I am having an issue training my Naive Bayes Classifier. I have a feature set and targets that I want to use but I keep getting errors. I've had a look at other people who have similar problems but I can't seem to figure out the issue. I'm sure there's a simple solution but I'm yet to find it.
Here's an example of the structure of the data that I'm trying to use to train the classifier.
In [1] >> train[0]
Out[1] ({
u'profici': [False],
u'saver': [False],
u'four': [True],
u'protest': [False],
u'asian': [True],
u'upsid': [False],
.
.
.
u'captain': [False],
u'payoff': [False],
u'whose': [False]
},
0)
Where train[0] is the first tuple in a list and contains:
A dictionary of features and boolean values to indicate the presence or absence of words in document[0]
The target label for the binary classification of document[0]
Obviously, the rest of the train list has the features and labels for the other documents that I want to classify.
When running the following code
from nltk.classify.scikitlearn import SklearnClassifier
from sklearn.naive_bayes import MultinomialNB
MNB_clf = SklearnClassifier(MultinomialNB())
MNB_clf.train(train)
I get the error message:
TypeError: float() argument must be a string or a number
Edit:
features are created here. From a dataframe post_sent that contains the posts in column 1 and the sentiment classification in column 2.
stopwords = set(stopwords.words('english'))
tokenized = []
filtered_posts = []
punc_tokenizer = RegexpTokenizer(r'\w+')
# tokenizing and removing stopwords
for post in post_sent.post:
tokenized = [word.lower() for word in.
punc_tokenizer.tokenize(post)]
filtered = ([w for w in tokenized if not w in stopwords])
filtered_posts.append(filtered)
# stemming
tokened_stemmed = []
for post in filtered_posts:
stemmed = []
for w in post:
stemmed.append(PorterStemmer().stem_word(w))
tokened_stemmed.append(stemmed)
#frequency dist
all_words =.
list(itertools.chain.from_iterable(tokened_stemmed))
frequency = FreqDist(all_words)
# Feature selection
word_features = list(frequency.keys())[:3000]
# IMPORTANT PART
#######################
#------ featuresets creation ---------
def find_features(list_of_posts):
features = {}
wrds = set(post)
for w in word_features:
features[w] = [w in wrds]
return features
# zipping inputs with targets
words_and_sent = zip(tokened_stemmed,
post_sent.sentiment)
# IMPORTANT PART
##########################
# feature sets created here
featuresets = [(find_features(words), sentiment) for
words, sentiment in
words_and_sent]
Thanks to help from both Vivek & Lenz, who explained to me the problem, I was able to reorganise my training set and thankfully it now works. Thanks guys!
The problem was very well explained in Vivek's post. This is the code that reorganised the train data into the correct format.
features_targ = []
for feature in range(0,len(featuresets)):
dict_test = featuresets[feature]
values = list(itertools.chain.from_iterable(dict_test[0].values()))
keys = dict_test[0].keys()
target = dict_test[1]
dict_ion = {}
for key in range(x,len(keys)):
dict_ion[keys[key]] = values[key]
features_targ.append((dict_ion,target))
You are setting the train wrong. As #lenz said in comment, remove the parentheses in the feature dict values and only use single values.
As given in the official documentation:
labeled_featuresets – A list of (featureset, label) where each
featureset is a dict mapping strings to either numbers, booleans or
strings.
But you are setting the mapping (value of key in dict) as a list.
You correct train should look like :
[({u'profici':False,
u'saver':False,
u'four':True,
u'protest':False,
u'asian':True,
u'upsid':False,
.
.
}, 0),
..
..
({u'profici':True,
u'saver':False,
u'four':False,
u'protest':False,
u'asian':True,
u'upsid':False,
.
.
}, 1)]
You can take a look at more examples here:
- http://www.nltk.org/howto/classify.html
Related
I'm trying to run a simple XGBoost Prediction based on Google Cloud using this simple example https://cloud.google.com/ml-engine/docs/scikit/getting-predictions-xgboost#get_online_predictions
The model is building fine, but when I try to run a prediction with a sample input JSON it fails with error "Could not initialize DMatrix from inputs: could not convert string to float:" as shown in the screen below. I understand this is happening because the test-input has strings, I was hoping the Google machine learning model should have information to convert the categorical values to floats. I cannot expect my user to submit-online-prediction-request with float values.
Based on the tutorial it should work without converting the categorical values to floats. Please advise, I have attached the GIF with more details. Thanks
import json
import numpy as np
import os
import pandas as pd
import pickle
import xgboost as xgb
from sklearn.preprocessing import LabelEncoder
# these are the column labels from the census data files
COLUMNS = (
'age',
'workclass',
'fnlwgt',
'education',
'education-num',
'marital-status',
'occupation',
'relationship',
'race',
'sex',
'capital-gain',
'capital-loss',
'hours-per-week',
'native-country',
'income-level'
)
# categorical columns contain data that need to be turned into numerical
# values before being used by XGBoost
CATEGORICAL_COLUMNS = (
'workclass',
'education',
'marital-status',
'occupation',
'relationship',
'race',
'sex',
'native-country'
)
# load training set
with open('./census_data/adult.data', 'r') as train_data:
raw_training_data = pd.read_csv(train_data, header=None, names=COLUMNS)
# remove column we are trying to predict ('income-level') from features list
train_features = raw_training_data.drop('income-level', axis=1)
# create training labels list
train_labels = (raw_training_data['income-level'] == ' >50K')
# load test set
with open('./census_data/adult.test', 'r') as test_data:
raw_testing_data = pd.read_csv(test_data, names=COLUMNS, skiprows=1)
# remove column we are trying to predict ('income-level') from features list
test_features = raw_testing_data.drop('income-level', axis=1)
# create training labels list
test_labels = (raw_testing_data['income-level'] == ' >50K.')
# convert data in categorical columns to numerical values
encoders = {col:LabelEncoder() for col in CATEGORICAL_COLUMNS}
for col in CATEGORICAL_COLUMNS:
train_features[col] = encoders[col].fit_transform(train_features[col])
for col in CATEGORICAL_COLUMNS:
test_features[col] = encoders[col].fit_transform(test_features[col])
# load data into DMatrix object
dtrain = xgb.DMatrix(train_features, train_labels)
dtest = xgb.DMatrix(test_features)
# train XGBoost model
bst = xgb.train({}, dtrain, 20)
bst.save_model('./model.bst')
Here is a fix. Put the input shown in the Google documentation in a file input.json, then run this. The output is input_numerical.json and prediction will succeed if you use that in place of input.json.
This code is just preprocessing categorical columns to numerical forms using the same procedure as was done with training and test data.
import json
import pandas as pd
from sklearn.preprocessing import LabelEncoder
COLUMNS = (
"age",
"workclass",
"fnlwgt",
"education",
"education-num",
"marital-status",
"occupation",
"relationship",
"race",
"sex",
"capital-gain",
"capital-loss",
"hours-per-week",
"native-country",
"income-level",
)
# categorical columns contain data that need to be turned into numerical
# values before being used by XGBoost
CATEGORICAL_COLUMNS = (
"workclass",
"education",
"marital-status",
"occupation",
"relationship",
"race",
"sex",
"native-country",
)
with open("./input.json", "r") as json_lines:
rows = [json.loads(line) for line in json_lines]
prediction_features = pd.DataFrame(rows, columns=(COLUMNS[:-1]))
encoders = {col: LabelEncoder() for col in CATEGORICAL_COLUMNS}
for col in CATEGORICAL_COLUMNS:
prediction_features[col] = encoders[col].fit_transform(prediction_features[col])
with open("input_numerical.json", "w") as input_numerical:
for index, row in prediction_features.iterrows():
input_numerical.write(row.to_json(orient="values") + "\n")
I created this Google Issues Tracker ticket as the Google documentation is missing this important step.
You can use pandas to convert categorical strings into codes for model inputs. For prediction input you can define a dictionary for each category with corresponding category values and codes. For example, for workclass:
df['workclass_cat'] = df['workclass'].astype('category')
df['workclass_cat'] = df['workclass_cat'].cat.codes
workclass_dict = dict(zip(list(df['workclass'].values), list(df['workclass_cat'].values)))
If a prediction input is 'somestring' you can access its code as follows:
category_input = workclass_dict['somestring']
XGBoost models take floats as input. In your training script you converted the categorical variables into numbers. The same transformation needs to be done when submitting a prediction.
I'm getting the following warning repeatedly when using GridsearchCV in Sklearn
"DataConversionWarning: Copying input dataframe for slicing."
I tried running some of the models separately outside of Gridsearch and didn't get any warnings. It also didn't prevent Gridsearch from finding a model.
I have 2 Questions:
1) What does this error mean?
2) What are the implications for my output, if any?
The relevant parts of the code are below:
df = pd.read_csv(os.path.join(filepath, "Modeling_Set.csv")) #loads main data
keep_vars = pd.read_csv(os.path.join(filepath, "keep_vars.csv")) #loads a list of variables to keep from a CSV list
model_vars = keep_vars[keep_vars['keep']==1]['name'] #creates a list of vars to keep
modeling_df = df[model_vars] #creates the df with only keep vars
model_feature_vars = model_vars[:-1]
#Splits test and train data
X_train, X_test, y_train, y_test = train_test_split(modeling_df[model_feature_vars], modeling_df['Segment'], test_size=0.30, random_state=42)
#sets up models
#Range of parameters for gridsearch with decision trees
max_depth = range(2,20,2)
min_samples_split = range(2,10,2)
features = range(2, len(X_train.columns))
#set up for decision trees with gridsearch
parametersDT ={'feature_selection__k':features,
'feature_selection__score_func':(chi2, f_classif),
'classification__criterion':('gini','entropy'),
'classification__max_depth':max_depth,
'classification__min_samples_split':min_samples_split}
DT_with_K_Best = Pipeline([
('feature_selection', SelectKBest()),
('classification', DecisionTreeClassifier())
])
clf_DT = GridSearchCV(DT_with_K_Best, parametersDT, cv=10, verbose=2, scoring='f1_weighted', n_jobs = -2)
clf_DT.fit(X_train,y_train)
As far as I can tell it only means that the DataFrame you're using is copied before being fed to the model.
This shouldn't affect the training results. It's only an efficiency problem, unrelated to the performance of the classifier.
When i use * i receive the error
raise error, v # invalid expression
error: nothing to repeat
other wildcard characters such as ^ work fine.
the line of code:
df.columns = df.columns.str.replace('*agriculture', 'agri')
am using pandas and python
edit:
when I try using / to escape, the wildcard does not work as i intend
In[44]df = pd.DataFrame(columns=['agriculture', 'dfad agriculture df'])
In[45]df
Out[45]:
Empty DataFrame
Columns: [agriculture, dfad agriculture df]
Index: []
in[46]df.columns.str.replace('/*agriculture*','agri')
Out[46]: Index([u'agri', u'dfad agri df'], dtype='object')
I thought the wildcard should output Index([u'agri', u'agri'], dtype='object)
edit:
I am currently using hierarchical columns and would like to only replace agri for that specific level (level = 2).
original:
df.columns[0] = ('grand total', '2005', 'agriculture')
df.columns[1] = ('grand total', '2005', 'other')
desired:
df.columns[0] = ('grand total', '2005', 'agri')
df.columns[1] = ('grand total', '2005', 'other')
I'm looking at this link right now: Changing columns names in Pandas with hierarchical columns
and that author says it will get easier at 0.15.0 so I am hoping there are more recent updated solutions
You need to the asterisk * at the end in order to match the string 0 or more times, see the docs:
In [287]:
df = pd.DataFrame(columns=['agriculture'])
df
Out[287]:
Empty DataFrame
Columns: [agriculture]
Index: []
In [289]:
df.columns.str.replace('agriculture*', 'agri')
Out[289]:
Index(['agri'], dtype='object')
EDIT
Based on your new and actual requirements, you can use str.contains to find matches and then use this to build a dict to map the old against new names and then call rename:
In [307]:
matching_cols = df.columns[df.columns.str.contains('agriculture')]
df.rename(columns = dict(zip(matching_cols, ['agri'] * len(matching_cols))))
Out[307]:
Empty DataFrame
Columns: [agri, agri]
Index: []
I am trying to do onevsrest classification like below:
classifier = Pipeline([('vectorizer', CountVectorizer()),('tfidf', TfidfTransformer()),('clf', OneVsRestClassifier(SVC(kernel='rbf')))])
classifier.fit(X_train, Y)
predicted = classifier.predict(X_test)
And I get the error 'predict_proba is not available when probability = false'. I saw that there was a bug reported, the one below:
https://github.com/scikit-learn/scikit-learn/issues/1946
And it was closed as fixed, so I killed scikit-learn from my Windows PC and completely re-downloaded scikit-learn to have version 0.15.2. But I still get this error. Any suggestions? Or I understood this wrong, and I still can't use SVC with OneVSRestClassifier unless I specify probability=true?
UPDATE: just to clarify, I am trying to actually achieve multi-label classification, here is data source:
df = pd.read_csv(fileIn, header = 0, encoding='utf-8-sig')
rows = random.sample(df.index, int(len(df) * 0.9))
work = df.ix[rows]
work_test = df.drop(rows)
X_train = []
y_train = []
X_test = []
y_test = []
for i in work[[i for i in list(work.columns.values) if i.startswith('Change')]].values:
X_train.append(','.join(i.T.tolist()))
X_train = np.array(X_train)
for i in work[[i for i in list(work.columns.values) if i.startswith('Corax')]].values:
y_train.append(list(i))
for i in work_test[[i for i in list(work_test.columns.values) if i.startswith('Change')]].values:
X_test.append(','.join(i.T.tolist()))
X_test = np.array(X_test)
for i in work_test[[i for i in list(work_test.columns.values) if i.startswith('Corax')]].values:
y_test.append(list(i))
lb = preprocessing.MultiLabelBinarizer()
Y = lb.fit_transform(y_train)
And after that I send it to pipeline mentioned earlier
Ok, I did some investigation in code. OneVsRestClassifier tries to call decision_function first and if it fails - it goes for predict_proba function of base classifier (svm.svc in our case).
As far as I see, my X_test is numpy.array of lists of strings. After it undergoes a sequence of transformations specified in pipeline CountVectorizer -> TfidfTransformer it becomes a sparse matrix (by design of these things). As I see currently decision_function is not available for sparse matrices, and there is even an open suggestion on github: https://github.com/scikit-learn/scikit-learn/issues/73
So, to summarize, looks like you can't make a multilabel classification using svm.svc unless you specify probability=True. If you do this you introduce some overhead to the classifier.fit process but it will work.
I am trying to use networkx to create a DiGraph. I want to use add_edges_from(), and I want the edges and their data to be generated from three tuples.
I am importing the data from a CSV file. I have three columns: one for ids (first set of nodes), one for a set of names (second set of nodes), and another for capacities (no headers in the file). So, I created a dictionary for the ids and capacities.
dictionary = dict(zip(id, capacity))
then I zipped the tuples containing the edges data:
List = zip(id, name, capacity)
but when I execute the next line, it gives me an assertion error.
G.add_edges_from(List, 'weight': 1)
Can someone help me with this problem? I have been trying for a week with no luck.
P.S. I'm a newbie in programming.
EDIT:
so, i found the following solution. I am honestly not sure how it works, but it did the job!
Here is the code:
import networkx as nx
import csv
G = nx.DiGraph()
capacity_dict = dict(zip(zip(id, name),capacity))
List = zip(id, name, capacity)
G.add_edges_from(capacity_dict, weight=1)
for u,v,d in List:
G[u][v]['capacity']=d
Now when I run:
G.edges(data=True)
The result will be:
[(2.0, 'First', {'capacity': 1.0, 'weight': 1}), (3.0, 'Second', {'capacity': 2.0, 'weight': 1})]
I am using the network simplex. Now, I am trying to find a way to make the output of the flowDict more understandable, because it is only showing the ids of the flow. (Maybe i'll try to input them in a database and return the whole row of data instead of using the ids only).
A few improvements on your version. (1) NetworkX algorithms assume that weight is 1 unless you specifically set it differently. Hence there is no need to set it explicitly in your case. (2) Using the generator allows the capacity attribute to be set explicitly and other attributes to also be set once per record. (3) The use of a generator to process each record as it comes through saves you having to iterate through the whole list twice. The performance improvement is probably negligible on small datasets but still it feels more elegant. Having said that -- your method clearly works!
import networkx as nx
import csv
# simulate a csv file.
# This makes a multi-line string behave as a file.
from StringIO import StringIO
filehandle = StringIO('''a,b,30
b,c,40
d,a,20
''')
# process each row in the file
# and generate an edge from each
def edge_generator(fh):
reader = csv.reader(fh)
for row in reader:
row[-1] = float(row[-1]) # convert capacity to float
# add other attributes to the dict() below as needed...
# e.g. you might add weights here as well.
yield (row[0],
row[1],
dict(capacity=row[2]))
# create the graph
G = nx.DiGraph()
G.add_edges_from(edge_generator(filehandle))
print G.edges(data=True)
Returns this:
[('a', 'b', {'capacity': 30.0}),
('b', 'c', {'capacity': 40.0}),
('d', 'a', {'capacity': 20.0})]