causarray 0.0.1__tar.gz

causarray-0.0.1/.gitignore

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causarray-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 Du Jinhong
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

causarray-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: causarray
+Version: 0.0.1
+Summary: causarray is a Python module for A Python package for simultaneous causal inference with an array of outcomes.
+Author-email: Jin-Hong Du <jinhongd@andrew.cmu.com>, Maya Shen <myshen@andrew.cmu.edu>, Hansruedi Mathys <mathysh@pitt.edu>, Kathryn Roeder <jinhongd@andrew.cmu.com>
+Maintainer-email: Jin-Hong Du <jinhongd@andrew.cmu.com>
+License: MIT License
+License-File: LICENSE
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Requires-Dist: joblib
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pip
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: sklearn-ensemble-cv
+Requires-Dist: statsmodels
+Requires-Dist: tqdm
+Description-Content-Type: text/markdown
+
+# causarray
+
+Advances in single-cell sequencing and CRISPR technologies have enabled detailed case-control comparisons and experimental perturbations at single-cell resolution. However, uncovering causal relationships in observational genomic data remains challenging due to selection bias and inadequate adjustment for unmeasured confounders, particularly in heterogeneous datasets. To address these challenges, we introduce `causarray` [Du25], a doubly robust causal inference framework for analyzing array-based genomic data at both bulk-cell and single-cell levels. `causarray` integrates a generalized confounder adjustment method to account for unmeasured confounders and employs semiparametric inference with flexible machine learning techniques to ensure robust statistical estimation of treatment effects.
+
+
+# Requirements
+
+The dependencies for running `causarray` method are listed in `environment.yml` and can be installed by running
+
+```cmd
+PIP_NO_DEPS=1 conda env create -f environment.yml
+```
+
+
+
+
+<!-- 
+# Development
+
+## Build
+```cmd
+git tag 0.0.0
+git tag --delete 1.0.0
+python -m pip install .
+```
+
+## Testing
+```cmd
+python -m pytest tests/test_gcate.py
+python -m pytest tests/test_DR_learner.py
+```
+
+## Documentation
+
+```cmd
+mkdir docs
+sphinx-quickstart
+cd docs
+make html # sphinx-build source build
+```
+-->
+
+
+# References
+[Du25] Jin-Hong Du, Maya Shen, Hansruedi Mathys, and Kathryn Roeder (2025). Causal differential expression analysis under unmeasured confounders with causarray. bioRxiv, 2025-01.

causarray-0.0.1/README.md

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+# causarray
+
+Advances in single-cell sequencing and CRISPR technologies have enabled detailed case-control comparisons and experimental perturbations at single-cell resolution. However, uncovering causal relationships in observational genomic data remains challenging due to selection bias and inadequate adjustment for unmeasured confounders, particularly in heterogeneous datasets. To address these challenges, we introduce `causarray` [Du25], a doubly robust causal inference framework for analyzing array-based genomic data at both bulk-cell and single-cell levels. `causarray` integrates a generalized confounder adjustment method to account for unmeasured confounders and employs semiparametric inference with flexible machine learning techniques to ensure robust statistical estimation of treatment effects.
+
+
+# Requirements
+
+The dependencies for running `causarray` method are listed in `environment.yml` and can be installed by running
+
+```cmd
+PIP_NO_DEPS=1 conda env create -f environment.yml
+```
+
+
+
+
+<!-- 
+# Development
+
+## Build
+```cmd
+git tag 0.0.0
+git tag --delete 1.0.0
+python -m pip install .
+```
+
+## Testing
+```cmd
+python -m pytest tests/test_gcate.py
+python -m pytest tests/test_DR_learner.py
+```
+
+## Documentation
+
+```cmd
+mkdir docs
+sphinx-quickstart
+cd docs
+make html # sphinx-build source build
+```
+-->
+
+
+# References
+[Du25] Jin-Hong Du, Maya Shen, Hansruedi Mathys, and Kathryn Roeder (2025). Causal differential expression analysis under unmeasured confounders with causarray. bioRxiv, 2025-01.

causarray-0.0.1/causarray/DR_estimation.py

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+import numpy as np
+from sklearn.linear_model import LogisticRegression
+from sklearn.ensemble import RandomForestClassifier
+from causarray.gcate_glm import fit_glm
+from causarray.utils import *
+from causarray.utils import _filter_params
+import pprint
+
+from sklearn.model_selection import KFold, ShuffleSplit
+
+def _get_func_ps(ps_model, **kwargs):
+    if ps_model=='random_forest_cv':
+        params_ps = _filter_params(fit_rf, kwargs)
+        func_ps = lambda X, Y, X_test:fit_rf_ind_ps(X, Y[:,None], X_test=X_test, **params_ps)[:,0]
+    elif ps_model=='logistic':
+        clf_ps = LogisticRegression
+        kwargs = {**{'fit_intercept':False, 'C':1e0, 'class_weight':'balanced', 'random_state':0}, **kwargs}
+        params_ps = _filter_params(clf_ps().get_params(), kwargs)
+        func_ps = lambda X, Y, X_test: clf_ps(**params_ps).fit(X, Y).predict_proba(X_test)[:,1]
+    elif ps_model=='ensemble':
+        params_ps_rf = _filter_params(fit_rf, kwargs)
+        clf_ps = LogisticRegression
+        kwargs = {**{'fit_intercept':False, 'C':1e0, 'class_weight':'balanced', 'random_state':0}, **kwargs}
+        params_ps_lr = _filter_params(clf_ps().get_params(), kwargs)
+        params_ps = {'params_ps_rf':params_ps_rf, 'params_ps_lr':params_ps_lr}
+        func_ps = lambda X, Y, X_test:(fit_rf_ind(X, Y[:,None], X_test=X_test, **params_ps_rf)[:,0] + clf_ps(**params_ps_lr).fit(X, Y).predict_proba(X_test)[:,1])/2
+    else:
+        raise ValueError('Invalid propensity score model.')
+
+    return func_ps, params_ps
+
+
+def cross_fitting(
+    Y, A, X, X_A, family='poisson', K=1, glm_alpha=1e-4,
+    ps_model='logistic', 
+    pi_hat=None, Y_hat=None, verbose=False, **kwargs):
+    '''
+    Cross-fitting for causal estimands.
+
+    Parameters
+    ----------
+    Y : array
+        Outcomes.    
+    A : array
+        Binary treatment indicator.
+    X : array
+        Covariates.
+    X_A : array
+        Covariates for the propensity score model.
+    family : str, optional
+        The family of the generalized linear model. The default is 'poisson'.
+    K : int, optional
+        The number of folds for cross-validation. The default is 1.
+    glm_alpha : float, optional
+        The regularization parameter for the generalized linear model. The default is 1e-4.
+    ps_model : str, optional
+        The propensity score model. The default is 'logistic'.
+    pi_hat : array, optional
+        Propensity score of shape (n, a). The default is None.
+    Y_hat : array, optional
+        Estimated potential outcome of shape (n, p, a, 2). The default is None.
+    **kwargs : dict
+        Additional arguments to pass to the model.
+
+    Returns
+    -------    
+    Y_hat : array
+        Estimated potential outcome under control.
+    pi_hat : array
+        Estimated propensity score.
+    '''
+    func_ps, params_ps = _get_func_ps(ps_model, **kwargs)
+    params_glm = _filter_params(fit_glm, kwargs)
+
+    if verbose:
+        pprint.pprint(params_ps)
+        pprint.pprint(params_glm)
+    
+    if K>1:
+        # Initialize KFold cross-validator
+        kf = KFold(n_splits=K, random_state=0, shuffle=True)
+        folds = kf.split(X)
+    else:
+        folds = [(np.arange(X.shape[0]), np.arange(X.shape[0]))]
+
+    # Initialize lists to store results
+    fit_pi = True if pi_hat is None else False
+    pi_hat = np.zeros_like(A, dtype=float) if fit_pi else pi_hat
+    Y_hat = np.zeros((Y.shape[0],Y.shape[1],A.shape[1],2), dtype=float)
+
+    # Perform cross-fitting
+    for train_index, test_index in folds:
+        # Split data
+        X_train, X_test = X[train_index], X[test_index]
+        XA_train, XA_test = X_A[train_index], X_A[test_index]
+        A_train, A_test = A[train_index], A[test_index]
+        Y_train, Y_test = Y[train_index], Y[test_index]
+
+        if fit_pi:
+            i_ctrl = (np.sum(A_train, axis=1) == 0.)
+
+            pi = np.zeros_like(A_test, dtype=float)
+            for j in range(A.shape[1]):
+                i_case = (A_train[:,j] == 1.)
+                i_cells = i_ctrl | i_case
+
+                if ps_model=='logistic' and XA_train.shape[1]==1 and np.all(XA_train==1):
+                    prob = np.sum(i_case)/np.sum(i_cells)
+                    pi[A_train[:,j] == 1., j] = prob
+                    pi[A_train[:,j] == 0., j] = 1 - prob
+                else:
+                    pi[:,j] = func_ps(XA_train[i_cells], A_train[i_cells][:,j], XA_test)
+
+        # Fit GLM on training data and predict on test data
+        res = fit_glm(Y_train, X_train, A_train, family=family, alpha=glm_alpha,
+            impute=X_test, **params_glm)
+        
+        # Store results
+        if fit_pi:
+            pi_hat[test_index] = pi
+
+        Y_hat[test_index,:,:,0] = res[1][0]
+        Y_hat[test_index,:,:,1] = res[1][1]
+
+    pi_hat = np.clip(pi_hat, 0.01, 0.99)
+    Y_hat = np.clip(Y_hat, None, 1e5)
+    return Y_hat, pi_hat
+
+
+
+
+
+def AIPW_mean(Y, A, mu, pi, positive=False):
+    '''
+    Augmented inverse probability weighted estimator (AIPW)
+
+    Parameters
+    ----------
+    Y : array
+        Outcomes of shape (n, p).
+    A : array
+        Binary treatment indicator of shape (n, a, 2).
+    mu : array
+        Conditional outcome distribution estimate of shape (n, p, a, 2).
+    pi : array
+        Propensity score of shape (n, a, 2).
+    positive : bool, optional
+        Whether to restrict the pseudo-outcome to be positive.
+
+    Returns
+    -------
+    tau : array
+        A point estimate of the expected potential outcome of shape (p, a, 2).
+    pseudo_y : array
+        Pseudo-outcome of shape (n, p, a, 2).
+    '''
+    
+    weight = A / pi
+    weight = weight[:, None, ...]
+    Y = Y[:, :, None, None]
+
+    pseudo_y = weight * (Y - mu) + mu
+    
+    if positive:
+        pseudo_y = np.clip(pseudo_y, 0, None)
+
+    tau = np.mean(pseudo_y, axis=0)
+
+    return tau, pseudo_y
+    
+
+
+
+
+
+
+
+
+
+from joblib import Parallel, delayed
+from tqdm import tqdm
+from sklearn_ensemble_cv import reset_random_seeds, Ensemble, ECV
+from sklearn.tree import DecisionTreeRegressor
+
+def fit_rf(X, y, X_test=None, sample_weight=None, M=100, M_max=1000,
+    # fixed parameters for bagging regressor
+    kwargs_ensemble={'verbose':1},
+    # fixed parameters for decision tree
+    kwargs_regr={'min_samples_leaf': 3}, # 'min_samples_split': 10, 'max_features':'sqrt'
+    # grid search parameters
+    grid_regr = {'max_depth': [11]},
+    grid_ensemble = {'random_state': 0}, #'max_samples':np.linspace(0.25, 1., 4)
+    ):
+
+    # Validate integer parameters
+    M = int(M)
+    M_max = int(M_max)
+    # for kwargs in [kwargs_regr, kwargs_ensemble, grid_regr, grid_ensemble]:
+    #     for param in kwargs:
+    #         if param in ['max_depth', 'random_state', 'max_leaf_nodes'] and isinstance(kwargs[param], float):
+    #             kwargs[param] = int(kwargs[param])
+
+    # Make sure y is 2D
+    y = y.reshape(-1, 1) if y.ndim == 1 else y
+
+    # Run ECV
+    res_ecv, info_ecv = ECV(
+        X, y, DecisionTreeRegressor, grid_regr, grid_ensemble, 
+        kwargs_regr, kwargs_ensemble, 
+        M=M, M0=M, M_max=M_max, return_df=True
+    )
+
+    # Replace the in-sample best parameter for 'n_estimators' with extrapolated best parameter
+    info_ecv['best_params_ensemble']['n_estimators'] = info_ecv['best_n_estimators_extrapolate']
+
+    # Fit the ensemble with the best CV parameters
+    regr = Ensemble(
+        estimator=DecisionTreeRegressor(**info_ecv['best_params_regr']),
+        **info_ecv['best_params_ensemble']).fit(X, y, sample_weight=sample_weight)
+        
+    # Predict
+    if X_test is None:
+        X_test = X
+    return regr.predict(X_test).reshape(-1, y.shape[1])
+
+
+
+def fit_rf_ind(X, Y, *args, **kwargs):
+    Y_hat = Parallel(n_jobs=-1)(delayed(fit_rf)(X, Y[:,j], *args, **kwargs)
+        for j in tqdm(range(Y.shape[1])))
+    Y_pred = np.concatenate(Y_hat, axis=-1)
+    return Y_pred
+
+
+def fit_rf_ind_ps(X, Y, *args, **kwargs):
+    i_ctrl = (np.sum(Y, axis=1) == 0.)
+
+    if 'X_test' not in kwargs:
+        kwargs['X_test'] = X
+
+    def _fit(X, y, i_ctrl, *args, **kwargs):        
+        i_case = (y == 1.)
+        i_cells = i_ctrl | i_case
+        sample_weight = np.ones(y.shape[0])
+        class_weight =  len(y) / (2 * np.bincount(y.astype(int)))  
+        for a in range(2):
+            sample_weight[y == a] = class_weight[a]     
+        return fit_rf(X[i_cells], y[i_cells], sample_weight=sample_weight[i_cells], *args, **kwargs)
+
+    Y_hat = Parallel(n_jobs=-1)(delayed(_fit)(X, Y[:,j], i_ctrl, *args, **kwargs)
+        for j in tqdm(range(Y.shape[1])))
+    Y_pred = np.concatenate(Y_hat, axis=-1)
+
+    return Y_pred
+
+
+def fit_rf_ind_outcome(W, Y, A, *args, **kwargs):
+    d = W.shape[1]
+    a = A.shape[1]
+    X = np.c_[W, A]
+    X_test = np.tile(np.c_[W, np.zeros_like(A)][:,None,:], (1,1+a,1))
+    for j in range(a):
+        X_test[:,1+j,d+j] = 1
+    X_test = X_test.reshape(-1, X_test.shape[-1])
+    Y_pred = fit_rf_ind(X, Y, X_test=X_test)
+    Y_pred = Y_pred.reshape(X.shape[0],1+a,Y.shape[1])
+    Yhat_1 = Y_pred[:,1:,:].transpose(0,2,1)
+    Yhat_0 = np.tile(Y_pred[:,0,:][:,:,None], (1,1,a))
+    return Yhat_0, Yhat_1