Changed linear fit to lasso regression (#93)

This was done to help fitting of underdetermined cases, such as when the chemical composition never or rarely changes (md snapshots etc).
Also a slight restructure was done to avoid repeated code.

Author: larsbratholm

qml/qmlearn/preprocessing.py

@@ -26,7 +26,7 @@
 
 import numpy as np
 from sklearn.base import BaseEstimator
-from sklearn.linear_model import LinearRegression
+from sklearn.linear_model import Lasso
 
 from .data import Data
 from ..utils import is_numeric_array, get_unique, is_positive_integer_or_zero_array
@@ -50,7 +50,7 @@ def __init__(self, data=None, elements='auto'):
         self.elements = elements
 
         # Initialize model
-        self.model = LinearRegression()
+        self.model = Lasso(alpha=1e-9)
 
     def _preprocess_input(self, X):
         """
@@ -117,15 +117,25 @@ def _check_data(self, X):
             print("Error: Expected Data object to have non-empty attribute 'energies'" % self.__class__.__name__)
             raise SystemExit
 
-
     def _set_data(self, data):
         if data:
             self._check_data(data)
         self.data = data
 
-    def fit_transform(self, X, y=None):
+    def _parse_input(self, X, y):
+        if not isinstance(X, Data) and y is not None:
+            data = None
+            nuclear_charges = X
+        else:
+            data = self._preprocess_input(X)
+            nuclear_charges = data.nuclear_charges[data._indices]
+            y = data.energies[data._indices]
+
+        return data, nuclear_charges, y
+
+    def fit(self, X, y=None):
         """
-        Fit and transform the data with a linear model.
+        Fit the data with a linear model.
         Supports three different types of input.
         1) X is a list of nuclear charges and y is values to transform.
         2) X is an array of indices of which to transform.
@@ -135,27 +145,58 @@ def fit_transform(self, X, y=None):
         :type X: list
         :param y: Values to transform
         :type y: array or None
-        :return: Array of transformed values or Data object, depending on input
-        :rtype: array or Data object
         """
 
-        if not isinstance(X, Data) and y is not None:
-            data = None
-            nuclear_charges = X
-        else:
-            data = self._preprocess_input(X)
-            nuclear_charges = data.nuclear_charges[data._indices]
-            y = data.energies[data._indices]
+        self._fit(X, y)
+
+        return self
+
+    def _fit(self, X, y=None):
+        """
+        Does the work of the fit method, but returns variables
+        that the fit_transform method can reuse.
+        """
+
+        data, nuclear_charges, y = self._parse_input(X, y)
 
         if self.elements == 'auto':
             self.elements = get_unique(nuclear_charges)
         else:
             self._check_elements(nuclear_charges)
 
-
         features = self._featurizer(nuclear_charges)
 
-        delta_y = y - self.model.fit(features, y).predict(features)
+        self.model.fit(features, y)
+
+        return data, features, y
+
+    def fit_transform(self, X, y=None):
+        """
+        Fit and transform the data with a linear model.
+        Supports three different types of input.
+        1) X is a list of nuclear charges and y is values to transform.
+        2) X is an array of indices of which to transform.
+        3) X is a data object
+
+        :param X: List with nuclear charges or Data object.
+        :type X: list
+        :param y: Values to transform
+        :type y: array or None
+        :return: Array of transformed values or Data object, depending on input
+        :rtype: array or Data object
+        """
+
+        data, features, y = self._fit(X, y)
+
+        return self._transform(data, features, y)
+
+    def _transform(self, data, features, y):
+        """
+        Does the work of the transform method, but can be reused by
+        the fit_transform method.
+        """
+
+        delta_y = y - self.model.predict(features)
 
         if data:
             # Force copy
@@ -213,25 +254,10 @@ def transform(self, X, y=None):
         :rtype: array or Data object
         """
 
-        if not isinstance(X, Data) and y is not None:
-            data = None
-            nuclear_charges = X
-        else:
-            data = self._preprocess_input(X)
-            nuclear_charges = data.nuclear_charges[data._indices]
-            y = data.energies[data._indices]
+        data, nuclear_charges, y = self._parse_input(X, y)
 
         self._check_elements(nuclear_charges)
 
         features = self._featurizer(nuclear_charges)
 
-        delta_y = y - self.model.predict(features)
-
-        if data:
-            # Force copy
-            data.energies = data.energies.copy()
-            data.energies[data._indices] = delta_y
-            return data
-        else:
-            return delta_y
-
+        return self._transform(data, features, y)