ValueError:在LinearSVC期间,数组在_assert_all_finite中包含NaN或无穷大

时间:2014-01-27 19:40:48

标签: python-2.7 pandas scikit-learn svc

我试图对此处的葡萄酒数据集进行分类 - http://archive.ics.uci.edu/ml/datasets/Wine+Quality 使用逻辑回归(使用method ='bfgs'和l1 norm)并捕获奇异值矩阵错误(提升LinAlgError('奇异矩阵'),尽管满级[我使用np.linalg.matrix_rank进行测试(数据[ train_cols] .values)]。

这就是我得出的结论,即某些功能可能是其他功能的线性组合。为此,我尝试使用网格搜索/ LinearSVC - 我得到下面的错误,以及我的代码&数据集。

我可以看到只有6/7个功能实际上是“独立的” - 我在比较x_train_new [0]和x_train的行时会解释(所以我可以得到哪些列是多余的)

    # Train & test DATA CREATION
    from sklearn.svm import LinearSVC
    import numpy, random
    import pandas as pd
    df = pd.read_csv("https://github.com/ekta1007/Predicting_wine_quality/blob/master/wine_red_dataset.csv")
#,skiprows=0, sep=',')


    df=df.dropna(axis=1,how='any') # also tried how='all' - still get NaN errors as below
    header=list(df.columns.values) # or df.columns
    X = df[df.columns - [header[-1]]] # header[-1] = ['quality'] - this is to make the code genric enough
    Y = df[header[-1]] # df['quality']
    rows = random.sample(df.index, int(len(df)*0.7)) # indexing the rows that will be picked in the train set
    x_train, y_train = X.ix[rows],Y.ix[rows] # Fetching the data frame using indexes
    x_test,y_test  = X.drop(rows),Y.drop(rows)


# Training the classifier using C-Support Vector Classification.
clf = LinearSVC(C=0.01, penalty="l1", dual=False) #,tol=0.0001,fit_intercept=True, intercept_scaling=1)
clf.fit(x_train, y_train)
x_train_new = clf.fit_transform(x_train, y_train)
#print x_train_new #works
clf.predict(x_test) # does NOT work and gives NaN errors for some x_tests


clf.score(x_test, y_test) # Does NOT work
clf.coef_ # Works, but I am not sure, if this is OK, given huge NaN's - or does the coef's get impacted ?

clf.predict(x_train)
552   NaN
209   NaN
427   NaN
288   NaN
175   NaN
427   NaN
748     7
552   NaN
429   NaN
[... and MORE]
Name: quality, Length: 1119

clf.predict(x_test)
76    NaN
287   NaN
420     7
812   NaN
443     7
420     7
430   NaN
373     5
624     5
[..and More]
Name: quality, Length: 480

奇怪的是,当我运行clf.predict(x_train)时,我仍然看到一些NaN - 我做错了什么?毕竟模型是用这个训练的,这不应该发生,对吧? /强>

根据这个帖子,我还检查了我的csv文件中没有空白(虽然我将“质量”重新标记为5和7标签(从范围(3,10)) How to fix "NaN or infinity" issue for sparse matrix in python?

此外 - 这是x_test&的数据类型y_test /火车...

x_test
<class 'pandas.core.frame.DataFrame'>
Int64Index: 480 entries, 1 to 1596
Data columns:
alcohol                 480  non-null values
chlorides               480  non-null values
citric acid             480  non-null values
density                 480  non-null values
fixed acidity           480  non-null values
free sulfur dioxide     480  non-null values
pH                      480  non-null values
residual sugar          480  non-null values
sulphates               480  non-null values
total sulfur dioxide    480  non-null values
volatile acidity        480  non-null values
dtypes: float64(11)

y_test
1     5
10    5
18    5
21    5
30    5
31    7
36    7
40    5
50    5
52    7
53    5
55    5
57    5
60    5
61    5
[..And MORE]
Name: quality, Length: 480

最后..

clf.score(x_test, y_test)

Traceback (most recent call last):
  File "<pyshell#31>", line 1, in <module>
    clf.score(x_test, y_test)
  File "C:\Python27\lib\site-packages\sklearn\base.py", line 279, in score
    return accuracy_score(y, self.predict(X))
  File "C:\Python27\lib\site-packages\sklearn\metrics\metrics.py", line 742, in accuracy_score
    y_true, y_pred = check_arrays(y_true, y_pred)
  File "C:\Python27\Lib\site-packages\sklearn\utils\validation.py", line 215, in check_arrays
  File "C:\Python27\Lib\site-packages\sklearn\utils\validation.py", line 18, in _assert_all_finite
ValueError: Array contains NaN or infinity.


#I also explicitly checked for NaN's as here -:
for i in df.columns:
    df[i].isnull()

提示:还请提一下,根据我的使用案例,我对使用LinearSVC的思考过程是否正确,还是应该使用网格搜索?

免责声明:此代码的部分内容是基于StackOverflow和其他来源的类似上下文中的建议构建的 - 我的实际用例只是尝试访问此方法是否适合我的方案。就是这样。

1 个答案:

答案 0 :(得分:2)

这很有用。我必须真正改变的是使用x_test * .values *以及其余的pandas Dataframes(x_train,y_train,y_test)。正如所指出的,唯一的原因是pandas df和scikit-learn(使用numpy数组)之间的不兼容性

 #changing your Pandas Dataframe elegantly to work with scikit-learn by transformation to  numpy arrays
>>> type(x_test)
<class 'pandas.core.frame.DataFrame'>
>>> type(x_test.values)
<type 'numpy.ndarray'>

这个黑客来自这篇帖子http://python.dzone.com/articles/python-making-scikit-learn-and和@AndreasMueller--他指出了这种不一致。