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+{"nbformat":4,"nbformat_minor":0,"metadata":{"kernelspec":{"display_name":"Python 3","language":"python","name":"python3"},"language_info":{"codemirror_mode":{"name":"ipython","version":3},"file_extension":".py","mimetype":"text/x-python","name":"python","nbconvert_exporter":"python","pygments_lexer":"ipython3","version":"3.8.10"},"colab":{"name":"feature_selection_with_SelectKBest_with_data_Norm.ipynb","provenance":[],"collapsed_sections":[]}},"cells":[{"cell_type":"code","metadata":{"id":"5T5tLCBgHYK-","executionInfo":{"status":"ok","timestamp":1638487394403,"user_tz":300,"elapsed":13860,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["import pandas as pd \n","import seaborn as sns\n","import numpy as np\n","import matplotlib.pyplot as plt\n","import scipy\n","from scipy.spatial.distance import cdist\n","import sklearn \n","from sklearn.cluster import KMeans\n","from sklearn.model_selection import train_test_split\n","from sklearn.feature_selection import mutual_info_classif, SelectKBest\n","import xgboost as xgb\n","from xgboost import XGBClassifier, plot_importance\n","\n","#data = pd.read_csv('train_data.csv') # load original dataset \n","\n","# split dataset into 75/25 train test split \n","#train, test = sklearn.model_selection.train_test_split(data, test_size=.25, random_state=42, shuffle=True, stratify=data['Label'])\n","#train.to_csv('split_train_data.csv', index = False) # save train data for future use \n","#test.to_csv('split_test_data.csv', index = False) # save test data for future use \n","\n","train_split = pd.read_csv('split_train_data.csv')\n","\n","\n"],"execution_count":15,"outputs":[]},{"cell_type":"code","metadata":{"id":"mJXtj0sV1Xn8"},"source":["corr = train_split.corr(method='pearson')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"QFa1oX3e1bL8","executionInfo":{"status":"ok","timestamp":1638394045375,"user_tz":300,"elapsed":152,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"3a41b2bf-974c-4a3c-f9f2-42369e6c21bb"},"source":["print(corr.iloc[:,0])"],"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["G26                                   1.000000\n","G26_Target Sequence_in_SMILES_perc   -0.658644\n","G26_SMILES_in_Target Sequence_perc   -0.633055\n","G26_ARRO                              0.169460\n","G26_SMILES_base                       0.317016\n","                                        ...   \n","G10_fd_Target Sequence_base           0.159265\n","G10_std_SMILES_dist                   0.430174\n","G10_std_Target Sequence_dist          0.111489\n","KIBA                                  0.201958\n","Label                                 0.152989\n","Name: G26, Length: 338, dtype: float64\n"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"MSAEiUx80PS0","executionInfo":{"status":"ok","timestamp":1638394074040,"user_tz":300,"elapsed":192,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"1d30dd87-a8a5-4a9f-de9a-19263bbf85c4"},"source":["print(data.shape)"],"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["(109479, 338)\n"]}]},{"cell_type":"code","metadata":{"id":"qNZtNRk4nCcn","executionInfo":{"status":"ok","timestamp":1638487443917,"user_tz":300,"elapsed":595,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["train_split = train_split.drop('KIBA', axis = 1)\n","train, test = sklearn.model_selection.train_test_split(train_split, test_size=.25, random_state=42, shuffle=True, stratify=train_split['Label'])"],"execution_count":16,"outputs":[]},{"cell_type":"code","metadata":{"id":"o1GnGYd8juC6","executionInfo":{"status":"ok","timestamp":1638487489284,"user_tz":300,"elapsed":605,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["from sklearn.feature_selection import f_classif"],"execution_count":19,"outputs":[]},{"cell_type":"code","metadata":{"id":"0_vbHgv9whZm"},"source":["from sklearn.feature_selection import f_regression"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"rJSFsqtRxHXU"},"source":["from sklearn.feature_selection import mutual_info_regression"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"q30ZDm8cROai","executionInfo":{"status":"ok","timestamp":1638487455646,"user_tz":300,"elapsed":267,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"ae63a960-1c2f-4375-f056-ce9fbfb594da"},"source":["print(train_split.shape)"],"execution_count":17,"outputs":[{"output_type":"stream","name":"stdout","text":["(82109, 337)\n"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"2aWu9FPVnATV","executionInfo":{"status":"ok","timestamp":1638489928271,"user_tz":300,"elapsed":309,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"34ed06cb-b02c-4ad9-b251-28ba25532aa1"},"source":["print(train)"],"execution_count":27,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  ...  Label\n","62386  5.771787  ...  False\n","63350  5.051778  ...  False\n","8881   5.648391  ...  False\n","15956  5.139381  ...  False\n","56441  5.467752  ...  False\n","...         ...  ...    ...\n","17916  5.220579  ...  False\n","8252   5.163831  ...   True\n","59884  5.036404  ...  False\n","39791  6.872042  ...  False\n","6867   5.609244  ...   True\n","\n","[61581 rows x 337 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"KaNiSiKxHYLC","executionInfo":{"status":"ok","timestamp":1638487492177,"user_tz":300,"elapsed":460,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["# Feature Selection \n","X = train.drop('Label', axis = 1)\n","y = train['Label']\n","\n","k_best = SelectKBest(f_classif, k=100) # might want to update feature selection method / change k val\n","train_fs = k_best.fit(X, y)\n","cols = k_best.get_support(indices=True)\n","train_fs = train.iloc[:,cols]"],"execution_count":20,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"MhjJCc0KxiP1","executionInfo":{"status":"ok","timestamp":1638486707049,"user_tz":300,"elapsed":32010,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"4e16e189-2c47-4a28-cc04-67c293f98066"},"source":["from google.colab import drive\n","drive.mount('/content/drive')"],"execution_count":1,"outputs":[{"output_type":"stream","name":"stdout","text":["Mounted at /content/drive\n"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"CLhYxCbMbDJa","executionInfo":{"status":"ok","timestamp":1638487328440,"user_tz":300,"elapsed":278,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"e0c63250-5748-461d-8aed-87284faae87b"},"source":["%cd ../"],"execution_count":14,"outputs":[{"output_type":"stream","name":"stdout","text":["/content/drive/MyDrive/SYSC5405/Project\n"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Emqj471mhiVd","executionInfo":{"status":"ok","timestamp":1638487506098,"user_tz":300,"elapsed":271,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"c5c641ed-a426-4b64-afc8-c7fba621e186"},"source":["print(cols)"],"execution_count":21,"outputs":[{"output_type":"stream","name":"stdout","text":["[  0  10  13  14  15  16  18  20  22  23  24  25  26  27  42  43  48  49\n","  50  52  54  56  57  58  60  62  64  65  66  67  68  69  70  71  76  78\n"," 140 141 142 146 148 149 150 151 152 153 196 203 210 211 218 220 222 224\n"," 225 232 234 238 239 244 246 248 250 252 253 258 259 260 262 264 266 267\n"," 268 274 275 276 278 279 280 281 286 287 288 292 295 300 308 309 314 315\n"," 316 318 320 321 322 323 328 330 332 334]\n"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"i5B05ma4h3tB","executionInfo":{"status":"ok","timestamp":1638490454217,"user_tz":300,"elapsed":460,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"870faa31-e124-4c56-933c-c9db78d55b03"},"source":["print(train_fs)"],"execution_count":29,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  G26_fd_SMILES_base  ...  G10_fd_SMILES_base  G10_std_SMILES_dist\n","62386  5.771787            0.076806  ...           -0.039719            -0.656573\n","63350  5.051778           -0.079144  ...           -0.036837            -0.573908\n","8881   5.648391            0.050248  ...           -0.007045             0.467020\n","15956  5.139381           -0.028619  ...            0.067213             2.927458\n","56441  5.467752           -0.015724  ...            0.004252             0.826105\n","...         ...                 ...  ...                 ...                  ...\n","17916  5.220579            0.020019  ...            0.084854             3.423547\n","8252   5.163831           -0.124667  ...            0.000754             0.752722\n","59884  5.036404           -0.023823  ...           -0.043870            -0.802460\n","39791  6.872042            0.221234  ...            0.075078             3.385024\n","6867   5.609244            0.045507  ...           -0.051585            -0.988755\n","\n","[61581 rows x 100 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"9NCZ2UJuHYLD","executionInfo":{"status":"ok","timestamp":1638490483566,"user_tz":300,"elapsed":875,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["# Outlier Removal \n","\n","# box plot pre-OR ?\n","preOL_mean = train_fs.mean()\n","preOL_med = train_fs.median()\n","\n","Q1 = train_fs.quantile(0.25)\n","Q3 = train_fs.quantile(0.75)\n","\n","IQR = Q3-Q1\n","\n","# this sets outliers to Nan\n","# train_or=train_fs[~((train_fs<(Q1-1.5*IQR)) | (train_fs>(Q3+1.5*IQR)))]\n","\n","# this relaces outliers with the corresponding bound \n","train_or = train_fs[(train_fs>(Q1-1.5*IQR))]\n","train_or = train_or.fillna(Q1-1.5*IQR)\n","train_or = train_or[(train_fs<(Q3+1.5*IQR))]\n","train_or = train_or.fillna(Q3+1.5*IQR)\n","\n","postOL_mean = train_or.mean()\n","postOL_med = train_or.median()\n","# box plot post OR ?\n","\n","OLdescriptor_frames = [preOL_mean, preOL_med, postOL_mean, postOL_med]\n","OLdescriptor_names = ['preOL_mean', 'preOL_med', 'postOL_mean', 'postOL_med']\n","\n","OLdescriptor = pd.concat(OLdescriptor_frames, axis = 1)\n","OLdescriptor.columns = OLdescriptor_names\n","#print(OLdescriptor)"],"execution_count":30,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"eRYZgpBIhCni","executionInfo":{"status":"ok","timestamp":1638491712519,"user_tz":300,"elapsed":272,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"4e1042f3-489c-42e2-9f61-79fa5e518565"},"source":["print(train_or)"],"execution_count":49,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  G26_fd_SMILES_base  ...  G10_fd_SMILES_base  G10_std_SMILES_dist\n","62386  5.771787            0.076806  ...           -0.039719            -0.656573\n","63350  5.051778           -0.079144  ...           -0.036837            -0.573908\n","8881   5.648391            0.050248  ...           -0.007045             0.467020\n","15956  5.139381           -0.028619  ...            0.067213             2.927458\n","56441  5.467752           -0.015724  ...            0.004252             0.826105\n","...         ...                 ...  ...                 ...                  ...\n","17916  5.220579            0.020019  ...            0.084854             3.423547\n","8252   5.163831           -0.124667  ...            0.000754             0.752722\n","59884  5.036404           -0.023823  ...           -0.043870            -0.802460\n","39791  6.175706            0.104837  ...            0.075078             3.385024\n","6867   5.609244            0.045507  ...           -0.051585            -0.988755\n","\n","[61581 rows x 100 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"hf_AHYSmpM08","executionInfo":{"status":"ok","timestamp":1638490510937,"user_tz":300,"elapsed":256,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["from sklearn import preprocessing"],"execution_count":32,"outputs":[]},{"cell_type":"code","metadata":{"id":"zumDLJOY0mCp","executionInfo":{"status":"ok","timestamp":1638493590311,"user_tz":300,"elapsed":300,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["train_norm = train_or.values"],"execution_count":65,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"lp9AUKnp0uNw","executionInfo":{"status":"ok","timestamp":1638493601353,"user_tz":300,"elapsed":293,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"dcc40ca3-7d90-4608-a12b-84d38dc6746e"},"source":["print(train_norm)"],"execution_count":66,"outputs":[{"output_type":"stream","name":"stdout","text":["[[ 5.77178669  0.0768065   2.17615677 ... -0.69013272 -0.03971912\n","  -0.65657302]\n"," [ 5.05177784 -0.07914385 -1.10831977 ... -0.6508944  -0.0368367\n","  -0.57390836]\n"," [ 5.64839125  0.05024753  0.67865392 ... -0.03981535 -0.00704541\n","   0.46701991]\n"," ...\n"," [ 5.03640413 -0.02382321 -1.74964522 ... -0.76514714 -0.04386997\n","  -0.80245971]\n"," [ 6.17570639  0.10483736  0.60116087 ...  0.1084824   0.07507801\n","   3.3850238 ]\n"," [ 5.60924435  0.04550669  0.69142603 ... -0.80957877 -0.05158534\n","  -0.98875548]]\n"]}]},{"cell_type":"code","metadata":{"id":"pOCIE4Uf1MU4","executionInfo":{"status":"ok","timestamp":1638493656327,"user_tz":300,"elapsed":277,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["min_max_scaler = preprocessing.MinMaxScaler()"],"execution_count":67,"outputs":[]},{"cell_type":"code","metadata":{"id":"4lqoo8ot1R2L","executionInfo":{"status":"ok","timestamp":1638493683010,"user_tz":300,"elapsed":270,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["x_scaled = min_max_scaler.fit_transform(train_norm)"],"execution_count":68,"outputs":[]},{"cell_type":"code","metadata":{"id":"xPkpRwB21Y-a","executionInfo":{"status":"ok","timestamp":1638494007914,"user_tz":300,"elapsed":291,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["df = pd.DataFrame(x_scaled, columns=train_or.columns)"],"execution_count":72,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"odlVY0ap1d7u","executionInfo":{"status":"ok","timestamp":1638494011276,"user_tz":300,"elapsed":277,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"d4612449-d07a-4a9e-f44c-26c191f788c1"},"source":["print(df)"],"execution_count":73,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  G26_fd_SMILES_base  ...  G10_fd_SMILES_base  G10_std_SMILES_dist\n","0      0.697589            0.889907  ...            0.348102             0.323693\n","1      0.158524            0.277403  ...            0.361077             0.335169\n","2      0.605204            0.785595  ...            0.495174             0.479687\n","3      0.224112            0.475842  ...            0.829430             0.821281\n","4      0.469960            0.526489  ...            0.546028             0.529540\n","...         ...                 ...  ...                 ...                  ...\n","61576  0.284904            0.666870  ...            0.908838             0.890156\n","61577  0.242418            0.098607  ...            0.530282             0.519352\n","61578  0.147014            0.494678  ...            0.329418             0.303438\n","61579  1.000000            1.000000  ...            0.864832             0.884808\n","61580  0.575895            0.766975  ...            0.294689             0.277574\n","\n","[61581 rows x 100 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"klCz1EqK23gz"},"source":[""],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"ryhQ7cffpR1B","executionInfo":{"status":"ok","timestamp":1638492862878,"user_tz":300,"elapsed":295,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["train_norm = preprocessing.Normalizer().fit(train_or)"],"execution_count":61,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"DLqEQBWkpl4q","executionInfo":{"status":"ok","timestamp":1638492893855,"user_tz":300,"elapsed":265,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"e14a77a8-020a-499d-db57-348d43563578"},"source":["print(train_norm.transform(train_or))"],"execution_count":63,"outputs":[{"output_type":"stream","name":"stdout","text":["[[ 0.19753808  0.00262868  0.07447847 ... -0.02361963 -0.00135938\n","  -0.02247106]\n"," [ 0.16845295 -0.00263907 -0.03695723 ... -0.02170426 -0.00122833\n","  -0.01913714]\n"," [ 0.18715873  0.00166495  0.02248711 ... -0.00131928 -0.00023345\n","   0.01547465]\n"," ...\n"," [ 0.16881012 -0.00079851 -0.05864458 ... -0.02564619 -0.00147043\n","  -0.02689683]\n"," [ 0.18062656  0.00306627  0.0175827  ...  0.00317288  0.00219588\n","   0.0990049 ]\n"," [ 0.18628563  0.0015113   0.02296258 ... -0.02688649 -0.00171317\n","  -0.03283703]]\n"]}]},{"cell_type":"code","metadata":{"id":"S8xXZwqNuMBL","executionInfo":{"status":"ok","timestamp":1638498686328,"user_tz":300,"elapsed":290,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}}},"source":["scaled_df = pd.DataFrame(train_norm, columns=train_or.columns)"],"execution_count":74,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"4SwtNsxhId7i","executionInfo":{"status":"ok","timestamp":1638498703797,"user_tz":300,"elapsed":292,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"89f44258-9f40-4883-b492-30c0b53f18d0"},"source":["print(scaled_df)"],"execution_count":75,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  G26_fd_SMILES_base  ...  G10_fd_SMILES_base  G10_std_SMILES_dist\n","0      5.771787            0.076806  ...           -0.039719            -0.656573\n","1      5.051778           -0.079144  ...           -0.036837            -0.573908\n","2      5.648391            0.050248  ...           -0.007045             0.467020\n","3      5.139381           -0.028619  ...            0.067213             2.927458\n","4      5.467752           -0.015724  ...            0.004252             0.826105\n","...         ...                 ...  ...                 ...                  ...\n","61576  5.220579            0.020019  ...            0.084854             3.423547\n","61577  5.163831           -0.124667  ...            0.000754             0.752722\n","61578  5.036404           -0.023823  ...           -0.043870            -0.802460\n","61579  6.175706            0.104837  ...            0.075078             3.385024\n","61580  5.609244            0.045507  ...           -0.051585            -0.988755\n","\n","[61581 rows x 100 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"9R0GKCvAHYLE","colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"status":"ok","timestamp":1638487684934,"user_tz":300,"elapsed":626,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"1a666db2-b161-40ad-81d7-7911a8e7946a"},"source":["# Normalization \n","\n","# min max normalization \n","train_mmnorm = train_or\n","for column in train_mmnorm.columns:\n","    col = train_mmnorm[column]\n","    num = col - col.min()\n","    denom = col.max()-col.min()\n","    train_mmnorm[column] = num/denom\n","print(train_mmnorm)\n","\n","# z-score normalization \n","#train_znorm = train_or\n","#for column in train_znorm.columns:\n","#    col = train_znorm[column]\n","#    num = col - col.mean()\n","#    denom = col.std()\n","#    train_znorm[column] = num/denom\n","\n","#print(train_znorm)"],"execution_count":23,"outputs":[{"output_type":"stream","name":"stdout","text":["            G26  G26_fd_SMILES_base  ...  G10_fd_SMILES_base  G10_std_SMILES_dist\n","62386  0.697589            0.889907  ...            0.348102             0.323693\n","63350  0.158524            0.277403  ...            0.361077             0.335169\n","8881   0.605204            0.785595  ...            0.495174             0.479687\n","15956  0.224112            0.475842  ...            0.829430             0.821281\n","56441  0.469960            0.526489  ...            0.546028             0.529540\n","...         ...                 ...  ...                 ...                  ...\n","17916  0.284904            0.666870  ...            0.908838             0.890156\n","8252   0.242418            0.098607  ...            0.530282             0.519352\n","59884  0.147014            0.494678  ...            0.329418             0.303438\n","39791  1.000000            1.000000  ...            0.864832             0.884808\n","6867   0.575895            0.766975  ...            0.294689             0.277574\n","\n","[61581 rows x 100 columns]\n"]}]},{"cell_type":"code","metadata":{"id":"lF4ctUetHYLG"},"source":["# k means classifier \n","k_means = KMeans(init='k-means++', n_clusters=3, n_init=10) # n_clusters based on elbow plots! \n","km_classiier = k_means.fit(train_mmnorm)\n","\n","km_train = k_means.predict(train_mmnorm)\n","\n","train_cluster = train_mmnorm\n","train_cluster['Cluster'] = list(km_train)\n","train_cluster['Label'] = y # if outliers are handeled differently (dropped) this will break "],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"x244IfunHYLI"},"source":["# for test set \n","X = test.drop('Label', axis = 1)\n","y = test['Label']\n","\n","# feature selection fron train\n","test_fs = k_best.fit(X, y)\n","test_fs = train.iloc[:,cols]\n","\n","# outlier replacement using train set \n","#test_or = test_fs[(test_fs>(Q1-1.5*IQR))]\n","#test_or = test_or.fillna(Q1-1.5*IQR)\n","#test_or = test_or[(test_fs<(Q3+1.5*IQR))]\n","#test_or = test_or.fillna(Q3+1.5*IQR)\n","\n","# normalization?\n","# create test_mmnorm\n","\n","km_test = k_means.predict(test_mmnorm)\n","\n","test_cluster = test_mmnorm\n","test_cluster['Cluster'] = list(km_test)\n","test_cluster['Label'] = y\n","\n","cluster1 = test_cluster[test_cluster['Cluster']==0]\n","yc1 = cluster1['Label']\n","Xc1 = cluster1.drop(['Label', 'Cluster'], axis = 1)\n","xgb_c1test = xgb.DMatrix(Xc1, label=yc1)\n","\n","xgb_c1model.predict() \n","#etccccc"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"2QeZPEMhHYLJ"},"source":[""],"execution_count":null,"outputs":[]}]}
\ No newline at end of file
diff --git a/select_feature_using_SPEC.ipynb b/select_feature_using_SPEC.ipynb
new file mode 100644
index 0000000..0befca7
--- /dev/null
+++ b/select_feature_using_SPEC.ipynb
@@ -0,0 +1 @@
+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"name":"select_feature_using_SPEC.ipynb","provenance":[],"toc_visible":true,"mount_file_id":"1GEzDDTnBnMh75ry3voVsahydH2P9KKnR","authorship_tag":"ABX9TyMOZ1VPEFJu2kuCiV+tuad9"},"kernelspec":{"name":"python2","display_name":"Python 2"},"language_info":{"name":"python"}},"cells":[{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"m6WNKn_e4Q7j","executionInfo":{"status":"ok","timestamp":1638428020145,"user_tz":300,"elapsed":168,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"39d4021d-492b-4a8f-e8c3-416f0ae24b16"},"source":["!ls"],"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["drive  sample_data\n"]}]},{"cell_type":"code","metadata":{"id":"KIP52Hzb4UP0"},"source":["import pandas as pd"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"iUC_QAfs4W16"},"source":["data = pd.read_csv('../data/train_data.csv')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"gHWYHaIH4kz2"},"source":["from skfeature.function.similarity_based import SPEC"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"xgBMqW5y4n74"},"source":["import sklearn"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"IVgbNRTS4qN0"},"source":["from sklearn.model_selection import train_test_split"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"p9aeXlDm4sFS"},"source":["train, test = sklearn.model_selection.train_test_split(data, test_size=.25, random_state=42, shuffle=True, stratify=data['Label'])"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"WEDGRjzd44HO"},"source":["train.to_csv('../data/split_train_data.csv', index=False)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"GULGyyTE5F9J"},"source":["test.to_csv('../data/split_test_data.csv', index=False)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"dlW50z9_5YW_"},"source":["train_split = pd.read_csv('../data/split_train_data.csv')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"_J915zd-5d1t"},"source":["train_split = train_split.drop('KIBA', axis=1)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"nlA_uXom5gpA"},"source":["train, test = sklearn.model_selection.train_test_split(train_split, test_size=.25, random_state=42, shuffle=True, stratify=train_split['Label'])"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"br7iXxUm5pwG"},"source":["X = train.drop('Label', axis=1)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"ejumjVLU5qlE"},"source":["y = train['Label']"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"fciRjdGq5sdO"},"source":["kwargs = {'style': 0}"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"nPtJERSd5ucu","colab":{"base_uri":"https://localhost:8080/","height":175},"executionInfo":{"status":"error","timestamp":1638427827185,"user_tz":300,"elapsed":179,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"343920bc-abfe-441e-9cd9-7b270686b30a"},"source":["score = SPEC.spec(X, **kwargs)"],"execution_count":null,"outputs":[{"output_type":"error","ename":"NameError","evalue":"ignored","traceback":["\u001b[0;31m---------------------------------------------------------------------------\u001b[0m","\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)","\u001b[0;32m<ipython-input-2-eec3ac39c71a>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mscore\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSPEC\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspec\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mX\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m","\u001b[0;31mNameError\u001b[0m: name 'SPEC' is not defined"]}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"6PvMkRnw6E2p","executionInfo":{"status":"ok","timestamp":1638427816832,"user_tz":300,"elapsed":322,"user":{"displayName":"Ziqiang Wang","photoUrl":"https://lh3.googleusercontent.com/a-/AOh14GiweiPeMwOjHmnxkMvA-huMaqUyaI1DrHObBMhHog=s64","userId":"15738722149016886899"}},"outputId":"9e799e98-4dd2-45d6-aad7-8b15d7f1933d"},"source":["!ls"],"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["drive  sample_data\n"]}]}]}
\ No newline at end of file