Refactor gauss kernel, more natural syntax

2 files changed, 12 insertions, 14 deletions

diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py
index dcb10a1df..e9dd83eae 100644
--- a/ml_exp/__init__.py
+++ b/ml_exp/__init__.py
@@ -23,6 +23,7 @@ SOFTWARE.
 from ml_exp.compound import Compound
 from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
     first_neighbor_matrix, adjacency_matrix, check_bond, bag_of_stuff
+from ml_exp.math import cholesky_solve
 
 # If somebody does "from package import *", this is what they will
 # be able to access:
@@ -32,4 +33,5 @@ __all__ = ['Compound',
            'first_neighbor_matrix',
            'adjacency_matrix',
            'check_bond',
-           'bag_of_stuff']
+           'bag_of_stuff',
+           'cholesky_solve']
diff --git a/ml_exp/kernels.py b/ml_exp/kernels.py
index 834d62408..7a61a1e1e 100644
--- a/ml_exp/kernels.py
+++ b/ml_exp/kernels.py
@@ -22,27 +22,23 @@ SOFTWARE.
 """
 import math
 import numpy as np
-from ml_exp.frob_norm import frob_norm
 
 
-def gauss_kernel(X_1, X_2, sigma):
+def gaussian_kernel(X1,
+                    X2,
+                    sigma):
     """
     Calculates the Gaussian Kernel.
-    X_1: first representations.
-    X_2: second representations.
+    X1: first representations.
+    X2: second representations.
     sigma: kernel width.
     """
-    x1_l = len(X_1)
-    x1_range = range(x1_l)
-    x2_l = len(X_2)
-    x2_range = range(x2_l)
-
     inv_sigma = -0.5 / (sigma*sigma)
 
-    K = np.zeros((x1_l, x2_l))
-    for i in x1_range:
-        for j in x2_range:
-            f_norm = frob_norm(X_1[i] - X_2[j])
+    K = np.zeros((X1.shape[0], X2.shape[0]), dtype=float)
+    for i in X1:
+        for j in X2:
+            f_norm = np.linalg.norm(i - j)
             # print(f_norm)
             K[i, j] = math.exp(inv_sigma * f_norm)