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fix: fix issue#221 #223

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Merged
merged 1 commit into from
Feb 28, 2025
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Merged

fix: fix issue#221 #223

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10 changes: 5 additions & 5 deletions causallearn/score/LocalScoreFunction.py
View file
Original file line number Diff line number Diff line change
@@ -206,7 +206,7 @@ def local_score_cv_general(
Thresh = 1e-5

if len(PAi):
PA = Data[:, PAi].reshape(-1, 1)
PA = Data[:, PAi]

# set the kernel for X
GX = np.multiply(X, X).reshape(-1, 1)
@@ -354,7 +354,7 @@ def local_score_cv_general(
CV = CV / k
else:
# set the kernel for X
GX = np.sum(np.multiply(X, X), axis=1)
GX = np.sum(np.multiply(X, X), axis=1).reshape(-1, 1)
Q = np.tile(GX, (1, T))
R = np.tile(GX.T, (T, 1))
dists = Q + R - 2 * X * X.T
@@ -416,8 +416,8 @@ def local_score_cv_general(
- 1
/ (gamma * n1)
* Kx_tr_te.T
* pdinv(np.eye(n1) + 1 / (gamma * n1) * Kx_tr)
* Kx_tr_te
@ pdinv(np.eye(n1) + 1 / (gamma * n1) * Kx_tr)
@ Kx_tr_te
) / gamma
B = 1 / (gamma * n1) * Kx_tr + np.eye(n1)
L = np.linalg.cholesky(B)
@@ -604,7 +604,7 @@ def local_score_cv_multi(
CV = CV / k
else:
# set the kernel for X
GX = np.sum(np.multiply(X, X), axis=1)
GX = np.sum(np.multiply(X, X), axis=1).reshape(-1, 1)
Q = np.tile(GX, (1, T))
R = np.tile(GX.T, (T, 1))
dists = Q + R - 2 * X * X.T

Unchanged files with check annotations Beta

View file
causallearn/utils/ScoreUtils.py
# nlml is the returned value of the negative log marginal likelihood
# dnlml is a (column) vector of partial derivatives of the negative
# log marginal likelihood wrt each log hyperparameter
# mu is a (column) vector (of size nn) of prediced means

Check failure on line 462 in causallearn/utils/ScoreUtils.py

GitHub Actions / Check for spelling errors 

prediced ==> predicted
# S2 is a (column) vector (of size nn) of predicted variances
#
# For more help on covariance functions, see "covFunctions".
View file
causallearn/utils/PCUtils/Helper.py
common_neighbor = (X_child == 1) & (Y_child == 1)
if sum(common_neighbor) > 0: # have at least one common neighbor
indx = np.array([i for i in range(len(Y_child))])

Check failure on line 600 in causallearn/utils/PCUtils/Helper.py

GitHub Actions / Check for spelling errors 

indx ==> index
common_neighbor_indx = indx[common_neighbor]

Check failure on line 601 in causallearn/utils/PCUtils/Helper.py

GitHub Actions / Check for spelling errors 

indx ==> index
var = [X] + [Y] + list(condition_set)
prt_ls = get_prt_mvars(var, prt_m)
if len(list(set(common_neighbor_indx) & set(prt_ls))):
View file
causallearn/search/ConstraintBased/PC.py
prt: list, parents of the missingness indicator r
"""
num_var = len(cg_skel_adj[0, :])
indx = np.array([i for i in range(num_var)])

Check failure on line 402 in causallearn/search/ConstraintBased/PC.py

GitHub Actions / Check for spelling errors 

indx ==> index
prt = indx[cg_skel_adj[r, :] == 1]

Check failure on line 403 in causallearn/search/ConstraintBased/PC.py

GitHub Actions / Check for spelling errors 

indx ==> index
return prt