I am attempting to use collect_list to collect arrays (and maintain order) from two different data frames.
Test_Data and Train_Data have the same format.
from pyspark.sql import functions as F
from pyspark.sql import Window
w = Window.partitionBy('Group').orderBy('date')
# Train_Data has 4 data points
# Test_Data has 7 data points
# desired target array: [1, 1, 2, 3]
# desired MarchMadInd array: [0, 0, 0, 1, 0, 0, 1]
sorted_list_diff_array_lens = train_data.withColumn('target',
F.collect_list('target').over(w)
)\
test_data.withColumn('MarchMadInd', F.collect_list('MarchMadInd').over(w))\
.groupBy('Group')\
.agg(F.max('target').alias('target'),
F.max('MarchMadInd').alias('MarchMadInd')
)
I realize the syntax is incorrect with "test_data.withColumn", but I want to select the array for the MarchMadInd from the test_date, but the array for the target from the train_data. The desired output would look like the following:
{"target":[1, 1, 2, 3], "MarchMadInd":[0, 0, 0, 1, 0, 0, 1]}
Context: this is for a DeepAR time series model (using AWS) that requires dynamic features to include the prediction period, but the target should be historical data.
The solution involves using a join as recommended by pault.
Create a dataframe with dynamic features of length equal to Training + Prediction period
Create a dataframe with target values of length equal to just the Training period.
Use a LEFT JOIN (with the dynamic feature data on LEFT) to bring these dataframes together
Now, using collect_list will create the desired result.
Related
Decision Tree supports multi label classification right? my y labels are of type [['brufen','amoxil'],['brufen'],['xanex']]. Now y labels can be of the type list of list of labels as mentioned in the sklearn documentation, so why does it gives me error of unknown label type?
This error is resolved in a way that the length of list should be consistent, but how else should I handle this problem apart from one hot encoding it?
You need to convert the labels to label-indicator format first. Then you can use them with decision trees.
For converting, you can use MultiLabelBinarizer.
from sklearn.preprocessing import MultiLabelBinarizer
mlb = MultiLabelBinarizer()
y_converted = mlb.fit_transform([['brufen','amoxil'], ['brufen'], ['xanex']])
# Output: array([[1, 1, 0],
# [0, 1, 0],
# [0, 0, 1]])
mlb.classes_
# OutPut: array(['amoxil', 'brufen', 'xanex'], dtype=object)
Now use this y_converted instead of original y in decision tree.
Based on the information here: https://scikit-learn.org/stable/modules/multiclass.html#multioutputclassifier
You can use sklearn.multioutput.MultiOutputClassifier with a decision tree to get multi-label behavior. If I understand correctly, it works by internally creating a separate tree for each label.
In order to split my data into train and test data separately, I'm using
sklearn.cross_validation.train_test_split function.
When I supply my data and labels as list of lists to this function, it returns train and test data in two separate lists.
I want to get the indices of the train and test data elements from the original data list.
Can anyone help me out with this?
Thanks in advance
You can supply the index vector as an additional argument. Using the example from sklearn:
import numpy as np
from sklearn.cross_validation import train_test_split
X, y,indices = (0.1*np.arange(10)).reshape((5, 2)),range(10,15),range(5)
X_train, X_test, y_train, y_test,indices_train,indices_test = train_test_split(X, y,indices, test_size=0.33, random_state=42)
indices_train,indices_test
#([2, 0, 3], [1, 4])
Try the below solutions (depending on whether you have imbalance):
NUM_ROWS = train.shape[0]
TEST_SIZE = 0.3
indices = np.arange(NUM_ROWS)
# usual train-val split
train_idx, val_idx = train_test_split(indices, test_size=TEST_SIZE, train_size=None)
# stratified train-val split as per Response's proportion (if imbalance)
strat_train_idx, strat_val_idx = train_test_split(indices, test_size=TEST_SIZE, stratify=y)
Say that I have the dataset like this
1, 3, 2015-03-25 11-15-13
1, 4, 2015-03-26 11-16-14
1, 4, 2015-03-25 11-16-15
1, 5, 2015-03-27 11-17-11
...
I want to store the data by datetime
so I will have the following output folders
2015-03-25/
2015-03-26/
2015-03-27/
...
How to do that with pig?
Thank you
You can use MultiStorage for this.
Use a FOREACH GENERATE to create a column that contains the date part that you are interested and then something like
STORE X INTO '/my/home/output' USING MultiStorage('/my/home/output','2');
scikit-learn provides various methods to remove descriptors, a basic method for this purpose has been provided by the given tutorial below,
http://scikit-learn.org/stable/modules/feature_selection.html
but the tutorial does not provide any method or a way that can tell you the way to keep the list of features that either removed or kept.
The code below has been taken from the tutorial.
from sklearn.feature_selection import VarianceThreshold
X = [[0, 0, 1], [0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 1, 0], [0, 1, 1]]
sel = VarianceThreshold(threshold=(.8 * (1 - .8)))
sel.fit_transform(X)
array([[0, 1],
[1, 0],
[0, 0],
[1, 1],
[1, 0],
[1, 1]])
The given example code above depicts only two descriptors "shape(6, 2)", but in my case, I have a huge data frames with a shape of (rows 51, columns 9000). After finding a suitable model I want to keep the track of useful and useless features because I can save computational time during the computation of the features of test data set by calculating only useful features.
For example, when you perform machine learning modeling with WEKA 6.0, it provided with remarkable flexibility over feature selection and after removing the useless feature you can get a list of a discarded features along with the useful features.
thanks
Then, what you can do, if I'm not wrong is:
In the case of the VarianceThreshold, you can call the method fit instead of fit_transform. This will fit data, and the resulting variances will be stored in vt.variances_ (assuming vt is your object).
Having a threhold, you can extract the features of the transformation as fit_transform would do:
X[:, vt.variances_ > threshold]
Or get the indexes as:
idx = np.where(vt.variances_ > threshold)[0]
Or as a mask
mask = vt.variances_ > threshold
PS: default threshold is 0
EDIT:
A more straight forward to do, is by using the method get_support of the class VarianceThreshold. From the documentation:
get_support([indices]) Get a mask, or integer index, of the features selected
You should call this method after fit or fit_transform.
import numpy as np
import pandas as pd
from sklearn.feature_selection import VarianceThreshold
# Just make a convenience function; this one wraps the VarianceThreshold
# transformer but you can pass it a pandas dataframe and get one in return
def get_low_variance_columns(dframe=None, columns=None,
skip_columns=None, thresh=0.0,
autoremove=False):
"""
Wrapper for sklearn VarianceThreshold for use on pandas dataframes.
"""
print("Finding low-variance features.")
try:
# get list of all the original df columns
all_columns = dframe.columns
# remove `skip_columns`
remaining_columns = all_columns.drop(skip_columns)
# get length of new index
max_index = len(remaining_columns) - 1
# get indices for `skip_columns`
skipped_idx = [all_columns.get_loc(column)
for column
in skip_columns]
# adjust insert location by the number of columns removed
# (for non-zero insertion locations) to keep relative
# locations intact
for idx, item in enumerate(skipped_idx):
if item > max_index:
diff = item - max_index
skipped_idx[idx] -= diff
if item == max_index:
diff = item - len(skip_columns)
skipped_idx[idx] -= diff
if idx == 0:
skipped_idx[idx] = item
# get values of `skip_columns`
skipped_values = dframe.iloc[:, skipped_idx].values
# get dataframe values
X = dframe.loc[:, remaining_columns].values
# instantiate VarianceThreshold object
vt = VarianceThreshold(threshold=thresh)
# fit vt to data
vt.fit(X)
# get the indices of the features that are being kept
feature_indices = vt.get_support(indices=True)
# remove low-variance columns from index
feature_names = [remaining_columns[idx]
for idx, _
in enumerate(remaining_columns)
if idx
in feature_indices]
# get the columns to be removed
removed_features = list(np.setdiff1d(remaining_columns,
feature_names))
print("Found {0} low-variance columns."
.format(len(removed_features)))
# remove the columns
if autoremove:
print("Removing low-variance features.")
# remove the low-variance columns
X_removed = vt.transform(X)
print("Reassembling the dataframe (with low-variance "
"features removed).")
# re-assemble the dataframe
dframe = pd.DataFrame(data=X_removed,
columns=feature_names)
# add back the `skip_columns`
for idx, index in enumerate(skipped_idx):
dframe.insert(loc=index,
column=skip_columns[idx],
value=skipped_values[:, idx])
print("Succesfully removed low-variance columns.")
# do not remove columns
else:
print("No changes have been made to the dataframe.")
except Exception as e:
print(e)
print("Could not remove low-variance features. Something "
"went wrong.")
pass
return dframe, removed_features
this worked for me if you want to see exactly which columns are remained after thresholding you may use this method:
from sklearn.feature_selection import VarianceThreshold
threshold_n=0.95
sel = VarianceThreshold(threshold=(threshold_n* (1 - threshold_n) ))
sel_var=sel.fit_transform(data)
data[data.columns[sel.get_support(indices=True)]]
When testing features I wrote this simple function that tells me which variables remained in the data frame after the VarianceThreshold is applied.
from sklearn.feature_selection import VarianceThreshold
from itertools import compress
def fs_variance(df, threshold:float=0.1):
"""
Return a list of selected variables based on the threshold.
"""
# The list of columns in the data frame
features = list(df.columns)
# Initialize and fit the method
vt = VarianceThreshold(threshold = threshold)
_ = vt.fit(df)
# Get which column names which pass the threshold
feat_select = list(compress(features, vt.get_support()))
return feat_select
which returns a list of column names which are selected. For example: ['col_2','col_14', 'col_17'].
The following code generates a simple hierarchical cluster dendrogram with 10 leaf nodes:
import scipy
import scipy.cluster.hierarchy as sch
import matplotlib.pylab as plt
X = scipy.randn(10,2)
d = sch.distance.pdist(X)
Z= sch.linkage(d,method='complete')
P =sch.dendrogram(Z)
plt.show()
I generate three flat clusters like so:
T = sch.fcluster(Z, 3, 'maxclust')
# array([3, 1, 1, 2, 2, 2, 2, 2, 1, 2])
However, I'd like to see the cluster labels 1,2,3 on the dendrogram. It's easy for me to visualize with just 10 leaf nodes and three clusters, but when I have 1000 nodes and 10 clusters, I can't see what's going on.
How do I show the cluster numbers on the dendrogram? I'm open to other packages. Thanks.
Here is a solution that appropriately colors the clusters and labels the leaves of the dendrogram with the appropriate cluster name (leaves are labeled: 'point number, cluster number'). These techniques can be used independently or together. I modified your original example to include both:
import scipy
import scipy.cluster.hierarchy as sch
import matplotlib.pylab as plt
n=10
k=3
X = scipy.randn(n,2)
d = sch.distance.pdist(X)
Z= sch.linkage(d,method='complete')
T = sch.fcluster(Z, k, 'maxclust')
# calculate labels
labels=list('' for i in range(n))
for i in range(n):
labels[i]=str(i)+ ',' + str(T[i])
# calculate color threshold
ct=Z[-(k-1),2]
#plot
P =sch.dendrogram(Z,labels=labels,color_threshold=ct)
plt.show()