From d1b84b91f4b94b717de477e47b22946fd42be0db Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 25 Feb 2020 20:52:08 -0700
Subject: Refactor gauss kernel, more natural syntax
---
ml_exp/__init__.py | 4 +++-
ml_exp/kernels.py | 22 +++++++++-------------
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)
--
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