From 06c0c76f8f4e1fafa31ea16c610c3a36b20e294f Mon Sep 17 00:00:00 2001
From: Johan Larsson <johanlarsson@outlook.com>
Date: Wed, 2 Nov 2022 16:44:08 +0100
Subject: [PATCH] feat: add standardization as parameter for dataset

---
 datasets/breheny.py   |  7 +++++--
 datasets/libsvm.py    |  7 +++++--
 datasets/simulated.py | 13 +++++++++++--
 3 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/datasets/breheny.py b/datasets/breheny.py
index 8bacbd6..21a8110 100644
--- a/datasets/breheny.py
+++ b/datasets/breheny.py
@@ -44,17 +44,20 @@ class Dataset(BaseDataset):
 
     parameters = {
         "dataset": ["Scheetz2006", "Rhee2006", "bcTCGA"],
+        "standardize" : [True, False]
     }
 
     install_cmd = "conda"
     requirements = ["rpy2", "numpy", "scipy", "appdirs", "r"]
 
-    def __init__(self, dataset="bcTCGA"):
+    def __init__(self, dataset="bcTCGA", standardize=True):
         self.dataset = dataset
         self.X, self.y = None, None
+        self.standardize = standardize
 
     def get_data(self):
         X, y = fetch_breheny(self.dataset)
-        X, y = preprocess_data(X, y)
+        if self.standardize:
+            X, y = preprocess_data(X, y)
 
         return dict(X=X, y=y)
diff --git a/datasets/libsvm.py b/datasets/libsvm.py
index 578dc52..f71b372 100644
--- a/datasets/libsvm.py
+++ b/datasets/libsvm.py
@@ -12,17 +12,20 @@ class Dataset(BaseDataset):
 
     parameters = {
         "dataset": ["finance", "finance-tf-idf", "YearPredictionMSD"],
+        "standardize" : [True, False]
     }
 
     install_cmd = "conda"
     requirements = ["pip:libsvmdata"]
 
-    def __init__(self, dataset="bodyfat"):
+    def __init__(self, dataset="bodyfat", standardize=True):
         self.dataset = dataset
         self.X, self.y = None, None
+        self.standardize = standardize
 
     def get_data(self):
         X, y = fetch_libsvm(self.dataset)
-        X, y = preprocess_data(X, y)
+        if self.standardize:
+            X, y = preprocess_data(X, y)
 
         return dict(X=X, y=y)
diff --git a/datasets/simulated.py b/datasets/simulated.py
index f2eba28..da9921d 100644
--- a/datasets/simulated.py
+++ b/datasets/simulated.py
@@ -15,16 +15,24 @@ class Dataset(BaseDataset):
             (200, 10_000, 20),
         ],
         "rho": [0, 0.5],
+        "standardize": [True, False],
     }
 
     def __init__(
-        self, n_samples=10, n_features=50, n_signals=5, rho=0, random_state=27
+        self,
+        n_samples=10,
+        n_features=50,
+        n_signals=5,
+        rho=0,
+        random_state=27,
+        standardize=True,
     ):
         self.n_samples = n_samples
         self.n_features = n_features
         self.n_signals = n_signals
         self.random_state = random_state
         self.rho = rho
+        self.standardize = standardize
 
     def get_data(self):
         X, y, _ = make_correlated_data(
@@ -35,6 +43,7 @@ def get_data(self):
             random_state=self.random_state,
         )
 
-        X, y = preprocess_data(X, y)
+        if self.standardize:
+            X, y = preprocess_data(X, y)
 
         return dict(X=X, y=y)