Yet Another Blog in Statistical Computing

I can calculate the motion of heavenly bodies but not the madness of people. -Isaac Newton

Archive for the ‘PYTHON’ Category

Autoencoder for Dimensionality Reduction

We often use ICA or PCA to extract features from the high-dimensional data. The autoencoder is another interesting algorithm to achieve the same purpose in the context of Deep Learning.

with the purpose of learning a function to approximate the input data itself such that F(X) = X, an autoencoder consists of two parts, namely encoder and decoder. While the encoder aims to compress the original input data into a low-dimensional representation, the decoder tries to reconstruct the original input data based on the low-dimension representation generated by the encoder. As a result, the autoencoder has been widely used to remove the data noise as well to reduce the data dimension.

First of all, we will show the basic structure of an autoencoder with 1-layer encoder and 1-layer decoder, as below. In the example, we will compress the input data with 10 columns into a compressed on with 3 columns.

from pandas import read_csv, DataFrame
from numpy.random import seed
from sklearn.preprocessing import minmax_scale
from sklearn.model_selection import train_test_split
from keras.layers import Input, Dense
from keras.models import Model

df = read_csv("credit_count.txt")
Y = df[df.CARDHLDR == 1].DEFAULTS
X = df[df.CARDHLDR == 1].ix[:, 2:12]
# SCALE EACH FEATURE INTO [0, 1] RANGE
sX = minmax_scale(X, axis = 0)
ncol = sX.shape[1]
X_train, X_test, Y_train, Y_test = train_test_split(sX, Y, train_size = 0.5, random_state = seed(2017))

### AN EXAMPLE OF SIMPLE AUTOENCODER ###
# InputLayer (None, 10)
#      Dense (None, 5)
#      Dense (None, 10)

input_dim = Input(shape = (ncol, ))
# DEFINE THE DIMENSION OF ENCODER ASSUMED 3
encoding_dim = 3
# DEFINE THE ENCODER LAYER
encoded = Dense(encoding_dim, activation = 'relu')(input_dim)
# DEFINE THE DECODER LAYER
decoded = Dense(ncol, activation = 'sigmoid')(encoded)
# COMBINE ENCODER AND DECODER INTO AN AUTOENCODER MODEL
autoencoder = Model(input = input_dim, output = decoded)
# CONFIGURE AND TRAIN THE AUTOENCODER
autoencoder.compile(optimizer = 'adadelta', loss = 'binary_crossentropy')
autoencoder.fit(X_train, X_train, nb_epoch = 50, batch_size = 100, shuffle = True, validation_data = (X_test, X_test))
# THE ENCODER TO EXTRACT THE REDUCED DIMENSION FROM THE ABOVE AUTOENCODER
encoder = Model(input = input_dim, output = encoded)
encoded_input = Input(shape = (encoding_dim, ))
encoded_out = encoder.predict(X_test)
encoded_out[0:2]
#array([[ 0.        ,  1.26510417,  1.62803197],
#       [ 2.32508397,  0.99735016,  2.06461048]], dtype=float32)

In the next example, we will relax the constraint of layers and employ a stack of layers to achievement the same purpose as above.

### AN EXAMPLE OF DEEP AUTOENCODER WITH MULTIPLE LAYERS
# InputLayer (None, 10)
#      Dense (None, 20)
#      Dense (None, 10)
#      Dense (None, 5)
#      Dense (None, 3)
#      Dense (None, 5)
#      Dense (None, 10)
#      Dense (None, 20)
#      Dense (None, 10)

input_dim = Input(shape = (ncol, ))
# DEFINE THE DIMENSION OF ENCODER ASSUMED 3
encoding_dim = 3
# DEFINE THE ENCODER LAYERS
encoded1 = Dense(20, activation = 'relu')(input_dim)
encoded2 = Dense(10, activation = 'relu')(encoded1)
encoded3 = Dense(5, activation = 'relu')(encoded2)
encoded4 = Dense(encoding_dim, activation = 'relu')(encoded3)
# DEFINE THE DECODER LAYERS
decoded1 = Dense(5, activation = 'relu')(encoded4)
decoded2 = Dense(10, activation = 'relu')(decoded1)
decoded3 = Dense(20, activation = 'relu')(decoded2)
decoded4 = Dense(ncol, activation = 'sigmoid')(decoded3)
# COMBINE ENCODER AND DECODER INTO AN AUTOENCODER MODEL
autoencoder = Model(input = input_dim, output = decoded4)
# CONFIGURE AND TRAIN THE AUTOENCODER
autoencoder.compile(optimizer = 'adadelta', loss = 'binary_crossentropy')
autoencoder.fit(X_train, X_train, nb_epoch = 100, batch_size = 100, shuffle = True, validation_data = (X_test, X_test))
# THE ENCODER TO EXTRACT THE REDUCED DIMENSION FROM THE ABOVE AUTOENCODER
encoder = Model(input = input_dim, output = encoded4)
encoded_input = Input(shape = (encoding_dim, ))
encoded_out = encoder.predict(X_test)
encoded_out[0:2]
#array([[ 3.74947715,  0.        ,  3.22947764],
#       [ 3.93903661,  0.17448257,  1.86618853]], dtype=float32)

Written by statcompute

January 15, 2017 at 6:19 pm

An Example of Merge Layer in Keras

The power of a DNN does not only come from its depth but also come from its flexibility of accommodating complex network structures. For instance, the DNN shown below consists of two branches, the left with 4 inputs and the right with 6 inputs. In addition, the right branch shows a more complicated structure than the left.

                                                InputLayer (None, 6)
                                                     Dense (None, 6)
                                        BatchNormalization (None, 6)
                                                     Dense (None, 6)
         InputLayer (None, 4)           BatchNormalization (None, 6)
              Dense (None, 4)                        Dense (None, 6)
 BatchNormalization (None, 4)           BatchNormalization (None, 6)
                    \____________________________________/
                                      |
                                 Merge (None, 10)
                                 Dense (None, 1)

To create a DNN as the above, both left and right branches are defined separately with corresponding inputs and layers. In the line 29, both branches would be combined with a MERGE layer. There are multiple benefits of such merged DNNs. For instance, the DNN has the flexibility to handle various inputs differently. In addition, new features can be added conveniently without messing around with the existing network structure.

from pandas import read_csv, DataFrame
from numpy.random import seed
from sklearn.preprocessing import scale
from keras.models import Sequential
from keras.constraints import maxnorm
from keras.optimizers import SGD
from keras.layers import Dense, Merge
from keras.layers.normalization import BatchNormalization
from keras_diagram import ascii

df = read_csv("credit_count.txt")
Y = df[df.CARDHLDR == 1].DEFAULTS
X1 = scale(df[df.CARDHLDR == 1][["MAJORDRG", "MINORDRG", "OWNRENT", "SELFEMPL"]])
X2 = scale(df[df.CARDHLDR == 1][["AGE", "ACADMOS", "ADEPCNT", "INCPER", "EXP_INC", "INCOME"]])

branch1 = Sequential()
branch1.add(Dense(X1.shape[1], input_shape = (X1.shape[1],), init = 'normal', activation = 'relu'))
branch1.add(BatchNormalization())

branch2 = Sequential()
branch2.add(Dense(X2.shape[1], input_shape =  (X2.shape[1],), init = 'normal', activation = 'relu'))
branch2.add(BatchNormalization())
branch2.add(Dense(X2.shape[1], init = 'normal', activation = 'relu', W_constraint = maxnorm(5)))
branch2.add(BatchNormalization())
branch2.add(Dense(X2.shape[1], init = 'normal', activation = 'relu', W_constraint = maxnorm(5)))
branch2.add(BatchNormalization())

model = Sequential()
model.add(Merge([branch1, branch2], mode = 'concat'))
model.add(Dense(1, init = 'normal', activation = 'sigmoid'))
sgd = SGD(lr = 0.1, momentum = 0.9, decay = 0, nesterov = False)
model.compile(loss = 'binary_crossentropy', optimizer = sgd, metrics = ['accuracy'])
seed(2017)
model.fit([X1, X2], Y.values, batch_size = 2000, nb_epoch = 100, verbose = 1)

Written by statcompute

January 8, 2017 at 4:42 pm

Dropout Regularization in Deep Neural Networks

The deep neural network (DNN) is a very powerful neural work with multiple hidden layers and is able to capture the highly complex relationship between the response and predictors. However, it is prone to the over-fitting due to a large number of parameters that makes the regularization crucial for DNNs. In the paper (https://www.cs.toronto.edu/~hinton/absps/JMLRdropout.pdf), an interesting regularization approach, e.g. dropout, was proposed with a simple and elegant idea. Basically, it suppresses the complexity of DNNs by randomly dropping units in both input and hidden layers.

Below is an example showing how to tune the hyper-parameter of dropout rates with Keras library in Python. Because of the long computing time required by the dropout, the parallelism is used to speed up the process.

from pandas import read_csv, DataFrame
from numpy.random import seed
from sklearn.preprocessing import scale
from sklearn.model_selection import train_test_split
from sklearn.metrics import roc_auc_score 
from keras.models import Sequential
from keras.constraints import maxnorm
from keras.optimizers import SGD
from keras.layers import Dense, Dropout
from multiprocessing import Pool, cpu_count
from itertools import product
from parmap import starmap

df = read_csv("credit_count.txt")
Y = df[df.CARDHLDR == 1].DEFAULT
X = df[df.CARDHLDR == 1][['AGE', 'ADEPCNT', 'MAJORDRG', 'MINORDRG', 'INCOME', 'OWNRENT', 'SELFEMPL']]
sX = scale(X)
ncol = sX.shape[1]
x_train, x_test, y_train, y_test = train_test_split(sX, Y, train_size = 0.5, random_state = seed(2017))

def tune_dropout(rate1, rate2):
  net = Sequential()
  ## DROPOUT AT THE INPUT LAYER
  net.add(Dropout(rate1, input_shape = (ncol,)))
  ## DROPOUT AT THE 1ST HIDDEN LAYER
  net.add(Dense(ncol, init = 'normal', activation = 'relu', W_constraint = maxnorm(4)))
  net.add(Dropout(rate2))
  ## DROPOUT AT THE 2ND HIDDER LAYER
  net.add(Dense(ncol, init = 'normal', activation = 'relu', W_constraint = maxnorm(4)))
  net.add(Dropout(rate2))
  net.add(Dense(1, init = 'normal', activation = 'sigmoid'))
  sgd = SGD(lr = 0.1, momentum = 0.9, decay = 0, nesterov = False)
  net.compile(loss='binary_crossentropy', optimizer = sgd, metrics = ['accuracy'])
  net.fit(x_train, y_train, batch_size = 200, nb_epoch = 50, verbose = 0)
  print rate1, rate2, "{:6.4f}".format(roc_auc_score(y_test, net.predict(x_test)))

input_dp = [0.1, 0.2, 0.3]
hidden_dp = [0.2, 0.3, 0.4, 0.5]
parms = [i for i in product(input_dp, hidden_dp)]

seed(2017)
starmap(tune_dropout, parms, pool = Pool(processes = cpu_count()))

As shown in the output below, the optimal dropout rate appears to be 0.2 incidentally for both input and hidden layers.

0.1 0.2 0.6354
0.1 0.4 0.6336
0.1 0.3 0.6389
0.1 0.5 0.6378
0.2 0.2 0.6419
0.2 0.4 0.6385
0.2 0.3 0.6366
0.2 0.5 0.6359
0.3 0.4 0.6313
0.3 0.2 0.6350
0.3 0.3 0.6346
0.3 0.5 0.6343

Written by statcompute

January 2, 2017 at 1:09 am

Flavors of SQL on Pandas DataFrame

In R, sqldf() provides a convenient interface of running SQL statement on data frames. Similarly, Python also offers multiple ways to interact between SQL and Pandas DataFrames by leveraging the lightweight SQLite engine. While pandasql (https://github.com/yhat/pandasql) works similarly to sqldf() in R, pysqldf (https://github.com/airtoxin/pysqldf) is even more powerful. In my experiments shown below, advantages of pysqldf over pandasql are two-fold. First of all, pysqldf is 2 – 3 times faster than pandasql. Secondly, pysqldf supports new function definitions, which is not available in pandasql. However, it is worth mentioning that the generic python interface to an in-memory SQLite database can be more efficient and flexible than both pysqldf and pandasql, as demonstrated below, as long as we are able to get the DataFrame into the SQLite and let it stay in-memory.

from sqlite3 import connect
from pandas import read_sql_query
import pandasql
import pysqldf
import numpy

# CREATE AN IN-MEMORY SQLITE DB
con = connect(":memory:")
cur = con.cursor()
cur.execute("attach 'my.db' as filedb")
cur.execute("create table df as select * from filedb.hflights")
cur.execute("detach filedb")

# IMPORT SQLITE TABLE INTO PANDAS DF
df = read_sql_query("select * from df", con)

# WRITE QUERIES
sql01 = "select * from df where DayofWeek = 1 and Dest = 'CVG';"
sql02 = "select DayofWeek, AVG(ArrTime) from df group by DayofWeek;"
sql03 = "select DayofWeek, median(ArrTime) from df group by DayofWeek;"

# SELECTION:
# 1. PANDASQL
%time t11 = pandasql.sqldf(sql01, globals())
# 2. PYSQLDF
%time t12 = pysqldf.SQLDF(globals()).execute(sql01)
# 3. GENERIC SQLITE CONNECTION
%time t13 = read_sql_query(sql01, con)

# AGGREGATION:
# 1. PANDASQL
%time t21 = pandasql.sqldf(sql02, globals())
# 2. PYSQLDF
%time t22 = pysqldf.SQLDF(globals()).execute(sql02)
# 3. GENERIC SQLITE CONNECTION
%time t23 = read_sql_query(sql02, con)

# DEFINING A NEW FUNCTION:
# DEFINE A FUNCTION NOT SUPPORTED IN SQLITE
class median(object):
  def __init__(self):
    self.a = []
  def step(self, x):
    self.a.append(x)
  def finalize(self):
    return numpy.median(self.a)

# 1. PYSQLDF
udafs = {"median": median}
%time t31 = pysqldf.SQLDF(globals(), udafs = udafs).execute(sql03)
# 2 GENERIC SQLITE CONNECTION
con.create_aggregate("median", 1, median)
%time t32 = read_sql_query(sql03, con)

Written by statcompute

October 17, 2016 at 10:34 pm

Posted in Big Data, pandas, PYTHON, SQL, SQLite

Tagged with , , , ,

SAS Macro Calculating Mutual Information

In statistics, various correlation functions, either Spearman or Pearson, have been used to measure the dependence between two data vectors under the linear or monotonic assumption. Mutual Information (MI) is an alternative widely used in Information Theory and is considered a more general measurement of the dependence between two vectors. More specifically, MI quantifies how much information two vectors, regardless of their actual values, might share based on their joint and marginal probability distribution functions.

Below is a sas macro implementing MI and Normalized MI by mimicking functions in Python, e.g. mutual_info_score() and normalized_mutual_info_score(). Although MI is used to evaluate the cluster analysis performance in sklearn package, it can also be used as an useful tool for Feature Selection in the context of Machine Learning and Statistical Modeling.

%macro mutual(data = , x = , y = );
***********************************************************;
* SAS MACRO CALCULATING MUTUAL INFORMATION AND ITS        *;
* NORMALIZED VARIANT BETWEEN TWO VECTORS BY MIMICKING     *;
* SKLEARN.METRICS.NORMALIZED_MUTUAL_INFO_SCORE()          *;
* SKLEARN.METRICS.MUTUAL_INFO_SCORE() IN PYTHON           *;
* ======================================================= *;
* INPUT PAREMETERS:                                       *;
*  DATA : INPUT SAS DATA TABLE                            *;
*  X    : FIRST INPUT VECTOR                              *;
*  Y    : SECOND INPUT VECTOR                             *;
* ======================================================= *;
* AUTHOR: WENSUI.LIU@53.COM                               *;
***********************************************************;

data _1;
  set &data;
  where &x ~= . and &y ~= .;
  _id = _n_;
run;

proc sql;
create table
  _2 as
select
  _id,
  &x,
  &y,
  1 / (select count(*) from _1) as _p_xy
from
  _1;

create table
  _3 as
select
  _id,
  &x         as _x,
  sum(_p_xy) as _p_x,
  sum(_p_xy) * log(sum(_p_xy)) / count(*) as _h_x
from 
  _2
group by
  &x;

create table
  _4 as
select
  _id,
  &y         as _y,
  sum(_p_xy) as _p_y,
  sum(_p_xy) * log(sum(_p_xy)) / count(*) as _h_y
from 
  _2
group by
  &y;

create table
  _5 as
select
  a.*,
  b._p_x,
  b._h_x,
  c._p_y,
  c._h_y,
  a._p_xy * log(a._p_xy / (b._p_x * c._p_y)) as mutual
from
  _2 as a, _3 as b, _4 as c
where
  a._id = b._id and a._id = c._id;

select
  sum(mutual) as MI format = 12.8,
  case 
    when sum(mutual) = 0 then 0
    else sum(mutual) / (sum(_h_x) * sum(_h_y)) ** 0.5 
  end as NMI format = 12.8
from
  _5;
quit;

%mend mutual;

Written by statcompute

August 7, 2016 at 5:18 pm

Python Prototype of Grid Search for SVM Parameters

from itertools import product
from pandas import read_table, DataFrame
from sklearn.cross_validation import KFold as kfold
from sklearn.svm import SVC as svc
from sklearn.metrics import roc_auc_score as auc

df = read_table('credit_count.txt', sep = ',')
Y = df[df.CARDHLDR == 1].DEFAULT
X = df[df.CARDHLDR == 1][['AGE', 'ADEPCNT', 'MAJORDRG', 'MINORDRG', 'INCOME', 'OWNRENT', 'SELFEMPL']]

c = [1, 10]
g = [0.01, 0.001]
parms = [i for i in product(c, g)]
kf = [i for i in kfold(Y.count(), n_folds = 3, shuffle = True, random_state = 0)]
final = DataFrame()

for i in parms:
  result = DataFrame()	
  mdl = svc(C = i[0], gamma = i[1], probability = True, random_state = 0)
  for j in kf:
    X1 = X.iloc[j[0]]
    Y1 = Y.iloc[j[0]]
    X2 = X.iloc[j[1]]
    Y2 = Y.iloc[j[1]]
    mdl.fit(X1, Y1)
    pred = mdl.predict_proba(X2)[:, 1]
    out = DataFrame({'pred': pred, 'y': Y2})
    result = result.append(out)
  perf = DataFrame({'Cost': i[0], 'Gamma': i[1], 'AUC': [auc(result.y, result.pred)]}) 
  final = final.append(perf)

Written by statcompute

March 27, 2016 at 2:40 pm

Parallelize Map()

Map() is a convenient routine in Python to apply a function to all items from one or more lists, as shown below. This specific nature also makes map() a perfect candidate for the parallelism.

In [1]: a = (1, 2, 3)

In [2]: b = (10, 20, 30)

In [3]: def func(a, b):
...:      print "a -->", a, "b -->", b
...:

In [4]: ### SERIAL CALL ###

In [5]: map(func, a, b)
a --> 1 b --> 10
a --> 2 b --> 20
a --> 3 b --> 30

Pool.map() function in Multiprocessing Package is the parallel implementation of map(). However, a drawback is that Pool.map() doesn’t support more than one arguments in the function call. Therefore, in case of a functional call with multiple arguments, a wrapper function is necessary to make it working, which however should be defined before importing Multiprocessing package.

In [6]: ### PARALLEL CALL ###

In [7]: ### SINCE POOL.MAP() DOESN'T TAKE MULTIPLE ARGUMENTS, A WRAPPER IS NEEDED

In [8]: def f2(ab):
...:      a, b = ab
...:      return func(a, b)
...:

In [9]: from multiprocessing import Pool, cpu_count

In [10]: pool = Pool(processes = cpu_count())

In [11]: ### PARALLEL MAP() ON ALL CPUS

In [12]: pool.map(f2, zip(a, b))
a --> 1 b --> 10
a --> 2 b --> 20
a --> 3 b --> 30

In addition, Pool.apply() function, with some tweaks, can also be employed to mimic the parallel version of map(). The advantage of this approach is that, different from Pool.map(), Pool.apply() is able to handle multiple arguments by using the list comprehension.

In [13]: ### POOL.APPLY() CAN ALSO MIMIC MAP()

In [14]: [pool.apply(func, args = (i, j)) for i, j in zip(a, b)]
a --> 1 b --> 10
a --> 2 b --> 20
a --> 3 b --> 30

Alternatively, starmap() function in the parmap package (https://github.com/zeehio/parmap), which is specifically designed to overcome limitations in Pool.map(), provides a more friendly and elegant interface to implement the parallelized map() with multiple arguments at the cost of a slight computing overhead.

In [15]: ### ALTERNATIVELY, PARMAP PACKAGE IS USED

In [16]: from parmap import starmap

In [17]: starmap(func, zip(a, b), pool = Pool(processes = cpu_count()))
a --> 1 b --> 10
a --> 2 b --> 20
a --> 3 b --> 30

Written by statcompute

December 31, 2015 at 4:00 pm

Posted in Big Data, Parallelism, PYTHON

Tagged with ,