From 7bfdb65d892b3e292f9066d1afc6419521da20b0 Mon Sep 17 00:00:00 2001
From: Michele Nottoli <michele.nottoli@gmail.com>
Date: Thu, 9 Nov 2023 11:42:50 +0100
Subject: [PATCH] Changed default for regularization, added a test.
---
gext/fitting.py | 4 +-
tests/test_descriptor_fitting.py | 68 ++++++++++++++++++++++++++++++++
tests/utils.py | 55 ++++++++++++++++++++++++++
3 files changed, 125 insertions(+), 2 deletions(-)
diff --git a/gext/fitting.py b/gext/fitting.py
index efd09f0..21fa5a3 100644
--- a/gext/fitting.py
+++ b/gext/fitting.py
@@ -64,7 +64,7 @@ class LeastSquare(AbstractFitting):
a = matrix.T @ matrix
b = matrix.T @ target
if self.options["regularization"] > 0.0:
- a += np.identity(len(b))*self.options["regularization"]
+ a += np.identity(len(b))*self.options["regularization"]**2
coefficients = np.linalg.solve(a, b)
return np.array(coefficients, dtype=np.float64)
@@ -103,7 +103,7 @@ class QuasiTimeReversible(AbstractFitting):
b = time_reversible_matrix.T @ (target + past_target)
if self.options["regularization"] > 0.0:
- a += np.identity(len(b))*self.options["regularization"]
+ a += np.identity(len(b))*self.options["regularization"]**2
coefficients = np.linalg.solve(a, b)
if q == 1:
diff --git a/tests/test_descriptor_fitting.py b/tests/test_descriptor_fitting.py
index f0ae573..d0c78a0 100644
--- a/tests/test_descriptor_fitting.py
+++ b/tests/test_descriptor_fitting.py
@@ -129,3 +129,71 @@ def test_time_reversibility(datafile):
# check the time reversibility
assert np.linalg.norm(fitted_target - fitted_target_reverse, ord=np.inf) < SMALL
+
+@pytest.mark.parametrize("datafile", ["urea.json", "glucose.json"])
+@pytest.mark.parametrize("regularization", [0.001, 0.005, 0.01, 0.05, 0.1])
+def test_square_qtr_formulation(datafile, regularization):
+
+ # load test data from json file
+ data = utils.load_json(f"tests/{datafile}")
+ nelectrons = data["nelectrons"]
+ natoms = data["trajectory"].shape[1]
+ nbasis = data["overlaps"].shape[1]
+ nframes = data["trajectory"].shape[0]
+
+ # initialize an extrapolator
+ extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms,
+ nsteps=nframes, fitting="qtr", fitting_regularization=regularization)
+
+ # load data in the extrapolator
+ for (coords, coeff, overlap) in zip(data["trajectory"],
+ data["coefficients"], data["overlaps"]):
+ extrapolator.load_data(coords, coeff, overlap)
+
+ descriptors = extrapolator.descriptors.get(10)
+ target = descriptors[-1]
+
+ fitting_calculator = extrapolator.fitting_calculator
+ alt_fitting_calculator = utils.AlternativeQuasiTimeReversible()
+ alt_fitting_calculator.set_options(regularization=regularization)
+
+ # check if the two fittings give the same coefficients
+ for start in range(0, 8):
+ vectors = descriptors[start:-1]
+ fit_coefficients = fitting_calculator.fit(vectors, target)
+ alt_fit_coefficients = alt_fitting_calculator.fit(vectors, target)
+ assert np.linalg.norm(fit_coefficients - alt_fit_coefficients, ord=np.inf) < 1e-4
+
+@pytest.mark.parametrize("datafile", ["urea.json", "glucose.json"])
+@pytest.mark.parametrize("regularization", [0.001, 0.005, 0.01, 0.05, 0.1])
+def test_square_ls_formulation(datafile, regularization):
+
+ # load test data from json file
+ data = utils.load_json(f"tests/{datafile}")
+ nelectrons = data["nelectrons"]
+ natoms = data["trajectory"].shape[1]
+ nbasis = data["overlaps"].shape[1]
+ nframes = data["trajectory"].shape[0]
+
+ # initialize an extrapolator
+ extrapolator = gext.Extrapolator(nelectrons, nbasis, natoms,
+ nsteps=nframes, fitting="leastsquare", fitting_regularization=regularization)
+
+ # load data in the extrapolator
+ for (coords, coeff, overlap) in zip(data["trajectory"],
+ data["coefficients"], data["overlaps"]):
+ extrapolator.load_data(coords, coeff, overlap)
+
+ descriptors = extrapolator.descriptors.get(10)
+ target = descriptors[-1]
+
+ fitting_calculator = extrapolator.fitting_calculator
+ alt_fitting_calculator = utils.AlternativeLeastSquare()
+ alt_fitting_calculator.set_options(regularization=regularization)
+
+ # check if the two fittings give the same coefficients
+ for start in range(0, 8):
+ vectors = descriptors[start:-1]
+ fit_coefficients = fitting_calculator.fit(vectors, target)
+ alt_fit_coefficients = alt_fitting_calculator.fit(vectors, target)
+ assert np.linalg.norm(fit_coefficients - alt_fit_coefficients, ord=np.inf) < 1e-4
diff --git a/tests/utils.py b/tests/utils.py
index 80ba090..fdd0205 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -1,5 +1,11 @@
+import os
+import sys
import json
import numpy as np
+from typing import List
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+from gext.fitting import LeastSquare, QuasiTimeReversible
def load_json(path):
with open(path, "r") as json_file:
@@ -12,3 +18,52 @@ def load_json(path):
else:
data[key] = np.array(value)
return data
+
+class AlternativeLeastSquare(LeastSquare):
+
+ """Alternative least square minimization fitting."""
+
+ def fit(self, vectors: List[np.ndarray], target: np.ndarray):
+ """Given a set of vectors and a target return the fitting
+ coefficients."""
+ matrix = np.array(vectors).T
+ a = np.vstack((matrix, np.identity(len(vectors))*self.options["regularization"]))
+ b = np.concatenate((target, np.zeros(len(vectors))))
+ coefficients, _, _, _ = np.linalg.lstsq(a, b, rcond=-1)
+ return np.array(coefficients, dtype=np.float64)
+
+class AlternativeQuasiTimeReversible(QuasiTimeReversible):
+
+ """Quasi time reversible fitting scheme."""
+
+ def fit(self, vectors: List[np.ndarray], target: np.ndarray):
+ """Given a set of vectors and a target return the fitting
+ coefficients in a quasi time reversible scheme."""
+
+ past_target = vectors[0]
+ matrix = np.array(vectors[1:]).T
+
+ q = matrix.shape[1]
+ if q == 1:
+ time_reversible_matrix = matrix
+ elif q%2 == 0:
+ time_reversible_matrix = matrix[:, :q//2] + matrix[:, :q//2-1:-1]
+ else:
+ time_reversible_matrix = matrix[:, :q//2+1] + matrix[:, :q//2-1:-1]
+
+ a = np.vstack((time_reversible_matrix,
+ np.identity(time_reversible_matrix.shape[1])*self.options["regularization"]))
+ b = np.concatenate((target + past_target, np.zeros((time_reversible_matrix.shape[1]))))
+
+ coefficients, _, _, _ = np.linalg.lstsq(a, b, rcond=-1)
+
+
+ if q == 1:
+ full_coefficients = np.concatenate(([-1.0], coefficients))
+ elif q%2 == 0:
+ full_coefficients = np.concatenate(([-1.0], coefficients,
+ coefficients[::-1]))
+ else:
+ full_coefficients = np.concatenate(([-1.0], coefficients[:-1],
+ 2.0*coefficients[-1:], coefficients[-2::-1]))
+ return np.array(full_coefficients, dtype=np.float64)
--
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