet filter=lfs diff=lfs merge=lfs -text
+glaser.parquet filter=lfs diff=lfs merge=lfs -text
+kiba.parquet filter=lfs diff=lfs merge=lfs -text
+bindingdb-kd-filtered.parquet filter=lfs diff=lfs merge=lfs -text

README.md

@@ -11,35 +11,35 @@ configs:
   - split: train
     path: "affinity-data-combined.parquet"
   - split: davis
-    path: "davis.csv"
+    path: "davis.parquet"
   - split: davis_filtered
-    path: "davis-filtered.csv"
+    path: "davis-filtered.parquet"
   - split: kiba
-    path: "kiba.csv"
+    path: "kiba.parquet"
   - split: pdbbind_2020_combined
-    path: "pdbbind-2020-combined.csv"
+    path: "pdbbind-2020-combined.parquet"
   - split: pdbbind_2020_refined
-    path: "pdbbind-2020-refined.csv"
+    path: "pdbbind-2020-refined.parquet"
   - split: bindingdb_ic50
-    path: "bindingdb-ic50.csv"
+    path: "bindingdb-ic50.parquet"
   - split: bindingdb_ki
-    path: "bindingdb-ki.csv"
+    path: "bindingdb-ki.parquet"
   - split: bindingdb_kd_filtered
-    path: "bindingdb-kd-filtered.csv"
+    path: "bindingdb-kd-filtered.parquet"
   - split: bindingdb_kd
-    path: "bindingdb-kd.csv"
+    path: "bindingdb-kd.parquet"
   - split: glaser
-    path: "glaser.csv"
+    path: "glaser.parquet"
 ---
 
 ## Data Sources
-bindingdb_ic50.csv: https://tdcommons.ai/ (tdc python package)
-bindingdb_kd.csv: https://tdcommons.ai/ (tdc python package)
-bindingdb_kd_filtered.csv: filtered manually (see standardize_data.ipynb)
-bindingdb_ki.csv: https://tdcommons.ai/ (tdc python package)
-davis.csv: https://tdcommons.ai/ (tdc python package)
-davis_filtered.csv: https://www.kaggle.com/datasets/christang0002/davis-and-kiba
-kiba.csv: https://tdcommons.ai/ (tdc python package)
-pdbbind_2020_combined.csv: https://www.pdbbind.org.cn/
-pdbbind_2020_refined.csv: https://www.pdbbind.org.cn/
-glaser.csv: https://huggingface.co/datasets/jglaser/binding_affinity
+bindingdb_ic50.parquet: https://tdcommons.ai/ (tdc python package)
+bindingdb_kd.parquet: https://tdcommons.ai/ (tdc python package)
+bindingdb_kd_filtered.parquet: filtered manually (see standardize_data.ipynb)
+bindingdb_ki.parquet: https://tdcommons.ai/ (tdc python package)
+davis.parquet: https://tdcommons.ai/ (tdc python package)
+davis_filtered.parquet: https://www.kaggle.com/datasets/christang0002/davis-and-kiba
+kiba.parquet: https://tdcommons.ai/ (tdc python package)
+pdbbind_2020_combined.parquet: https://www.pdbbind.org.cn/
+pdbbind_2020_refined.parquet: https://www.pdbbind.org.cn/
+glaser.parquet: https://huggingface.co/datasets/jglaser/binding_affinity

bindingdb-ic50.csv → bindingdb-ic50.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:25a6488d678b3a1a2b83d78ab900fe5c49b96ad6b116efde158b5c5bdd39b557
-size 899074544
+oid sha256:f1d2e2220fecf27a4127de3e038d4d248cdf10dcb4e051f4f5b49bb7ff6fbdf2
+size 567925247

davis-filtered.csv → bindingdb-kd-filtered.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:484eaefff41f82de0f39811b589db7ed390061c952bc4199353d9e1c3700cfff
-size 8948685
+oid sha256:8a9b82dbe2d1349d8f0383d01c0eef8f1ac4896fcc4eb23ffbf2510821c0eb43
+size 1359656

pdbbind-2020-refined.csv → bindingdb-kd.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:46ef8fb491e31ca6b9e6256742300b14d0cc545d0ebdf83cdd097155f98bbd99
-size 3025349
+oid sha256:302cbd91af1ab1b414f79d683cda68786bb0fdb769343cf6761776878ceb5185
+size 1438234

bindingdb-kd-filtered.csv → bindingdb-ki.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:541f7d1392c64a8b74f51bc08dbc5f8c619d832cb1a982f6f5d45837890adef7
-size 29878994
+oid sha256:5c11ebb80d61ccd6d6dc631c5f5badd2c6dc584c9682d71cefed5638e8fc2b8f
+size 77601662

combine_data.py

@@ -32,5 +32,5 @@ def combine_csv_files(csv_file_list):
     
     return combined_df
 
-combined_df = combine_csv_files(['glaser.csv', 'davis-filtered.csv', 'pdbbind-2020-combined.csv', 'bindingdb-kd-filtered.csv', 'bindingdb-ki.csv', 'bindingdb-ic50.csv'])
+combined_df = combine_csv_files(['glaser.parquet', 'davis-filtered.parquet', 'pdbbind-2020-combined.parquet', 'bindingdb-kd-filtered.parquet', 'bindingdb-ki.parquet', 'bindingdb-ic50.parquet'])
 combined_df.to_parquet('affinity-data-combined.parquet', index=False)

bindingdb-kd.csv → davis-filtered.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e18aaba78a1e2c0e9584fbc831954312d65e02deca70ce01b7514b5004a4c216
-size 57281302
+oid sha256:e12377bc3c56a0cffd9eb48b58c221172e87e3d42f2ee28929b08417dcc96dc0
+size 319846

davis.csv → davis.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:34f698180a386c92ecc160da984d9d2c31bf1d153cb26a2d91d8eab4d7ec5fd7
-size 22441866
+oid sha256:5136c1949cfd332496e87db8029664b3d255f69a1cb69b96094a140d5c9e009e
+size 345287

glaser.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:73550c83f7fc9315bbcfa363304231f00f88dbd503222d241a47c8551ef65cd8
-size 1433278852

bindingdb-ki.csv → glaser.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c8b08f64f5954c6189561014f802c103a86bb78d6644460e3f6f31697376a1f6
-size 259031100
+oid sha256:5f91591b1896928fb860e03ced086ad225b3f66ac1d13363c6c6b59d0d8bc351
+size 1034508980

kiba.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:56ac9893cbdc98ddc137a7ef4f5a5f00756da6ec5792b7ce9b2ccd270e4244d2
-size 102460723

kiba.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:39c9b84755218c501647b3e5a7a4885192d061f043d57532dd7d9aa081b7e35a
+size 597576

pdbbind-2020-combined.csv

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:7221192655553cdfd07df4a71386aad31873bb8e0f27ec7fe26536a56a9df868
-size 11802666

pdbbind-2020-combined.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:82ea985d30e9e7102effdf8053275fec7a7473a32437857d3cf748642ee01814
+size 7215274

pdbbind-2020-refined.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5d4fc1c1eae3a0c9b9a5db6dc6469dfce35672173b45605b19fa47c4a1a44b79
+size 1432703

standardize_data.ipynb

@@ -102,7 +102,7 @@
     "    affinity_unit=\"nM\",\n",
     "    delimiter=\",\"\n",
     ")\n",
-    "dataset.to_csv(\"data/bindingdb-ic50.csv\", index=False)\n"
+    "dataset.to_parquet(\"data/bindingdb-ic50.parquet\", index=False)\n"
    ]
   },
   {
@@ -323,6 +323,48 @@
     "bindingdb_df.to_csv('bindingdb-kd-filtered.csv', index=False)\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 96,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Converted bindingdb-ki.csv to bindingdb-ki.parquet\n",
+      "Converted pdbbind-2020-refined.csv to pdbbind-2020-refined.parquet\n",
+      "Converted davis-filtered.csv to davis-filtered.parquet\n",
+      "Converted bindingdb-kd-filtered.csv to bindingdb-kd-filtered.parquet\n",
+      "Converted glaser.csv to glaser.parquet\n",
+      "Converted bindingdb-ic50.csv to bindingdb-ic50.parquet\n",
+      "Converted pdbbind-2020-combined.csv to pdbbind-2020-combined.parquet\n",
+      "Converted bindingdb-kd.csv to bindingdb-kd.parquet\n",
+      "Converted davis.csv to davis.parquet\n",
+      "Converted kiba.csv to kiba.parquet\n"
+     ]
+    }
+   ],
+   "source": [
+    "import pandas as pd\n",
+    "import glob\n",
+    "\n",
+    "# Get all CSV files in current directory\n",
+    "csv_files = glob.glob('*.csv')\n",
+    "\n",
+    "# Convert each CSV to parquet\n",
+    "for csv_file in csv_files:\n",
+    "    # Read CSV\n",
+    "    df = pd.read_csv(csv_file)\n",
+    "    \n",
+    "    # Create parquet filename by replacing .csv extension\n",
+    "    parquet_file = csv_file.replace('.csv', '.parquet')\n",
+    "    \n",
+    "    # Save as parquet\n",
+    "    df.to_parquet(parquet_file, index=False)\n",
+    "    print(f\"Converted {csv_file} to {parquet_file}\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,