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import itertools |
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import json |
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import os |
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import warnings |
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from typing import Callable, Optional, List, Tuple, Dict, Any |
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|
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import numpy as np |
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import pandas as pd |
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from sklearn.exceptions import ConvergenceWarning |
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from sklearn.linear_model import Lasso |
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from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, r2_score |
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from sparse_lmm import LMM |
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from statsmodels.stats.multitest import multipletests |
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warnings.simplefilter('ignore', ConvergenceWarning) |
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def read_json_to_dataframe(json_file: str) -> pd.DataFrame: |
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""" |
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Reads a JSON file storing cohort information, and converts it into a pandas DataFrame. |
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Args: |
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json_file (str): The path to the JSON file containing the data. |
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Returns: |
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DataFrame: A pandas DataFrame with the JSON data. |
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""" |
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with open(json_file, 'r') as file: |
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data = json.load(file) |
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return pd.DataFrame.from_dict(data, orient='index').reset_index().rename(columns={'index': 'cohort_id'}) |
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def filter_and_rank_cohorts(json_file: str, condition: Optional[str] = None) -> Tuple[ |
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Optional[str], pd.DataFrame]: |
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""" |
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Reads a JSON file storing cohort information, filters cohorts based on usability and an optional condition, then |
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ranks them by sample size. |
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Args: |
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json_file (str): The path to the JSON file containing the data. |
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condition (str, optional): A specific attribute that needs to be available in the cohort. If None, only filters |
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cohorts by the 'is_usable' flag. |
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Returns: |
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Tuple: A tuple containing the best cohort ID (str or None if no suitable cohort is found), and |
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the filtered and ranked DataFrame. |
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""" |
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df = read_json_to_dataframe(json_file) |
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if df.empty: |
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return None, df |
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if condition: |
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condition = condition.lower() |
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assert condition in ['age', 'gender'] |
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condition_available = 'has_' + condition |
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filtered_df = df[(df['is_usable'] == True) & (df[condition_available] == True)] |
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else: |
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filtered_df = df[df['is_usable'] == True] |
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ranked_df = filtered_df.sort_values(by='sample_size', ascending=False) |
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best_cohort_id = ranked_df.iloc[0]['cohort_id'] if not ranked_df.empty else None |
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return best_cohort_id, ranked_df |
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def select_and_load_cohort(data_root: str, trait: str, condition=None, is_two_step=True, gene_info_path=None) -> Tuple[ |
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Optional[pd.DataFrame], Optional[pd.DataFrame], Optional[List]]: |
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""" |
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Selects the best cohort data for specified trait (and optionally condition) from a given data root directory, load |
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the data and find the gene regressors if in two-step mode. This function supports data selection for both single-step |
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and two-step regression based on the is_two_step flag. |
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Args: |
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data_root (str): The root directory containing cohort data. |
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trait (str): The trait of interest. |
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condition (str, optional): The condition of interest; required if is_two_step is True. |
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is_two_step (bool, optional): If True, will be used in two-step regression using data from both trait and condition |
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along with gene information. Requires condition and gene_info_path to be specified. |
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gene_info_path (str, optional): Path to gene information file; required if is_two_step is True. |
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Returns: |
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tuple: A tuple containing: |
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- trait_data (Optional[pd.DataFrame]): Data for the selected trait cohort. |
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- condition_data (Optional[pd.DataFrame]): Data for the selected condition cohort if in two-step mode, otherwise None. |
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- gene_regressors (Optional[pd.DataFrame]): Gene regression data if in two-step mode, otherwise None. |
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""" |
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trait_dir = os.path.join(data_root, trait) |
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if (not condition) or condition in ['Age', 'Gender']: |
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is_two_step = False |
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if not is_two_step: |
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trait_cohort_id, trait_info_df = filter_and_rank_cohorts(os.path.join(trait_dir, 'cohort_info.json'), condition) |
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if trait_cohort_id is None: |
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return None, None, None |
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else: |
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trait_data = pd.read_csv(os.path.join(trait_dir, trait_cohort_id + '.csv'), index_col=0).astype('float') |
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return trait_data, None, None |
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else: |
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assert gene_info_path is not None, "A path to gene information file must be specified for two-step regression" |
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trait_cohort_id, trait_info_df = filter_and_rank_cohorts(os.path.join(trait_dir, 'cohort_info.json'), None) |
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condition_dir = os.path.join(data_root, condition) |
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condition_cohort_id, condition_info_df = filter_and_rank_cohorts( |
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os.path.join(condition_dir, 'cohort_info.json'), None) |
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if trait_cohort_id is None or condition_cohort_id is None: |
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print( |
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f"No available data, best cohorts being '{trait_cohort_id}' for the trait '{trait}' and " |
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f"'{condition_cohort_id}' for the condition '{condition}'") |
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return None, None, None |
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merged_df = pd.merge(trait_info_df.assign(key=1), condition_info_df.assign(key=1), on='key').drop(columns='key') |
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merged_df['sample_product'] = merged_df['sample_size_x'] * merged_df['sample_size_y'] |
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merged_df = merged_df.sort_values(by='sample_product', ascending=False) |
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for index, row in merged_df.iterrows(): |
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trait_data_path = os.path.join(trait_dir, row['cohort_id_x'] + '.csv') |
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condition_data_path = os.path.join(condition_dir, row['cohort_id_y'] + '.csv') |
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trait_data = pd.read_csv(trait_data_path, index_col=0).astype('float') |
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condition_data = pd.read_csv(condition_data_path, index_col=0).astype('float') |
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gene_regressors = get_gene_regressors(trait, condition, trait_data, condition_data, gene_info_path) |
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if gene_regressors: |
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print( |
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f"Found {len(gene_regressors)} candidate genes that can be used in two-step regression analysis, such as {gene_regressors[:10]}.") |
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return trait_data, condition_data, gene_regressors |
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print(f"No available cohorts with common regressors for the trait '{trait}' and the condition '{condition}'") |
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return None, None, None |
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|
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def normalize_data(X_train: np.ndarray, X_test: Optional[np.ndarray] = None) -> Tuple[np.ndarray, Optional[np.ndarray]]: |
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""" |
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Normalize features by centering and scaling using training set statistics. |
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Args: |
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X_train (np.ndarray): Training feature matrix of shape (n_samples, n_features). |
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X_test (np.ndarray, optional): Test feature matrix of shape (n_samples, n_features). |
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Returns: |
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Tuple[np.ndarray, Optional[np.ndarray]]: Normalized training features and test features (if provided). |
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For features with zero standard deviation, no scaling is applied. |
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""" |
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mean = np.mean(X_train, axis=0) |
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std = np.std(X_train, axis=0) |
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std_no_zero = np.where(std == 0, 1, std) |
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X_train_normalized = (X_train - mean) / std_no_zero |
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if X_test is not None: |
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X_test_normalized = (X_test - mean) / std_no_zero |
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else: |
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X_test_normalized = None |
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return X_train_normalized, X_test_normalized |
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def detect_batch_effect(X: np.ndarray) -> bool: |
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""" |
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Detect potential batch effects in a dataset by analyzing eigenvalue distribution of the covariance matrix. |
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A large gap between consecutive eigenvalues may indicate presence of batch effects. |
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Args: |
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X (np.ndarray): Feature matrix with shape (n_samples, n_features). |
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Returns: |
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bool: True if a potential batch effect is detected based on eigenvalue gap threshold, False otherwise. |
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""" |
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n_samples, n_features = X.shape |
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X_centered = X - X.mean(axis=0) |
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XXt = np.dot(X_centered, X_centered.T) |
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eigen_values = np.linalg.eigvalsh(XXt) |
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eigen_values = sorted(eigen_values, reverse=True)[:10] |
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eigen_values = np.array(eigen_values) |
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normalized_ev = eigen_values / eigen_values[0] |
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for i in range(len(normalized_ev) - 1): |
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gap = normalized_ev[i] - normalized_ev[i + 1] |
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if gap > 200 / n_samples: |
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return True |
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return False |
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class ResidualizationRegressor: |
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def __init__(self, model_constructor, params=None): |
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if params is None: |
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params = {} |
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self.regression_model = model_constructor(**params) |
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self.beta_Z = None |
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self.beta_X = None |
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self.neg_log_p_values = None |
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self.p_values = None |
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def _reshape_data(self, data): |
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""" |
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Reshape the data to ensure it's in the correct format (2D array). |
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:param data: The input data (can be 1D or 2D array). |
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:return: Reshaped 2D array. |
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""" |
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if data.ndim == 1: |
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return data.reshape(-1, 1) |
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return data |
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def _reshape_output(self, data): |
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""" |
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Reshape the output data to ensure it's in the correct format (1D array). |
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:param data: The output data (can be 1D or 2D array). |
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:return: Reshaped 1D array. |
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""" |
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if data.ndim == 2 and data.shape[1] == 1: |
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return data.ravel() |
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return data |
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|
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def fit(self, X, Y, Z=None): |
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X = self._reshape_data(X) |
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Y = self._reshape_data(Y) |
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if Z is not None: |
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Z = self._reshape_data(Z) |
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Z_ones = np.column_stack((np.ones(Z.shape[0]), Z)) |
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self.beta_Z = np.linalg.pinv(Z_ones.T @ Z_ones) @ Z_ones.T @ Y |
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Y_hat = Z_ones @ self.beta_Z |
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e_Y = Y - Y_hat |
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else: |
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e_Y = Y |
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self.regression_model.fit(X, e_Y) |
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if hasattr(self.regression_model, 'coef_'): |
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self.beta_X = self.regression_model.coef_ |
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elif hasattr(self.regression_model, 'getBeta'): |
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beta_output = self.regression_model.getBeta() |
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self.beta_X = self._reshape_output(beta_output) |
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if hasattr(self.regression_model, 'getNegLogP'): |
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neg_log_p_output = self.regression_model.getNegLogP() |
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if neg_log_p_output is not None: |
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self.neg_log_p_values = self._reshape_output(neg_log_p_output) |
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self.p_values = np.exp(-self.neg_log_p_values) |
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if Z is not None: |
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p_values_Z = np.full(Z.shape[1], np.nan) |
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self.p_values = np.concatenate((p_values_Z, self.p_values)) |
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def predict(self, X, Z=None): |
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X = self._reshape_data(X) |
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e_Y = self.regression_model.predict(X) |
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if Z is not None: |
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Z = self._reshape_data(Z) |
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Z_ones = np.column_stack((np.ones(Z.shape[0]), Z)) |
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Y = e_Y + Z_ones @ self.beta_Z.ravel() |
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else: |
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Y = e_Y |
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return Y |
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|
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def get_coefficients(self): |
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if self.beta_Z is not None: |
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return np.concatenate((self.beta_Z[1:].ravel(), self.beta_X.ravel())) |
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return self.beta_X.ravel() |
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def get_p_values(self): |
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return self.p_values |
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def gene_jaccard(pred: List[str], ref: List[str]) -> float: |
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""" |
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Calculate Jaccard similarity between predicted and reference gene sets. |
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""" |
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p = set(pred) |
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r = set(ref) |
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if len(p.union(r)): |
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iou = len(p.intersection(r)) / len(p.union(r)) |
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else: |
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iou = 0 |
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return iou |
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def gene_precision(pred: List[str], ref: List[str]) -> float: |
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""" |
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Calculate precision of predicted genes against reference set. |
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""" |
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if len(pred): |
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precision = sum([p in ref for p in pred]) / len(pred) |
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else: |
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precision = 0 |
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return precision |
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def gene_recall(pred: List[str], ref: List[str]) -> float: |
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""" |
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Calculate recall of predicted genes against reference set. |
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""" |
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if len(ref): |
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recall = sum([p in pred for p in ref]) / len(ref) |
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else: |
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recall = 0 |
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return recall |
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def gene_f1(pred: List[str], ref: List[str]) -> float: |
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""" |
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Calculate F1 score between predicted and reference gene sets. |
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""" |
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prec = gene_precision(pred, ref) |
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rec = gene_recall(pred, ref) |
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if prec + rec == 0: |
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return 0 |
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f1 = 2 * (prec * rec) / (prec + rec) |
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return f1 |
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def evaluate_gene_selection(pred: List[str], ref: List[str]) -> Dict[str, float]: |
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""" |
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Evaluate the performance of predicted gene selection against a reference set. |
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Args: |
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pred (List[str]): List of predicted gene symbols. |
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ref (List[str]): List of reference (ground truth) gene symbols. |
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Returns: |
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Dict[str, float]: Dictionary containing precision, recall, F1 score, and Jaccard similarity. |
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""" |
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return { |
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'precision': gene_precision(pred, ref) * 100, |
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'recall': gene_recall(pred, ref) * 100, |
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'f1': gene_f1(pred, ref) * 100, |
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'jaccard': gene_jaccard(pred, ref) * 100 |
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} |
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def cross_validation( |
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model_constructor: Callable, |
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model_params: Dict[str, Any], |
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X: np.ndarray, |
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Y: np.ndarray, |
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var_names: List[str], |
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trait: str, |
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gene_info_path: str, |
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condition: Optional[str] = None, |
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Z: Optional[np.ndarray] = None, |
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k: int = 5 |
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) -> Dict[str, Any]: |
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""" |
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Perform k-fold cross-validation for either classification or regression models, |
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assessing both prediction accuracy and variable selection precision. |
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|
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Parameters: |
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- model_constructor: Callable that constructs a model instance. |
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- model_params: Dictionary of parameters to pass to the model constructor. |
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- X: Input features as a numpy array. |
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- Y: Target variable as a numpy array. |
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- var_names: List of names of all variables considered in the model. |
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- trait: Name of the trait under analysis. |
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- gene_info_path: Path to the file containing gene information. |
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- condition: Optional; name of the condition considered in the model, if applicable. |
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- Z: Optional; conditions as a numpy array, if applicable. |
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- k: Number of folds for cross-validation. |
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|
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Returns: |
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- A dictionary containing the averaged results from the cross-validation, |
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including metrics like accuracy, precision, recall, F1 score, NMSE, and R-squared, |
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along with variable selection metrics based on gene identification. |
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""" |
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np.random.seed(42) |
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indices = np.arange(X.shape[0]) |
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np.random.shuffle(indices) |
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|
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fold_size = len(X) // k |
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performances = [] |
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|
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target_type = 'binary' if len(np.unique(Y)) == 2 else 'continuous' |
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for i in range(k): |
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|
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test_indices = indices[i * fold_size: (i + 1) * fold_size] |
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train_indices = np.setdiff1d(indices, test_indices) |
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X_train, X_test = X[train_indices], X[test_indices] |
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Y_train, Y_test = Y[train_indices], Y[test_indices] |
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normalized_X_train, normalized_X_test = normalize_data(X_train, X_test) |
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|
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if Z is not None: |
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Z_train, Z_test = Z[train_indices], Z[test_indices] |
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normalized_Z_train, normalized_Z_test = normalize_data(Z_train, Z_test) |
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else: |
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normalized_Z_train = normalized_Z_test = None |
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model = ResidualizationRegressor(model_constructor, model_params) |
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model.fit(normalized_X_train, Y_train, normalized_Z_train) |
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predictions = model.predict(normalized_X_test, normalized_Z_test) |
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performance = {} |
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if target_type == 'binary': |
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predictions = (predictions > 0.5).astype(int) |
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Y_test = (Y_test > 0.5).astype(int) |
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performance['prediction'] = { |
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"accuracy": accuracy_score(Y_test, predictions) * 100, |
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"precision": precision_score(Y_test, predictions, zero_division=0) * 100, |
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"recall": recall_score(Y_test, predictions, zero_division=0) * 100, |
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"f1": f1_score(Y_test, predictions, zero_division=0) * 100 |
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} |
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elif target_type == 'continuous': |
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nmse = np.sum((Y_test - predictions) ** 2) / np.sum((Y_test - np.mean(Y_test)) ** 2) |
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rsq = r2_score(Y_test, predictions) |
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performance['prediction'] = { |
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"nmse": nmse, |
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"r_squared": rsq |
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} |
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|
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pred_genes = interpret_result(model, var_names, trait, condition)["Variable"] |
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ref_genes = get_known_related_genes(gene_info_path, trait) |
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var_genes = [v for v in var_names if v not in [trait, condition]] |
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ref_genes = [r for r in ref_genes if r in var_genes] |
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performance["selection"] = evaluate_gene_selection(pred_genes, ref_genes) |
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performances.append(performance) |
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|
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cv_means = {} |
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for metric in performances[0]: |
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if isinstance(performances[0][metric], dict): |
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cv_means[metric] = {} |
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for submetric in performances[0][metric]: |
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cv_means[metric][submetric] = np.mean([p[metric][submetric] for p in performances]) |
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else: |
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cv_means[metric] = np.mean([p[metric] for p in performances]) |
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|
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print(f'The cross-validation performance: {cv_means}') |
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|
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return cv_means |
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|
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def tune_hyperparameters( |
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model_constructor: Callable, |
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param_values: List[float], |
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X: np.ndarray, |
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Y: np.ndarray, |
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var_names: list, |
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trait: str, |
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gene_info_path: str, |
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condition: Optional[str] = None, |
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Z: Optional[np.ndarray] = None, |
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fixed_params: Optional[Dict[str, Any]] = {}, |
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k: int = 5 |
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) -> Tuple[Dict[str, Any], Dict[str, Dict[str, float]]]: |
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""" |
|
Tune hyperparameters for a given model by exploring combinations of parameter values. |
|
|
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This function performs cross-validation to find the best hyperparameter settings based on the precision |
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of gene identification. It returns the best configuration along with the top performance metrics for both |
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prediction and gene identification. |
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|
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Parameters: |
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- model_constructor: A callable that returns an instance of the model to be used. |
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- param_values: List specifying the possible values of hyperparameter(s) to be tuned. |
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- X: Input features as a numpy array. |
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- Y: Target variable as a numpy array. |
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- var_names: List of names of all variables considered in the model. |
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- trait: Name of the trait under analysis. |
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- gene_info_path: File path to the gene information data. |
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- condition: Optional; name of the condition considered in the model, if applicable. |
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- Z: Optional; conditions as a numpy array, if applicable. |
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- fixed_params: Dictionary specifying hyperparameters and their values that are set different from default, but do |
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not need to be tuned. |
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- k: Number of folds for cross-validation. |
|
|
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Returns: |
|
- Tuple containing: |
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1. Dictionary of the best hyperparameters based on gene identification precision. |
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2. Dictionary of the best performances for 'selection' and 'prediction'. |
|
""" |
|
best_selection_score = -np.inf |
|
best_prediction_score = -np.inf |
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best_config = {} |
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best_performance = {} |
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prediction_metric = "f1" if len(np.unique(Y)) == 2 else "r_squared" |
|
|
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if model_constructor == LMM: |
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param = "lamda" |
|
elif model_constructor == Lasso: |
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param = "alpha" |
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tune_params = {param: param_values} |
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keys, values = zip(*tune_params.items()) |
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for combination in itertools.product(*values): |
|
|
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current_params = dict(zip(keys, combination)) |
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current_params.update(fixed_params) |
|
|
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results = cross_validation(model_constructor, current_params, X, Y, var_names, trait, gene_info_path, condition, |
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Z, k) |
|
|
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current_prediction_score = results["prediction"][prediction_metric] |
|
if current_prediction_score > best_prediction_score: |
|
best_prediction_score = current_prediction_score |
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best_performance["prediction"] = results["prediction"] |
|
|
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current_selection_score = results["selection"]["precision"] |
|
if current_selection_score > best_selection_score: |
|
best_selection_score = current_selection_score |
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best_config = current_params |
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best_performance["selection"] = results["selection"] |
|
|
|
|
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if best_selection_score <= 0: |
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best_config[param] = 0.1 |
|
|
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return best_config, best_performance |
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|
|
|
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def get_known_related_genes(file_path, entity): |
|
"""Read a JSON file recording gene-trait association, and get the gene symbols related to a given |
|
phenotypic entity""" |
|
with open(file_path, "r") as f: |
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data = json.load(f) |
|
|
|
if entity not in data: |
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print(f"The gene info file does not contain genes related to the entity '{entity}'.") |
|
return [] |
|
related_genes = data[entity]['related_genes'] |
|
|
|
return related_genes |
|
|
|
|
|
def get_gene_regressors(trait: str, condition: str, trait_df: pd.DataFrame, condition_df: pd.DataFrame, |
|
gene_info_path: str) -> List[str]: |
|
""" |
|
Find genes suitable for two-step regression analysis by identifying genes that are: |
|
1. Present in both trait and condition datasets |
|
2. Known to be related to the condition based on prior knowledge |
|
|
|
Args: |
|
trait (str): Name of the target trait. |
|
condition (str): Name of the condition being analyzed. |
|
trait_df (pd.DataFrame): DataFrame containing gene expression data for the trait. |
|
condition_df (pd.DataFrame): DataFrame containing gene expression data for the condition. |
|
gene_info_path (str): Path to JSON file containing known gene-trait associations. |
|
|
|
Returns: |
|
List[str]: List of gene symbols that can be used as regressors in two-step analysis. |
|
Returns empty list if no suitable genes are found. |
|
""" |
|
gene_regressors = [] |
|
related_genes = get_known_related_genes(gene_info_path, condition) |
|
genes_in_trait_data = set(trait_df.columns) - {'Age', 'Gender', trait} |
|
genes_in_condition_data = set(condition_df.columns) - {'Age', 'Gender', condition} |
|
|
|
common_genes_across_data = genes_in_trait_data.intersection(genes_in_condition_data) |
|
if len(common_genes_across_data) != 0 and len(related_genes) != 0: |
|
gene_regressors = [g for g in related_genes if g in common_genes_across_data] |
|
|
|
return gene_regressors |
|
|
|
|
|
def interpret_result(model: ResidualizationRegressor, var_names: List[str], trait: str, condition=None, |
|
threshold: float = 0.05, print_output=False) -> dict: |
|
"""This function interprets and reports the result of a trained linear regression model, where the regressor |
|
consists of one variable about some biomedical condition and multiple variables about genetic factors. |
|
The function extracts coefficients and p-values from the model, identifies significant genes based on |
|
p-values or non-zero coefficients, depending on the availability of p-values, and optionally prints the output. |
|
|
|
Parameters: |
|
model (Any): The trained regression Model. |
|
var_names (List[str]): List of names of all the variables involved in the regression analysis. |
|
trait (str): The target trait of interest. |
|
condition (str): The specific condition to examine within the model. |
|
threshold (float): Significance level for p-value correction. Defaults to 0.05. |
|
print_output (bool): Flag to determine whether to print the output to the console. Defaults to False. |
|
|
|
Returns: |
|
dict: A dictionary containing the list of significant genes, sorted by their importance, and the corresponding |
|
coefficient magnitude or corrected p-value. |
|
""" |
|
assert isinstance(model, ResidualizationRegressor), "The model must be an instance of the ResidualizationRegressor" \ |
|
"class." |
|
feature_names = [var for var in var_names if var != trait] |
|
|
|
|
|
if condition: |
|
if condition in feature_names: |
|
feature_names.remove(condition) |
|
feature_names.insert(0, condition) |
|
|
|
coefficients = model.get_coefficients().reshape(-1).tolist() |
|
p_values = model.get_p_values() |
|
if p_values is None: |
|
regression_df = pd.DataFrame({ |
|
'Variable': feature_names, |
|
'Coefficient': coefficients |
|
}) |
|
else: |
|
regression_df = pd.DataFrame({ |
|
'Variable': feature_names, |
|
'Coefficient': coefficients, |
|
'p_value': p_values.reshape(-1).tolist() |
|
}) |
|
|
|
if condition is not None: |
|
condition_effect = regression_df[regression_df['Variable'] == condition].iloc[0] |
|
if print_output: |
|
print(f"Effect of the condition on the target variable:") |
|
print(f"Variable: {condition}, Coefficient: {condition_effect['Coefficient']:.4f}") |
|
gene_regression_df = regression_df[regression_df['Variable'] != condition] |
|
else: |
|
gene_regression_df = regression_df |
|
|
|
if p_values is None: |
|
significant_genes_df = gene_regression_df[gene_regression_df['Coefficient'] != 0].copy() |
|
significant_genes_df['Absolute Coefficient'] = significant_genes_df['Coefficient'].abs() |
|
significant_genes_df = significant_genes_df.sort_values('Absolute Coefficient', ascending=False) |
|
else: |
|
corrected_p_values = multipletests(gene_regression_df['p_value'], alpha=threshold, method='fdr_bh')[1] |
|
gene_regression_df.loc[:, 'corrected_p_value'] = corrected_p_values |
|
significant_genes_df = gene_regression_df[gene_regression_df['corrected_p_value'] < threshold] |
|
significant_genes_df = significant_genes_df.sort_values('corrected_p_value', ascending=True) |
|
|
|
if print_output: |
|
print(f"Found {len(significant_genes_df)} significant genes associated with the trait '{trait}', " |
|
f"conditional on the factor '{condition}'.") |
|
|
|
return significant_genes_df.to_dict(orient="list") |
|
|
|
|
|
def save_result(significant_genes: Dict[str, any], performance: Dict[str, any], output_root: str, |
|
trait: str, condition: Optional[str] = None): |
|
""" |
|
Saves the results of gene identification and model performance metrics to a JSON file. |
|
|
|
Args: |
|
significant_genes (dict): Dictionary containing identified significant genes and their related metrics. |
|
performance (dict): Dictionary containing performance metrics from cross-validation. |
|
output_root (str): The root directory where all output files will be saved. |
|
trait (str, optional): Specifies the trait in the gene identification question. |
|
condition (str, optional): Specifies the condition related to the gene identification. Include this parameter if |
|
the model considers a specific condition; otherwise, leave it as None. |
|
|
|
Outputs: |
|
A JSON file named 'significant_genes_condition_{condition}.json' in the specified directory, containing both the |
|
significant genes and cross-validation performance data. |
|
""" |
|
output_dir = os.path.join(output_root, trait) |
|
os.makedirs(output_dir, exist_ok=True) |
|
output_path = os.path.join(output_dir, f'significant_genes_condition_{condition}.json') |
|
output_data = {'significant_genes': significant_genes, 'cv_performance': performance} |
|
|
|
with open(output_path, 'w') as f: |
|
json.dump(output_data, f, indent=4) |
|
|