Refactor Gram matrix normalization for memory efficiency

barakcohenlab · May 6, 2022 · f88e917 · f88e917
1 parent f86a567
commit f88e917
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/preimage/kernels/generic_string.py b/preimage/kernels/generic_string.py
@@ -260,7 +260,7 @@ def _normalize(self, gram_matrix, X1, x1_lengths, X2, x2_lengths, is_symmetric,
             else:
                 x1_norm = c_norm_fun(X1, x1_lengths)
                 x2_norm = c_norm_fun(X2, x2_lengths)
-            gram_matrix = ((gram_matrix / np.sqrt(x2_norm)).T / np.sqrt(x1_norm)).T
+            gram_matrix = gram_matrix / np.sqrt(x2_norm) / np.sqrt(x1_norm[:, np.newaxis])
         return gram_matrix
 
     def transform(self, x):