Team 13

Is_Centrosymmetric(Master).ipynb

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+{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"name":"Is_Centrosymmetric(Master).ipynb","provenance":[],"collapsed_sections":[]},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"markdown","metadata":{"id":"RV1EQWC6zz0N"},"source":["# DigiFab Datathon\n","\n","Aim: Centroid Distances"]},{"cell_type":"code","metadata":{"id":"Ls0c9tqtwqKb","executionInfo":{"status":"ok","timestamp":1616598250301,"user_tz":0,"elapsed":678,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["import pandas as pd\n","import numpy as np\n","import sklearn\n","import matplotlib.pyplot as plt\n","\n","from sklearn.model_selection import cross_val_score, GridSearchCV\n","from sklearn.impute import SimpleImputer\n","from sklearn.decomposition import PCA\n","from sklearn.preprocessing import OneHotEncoder, StandardScaler\n","from sklearn.metrics import mean_squared_error \n","from sklearn import *\n","from sklearn.linear_model import LogisticRegression\n","from sklearn.metrics import classification_report, confusion_matrix"],"execution_count":11,"outputs":[]},{"cell_type":"markdown","metadata":{"id":"a9DO3z7I3FHX"},"source":["## Imports"]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"7JujBtKv5w42","executionInfo":{"status":"ok","timestamp":1616598126932,"user_tz":0,"elapsed":28099,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"83b67840-83a1-40ba-b868-ca183307371a"},"source":["from google.colab import drive\n","drive.mount('/content/drive')"],"execution_count":5,"outputs":[{"output_type":"stream","text":["Mounted at /content/drive\n"],"name":"stdout"}]},{"cell_type":"code","metadata":{"id":"vvipWvQ4vkCJ","executionInfo":{"status":"ok","timestamp":1616598148719,"user_tz":0,"elapsed":11786,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["file_path = '/content/drive/MyDrive/DigiFab_Datathon/train_and_test_sets/'\n","save_path = '/content/drive/MyDrive/DigiFab_Datathon/'\n","\n","train_descriptors = pd.read_csv(file_path+\"train_descriptors.csv\")\n","train_mord3d = pd.read_csv(file_path+\"train_mord3d.csv\")\n","train_morgan = pd.read_csv(file_path+\"train_morgan.csv\")\n","train_rdk = pd.read_csv(file_path+\"train_rdk.csv\")\n","\n","train_crystals = pd.read_csv(file_path+\"train_crystals.csv\")\n","train_distances = pd.read_csv(file_path+\"train_distances.csv\")\n","train_centroid_distances = pd.read_csv(file_path+\"train_centroid_distances.csv\")"],"execution_count":6,"outputs":[]},{"cell_type":"code","metadata":{"id":"dyKbRmlv7JlP","executionInfo":{"status":"ok","timestamp":1616598152576,"user_tz":0,"elapsed":15029,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["test_descriptors = pd.read_csv(file_path+\"test_descriptors.csv\")\n","test_mord3d = pd.read_csv(file_path+\"test_mord3d.csv\")\n","test_morgan = pd.read_csv(file_path+\"test_morgan.csv\")\n","test_rdk = pd.read_csv(file_path+\"test_rdk.csv\")"],"execution_count":7,"outputs":[]},{"cell_type":"markdown","metadata":{"id":"eIfsdghU2l5K"},"source":["## Date Engineering Step\n","\n","* Look for NaN values.\n","* Look at magintude of values - do they need scaling?"]},{"cell_type":"code","metadata":{"id":"alrEPOXwwo9u","colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"status":"ok","timestamp":1616588310911,"user_tz":0,"elapsed":16468,"user":{"displayName":"Sophie Finnigan","photoUrl":"","userId":"10230321660225593837"}},"outputId":"67c2161b-37e0-476c-ab92-256c5975ac36"},"source":["print(train_descriptors.describe())\n","print(train_mord3d.describe())"],"execution_count":null,"outputs":[{"output_type":"stream","text":["         Unnamed: 0           ABC  ...      mZagreb1      mZagreb2\n","count  13449.000000  13449.000000  ...  13448.000000  13449.000000\n","mean   40464.558183      8.791685  ...      4.820664      2.709742\n","std    19446.921704      2.294386  ...      1.421185      0.606246\n","min        2.000000      0.000000  ...      0.750000      0.000000\n","25%    33281.000000      7.387307  ...      3.833333      2.333333\n","50%    43815.000000      9.289847  ...      4.722222      2.833333\n","75%    55711.000000     10.663621  ...      5.694444      3.194444\n","max    66123.000000     13.654635  ...     10.652778      4.000000\n","\n","[8 rows x 1614 columns]\n","         Unnamed: 0         PNSA1  ...        MOMI-Z           PBF\n","count  13449.000000  13432.000000  ...  13449.000000  13449.000000\n","mean   40464.558183    164.398549  ...    356.137203      0.383000\n","std    19446.921704     55.235914  ...    284.378542      0.304775\n","min        2.000000      0.000000  ...      0.000000      0.000000\n","25%    33281.000000    127.855661  ...    188.703461      0.111270\n","50%    43815.000000    160.405836  ...    303.942659      0.351683\n","75%    55711.000000    196.513934  ...    450.002580      0.605584\n","max    66123.000000    469.849929  ...   7084.018710      2.195392\n","\n","[8 rows x 214 columns]\n"],"name":"stdout"}]},{"cell_type":"code","metadata":{"id":"XvPVmxJPABOw"},"source":["# Data Preprocessing"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"IGzlc3kCALx3","executionInfo":{"status":"ok","timestamp":1616598173435,"user_tz":0,"elapsed":518,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"e59cb5f8-bbfa-4699-b78e-9f27366c0c23"},"source":["train_mord3d_full = train_mord3d.iloc[:, 1:-3].dropna(axis= 1, how=\"any\")\n","train_mord3d_full.shape"],"execution_count":8,"outputs":[{"output_type":"execute_result","data":{"text/plain":["(13449, 173)"]},"metadata":{"tags":[]},"execution_count":8}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"ks-QZ-giAwel","executionInfo":{"status":"ok","timestamp":1616598193341,"user_tz":0,"elapsed":690,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"2510135b-0a09-4925-d28c-440cbbad1e2d"},"source":["test_mord3d_full = test_mord3d[train_mord3d_full.columns]\n","test_mord3d_full.shape"],"execution_count":9,"outputs":[{"output_type":"execute_result","data":{"text/plain":["(3363, 173)"]},"metadata":{"tags":[]},"execution_count":9}]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"46tKyHLvAwoT","executionInfo":{"status":"ok","timestamp":1616598207599,"user_tz":0,"elapsed":872,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"16764fb2-093b-4313-b82d-d0d846f8cfbc"},"source":["train_PCA = decomposition.PCA(n_components=.95)\n","scaler_for_PCA = preprocessing.StandardScaler()\n","train_mord3d_PCA = train_PCA.fit_transform(scaler_for_PCA.fit_transform(train_mord3d_full))\n","test_mord3d_PCA = train_PCA.transform(scaler_for_PCA.transform(test_mord3d_full))\n","print(train_mord3d_PCA.shape, test_mord3d_PCA.shape)"],"execution_count":10,"outputs":[{"output_type":"stream","text":["(13449, 45) (3363, 45)\n"],"name":"stdout"}]},{"cell_type":"code","metadata":{"id":"h6_n2nGTw9OK","executionInfo":{"status":"ok","timestamp":1616598271819,"user_tz":0,"elapsed":465,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["train_crystals[\"is_centrosymmetric\"] = train_crystals[\"is_centrosymmetric\"].astype(int)"],"execution_count":12,"outputs":[]},{"cell_type":"markdown","metadata":{"id":"6t6t8uKK3ewx"},"source":["## Initial Models"]},{"cell_type":"markdown","metadata":{"id":"uu2z9RWM9ygY"},"source":[""]},{"cell_type":"code","metadata":{"id":"C71wz1cc3j3O","executionInfo":{"status":"ok","timestamp":1616600095974,"user_tz":0,"elapsed":409,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["#RandomForest"],"execution_count":25,"outputs":[]},{"cell_type":"code","metadata":{"id":"uycZmmBmFQQS","executionInfo":{"status":"ok","timestamp":1616600097174,"user_tz":0,"elapsed":476,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["target = \"is_centrosymmetric\""],"execution_count":26,"outputs":[]},{"cell_type":"code","metadata":{"id":"_uO4XyOO_MXF","executionInfo":{"status":"ok","timestamp":1616600098479,"user_tz":0,"elapsed":470,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["from sklearn.ensemble import RandomForestClassifier"],"execution_count":27,"outputs":[]},{"cell_type":"code","metadata":{"id":"7pcd6oIv_Ubw","executionInfo":{"status":"ok","timestamp":1616600130849,"user_tz":0,"elapsed":460,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["clf = RandomForestClassifier(n_estimators = 100)"],"execution_count":28,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"ToED_6dOxX0p","executionInfo":{"status":"ok","timestamp":1616600158264,"user_tz":0,"elapsed":10672,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"1ad34233-af38-4217-b972-75065e7e42de"},"source":["clf = RandomForestClassifier(n_estimators = 100)\n","clf.fit(train_mord3d_PCA,train_crystals[target])"],"execution_count":29,"outputs":[{"output_type":"execute_result","data":{"text/plain":["RandomForestClassifier(bootstrap=True, ccp_alpha=0.0, class_weight=None,\n","                       criterion='gini', max_depth=None, max_features='auto',\n","                       max_leaf_nodes=None, max_samples=None,\n","                       min_impurity_decrease=0.0, min_impurity_split=None,\n","                       min_samples_leaf=1, min_samples_split=2,\n","                       min_weight_fraction_leaf=0.0, n_estimators=100,\n","                       n_jobs=None, oob_score=False, random_state=None,\n","                       verbose=0, warm_start=False)"]},"metadata":{"tags":[]},"execution_count":29}]},{"cell_type":"code","metadata":{"id":"xBI8LVpQ4MyU","executionInfo":{"status":"ok","timestamp":1616600161860,"user_tz":0,"elapsed":664,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["y_pred = clf.predict(train_mord3d_PCA)"],"execution_count":30,"outputs":[]},{"cell_type":"code","metadata":{"id":"5fWwA46h4M7A"},"source":[""],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"a1uynQ7fGA-p"},"source":["#Cross-validation"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"THA2-XEg_Yz_","executionInfo":{"status":"ok","timestamp":1616600179354,"user_tz":0,"elapsed":506,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["from sklearn.model_selection import cross_val_score"],"execution_count":31,"outputs":[]},{"cell_type":"code","metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"9_LyyF3m4Ss_","executionInfo":{"status":"ok","timestamp":1616600286536,"user_tz":0,"elapsed":89737,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}},"outputId":"5c219c6c-a470-487b-8c1e-6bb23784cced"},"source":["np.mean(cross_val_score(clf, train_mord3d_PCA, train_crystals[target], cv=10))"],"execution_count":32,"outputs":[{"output_type":"execute_result","data":{"text/plain":["0.848762502212781"]},"metadata":{"tags":[]},"execution_count":32}]},{"cell_type":"markdown","metadata":{"id":"0BmlIJ3lKAUp"},"source":["### Outputting predictions for automated checking \n","Link: https://github.com/stevenkbennett/fons_datathon_testing"]},{"cell_type":"code","metadata":{"id":"dEhCsnCHGE8n","executionInfo":{"status":"ok","timestamp":1616600287183,"user_tz":0,"elapsed":638,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["predictions = logreg.predict(test_mord3d_PCA)"],"execution_count":33,"outputs":[]},{"cell_type":"code","metadata":{"id":"RuDLlv10KLr8","executionInfo":{"status":"ok","timestamp":1616600315535,"user_tz":0,"elapsed":497,"user":{"displayName":"Charlotte Breakwell","photoUrl":"","userId":"15588921800197350603"}}},"source":["# np.savetxt(\"is_centrosymmetric.csv\", predictions)\n","# Alternatively, if using pandas, you can use the following:\n","pd.DataFrame(predictions).to_csv(save_path+\"task_2_predictions.csv\", header=False, index=False)"],"execution_count":34,"outputs":[]},{"cell_type":"code","metadata":{"id":"KZOjGVb1M8nY"},"source":[""],"execution_count":null,"outputs":[]}]}