python-katlas 0.0.1__py3-none-any.whl

katlas/train.py

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+# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_ML.ipynb.
+
+# %% auto 0
+__all__ = ['get_splits', 'split_data', 'score_each', 'train_ml', 'train_ml_cv', 'predict_ml']
+
+# %% ../nbs/03_ML.ipynb 4
+# katlas
+from .core import Data
+from .feature import *
+
+# essentials
+import pandas as pd, numpy as np
+from joblib import dump, load
+import math,matplotlib.pyplot as plt
+from pathlib import Path
+
+# scipy
+from scipy.stats import spearmanr, pearsonr
+from scipy.stats import spearmanr,pearsonr
+
+# sklearn
+from sklearn.model_selection import *
+from sklearn.metrics import mean_squared_error
+from sklearn.linear_model import *
+from sklearn.svm import *
+from sklearn.ensemble import *
+from sklearn import set_config
+set_config(transform_output="pandas")
+
+# %% ../nbs/03_ML.ipynb 7
+def get_splits(df: pd.DataFrame, # df contains info for split
+               stratified: str=None, # colname to make stratified kfold; sampling from different groups
+               group: str=None, # colname to make group kfold; test and train are from different groups
+               nfold: int=5,
+               seed: int=123):
+    
+    "Split samples in a dataframe based on Stratified, Group, or StratifiedGroup Kfold method"
+    def _log(colname):
+        print(kf)
+        split=splits[0]
+        print(f'# kinase {colname} in train set: {df.loc[split[0]][colname].unique().shape[0]}')
+        print(f'# kinase {colname} in test set: {df.loc[split[1]][colname].unique().shape[0]}')
+        
+    splits = []
+    if stratified is not None and group is None:
+        kf = StratifiedKFold(nfold, shuffle=True, random_state=seed)
+        for split in kf.split(df.index, df[stratified]):
+            splits.append(split)
+            
+        _log(stratified)
+        
+    elif group is not None and stratified is None:
+        kf = GroupKFold(nfold)
+        for split in kf.split(df.index, groups=df[group]):
+            splits.append(split)
+            
+        _log(group)
+        
+    elif stratified is not None and group is not None:
+        kf = StratifiedGroupKFold(nfold, shuffle=True, random_state=seed)
+        for split in kf.split(df.index, groups=df[group], y=df[stratified]):
+            splits.append(split)
+            
+        _log(stratified)
+
+    else:
+        raise ValueError("Either 'stratified' or 'group' argument must be provided.")
+        
+        
+    print('---------------------------')
+    print(f'# kinase in train set: {df.loc[split[0]].kinase.unique().shape[0]}')
+    
+    print('---------------------------')
+    print(f'# kinase in test set: {df.loc[split[1]].kinase.unique().shape[0]}')
+    print('---------------------------')
+    print(f'test set: {df.loc[split[1]].kinase.unique()}')
+    
+    return splits
+
+# %% ../nbs/03_ML.ipynb 12
+def split_data(df: pd.DataFrame, # dataframe of values
+               feat_col: list, # feature columns
+               target_col: list, # target columns
+               split: tuple # one of the split in splits
+               ):
+    "Given split tuple, split dataframe into X_train, y_train, X_test, y_test"
+    
+    X_train = df.loc[split[0]][feat_col]
+    y_train = df.loc[split[0]][target_col]
+    
+    X_test = df.loc[split[1]][feat_col]
+    y_test = df.loc[split[1]][target_col]
+    
+    return X_train, y_train, X_test, y_test
+
+# %% ../nbs/03_ML.ipynb 16
+def score_each(target: pd.DataFrame, # target dataframe
+              pred: pd.DataFrame, # predicted dataframe
+              absolute = True, # if absolute, take average with absolute values for pearson/spearman
+              verbose=True, # whether or not display the error value
+              
+             ):
+    
+    "Calculate the overall MSE and average Pearson (per row) between two dataframes."
+    
+    # Calculate overall MSE
+    mse = mean_squared_error(target, pred)
+    
+    # Calculate RMSE
+    # rmse = math.sqrt(mse)
+
+    # Calculate the Spearman correlation coefficient
+    # spearman, _ = spearmanr(target.values.ravel(), pred.values.ravel())
+
+    # Calculate the Pearson correlation coefficient
+    # pearson, _ = pearsonr(target.values.ravel(), pred.values.ravel())
+    
+    # Calculate Spearman and Pearson per row 
+    # spearman_all = target.corrwith(pred,axis=1,method='spearman')
+    pearson_all = target.corrwith(pred,axis=1,method='pearson')
+    
+    # Calculate mean
+    # spearman_mean = spearman_all.abs().mean()
+    pearson_mean = pearson_all.abs().mean()
+    
+    metrics_df = pd.DataFrame({'Pearson':pearson_all})
+    
+    if verbose:
+        print(f'overall MSE: {mse:.4f}')
+        # print(f"Average Spearman:  {spearman_mean:.4f}")
+        print(f"Average Pearson: {pearson_mean:.4f} ")
+    
+    return mse,pearson_mean, metrics_df
+
+# %% ../nbs/03_ML.ipynb 21
+def train_ml(df, # dataframe of values
+             feat_col, # feature columns
+             target_col, # target columns
+             split, # one split in splits
+             model,  # a sklearn models
+             save = None, # file (.joblib) to save, e.g. 'model.joblib'
+             params={}, # parameters for model.fit from sklearn
+            ):
+    
+    "Fit and predict using sklearn model format, return target and pred of valid dataset."
+    
+    # split data
+    X_train, y_train, X_test, y_test = split_data(df, feat_col, target_col, split)
+    
+    # Fit the model
+    model.fit(X_train, y_train, **params) # better convert y_train to numpy array and flatten
+    print(model)
+    
+    if save is not None:
+        # Save the model to a file
+        # joblib.dump(model, save)
+        dump(model, save)
+        
+    # Predict train
+    y_train_pred = model.predict(X_train) # X_test is dataframe, y_pred is numpy array
+    
+    # Predict test
+    y_pred = model.predict(X_test) # X_test is dataframe, y_pred is numpy array
+
+    # Make dataframe
+    y_pred = pd.DataFrame(y_pred,index=y_test.index, columns = y_test.columns)
+    
+    return y_test, y_pred
+
+# %% ../nbs/03_ML.ipynb 24
+def train_ml_cv( df, # dataframe of values
+                 feat_col, # feature columns
+                 target_col,  # target columns
+                 splits, # splits
+                 model, # sklearn model
+                 save = None, # model name to be saved, e.g., 'LR'
+                 params = {}, # act as kwargs, for model.fit
+                ):
+    
+    "Cross-validation through the given splits"
+    
+    OOF = []
+    metrics = []
+    
+    for fold, split in enumerate(splits):
+        print(f'------ fold: {fold} --------')
+        
+        if save is not None: 
+            save = f'models/{save}_{fold}.joblib'
+            
+        target, pred = train_ml(df, feat_col, target_col, split, model,save,params=params)
+
+        mse, pearson_avg, _ = score_each(target,pred)
+        
+        # Store metrics in a dictionary for the current fold
+        fold_metrics = {
+            'fold': fold,
+            'mse': mse,
+            'pearson_avg': pearson_avg
+        }
+        
+        metrics.append(fold_metrics)
+
+        OOF.append(pred)
+        
+    # Concatenate OOF from each fold to a new dataframe
+    oof = pd.concat(OOF).sort_index()
+    
+    # Get metrics into a dataframe
+    metrics = pd.DataFrame(metrics)
+    
+    return oof, metrics
+
+# %% ../nbs/03_ML.ipynb 31
+def predict_ml(df, # Dataframe that contains features
+               feat_col, # feature columns
+               target_col=None,
+               model_pth = 'model.joblib'
+              ):
+    
+    "Make predictions based on trained model."
+    
+    test = df[feat_col]
+    
+    model = load(model_pth)
+    
+    pred = model.predict(test)
+    
+    pred_df = pd.DataFrame(pred,index=df.index,columns=target_col)
+    
+    return pred_df

python_katlas-0.0.1.dist-info/LICENSE

@@ -0,0 +1,201 @@
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