{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"# Install tsflex and seglearn\n!pip install tsflex --no-index --find-links=file:///kaggle/input/time-series-tools\n!pip install seglearn --no-index --find-links=file:///kaggle/input/time-series-tools","metadata":{"_kg_hide-input":true,"_kg_hide-output":true,"execution":{"iopub.status.busy":"2023-04-19T00:45:06.474113Z","iopub.execute_input":"2023-04-19T00:45:06.474570Z","iopub.status.idle":"2023-04-19T00:45:32.755494Z","shell.execute_reply.started":"2023-04-19T00:45:06.474530Z","shell.execute_reply":"2023-04-19T00:45:32.753810Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"# Data loading and feature extraction ","metadata":{}},{"cell_type":"code","source":"import numpy as np\nimport pandas as pd\nfrom tqdm.auto import tqdm\nfrom sklearn import *\nimport glob\n\np = '/kaggle/input/tlvmc-parkinsons-freezing-gait-prediction/'\n\ntrain = glob.glob(p+'train/**/**')\ntest = glob.glob(p+'test/**/**')\nsubjects = pd.read_csv(p+'subjects.csv')\ntasks = pd.read_csv(p+'tasks.csv')\nsub = pd.read_csv(p+'sample_submission.csv')\n\ntdcsfog_metadata=pd.read_csv('/kaggle/input/tlvmc-parkinsons-freezing-gait-prediction/tdcsfog_metadata.csv')\ndefog_metadata=pd.read_csv('/kaggle/input/tlvmc-parkinsons-freezing-gait-prediction/defog_metadata.csv')\n# daily_metadata=pd.read_csv('/kaggle/input/tlvmc-parkinsons-freezing-gait-prediction/daily_metadata.csv')\ntdcsfog_metadata['Module']='tdcsfog'\ndefog_metadata['Module']='defog'\n# daily_metadata['Module']='daily'\nmetadata=pd.concat([tdcsfog_metadata,defog_metadata])\n# metadata","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","execution":{"iopub.status.busy":"2023-04-19T00:45:32.758248Z","iopub.execute_input":"2023-04-19T00:45:32.758639Z","iopub.status.idle":"2023-04-19T00:45:34.950132Z","shell.execute_reply.started":"2023-04-19T00:45:32.758601Z","shell.execute_reply":"2023-04-19T00:45:34.948793Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"# https://www.kaggle.com/code/jazivxt/familiar-solvs\ntasks['Duration'] = tasks['End'] - tasks['Begin']\ntasks = pd.pivot_table(tasks, values=['Duration'], index=['Id'], columns=['Task'], aggfunc='sum', fill_value=0)\ntasks.columns = [c[-1] for c in tasks.columns]\ntasks = tasks.reset_index()\ntasks['t_kmeans'] = cluster.KMeans(n_clusters=10, random_state=3).fit_predict(tasks[tasks.columns[1:]])\n\nsubjects = subjects.fillna(0).groupby('Subject').median()\nsubjects = subjects.reset_index()\n# subjects.rename(columns={'Subject':'Id'}, inplace=True)\nsubjects['s_kmeans'] = cluster.KMeans(n_clusters=10, random_state=3).fit_predict(subjects[subjects.columns[1:]])\nsubjects=subjects.rename(columns={'Visit':'s_Visit','Age':'s_Age','YearsSinceDx':'s_YearsSinceDx','UPDRSIII_On':'s_UPDRSIII_On','UPDRSIII_Off':'s_UPDRSIII_Off','NFOGQ':'s_NFOGQ'})\n","metadata":{"_kg_hide-input":true,"execution":{"iopub.status.busy":"2023-04-19T00:45:34.971497Z","iopub.execute_input":"2023-04-19T00:45:34.971982Z","iopub.status.idle":"2023-04-19T00:45:35.118178Z","shell.execute_reply.started":"2023-04-19T00:45:34.971941Z","shell.execute_reply":"2023-04-19T00:45:35.116936Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"complex_featlist=['Visit','Test','Medication','s_Visit','s_Age','s_YearsSinceDx','s_UPDRSIII_On','s_UPDRSIII_Off','s_NFOGQ','s_kmeans']\nmetadata_complex=metadata.merge(subjects,how='left',on='Subject').copy()\nmetadata_complex['Medication']=metadata_complex['Medication'].factorize()[0]\n\n# display(metadata_complex)","metadata":{"_kg_hide-input":true,"execution":{"iopub.status.busy":"2023-04-19T00:45:35.193819Z","iopub.execute_input":"2023-04-19T00:45:35.194276Z","iopub.status.idle":"2023-04-19T00:45:35.210510Z","shell.execute_reply.started":"2023-04-19T00:45:35.194225Z","shell.execute_reply":"2023-04-19T00:45:35.209151Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"## Create a tsflex feature collection","metadata":{}},{"cell_type":"code","source":"from seglearn.feature_functions import base_features, emg_features\n\nfrom tsflex.features import FeatureCollection, MultipleFeatureDescriptors\nfrom tsflex.features.integrations import seglearn_feature_dict_wrapper\n\n\nbasic_feats = MultipleFeatureDescriptors(\n    functions=seglearn_feature_dict_wrapper(base_features()),\n    series_names=['AccV', 'AccML', 'AccAP'],\n    windows=[5_000],\n    strides=[5_000],\n)\n\nemg_feats = emg_features()\ndel emg_feats['simple square integral'] # is same as abs_energy (which is in base_features)\n\nemg_feats = MultipleFeatureDescriptors(\n    functions=seglearn_feature_dict_wrapper(emg_feats),\n    series_names=['AccV', 'AccML', 'AccAP'],\n    windows=[5_000],\n    strides=[5_000],\n)\n\nfc = FeatureCollection([basic_feats, emg_feats])","metadata":{"_kg_hide-input":true,"execution":{"iopub.status.busy":"2023-04-19T00:45:35.211895Z","iopub.execute_input":"2023-04-19T00:45:35.212311Z","iopub.status.idle":"2023-04-19T00:45:35.270089Z","shell.execute_reply.started":"2023-04-19T00:45:35.212275Z","shell.execute_reply":"2023-04-19T00:45:35.268960Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"## Extract the features (with Time_frac feature)","metadata":{}},{"cell_type":"code","source":"\nimport pathlib\ndef reader(f):\n    try:\n        df = pd.read_csv(f, index_col=\"Time\", usecols=['Time', 'AccV', 'AccML', 'AccAP', 'StartHesitation', 'Turn' , 'Walking'])\n        \n        df['Id'] = f.split('/')[-1].split('.')[0]\n        df['Module'] = pathlib.Path(f).parts[-2]\n        \n        df['Time_frac']=(df.index/df.index.max()).values#currently the index of data is actually \"Time\"\n        \n        df = pd.merge(df, tasks[['Id','t_kmeans']], how='left', on='Id').fillna(-1)\n#         df = pd.merge(df, subjects[['Id','s_kmeans']], how='left', on='Id').fillna(-1)\n        df = pd.merge(df, metadata_complex[['Id','Subject']+['Visit','Test','Medication','s_kmeans']], how='left', on='Id').fillna(-1)\n        df_feats = fc.calculate(df, return_df=True, include_final_window=True, approve_sparsity=True, window_idx=\"begin\").astype(np.float32)\n        df = df.merge(df_feats, how=\"left\", left_index=True, right_index=True)\n        df.fillna(method=\"ffill\", inplace=True)\n        return df\n    except: pass\ntrain = pd.concat([reader(f) for f in tqdm(train)]).fillna(0); print(train.shape)\ncols = [c for c in train.columns if c not in ['Id','Subject','Module', 'Time', 'StartHesitation', 'Turn' , 'Walking', 'Valid', 'Task','Event']]\npcols = ['StartHesitation', 'Turn' , 'Walking']\nscols = ['Id', 'StartHesitation', 'Turn' , 'Walking']","metadata":{"execution":{"iopub.status.busy":"2023-04-19T00:45:35.271973Z","iopub.execute_input":"2023-04-19T00:45:35.272505Z","iopub.status.idle":"2023-04-19T00:53:41.122237Z","shell.execute_reply.started":"2023-04-19T00:45:35.272468Z","shell.execute_reply":"2023-04-19T00:53:41.121111Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"train=train.reset_index(drop=True)","metadata":{"_kg_hide-input":true,"execution":{"iopub.status.busy":"2023-04-19T00:53:41.124206Z","iopub.execute_input":"2023-04-19T00:53:41.124859Z","iopub.status.idle":"2023-04-19T00:53:46.467551Z","shell.execute_reply.started":"2023-04-19T00:53:41.124818Z","shell.execute_reply":"2023-04-19T00:53:46.466066Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"## Train the model","metadata":{}},{"cell_type":"code","source":"import xgboost as xgb\nimport lightgbm as lgb\nfrom sklearn.multioutput import MultiOutputRegressor\nfrom sklearn.metrics import mean_squared_error, r2_score\n","metadata":{"execution":{"iopub.status.busy":"2023-04-19T00:53:48.012530Z","iopub.execute_input":"2023-04-19T00:53:48.013386Z","iopub.status.idle":"2023-04-19T00:53:49.560180Z","shell.execute_reply.started":"2023-04-19T00:53:48.013321Z","shell.execute_reply":"2023-04-19T00:53:49.558925Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"import numpy as np\nimport xgboost as xgb\nfrom sklearn.model_selection import RandomizedSearchCV, train_test_split\nfrom scipy.stats import uniform, randint\nfrom sklearn.metrics import average_precision_score, make_scorer\n\nbest_params_ = {'estimator__colsample_bytree': 0.5282057895135501, \n 'estimator__learning_rate': 0.22659963168004743, \n 'estimator__max_depth': 8, \n 'estimator__min_child_weight': 3.1233911067827616, \n 'estimator__n_estimators': 291, \n 'estimator__subsample': 0.9961057796456088}","metadata":{"execution":{"iopub.status.busy":"2023-04-19T00:53:49.561672Z","iopub.execute_input":"2023-04-19T00:53:49.562405Z","iopub.status.idle":"2023-04-19T00:53:49.569653Z","shell.execute_reply.started":"2023-04-19T00:53:49.562364Z","shell.execute_reply":"2023-04-19T00:53:49.568318Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"best_params_ = {kk: v for k, v in best_params_.items() for kk in k.split('__')}; del best_params_['estimator']","metadata":{"execution":{"iopub.status.busy":"2023-04-19T00:53:49.570970Z","iopub.execute_input":"2023-04-19T00:53:49.571453Z","iopub.status.idle":"2023-04-19T00:53:49.587808Z","shell.execute_reply.started":"2023-04-19T00:53:49.571414Z","shell.execute_reply":"2023-04-19T00:53:49.586420Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"from sklearn.base import clone\n\ndef custom_average_precision(y_true, y_pred):\n    score = average_precision_score(y_true, y_pred)\n    return 'average_precision', score, True\n\nclass LGBMMultiOutputRegressor(MultiOutputRegressor):\n    def fit(self, X, y, eval_set=None, **fit_params):\n        self.estimators_ = [clone(self.estimator) for _ in range(y.shape[1])]\n        \n        for i, estimator in enumerate(self.estimators_):\n            if eval_set:\n                fit_params['eval_set'] = [(eval_set[0], eval_set[1][:, i])]\n            estimator.fit(X, y[:, i], **fit_params, verbose=False)\n        \n        return self","metadata":{"execution":{"iopub.status.busy":"2023-04-19T00:53:49.589168Z","iopub.execute_input":"2023-04-19T00:53:49.589516Z","iopub.status.idle":"2023-04-19T00:53:49.603700Z","shell.execute_reply.started":"2023-04-19T00:53:49.589480Z","shell.execute_reply":"2023-04-19T00:53:49.602565Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"from sklearn.model_selection import GroupKFold\n\nN_FOLDS=5\nkfold = GroupKFold(N_FOLDS)\ngroup_var = train.Subject\ngroups=kfold.split(train, groups=group_var)\nregs=[]\ncvs=[]\nfor fold, (tr_idx,te_idx ) in enumerate(tqdm(groups, total=N_FOLDS, desc=\"Folds\")):\n    tr_idx=pd.Series(tr_idx).sample(n=2000000,random_state=42).values #2000000\n    \n    # Create a base XGBoost regressor with the common parameters\n    base_regressor = lgb.LGBMRegressor(**best_params_)\n\n    # Wrap the base regressor with the MultiOutputRegressor\n    multioutput_regressor = LGBMMultiOutputRegressor(base_regressor)\n    x_tr,y_tr=train.loc[tr_idx,cols].to_numpy(),train.loc[tr_idx,pcols].to_numpy()\n    x_te,y_te=train.loc[te_idx,cols].to_numpy(),train.loc[te_idx,pcols].to_numpy()\n\n    multioutput_regressor.fit(\n    x_tr,y_tr,\n    eval_set=(x_te,y_te),\n    eval_metric=custom_average_precision,\n    early_stopping_rounds=25\n    )\n    regs.append(multioutput_regressor)\n    cv=metrics.accuracy_score(y_te, multioutput_regressor.predict(x_te).clip(0.0,1.0)>5)\n    cvs.append(cv)\n    \n    \nprint(cvs)\nbest_acc = max(cvs)","metadata":{"_kg_hide-output":true,"execution":{"iopub.status.busy":"2023-04-19T01:13:58.683164Z","iopub.execute_input":"2023-04-19T01:13:58.683625Z","iopub.status.idle":"2023-04-19T01:29:20.704361Z","shell.execute_reply.started":"2023-04-19T01:13:58.683587Z","shell.execute_reply":"2023-04-19T01:29:20.702478Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"print(f\"the best accuracy is {best_acc}\")","metadata":{"execution":{"iopub.status.busy":"2023-04-19T01:35:38.292019Z","iopub.execute_input":"2023-04-19T01:35:38.293308Z","iopub.status.idle":"2023-04-19T01:35:46.694652Z","shell.execute_reply.started":"2023-04-19T01:35:38.293242Z","shell.execute_reply":"2023-04-19T01:35:46.693250Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"markdown","source":"## Predict for test","metadata":{}},{"cell_type":"code","source":"sub['t'] = 0\nsubmission = []\nfor f in test:\n    df = pd.read_csv(f)\n    df.set_index('Time', drop=True, inplace=True)\n\n    df['Id'] = f.split('/')[-1].split('.')[0]\n#     df = df.fillna(0).reset_index(drop=True)\n    df['Time_frac']=(df.index/df.index.max()).values#currently the index of data is actually \"Time\"\n    df = pd.merge(df, tasks[['Id','t_kmeans']], how='left', on='Id').fillna(-1)\n#     df = pd.merge(df, subjects[['Id','s_kmeans']], how='left', on='Id').fillna(-1)\n    df = pd.merge(df, metadata_complex[['Id','Subject']+['Visit','Test','Medication','s_kmeans']], how='left', on='Id').fillna(-1)\n    df_feats = fc.calculate(df, return_df=True, include_final_window=True, approve_sparsity=True, window_idx=\"begin\")\n    df = df.merge(df_feats, how=\"left\", left_index=True, right_index=True)\n    df.fillna(method=\"ffill\", inplace=True)\n#     res = pd.DataFrame(np.round(reg.predict(df[cols]).clip(0.0,1.0),3), columns=pcols)\n    \n    res_vals=[]\n    for i_fold in range(N_FOLDS):\n        res_val=np.round(regs[i_fold].predict(df[cols]).clip(0.0,1.0),3)\n        res_vals.append(np.expand_dims(res_val,axis=2))\n    res_vals=np.mean(np.concatenate(res_vals,axis=2),axis=2)\n    res = pd.DataFrame(res_vals, columns=pcols)\n    \n    df = pd.concat([df,res], axis=1)\n    df['Id'] = df['Id'].astype(str) + '_' + df.index.astype(str)\n    submission.append(df[scols])\nsubmission = pd.concat(submission)\nsubmission = pd.merge(sub[['Id']], submission, how='left', on='Id').fillna(0.0)\nsubmission[scols].to_csv('submission.csv', index=False)","metadata":{"execution":{"iopub.status.busy":"2023-04-19T01:08:47.474193Z","iopub.execute_input":"2023-04-19T01:08:47.475062Z","iopub.status.idle":"2023-04-19T01:08:56.162282Z","shell.execute_reply.started":"2023-04-19T01:08:47.475021Z","shell.execute_reply":"2023-04-19T01:08:56.160527Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"submission","metadata":{"execution":{"iopub.status.busy":"2023-04-19T01:08:56.164282Z","iopub.execute_input":"2023-04-19T01:08:56.164670Z","iopub.status.idle":"2023-04-19T01:08:56.185706Z","shell.execute_reply.started":"2023-04-19T01:08:56.164633Z","shell.execute_reply":"2023-04-19T01:08:56.184338Z"},"trusted":true},"execution_count":null,"outputs":[]}]}