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small rename
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psets/ps6-drug-screen/pset6_template.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -86,12 +86,12 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"cmap = pd.read_csv(\n",
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"prism = pd.read_csv(\n",
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" \"prism_train.csv\",\n",
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" header=\"infer\",\n",
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" index_col=0,\n",
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")\n",
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"cmap_test = pd.read_csv(\n",
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"prism_test = pd.read_csv(\n",
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" \"prism_test.csv\",\n",
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" header=\"infer\",\n",
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" index_col=0,\n",
@@ -124,8 +124,8 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"y = cmap.to_numpy()\n",
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"X = cmap.index.to_list()\n",
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"y = prism.to_numpy()\n",
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"X = prism.index.to_list()\n",
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"X[:10], y"
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]
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},
@@ -323,7 +323,7 @@
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"outputs": [],
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"source": [
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"def save_submission(model, X_test, csv_name):\n",
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" pred_df = pd.DataFrame(index=cmap_test[\"SMILES\"], columns=cmap.columns)\n",
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" pred_df = pd.DataFrame(index=prism_test[\"SMILES\"], columns=prism.columns)\n",
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" pred_df[:] = model.predict(X_test)\n",
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" # Annoyingly Kaggle can't seem to handle large matrix datasets \n",
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" # & so we need to cut down our submission to just the first 30 cell lines\n",
@@ -337,7 +337,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"X_test = cmap_test['SMILES'].to_list()\n",
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"X_test = prism_test['SMILES'].to_list()\n",
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"new_X_test = []\n",
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"for smiles in tqdm(X_test):\n",
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" morgan_fingerprints = AllChem.GetHashedMorganFingerprint(\n",

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