From 66c6f2420a5c5899b6c3b7214f18d5b16148784f Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 3 Jul 2023 23:28:34 +0200
Subject: [PATCH 1/2] bug in the covariance. Took the covariance_a_posteriori
instead of the covariance.
---
pyPLNmodels/models.py | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index 492c9106..c4189583 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -411,7 +411,7 @@ class _model(ABC):
centered_latent = self.latent_variables - torch.mean(
self.latent_variables, axis=0
)
- chol = torch.linalg.cholesky(torch.inverse(self.covariance))
+ chol = torch.linalg.cholesky(torch.inverse(self.covariance_a_posteriori))
residus = torch.matmul(centered_latent.unsqueeze(1), chol.unsqueeze(0))
stats.probplot(residus.ravel(), plot=plt)
plt.show()
@@ -3050,9 +3050,23 @@ class PlnPCA(_model):
return string
@property
- def covariance(self) -> Optional[torch.Tensor]:
+ def covariance(self) -> torch.Tensor:
"""
- Property representing the covariance.
+ Property representing the covariance a posteriori of the latent variables.
+
+ Returns
+ -------
+ Optional[torch.Tensor]
+ The covariance tensor or None if components are not present.
+ """
+ if hasattr(self, "_components"):
+ return self._components @ (self._components.T)
+ return None
+
+ @property
+ def covariance_a_posteriori(self) -> Optional[torch.Tensor]:
+ """
+ Property representing the covariance a posteriori of the latent variables.
Returns
-------
--
GitLab
From cfab2b90283125e19f353f2df82f8a57a7ab1c88 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Thu, 13 Jul 2023 09:51:26 +0200
Subject: [PATCH 2/2] model.covariance now returns a detached tensor.
---
pyPLNmodels/models.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index c4189583..9c2024ee 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -3060,7 +3060,7 @@ class PlnPCA(_model):
The covariance tensor or None if components are not present.
"""
if hasattr(self, "_components"):
- return self._components @ (self._components.T)
+ return self.components @ (self.components.T)
return None
@property
--
GitLab