cvmatrix 2.0.0__tar.gz → 2.0.2__tar.gz

{cvmatrix-2.0.0 → cvmatrix-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cvmatrix
-Version: 2.0.0
+Version: 2.0.2
 Summary: Fast computation of possibly weighted and possibly centered/scaled training set kernel matrices in a cross-validation setting.
 License: Apache-2.0
 Author: Sm00thix
@@ -118,7 +118,7 @@ Guidelines](https://github.com/Sm00thix/CVMatrix/blob/main/CONTRIBUTING.md).
 
 1. [Engstrøm, O.-C. G. and Jensen, M. H. (2025). Fast partition-based cross-validation with centering and scaling for $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$. *Journal of Chemometrics*, 39(3).](https://doi.org/10.1002/cem.70008)
 2. [Dayal, B. S. and MacGregor, J. F. (1997). Improved PLS algorithms. *Journal of Chemometrics*, 11(1), 73-85.](https://doi.org/10.1002/(SICI)1099-128X(199701)11:1%3C73::AID-CEM435%3E3.0.CO;2-%23?)
-3. [Engstrøm, O.-C. G. and Dreier, E. S. and Jespersen, B. M. and Pedersen, K. S. IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX. *Journal of Open Source Software*, 9(99).](https://doi.org/10.21105/joss.06533)
+3. [Engstrøm, O.-C. G. and Dreier, E. S. and Jespersen, B. M. and Pedersen, K. S. (2024). IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX. *Journal of Open Source Software*, 9(99).](https://doi.org/10.21105/joss.06533)
 
 ## Funding
 - Up until May 31st 2025, this work has been carried out as part of an industrial Ph. D. project receiving funding from [FOSS Analytical A/S](https://www.fossanalytics.com/) and [The Innovation Fund Denmark](https://innovationsfonden.dk/en). Grant number 1044-00108B.

{cvmatrix-2.0.0 → cvmatrix-2.0.2}/README.md

@@ -96,7 +96,7 @@ Guidelines](https://github.com/Sm00thix/CVMatrix/blob/main/CONTRIBUTING.md).
 
 1. [Engstrøm, O.-C. G. and Jensen, M. H. (2025). Fast partition-based cross-validation with centering and scaling for $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$. *Journal of Chemometrics*, 39(3).](https://doi.org/10.1002/cem.70008)
 2. [Dayal, B. S. and MacGregor, J. F. (1997). Improved PLS algorithms. *Journal of Chemometrics*, 11(1), 73-85.](https://doi.org/10.1002/(SICI)1099-128X(199701)11:1%3C73::AID-CEM435%3E3.0.CO;2-%23?)
-3. [Engstrøm, O.-C. G. and Dreier, E. S. and Jespersen, B. M. and Pedersen, K. S. IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX. *Journal of Open Source Software*, 9(99).](https://doi.org/10.21105/joss.06533)
+3. [Engstrøm, O.-C. G. and Dreier, E. S. and Jespersen, B. M. and Pedersen, K. S. (2024). IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX. *Journal of Open Source Software*, 9(99).](https://doi.org/10.21105/joss.06533)
 
 ## Funding
 - Up until May 31st 2025, this work has been carried out as part of an industrial Ph. D. project receiving funding from [FOSS Analytical A/S](https://www.fossanalytics.com/) and [The Innovation Fund Denmark](https://innovationsfonden.dk/en). Grant number 1044-00108B.

cvmatrix-2.0.2/cvmatrix/__init__.py

@@ -0,0 +1 @@
+__version__ = "2.0.2"

{cvmatrix-2.0.0 → cvmatrix-2.0.2}/cvmatrix/cvmatrix.py

@@ -99,8 +99,6 @@ class CVMatrix:
         self.N = None
         self.K = None
         self.M = None
-        self.X_total_mean = None
-        self.Y_total_mean = None
         self.XTX_total = None
         self.XTY_total = None
         self.sum_X_total = None
@@ -146,7 +144,6 @@ class CVMatrix:
         ValueError
             If `weights` is provided and contains negative values.
         """
-
         self._init_mats(X, Y, weights)
         self._init_weighted_mats()
         self._init_matrix_products()
@@ -353,26 +350,19 @@ class CVMatrix:
                         "The number of non-zero weights in the training set must be "
                         "greater than zero."
                     )
-            sum_w_total_over_sum_w_train = self.sum_w_total / sum_w_train
-            sum_w_val_over_sum_w_train = sum_w_val / sum_w_train
-
         if self.center_X or self.scale_X or (return_XTY and self.center_Y):
             sum_X_val = np.sum(X_val, axis=0, keepdims=True)
             X_train_mean = self._compute_training_mat_mean(
                 sum_X_val,
-                sum_w_val,
-                self.X_total_mean,
-                sum_w_total_over_sum_w_train,
-                sum_w_val_over_sum_w_train,
+                self.sum_X_total,
+                sum_w_train,
             )
         if return_XTY and (self.center_X or self.center_Y or self.scale_Y):
             sum_Y_val = np.sum(Y_val, axis=0, keepdims=True)
             Y_train_mean = self._compute_training_mat_mean(
                 sum_Y_val,
-                sum_w_val,
-                self.Y_total_mean,
-                sum_w_total_over_sum_w_train,
-                sum_w_val_over_sum_w_train,
+                self.sum_Y_total,
+                sum_w_train,
             )
         if self.scale_X or (self.scale_Y and return_XTY):
             divisor = self._compute_std_divisor(sum_w_train, num_nonzero_w_train)
@@ -519,10 +509,8 @@ class CVMatrix:
     def _compute_training_mat_mean(
         self,
         sum_mat_val: np.ndarray,
-        sum_w_val: float,
-        mat_total_mean: np.ndarray,
-        sum_w_total_over_sum_w_train: float,
-        sum_w_val_over_sum_w_train: float,
+        sum_mat_total: np.ndarray,
+        sum_w_train: float,
     ) -> np.ndarray:
         """
         Computes the row of column-wise means of a matrix for a given fold.
@@ -532,34 +520,18 @@ class CVMatrix:
         sum_mat_val : Array of shape (1, K) or (1, M)
             The row of column-wise sums of validation set of `Xw` or `Yw`.
 
-        sum_w_val : float
-            The sum of weights in the validation set.
-
-        mat_total_mean : Array of shape (1, K) or (1, M)
-            The row of column-wise weighted means of the total matrix.
-
-        sum_w_total_over_sum_w_train : float
-            The ratio of the sum of weights in the entire dataset to the sum of weights
-            in the training set.
-
-        sum_w_val_over_sum_w_train : float
-            The ratio of the sum of weights in the validation set to the sum of weights
-            in the training set.
+        sum_mat_total : Array of shape (1, K) or (1, M)
+            The row of column-wise sums of the total `Xw` or `Yw`.
 
-        sum_w_val : float
-            The sum of weights in the validation set.
+        sum_w_train : float
+            The sum of weights in the training set.
 
         Returns
         -------
         Array of shape (1, K) or (1, M)
             The row of column-wise means of the training set matrix.
         """
-        train_part_contribution = sum_w_total_over_sum_w_train * mat_total_mean
-        if sum_w_val <= self.eps:
-            return train_part_contribution
-        return train_part_contribution - sum_w_val_over_sum_w_train * (
-            sum_mat_val / sum_w_val
-        )
+        return (sum_mat_total - sum_mat_val) / sum_w_train
 
     def _compute_std_divisor(
         self, sum_w_train: float, num_nonzero_w_train: int
@@ -745,33 +717,28 @@ class CVMatrix:
         """
         Initializes the global statistics for `X` and `Y`.
         """
-        if self.w_total is not None:
-            self.sum_w_total = np.sum(self.w_total)
-            self.num_nonzero_w_total = np.count_nonzero(self.w_total)
-        else:
-            self.sum_w_total = self.N
-            self.num_nonzero_w_total = self.N
+        if self.center_X or self.center_Y or self.scale_X or self.scale_Y:
+            if self.w_total is not None:
+                self.sum_w_total = np.sum(self.w_total)
+                self.num_nonzero_w_total = np.count_nonzero(self.w_total)
+            else:
+                self.sum_w_total = self.N
+                self.num_nonzero_w_total = self.N
         if self.center_X or self.center_Y or self.scale_X:
             self.sum_X_total = np.sum(self.Xw_total, axis=0, keepdims=True)
-            self.X_total_mean = self.sum_X_total / self.sum_w_total
-        else:
-            self.X_total_mean = None
         if (
             self.center_X or self.center_Y or self.scale_Y
         ) and self.Y_total is not None:
             self.sum_Y_total = np.sum(self.Yw_total, axis=0, keepdims=True)
-            self.Y_total_mean = self.sum_Y_total / self.sum_w_total
-        else:
-            self.Y_total_mean = None
         if self.scale_X:
-            self.sum_sq_X_total = np.expand_dims(
-                np.einsum("ij, ij -> j", self.Xw_total, self.X_total), axis=0
+            self.sum_sq_X_total = np.sum(
+                self.Xw_total * self.X_total, axis=0, keepdims=True
             )
         else:
             self.sum_sq_X_total = None
         if self.scale_Y and self.Y_total is not None:
-            self.sum_sq_Y_total = np.expand_dims(
-                np.einsum("ij, ij -> j", self.Yw_total, self.Y_total), axis=0
+            self.sum_sq_Y_total = np.sum(
+                self.Yw_total * self.Y_total, axis=0, keepdims=True
             )
         else:
             self.sum_sq_Y_total = None
@@ -788,7 +755,6 @@ class CVMatrix:
             An iterable defining cross-validation splits. Each unique value in
             `folds` corresponds to a different fold.
         """
-
         folds_dict: "defaultdict[Hashable, list[int]]" = defaultdict(list)
         for i, num in enumerate(folds):
             folds_dict[num].append(i)

{cvmatrix-2.0.0 → cvmatrix-2.0.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cvmatrix"
-version = "2.0.0"
+version = "2.0.2"
 description = "Fast computation of possibly weighted and possibly centered/scaled training set kernel matrices in a cross-validation setting."
 authors = ["Sm00thix <oleemail@icloud.com>"]
 maintainers = ["Sm00thix <oleemail@icloud.com>"]

cvmatrix-2.0.0/cvmatrix/__init__.py

@@ -1 +0,0 @@
-__version__ = "2.0.0"