A Data Science Framework: To Achieve 99% Accuracy :Part 1

Part 1: Gathering Data

Table of Contents

1. Chapter 1 – How a Data Scientist Beat the Odds
2. Chapter 2 – A Data Science Framework
3. Chapter 3 – Step 1: Define the Problem and Step 2: Gather the Data
4. Chapter 4 – Step 3: Prepare Data for Consumption
5. Chapter 5 – The 4 C’s of Data Cleaning: Correcting, Completing, Creating, and Converting
6. Chapter 6 – Step 4: Perform Exploratory Analysis with Statistics
7. Chapter 7 – Step 5: Model Data
8. Chapter 8 – Evaluate Model Performance
9. Chapter 9 – Tune Model with Hyper-Parameters
10. Chapter 10 – Tune Model with Feature Selection
11. Chapter 11 – Step 6: Validate and Implement
12. Chapter 12 – Conclusion and Step 7: Optimize and Strategize
13. Change Log
14. Credits

How a Data Scientist Beat the Odds

It’s the classical problem, predict the outcome of a binary event. In laymen terms this means, it either occurred or did not occur. For example, you won or did not win, you passed the test or did not pass the test, you were accepted or not accepted, and you get the point. A common business application is churn or customer retention. Another popular use case is, healthcare’s mortality rate or survival analysis. Binary events create an interesting dynamic, because we know statistically, a random guess should achieve a 50% accuracy rate, without creating one single algorithm or writing one single line of code. However, just like autocorrect spellcheck technology, sometimes we humans can be too smart for our own good and actually underperform a coin flip. In this kernel, I use Kaggle’s Getting Started Competition, Titanic: Machine Learning from Disaster, to walk the reader through, how-to use the data science framework to beat the odds.

What happens when technology is too smart for its own good?

A Data Science Framework

1. Define the Problem: If data science, big data, machine learning, predictive analytics, business intelligence, or any other buzzword is the solution, then what is the problem? As the saying goes, don’t put the cart before the horse. Problems before requirements, requirements before solutions, solutions before design, and design before technology. Too often we are quick to jump on the new shiny technology, tool, or algorithm before determining the actual problem we are trying to solve.
2. Gather the Data: John Naisbitt wrote in his 1984 (yes, 1984) book Megatrends, we are “drowning in data, yet staving for knowledge.” So, chances are, the dataset(s) already exist somewhere, in some format. It may be external or internal, structured or unstructured, static or streamed, objective or subjective, etc. As the saying goes, you don’t have to reinvent the wheel, you just have to know where to find it. In the next step, we will worry about transforming “dirty data” to “clean data.”
3. Prepare Data for Consumption: This step is often referred to as data wrangling, a required process to turn “wild” data into “manageable” data. Data wrangling includes implementing data architectures for storage and processing, developing data governance standards for quality and control, data extraction (i.e. ETL and web scraping), and data cleaning to identify aberrant, missing, or outlier data points.
4. Perform Exploratory Analysis: Anybody who has ever worked with data knows, garbage-in, garbage-out (GIGO). Therefore, it is important to deploy descriptive and graphical statistics to look for potential problems, patterns, classifications, correlations and comparisons in the dataset. In addition, data categorization (i.e. qualitative vs quantitative) is also important to understand and select the correct hypothesis test or data model.
5. Model Data: Like descriptive and inferential statistics, data modeling can either summarize the data or predict future outcomes. Your dataset and expected results, will determine the algorithms available for use. It’s important to remember, algorithms are tools and not magical wands or silver bullets. You must still be the master craft (wo)man that knows how-to select the right tool for the job. An analogy would be asking someone to hand you a Philip screwdriver, and they hand you a flathead screwdriver or worst a hammer. At best, it shows a complete lack of understanding. At worst, it makes completing the project impossible. The same is true in data modelling. The wrong model can lead to poor performance at best and the wrong conclusion (that’s used as actionable intelligence) at worst.
6. Validate and Implement Data Model: After you’ve trained your model based on a subset of your data, it’s time to test your model. This helps ensure you haven’t overfit your model or made it so specific to the selected subset, that it does not accurately fit another subset from the same dataset. In this step we determine if our model overfit, generalize, or underfit our dataset.
7. Optimize and Strategize: This is the “bionic man” step, where you iterate back through the process to make it better…stronger…faster than it was before. As a data scientist, your strategy should be to outsource developer operations and application plumbing, so you have more time to focus on recommendations and design. Once you’re able to package your ideas, this becomes your “currency exchange” rate.

Step 1: Define the Problem

For this project, the problem statement is given to us on a golden plater, develop an algorithm to predict the survival outcome of passengers on the Titanic.

….

Project Summary: The sinking of the RMS Titanic is one of the most infamous shipwrecks in history. On April 15, 1912, during her maiden voyage, the Titanic sank after colliding with an iceberg, killing 1502 out of 2224 passengers and crew. This sensational tragedy shocked the international community and led to better safety regulations for ships.

One of the reasons that the shipwreck led to such loss of life was that there were not enough lifeboats for the passengers and crew. Although there was some element of luck involved in surviving the sinking, some groups of people were more likely to survive than others, such as women, children, and the upper-class.

In this challenge, we ask you to complete the analysis of what sorts of people were likely to survive. In particular, we ask you to apply the tools of machine learning to predict which passengers survived the tragedy.

Practice Skills

• Binary classification
• Python and R basics

Step 2: Gather the Data

The dataset is also given to us on a golden plater with test and train data at Kaggle’s Titanic: Machine Learning from Disasterlinkcode

Step 3: Prepare Data for Consumption

Since step 2 was provided to us on a golden plater, so is step 3. Therefore, normal processes in data wrangling, such as data architecture, governance, and extraction are out of scope. Thus, only data cleaning is in scope.

3.1 Import Libraries

The following code is written in Python 3.x. Libraries provide pre-written functionality to perform necessary tasks. The idea is why write ten lines of code, when you can write one line.

# This Python 3 environment comes with many helpful analytics libraries installed
# It is defined by the kaggle/python docker image: https://github.com/kaggle/docker-python

#load packages
import sys #access to system parameters https://docs.python.org/3/library/sys.html
print("Python version: {}". format(sys.version))

import pandas as pd #collection of functions for data processing and analysis modeled after R dataframes with SQL like features
print("pandas version: {}". format(pd.__version__))

import matplotlib #collection of functions for scientific and publication-ready visualization
print("matplotlib version: {}". format(matplotlib.__version__))

import numpy as np #foundational package for scientific computing
print("NumPy version: {}". format(np.__version__))

import scipy as sp #collection of functions for scientific computing and advance mathematics
print("SciPy version: {}". format(sp.__version__)) 

import IPython
from IPython import display #pretty printing of dataframes in Jupyter notebook
print("IPython version: {}". format(IPython.__version__)) 

import sklearn #collection of machine learning algorithms
print("scikit-learn version: {}". format(sklearn.__version__))

#misc libraries
import random
import time


#ignore warnings
import warnings
warnings.filterwarnings('ignore')
print('-'*25)



# Input data files are available in the "../input/" directory.
# For example, running this (by clicking run or pressing Shift+Enter) will list the files in the input directory

from subprocess import check_output
print(check_output(["ls", "../input"]).decode("utf8"))

# Any results you write to the current directory are saved as output.

3.11 Load Data Modelling Libraries

We will use the popular scikit-learn library to develop our machine learning algorithms. In sklearn, algorithms are called Estimators and implemented in their own classes. For data visualization, we will use the matplotlib and seaborn library. Below are common classes to load.

#Common Model Algorithms
from sklearn import svm, tree, linear_model, neighbors, naive_bayes, ensemble, discriminant_analysis, gaussian_process
from xgboost import XGBClassifier

#Common Model Helpers
from sklearn.preprocessing import OneHotEncoder, LabelEncoder
from sklearn import feature_selection
from sklearn import model_selection
from sklearn import metrics

#Visualization
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.pylab as pylab
import seaborn as sns
from pandas.tools.plotting import scatter_matrix

#Configure Visualization Defaults
#%matplotlib inline = show plots in Jupyter Notebook browser
%matplotlib inline
mpl.style.use('ggplot')
sns.set_style('white')
pylab.rcParams['figure.figsize'] = 12,8

3.2 Meet and Greet Data

This is the meet and greet step. Get to know your data by first name and learn a little bit about it. What does it look like (datatype and values), what makes it tick (independent/feature variables(s)), what’s its goals in life (dependent/target variable(s)). Think of it like a first date, before you jump in and start poking it in the bedroom.

To begin this step, we first import our data. Next we use the info() and sample() function, to get a quick and dirty overview of variable datatypes (i.e. qualitative vs quantitative). Click here for the Source Data Dictionary.

1. The Survived variable is our outcome or dependent variable. It is a binary nominal datatype of 1 for survived and 0 for did not survive. All other variables are potential predictor or independent variables. It’s important to note, more predictor variables do not make a better model, but the right variables.
2. The PassengerID and Ticket variables are assumed to be random unique identifiers, that have no impact on the outcome variable. Thus, they will be excluded from analysis.
3. The Pclass variable is an ordinal datatype for the ticket class, a proxy for socio-economic status (SES), representing 1 = upper class, 2 = middle class, and 3 = lower class.
4. The Name variable is a nominal datatype. It could be used in feature engineering to derive the gender from title, family size from surname, and SES from titles like doctor or master. Since these variables already exist, we’ll make use of it to see if title, like master, makes a difference.
5. The Sex and Embarked variables are a nominal datatype. They will be converted to dummy variables for mathematical calculations.
6. The Age and Fare variable are continuous quantitative datatypes.
7. The SibSp represents number of related siblings/spouse aboard and Parch represents number of related parents/children aboard. Both are discrete quantitative datatypes. This can be used for feature engineering to create a family size and is alone variable.
8. The Cabin variable is a nominal datatype that can be used in feature engineering for approximate position on ship when the incident occurred and SES from deck levels. However, since there are many null values, it does not add value and thus is excluded from analysis.

#import data from file: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_csv.html
data_raw = pd.read_csv('../input/train.csv')


#a dataset should be broken into 3 splits: train, test, and (final) validation
#the test file provided is the validation file for competition submission
#we will split the train set into train and test data in future sections
data_val  = pd.read_csv('../input/test.csv')


#to play with our data we'll create a copy
#remember python assignment or equal passes by reference vs values, so we use the copy function: https://stackoverflow.com/questions/46327494/python-pandas-dataframe-copydeep-false-vs-copydeep-true-vs
data1 = data_raw.copy(deep = True)

#however passing by reference is convenient, because we can clean both datasets at once
data_cleaner = [data1, data_val]


#preview data
print (data_raw.info()) #https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.info.html
#data_raw.head() #https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.head.html
#data_raw.tail() #https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.tail.html
data_raw.sample(10) #https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.sample.html

3.21 The 4 C’s of Data Cleaning: Correcting, Completing, Creating, and Converting

In this stage, we will clean our data by 1) correcting aberrant values and outliers, 2) completing missing information, 3) creating new features for analysis, and 4) converting fields to the correct format for calculations and presentation.

1. Correcting: Reviewing the data, there does not appear to be any aberrant or non-acceptable data inputs. In addition, we see we may have potential outliers in age and fare. However, since they are reasonable values, we will wait until after we complete our exploratory analysis to determine if we should include or exclude from the dataset. It should be noted, that if they were unreasonable values, for example age = 800 instead of 80, then it’s probably a safe decision to fix now. However, we want to use caution when we modify data from its original value, because it may be necessary to create an accurate model.
2. Completing: There are null values or missing data in the age, cabin, and embarked field. Missing values can be bad, because some algorithms don’t know how-to handle null values and will fail. While others, like decision trees, can handle null values. Thus, it’s important to fix before we start modeling, because we will compare and contrast several models. There are two common methods, either delete the record or populate the missing value using a reasonable input. It is not recommended to delete the record, especially a large percentage of records, unless it truly represents an incomplete record. Instead, it’s best to impute missing values. A basic methodology for qualitative data is impute using mode. A basic methodology for quantitative data is impute using mean, median, or mean + randomized standard deviation. An intermediate methodology is to use the basic methodology based on specific criteria; like the average age by class or embark port by fare and SES. There are more complex methodologies, however before deploying, it should be compared to the base model to determine if complexity truly adds value. For this dataset, age will be imputed with the median, the cabin attribute will be dropped, and embark will be imputed with mode. Subsequent model iterations may modify this decision to determine if it improves the model’s accuracy.
3. Creating: Feature engineering is when we use existing features to create new features to determine if they provide new signals to predict our outcome. For this dataset, we will create a title feature to determine if it played a role in survival.
4. Converting: Last, but certainly not least, we’ll deal with formatting. There are no date or currency formats, but datatype formats. Our categorical data imported as objects, which makes it difficult for mathematical calculations. For this dataset, we will convert object datatypes to categorical dummy variables.

print('Train columns with null values:\n', data1.isnull().sum())
print("-"*10)

print('Test/Validation columns with null values:\n', data_val.isnull().sum())
print("-"*10)

data_raw.describe(include = 'all')

Train columns with null values:
 PassengerId      0
Survived         0
Pclass           0
Name             0
Sex              0
Age            177
SibSp            0
Parch            0
Ticket           0
Fare             0
Cabin          687
Embarked         2
dtype: int64
----------
Test/Validation columns with null values:
 PassengerId      0
Pclass           0
Name             0
Sex              0
Age             86
SibSp            0
Parch            0
Ticket           0
Fare             1
Cabin          327
Embarked         0
dtype: int64
----------

3.22 Clean Data

Now that we know what to clean, let’s execute our code.

Developer Documentation:

• pandas.DataFrame
• pandas.DataFrame.info
• pandas.DataFrame.describe
• Indexing and Selecting Data
• pandas.isnull
• pandas.DataFrame.sum
• pandas.DataFrame.mode
• pandas.DataFrame.copy
• pandas.DataFrame.fillna
• pandas.DataFrame.drop
• pandas.Series.value_counts
• pandas.DataFrame.loc

###COMPLETING: complete or delete missing values in train and test/validation dataset
for dataset in data_cleaner:    
    #complete missing age with median
    dataset['Age'].fillna(dataset['Age'].median(), inplace = True)

    #complete embarked with mode
    dataset['Embarked'].fillna(dataset['Embarked'].mode()[0], inplace = True)

    #complete missing fare with median
    dataset['Fare'].fillna(dataset['Fare'].median(), inplace = True)
    
#delete the cabin feature/column and others previously stated to exclude in train dataset
drop_column = ['PassengerId','Cabin', 'Ticket']
data1.drop(drop_column, axis=1, inplace = True)

print(data1.isnull().sum())
print("-"*10)
print(data_val.isnull().sum())

Survived    0
Pclass      0
Name        0
Sex         0
Age         0
SibSp       0
Parch       0
Fare        0
Embarked    0
dtype: int64
----------
PassengerId      0
Pclass           0
Name             0
Sex              0
Age              0
SibSp            0
Parch            0
Ticket           0
Fare             0
Cabin          327
Embarked         0
dtype: int64

###CREATE: Feature Engineering for train and test/validation dataset
for dataset in data_cleaner:    
    #Discrete variables
    dataset['FamilySize'] = dataset ['SibSp'] + dataset['Parch'] + 1

    dataset['IsAlone'] = 1 #initialize to yes/1 is alone
    dataset['IsAlone'].loc[dataset['FamilySize'] > 1] = 0 # now update to no/0 if family size is greater than 1

    #quick and dirty code split title from name: http://www.pythonforbeginners.com/dictionary/python-split
    dataset['Title'] = dataset['Name'].str.split(", ", expand=True)[1].str.split(".", expand=True)[0]


    #Continuous variable bins; qcut vs cut: https://stackoverflow.com/questions/30211923/what-is-the-difference-between-pandas-qcut-and-pandas-cut
    #Fare Bins/Buckets using qcut or frequency bins: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.qcut.html
    dataset['FareBin'] = pd.qcut(dataset['Fare'], 4)

    #Age Bins/Buckets using cut or value bins: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.cut.html
    dataset['AgeBin'] = pd.cut(dataset['Age'].astype(int), 5)


    
#cleanup rare title names
#print(data1['Title'].value_counts())
stat_min = 10 #while small is arbitrary, we'll use the common minimum in statistics: http://nicholasjjackson.com/2012/03/08/sample-size-is-10-a-magic-number/
title_names = (data1['Title'].value_counts() < stat_min) #this will create a true false series with title name as index

#apply and lambda functions are quick and dirty code to find and replace with fewer lines of code: https://community.modeanalytics.com/python/tutorial/pandas-groupby-and-python-lambda-functions/
data1['Title'] = data1['Title'].apply(lambda x: 'Misc' if title_names.loc[x] == True else x)
print(data1['Title'].value_counts())
print("-"*10)


#preview data again
data1.info()
data_val.info()
data1.sample(10)

Train columns with null values: 
 Survived         0
Pclass           0
Name             0
Sex              0
Age              0
SibSp            0
Parch            0
Fare             0
Embarked         0
FamilySize       0
IsAlone          0
Title            0
FareBin          0
AgeBin           0
Sex_Code         0
Embarked_Code    0
Title_Code       0
AgeBin_Code      0
FareBin_Code     0
dtype: int64
----------
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 891 entries, 0 to 890
Data columns (total 19 columns):
Survived         891 non-null int64
Pclass           891 non-null int64
Name             891 non-null object
Sex              891 non-null object
Age              891 non-null float64
SibSp            891 non-null int64
Parch            891 non-null int64
Fare             891 non-null float64
Embarked         891 non-null object
FamilySize       891 non-null int64
IsAlone          891 non-null int64
Title            891 non-null object
FareBin          891 non-null category
AgeBin           891 non-null category
Sex_Code         891 non-null int64
Embarked_Code    891 non-null int64
Title_Code       891 non-null int64
AgeBin_Code      891 non-null int64
FareBin_Code     891 non-null int64
dtypes: category(2), float64(2), int64(11), object(4)
memory usage: 120.3+ KB
None
----------
Test/Validation columns with null values: 
 PassengerId        0
Pclass             0
Name               0
Sex                0
Age                0
SibSp              0
Parch              0
Ticket             0
Fare               0
Cabin            327
Embarked           0
FamilySize         0
IsAlone            0
Title              0
FareBin            0
AgeBin             0
Sex_Code           0
Embarked_Code      0
Title_Code         0
AgeBin_Code        0
FareBin_Code       0
dtype: int64
----------
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 418 entries, 0 to 417
Data columns (total 21 columns):
PassengerId      418 non-null int64
Pclass           418 non-null int64
Name             418 non-null object
Sex              418 non-null object
Age              418 non-null float64
SibSp            418 non-null int64
Parch            418 non-null int64
Ticket           418 non-null object
Fare             418 non-null float64
Cabin            91 non-null object
Embarked         418 non-null object
FamilySize       418 non-null int64
IsAlone          418 non-null int64
Title            418 non-null object
FareBin          418 non-null category
AgeBin           418 non-null category
Sex_Code         418 non-null int64
Embarked_Code    418 non-null int64
Title_Code       418 non-null int64
AgeBin_Code      418 non-null int64
FareBin_Code     418 non-null int64
dtypes: category(2), float64(2), int64(11), object(6)
memory usage: 63.1+ KB
None
----------

Out[6]:

3.25 Split Training and Testing Data

As mentioned previously, the test file provided is really validation data for competition submission. So, we will use sklearn function to split the training data in two datasets; 75/25 split. This is important, so we don’t overfit our model. Meaning, the algorithm is so specific to a given subset, it cannot accurately generalize another subset, from the same dataset. It’s important our algorithm has not seen the subset we will use to test, so it doesn’t “cheat” by memorizing the answers. We will use sklearn’s train_test_split function. In later sections we will also use sklearn’s cross validation functions, that splits our dataset into train and test for data modeling comparison.

#split train and test data with function defaults
#random_state -> seed or control random number generator: https://www.quora.com/What-is-seed-in-random-number-generation
train1_x, test1_x, train1_y, test1_y = model_selection.train_test_split(data1[data1_x_calc], data1[Target], random_state = 0)
train1_x_bin, test1_x_bin, train1_y_bin, test1_y_bin = model_selection.train_test_split(data1[data1_x_bin], data1[Target] , random_state = 0)
train1_x_dummy, test1_x_dummy, train1_y_dummy, test1_y_dummy = model_selection.train_test_split(data1_dummy[data1_x_dummy], data1[Target], random_state = 0)


print("Data1 Shape: {}".format(data1.shape))
print("Train1 Shape: {}".format(train1_x.shape))
print("Test1 Shape: {}".format(test1_x.shape))

train1_x_bin.head()

Data1 Shape: (891, 19)
Train1 Shape: (668, 8)
Test1 Shape: (223, 8)