scikit-learn / scikit-learn/scikit-learn

PCA, LDA, unexpected explained_variance_ratio

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Bug help wanted module:decomposition
Dominant language
Python
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Description

from sklearn import datasets
from sklearn.decomposition import PCA
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis

iris = datasets.load_iris()

X = iris.data
y = iris.target
target_names = iris.target_names

#### dimensionality reduction using PCA
pca = PCA(n_components=2)
X_r = pca.fit(X).transform(X)

#### Percentage of variance explained for each components
print('PCA: explained variance ratio (first two components): %s'
      % str(pca.explained_variance_ratio_))

#### dimensionality reduction using LDA
lda = LinearDiscriminantAnalysis(n_components=2)
X_r2 = lda.fit(X, y).transform(X)

print('LDA: explained variance ratio (first two components): %s'
      % str(lda.explained_variance_ratio_))
Expected Results

The first componet of the PCA has a larger variance ratio than that from the first componet from LDA.

Actual Results

PCA: explained variance ratio (first two components): [ 0.925 0.053]
LDA: explained variance ratio (first two components): [ 0.991 0.009]

Versions

Darwin-14.5.0-x86_64-i386-64bit
Python 3.5.3 |Anaconda custom (x86_64)| (default, Mar 6 2017, 12:15:08)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]
NumPy 1.12.1
SciPy 0.19.1
Scikit-Learn 0.18.2

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the reproducible iris example and the PCA and LinearDiscriminantAnalysis entry points shown in the issue. Compare the documented meaning of each explained_variance_ratio_ against the reported values, then determine whether the behavior is expected or indicates a defect. Done means a verified explanation and, if needed, a focused correction with regression coverage.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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