pymltoolkit 0.1.11
End-to-end Machine Learning Toolkit (MLToolkit/mltk) for Python
License: Apache License Version 2.0

# MLToolKit Project 

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<br>www.mltoolkit.org

## Current release: PyMLToolkit [v0.1.11]

<img src="https://raw.githubusercontent.com/mltoolkit/MLToolkit/master/MLToolkit.png" height="200">

MLToolKit (mltk) is a Python package providing a set of user-friendly functions to help building end-to-end machine learning models in data science research, teaching or production focused projects. 

## Introduction
MLToolKit supports all stages of the machine learning application development process.
<img src="https://raw.githubusercontent.com/mltoolkit/MLToolkit/master/MLToolkit/image/MLTKProcess.png" height="200">

## Installation
```
pip install pymltoolkit
```
If the installation failed with dependancy issues, execute the above command with --no-dependencies

```
pip install pymltoolkit --no-dependencies
```

## Functions
- Data Extraction (SQL, Flatfiles, Binary Files, Images, etc.)
- Exploratory Data Analysis (statistical summary, univariate analysis, visulize distributions, etc.)
- Feature Engineering (Supports numeric, text, date/time. Image data support will integrate in later releases of v0.1)
- Model Building (Currently supported for binary classification and regression only)
- Hyper Parameter Tuning [in development for v0.2]
- Cross Validation (will integrate in later releases of v0.1)
- Model Performance Analysis, Explain Predictions (LIME and SHAP) and Performance Comparison Between Models.
- JSON input script for executing model building and scoring tasks.
- Model Building UI [in development for v0.2]
- ML Model Building Project [in development for v0.2]
- Auto ML (automated machine learning) [in development for v0.2]
- Model Deploymet and Serving [included, will be imporved for v0.2]

## Supported Machine Learning Algorithms/Packages
- RandomForestClassifier: scikit-learn
- LogisticRegression: statsmodels
- Deep Feed Forward Neural Network (DFF): tensorflow
- Convlutional Neural Network (CNN): tensorflow
- Gradient Boost : catboost, xgboost, lightgbm
- Linear Regression: statsmodels
- RandomForestRegressor: scikit-learn
- ... More models will be added in the future releases ...

## Usage
```python
import mltk
```

### Warning: Python Variable, Function or Class names 
The Python interpreter has a number of built-in functions. It is possible to overwrite thier definitions when coding without any rasing a warning from the Python interpriter. (https://docs.python.org/3/library/functions.html)
Therfore, AVOID THESE NAMES as your variable, function or class names.
<table border="1">
<tr><td>abs</td><td>all</td><td>any</td><td>ascii</td><td>bin</td><td>bool</td><td>bytearray</td><td>bytes</td></tr>
<tr><td>callable</td><td>chr</td><td>classmethod</td><td>compile</td><td>complex</td><td>delattr</td><td>dict</td><td>dir</td></tr>
<tr><td>divmod</td><td>enumerate</td><td>eval</td><td>exec</td><td>filter</td><td>float</td><td>format</td><td>frozenset</td></tr>
<tr><td>getattr</td><td>globals</td><td>hasattr</td><td>hash</td><td>help</td><td>hex</td><td>id</td><td>input</td></tr>
<tr><td>int</td><td>isinstance</td><td>issubclass</td><td>iter</td><td>len</td><td>list</td><td>locals</td><td>map</td></tr>
<tr><td>max</td><td>memoryview</td><td>min</td><td>next</td><td>object</td><td>oct</td><td>open</td><td>ord</td></tr>
<tr><td>pow</td><td>print</td><td>property</td><td>range</td><td>repr</td><td>reversed</td><td>round</td><td>set</td></tr>
<tr><td>setattr</td><td>slice</td><td>sorted</td><td>staticmethod</td><td>str</td><td>sum</td><td>super</td><td>tuple</td></tr>
<tr><td>type</td><td>vars</td><td>zip</td><td>__import__</td></tr>
</table>

If you accedently overwrite any of the built-in function (e.g. list), execute the following to bring built-in defition.
```python
del(list)
```

Similarly, avoid using special charcters and spaces in the column names of the DataFrames.
Execute the following to remove special characters from the column names.
```python
Data = mltk.clean_column_names(Data, replace='')
```

## MLToolkit Example

### Data Loading and exploration
```python
import numpy as np
import pandas as pd
import mltk as mltk

Data = mltk.read_data_csv(file=r'C:\Projects\Data\incomedata.csv')
Data = mltk.clean_column_names(Data, replace='')
Data = mltk.add_identity_column(Data, id_label='ID', start=1, increment=1)
DataStats = mltk.data_description(Data)
```
### Data Pre-processing and Feature Engineering
```python
# Analyze Response Target
print(mltk.variable_frequency(DataFrame=Data, variable='income'))

# Set Target Variables
targetVariable = 'HighIncome'
targetCondition = "income=='>50K'" #For Binary Classification

Data=mltk.set_binary_target(Data, target_condition=targetCondition, target_variable=targetVariable)
print(mltk.variable_frequency(DataFrame=Data, variable=targetVariable))
```
```
        Counts  CountsFraction%
income                         
<=50K    24720         75.91904
>50K      7841         24.08096
TOTAL    32561        100.00000
```
```python
# Flag Records to Exclude
excludeCondition="age < 18"
action = 'flag' # 'drop' #
excludeLabel = 'EXCLUDE'
Data=mltk.exclude_records(Data, exclude_ondition=excludeCondition, action=action, exclude_label=excludeLabel) # )#

# Get list of uniques values in categorical variables
categoryVariables = set({'sex', 'nativecountry', 'race', 'occupation', 'workclass', 'maritalstatus', 'relationship'})
print(mltk.category_lists(Data, list(categoryVariables)))

# Merge unique categorical values
category_merges = [{'variable':'maritalstatus', 'category_variable':'maritalstatus', 'group_value':'Married', 'values':["Married-civ-spouse", "Married-spouse-absent", "Married-AF-spouse"]}]
Data = mltk.merge_categories(Data, category_merges)

# Show Frequency distribution of categorical variable
sourceVariable='maritalstatus'
table = mltk.variable_frequency(Data, variable=sourceVariable, show_plot=False)
table.style.background_gradient(cmap='Greens').set_precision(3)

# Response Rate For Categorical Variables
mltk.variable_responses(Data, variables=categoryVariables, target_variable=targetVariable, show_output=False, show_plot=True)
```
# Get numeric units list
```python
mltk.get_number_units()
```

# Variables Manipulations
```python
# General form
{
	'type':'category'
	'out_type':'cat',
	'include':True,
	'operation':'bucket',
	'variables': {
		'source':'age',
		'destination': None  # None for mult-variable operations, variable1 (for pair operations), variable1a (for pair sequence operation)
	},
        'parameters': {
        'labels_str': ['0', '20', '30', '40', '50', '60', 'INF'],
        'right_inclusive':True,
        "default":'OTHER',
        "null": 'NA'
    }
}
```

```	
List of Avaiable Transformation
 |- Date/Numeric Transformations (transform)
 | |- normalize
 | |- datepart
 | |- dateadd
 | |- log
 | |- exponent
 | |- segment (piecewise functions)
 |- String Transformation (str_transform)
 | |- normalize
 | |- strcount
 | |- extract
 |- Multi-variable Operations (operation_mult)
 | |- expression
 |- Sequence Order Check (seq_order)
 | |- seqorder
 |- Numeric/Date Comparison* (comparison)
 | |- numdiff
 | |- ratio
 | |- datediff
 | |- rowmin (pair)
 | |- rowmax (pair)
 |- String Comparison* (str_comparison)
 | |- levenshtein
 | |- jaccard
 | |- ..more to add ..
 |- Pair comparison

List of Avaiable Discrete Feature Transforms
 |- Binary Variable (condition)
 |- Numeric to Catergory (buckets)
 |- Entity Grouping (dictionary)
 |- Pair Equality/Existance (pair_equality)
 |- Category Merge(category_merge)
```

```python
# Transform numeric variable
rule_set = {
    "operation":"normalize", 
    'variables': {
        'source':'age', 
        'destination':'normalizedage'
    },
    "parameters":{"method":"zscore"}
}
Data, transformed_variable = mltk.create_transformed_variable_task(Data, rule_set, return_variable=True)

# Create Categorical Variables from continious variables
sourceVariable='age'
table = mltk.histogram(Data, sourceVariable, n_bins=10, orientation='vertical', density=True, show_plot=True)
print(table)

# Divide to categories
rule_set = {   
    'operation':'bucket',
    'variables': {
        'source':'age', 
        'destination':None
    },
    'parameters': {
        'labels_str': ['0', '20', '30', '40', '50', '60', 'INF'],
        'right_inclusive':True,
        "default":'OTHER',
        "null": 'NA'
    }
}
Data, categoryVariable = mltk.create_categorical_variable_task(Data, rule_set, return_variable=True)
mltk.variable_response(DataFrame=Data, variable=categoryVariable, target_variable=targetVariable, show_plot=True)
```
```
            Counts  HighIncome  CountsFraction%  ResponseFraction%  ResponseRate%
ageGRP                                                                           
1_(0,20]      2410           2          7.40149            0.02551        0.08299
2_(20,30]     8162         680         25.06680            8.67236        8.33129
3_(30,40]     8546        2406         26.24612           30.68486       28.15352
4_(40,50]     6983        2655         21.44590           33.86048       38.02091
5_(50,60]     4128        1547         12.67774           19.72963       37.47578
6_(60,INF)    2332         551          7.16194            7.02716       23.62779
TOTAL        32561        7841        100.00000          100.00000        0.24081
```

```python
# Create One Hot Encoded Variables
Data, featureVariables, targetVariable = mltk.to_one_hot_encode(Data, category_variables=categoryVariables, binary_variables=binaryVariables, target_variable=targetVariable)
Data[identifierColumns+featureVariables+[targetVariable]].sample(5).transpose()
```
### Correlation
```python
correlation=mltk.correlation_matrix(Data, featureVariables+[targetVariable], target_variable=targetVariable, method='pearson', return_type='list', show_plot=False)
```
### Split Train, Validate Test datasets
```python
TrainDataset, ValidateDataset, TestDataset = mltk.train_validate_test_split(Data, ratios=(0.6,0.2,0.2))
```
### Model Building
```python
identifierColumns = ['ID']
modelDataStats = mltk.data_description(TrainDataset)

sample_attributes = {
                    'SampleDescription':'Adult Census Income Dataset',
                    'NumClasses':2,
                    'ClassLabelsMap':{'<=50K':0, '>50K':1},
                    'DataFormat':'table',
                    'RecordIdentifiers':identifierColumns,
                    'ModelDataStats':modelDataStats
                }                 

score_parameters = {
                    'Edges':[0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
                    'Percentiles':[0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0],
                    'Threshold':0.5,
                    'Quantiles':10,
                    'TargetClass': '>50K',
                    'ScoreVariable':'Probability',
                    'ScoreLabel':'Score',
                    'QuantileLabel':'Quantile',
                    'PredictedLabel':'Predicted'
                }
````

# Classification Models

Model Attributes
```python
model_attributes = {
                    'ModelID': None,
                    'ModelType':'classification',# 'regression'
                    'EnumerationType': 'binary', # 'multi' 'mono' None
                    'ModelName': 'IncomeLevel',
                    'Version':'0.1',
                    'TrainingMethod': 'supervised'                   
                }
```

Losgistic Regression
```python
model_parameters = {
                    'MLAlgorithm':'LGR', # 'RF', #  'NN', # 'CATBST', (# 'CNN',  # 'XGBST')
                    'MaxIterations':50
                }  
```

Random Forest
```python
model_parameters = {
                    'MLAlgorithm':'RF', # 'LGR', #  'NN', # 'CATBST', (# 'CNN',  # 'XGBST')
                    'NTrees':500,
                    'MaxDepth':100,
                    'MinSamplesToSplit':10,
                    'Processors':2,
                    'Verbose':True
                } 
```

Neural Networks
```python
# Setup Architecture
# Binary classification
SimpleDFF_architecture = {'layers': [
        {'name': 'Dense1', 'class_name': 'Dense', 'position':'input', 'config':{'units': 512, 'activation':'relu', 'input_shape':(48,)}},
        {'name': 'Dense2', 'class_name': 'Dense', 'position':'hidden', 'config':{'units': 512, 'activation':'relu', 'kernel_regularizer':{'l1':0.01}}},
        {'name': 'Dropout1', 'class_name': 'Dropout', 'position':'hidden', 'config':{'rate':0.5, 'noise_shape':None, 'seed':None}},
        {'name': 'Dense3', 'class_name': 'Dense', 'position':'output',  'config':{'units': 2, 'activation':'softmax'}}
       ]}

# Binary classification 
LogisticRegressionNN_architecture = {'layers': [
        {'name': 'Dense1', 'class_name': 'Dense', 'position':'input',  'config':{'units': 2, 'activation':'softmax', 'input_shape':(32,)}}
       ]}

# Multi Class classification 
n_classes = 8
SimpleImageClassifier_architecture = {'layers': [
        {'name':'Conv2D1', 'type':'Conv2D', 'position':'input', 'config':{'filters':32, 'kernel_size':(3,3), 'strides':None, 'padding':'same', 'activation':'relu', 'input_shape':(128, 128, 1), 'data_format':'channels_last'}},
        {'name':'MaxPooling2D1', 'type':'MaxPooling2D', 'position':'hidden', 'config':{'pool_size':(2,2), 'strides':None, 'padding':'same', 'data_format':'channels_last'}},      
        {'name':'Conv2D2', 'type':'Conv2D', 'position':'hidden', 'config':{'filters': 64, 'kernel_size': (3,3), 'strides':None, 'padding':'same', 'activation':'relu', 'data_format':'channels_last'}},
        {'name':'MaxPooling2D2', 'type':'MaxPooling2D', 'position':'hidden', 'config':{'pool_size':(2,2), 'strides':None, 'padding':'same', 'data_format':'channels_last'}},       
        {'name':'Dropout1', 'type':'Dropout', 'position':'hidden', 'config':{'rate':0.5, 'noise_shape':None, 'seed':None}},
        {'name':'Flatten1', 'type':'Flatten', 'position':'hidden', 'config':{'data_format':'channels_last'}},
        {'name': 'Dense1', 'type':'Dense', 'position':'output',  'config':{'units': 256, 'activation':'relu', 'kernel_regularizer':None}}, 
        {'name':'Dropout2', 'type':'Dropout', 'position':'hidden', 'config':{'rate':0.5, 'noise_shape':None, 'seed':None}},
        {'name': 'Dense2', 'type':'Dense', 'position':'output',  'config':{'units':n_classes, 'activation':'softmax'}}
    ]}

model_parameters = {
                    'MLAlgorithm':'NN',
                    'BatchSize':512,
                    'InputShape':InputShape,
                    'num_classes':2, #change accordingly
                    'Epochs':10,
                    'metrics':['accuracy'],
                    'architecture':SimpleDFF_architecture,
                    'Verbose':True
                } 
```

CatBoost
```python
model_parameters = {
                    'MLAlgorithm':'CBST',
                    'NTrees': 500,
                    'MaxDepth':10,
                    'LearningRate':0.7,
                    'LossFunction':'Logloss',#crossEntropy
                    'EvalMatrics':'Accuracy',
                    'Imbalanced':False,
                    'TaskType':'GPU',
                    'Processors':2,
                    'UseBestModel':True,
                    'Verbose':True
                }
```

XGBoost
```python
model_parameters = {
                    'MLAlgorithm':'XGBST',
                    'NTrees': 500,
                    'MaxDepth':10,
                    'LearningRate':0.7,
                    'LossFunction':'binary:logistic',
                    'EvalMatrics':['auc', 'error'],
                    'Regularization': {'L1':0.0, 'L2' 1.0},
                    'SamplesRatioPerTree':0.8,
                    'FeaturesRatioPerTree':1.0,
                    'Processors':2,
                    'EarlyStopAttempts':5,
                    'Verbose':True
                }
```

LightGBM
```python
model_parameters = {
                    'MLAlgorithm':'XGBST',
                    'NTrees': 500,
                    'MaxDepth':10,
                    'LearningRate':0.7,
                    'LossFunction':'binary:logistic',
                    'EvalMatrics':['auc', 'error'],
                    'Regularization': {'L1':0.0, 'L2' 1.0},
                    'SamplesRatioPerTree':0.8,
                    'FeaturesRatioPerTree':1.0,
                    'Processors':2,
                    'EarlyStopAttempts':5,
                    'Verbose':True
                }
```   

### Build Model
```python
XModel = mltk.build_ml_model(TrainDataset, ValidateDataset, TestDataset, 
                                  model_variables=modelVariables,
                                  variable_setup = None,
                                  target_variable=targetVariable,
                                  model_attributes=model_attributes, 
                                  sample_attributes=sample_attributes, 
                                  model_parameters=model_parameters, 
                                  score_parameters=score_parameters, 
                                  return_model_object=True, 
                                  show_results=False, 
                                  show_plot=True
                                  )

print(XModel.model_attributes['ModelID'])
print(XModel.model_interpretation['ModelSummary'])
print('ROC AUC: ', XModel.get_auc(curve='roc'))
print('PRC AUC: ', XModel.get_auc(curve='prc'))
print(XModel.model_evaluation['RobustnessTable'])

XModel.plot_eval_matrics(comparison=False)
```

```
          minProbability  maxProbability  meanProbability  BucketCount  ResponseCount  BucketFraction  ResponseFraction  BucketPrecision  CumulativeBucketFraction  CumulativeResponseFraction  CumulativePrecision
Quantile                                                                                                                                                                                                           
1                0.00000         0.00008      3.85729e-06          652            3         0.10011           0.00192          0.00460                   1.00000                     1.00000              0.23967
2                0.00008         0.00432      1.52655e-03          651            9         0.09995           0.00577          0.01382                   0.89989                     0.99808              0.26582
3                0.00435         0.02042      1.10941e-02          652           14         0.10011           0.00897          0.02147                   0.79994                     0.99231              0.29731
4                0.02049         0.05702      3.58648e-02          650           20         0.09980           0.01281          0.03077                   0.69983                     0.98334              0.33677
5                0.05711         0.12075      8.51409e-02          652           65         0.10011           0.04164          0.09969                   0.60003                     0.97053              0.38767
6                0.12086         0.20457      1.63366e-01          651          109         0.09995           0.06983          0.16743                   0.49992                     0.92889              0.44533
7                0.20469         0.31870      2.61577e-01          651          190         0.09995           0.12172          0.29186                   0.39997                     0.85906              0.51478
8                0.31895         0.46840      4.03550e-01          666          259         0.10226           0.16592          0.38889                   0.30002                     0.73735              0.58905
9                0.46854         0.66965      5.68083e-01          641          377         0.09842           0.24151          0.58814                   0.19776                     0.57143              0.69255
10               0.66994         0.99967      8.06834e-01          647          515         0.09934           0.32992          0.79598                   0.09934                     0.32992              0.79598
DataSet          0.00000         0.99967      2.33167e-01         6513         1561         1.00000           1.00000          0.23967                   1.00000                     1.00000              0.23967
```

### Evaluate Model

Plot model performance curves
```python
RFModel.plot_eval_matrics(comparison=True)
LGRModel.plot_eval_matrics(comparison=True)
NNModel.plot_eval_matrics(comparison=True)
CBSTModel.plot_eval_matrics(comparison=True)
```

Area Under Curve (AUC) Comparison
```python
Models = [LGRModel, RFModel, CBSTModel, NNModel]
ModelsComp = mltk.model_guages_comparison(Models)
print(ModelsComp)
```

```
                           Model  PRC_AUC  ROC_AUC
0   INCOMELEVELLGR20190728113633  0.71971  0.88926
1    INCOMELEVELRF20190728113635  0.69348  0.88113
2  INCOMELEVELCBST20190728113703  0.71507  0.88975
3    INCOMELEVELNN20190728113641  0.71396  0.88890
```

Test Model
```python
score_variable = RFModel.get_score_variable()
score_label = RFModel.get_score_label()

TestDataset = mltk.score_processed_dataset(TestDataset, RFModel, edges=None, score_label=None, fill_missing=0)

threshold = 0.8
TestDataset = mltk.set_predicted_columns(TestDataset, score_variable, threshold=threshold)
ConfusionMatrix = mltk.confusion_matrix(TestDataset, actual_variable=targetVariable, predcted_variable='Predicted', labels=[0,1], sample_weight=None, totals=True)
print(ConfusionMatrix)
```

Comparing Models and Probability Thresholds
```python
Models = [LGRModel, RFModel, CBSTModel, NNModel]
thresholds=[0.7, 0.8, 0.9]
ConfusionMatrixComparison = mltk.confusion_matrix_comparison(TestDataset, Models, thresholds, score_variable=None, show_plot=True)
ConfusionMatrixComparison.style.background_gradient(cmap='RdYlGn').set_precision(3)
```

Comparing Models and Threshold Score (1-10 Scale)
```python
Models = [LGRModel, RFModel, CBSTModel, NNModel]
thresholds=[7, 8, 9]
ConfusionMatrixComparison = mltk.confusion_matrix_comparison(TestDataset, Models, thresholds, score_variable=score_label, show_plot=True)
ConfusionMatrixComparison.style.background_gradient(cmap='RdYlGn').set_precision(3)
```

Set Custom Score Edges
``` python
RobustnessTable, ROCCurve, PrecisionRecallCurve, roc_auc, prc_auc = mltk.model_performance_matrics(ResultsSet=TestDataset, target_variable=targetVariable, score_variable=score_variable, quantile_label='Quantile',  quantiles=100, show_plot=True)
print('ROC AUC', roc_auc)
print('PRC AUC', prc_auc)

print(RobustnessTable)

# Examine cutoffs
quantiles=[0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
edges, threshold = mltk.get_score_cutoffs(ResultsSet=TestDataset, quantiles=quantiles, target_variable=targetVariable, score_variable=scoreVariable)
print('Threshold', threshold)
print('Edges', edges)

# Re-bin score buckets
edges = [0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.75, 0.95, 1.0]
LGRModel.set_score_edges(edges)
```

# Regression Models

Model Attributes
```python
model_attributes = {
                    'ModelID': None,   
                    'ModelType':'regression',
                    'EnumerationType': None,
                    'ModelName': 'Income',
                    'Version':'0.1',
                    'TrainingMethod': 'supervised'  
                }
```                    

```python
model_parameters = {
                    'MLAlgorithm':'RFREG', # 'RFREG'
                    'NTrees':200,
                    'MaxDepth':10,
                    'MinSamplesToSplit':6,
                    'Processors':2
                } 
model_parameters = {'MLAlgorithm':'LREG', 'MaxIterations':100}
```

```python
REGModel = mltk.build_ml_model(TrainDataset, ValidateDataset, TestDataset, 
                                  model_variables=modelVariables,
                                  variable_setup = None,
                                  target_variable=targetVariable,
                                  model_attributes=model_attributes, 
                                  sample_attributes=sample_attributes, 
                                  model_parameters=model_parameters, 
                                  score_parameters=score_parameters, 
                                  return_model_object=True, 
                                  show_results=False, 
                                  show_plot=False
                                  )
```

```
print(REGModel.model_attributes['ModelID'])
print(REGModel.model_interpretation['ModelSummary'])
print('RMSE =', SelectModel.get_rmse())
print('R^2 =', SelectModel.get_r2())
REGModel.plot_eval_matrics(comparison=True)
SelectModel.plot_eval_matrics(comparison=True)
```

Save model
```python
saveFilePath = '{}.pkl'.format(XModel.get_model_id())
mltk.save_model(XModel, saveFilePath)
```

### Deployment
Simplified MLToolkit ETL pipeline for scoring and model re-building (Need to customize based on the project).
<img src="https://raw.githubusercontent.com/sptennak/MLToolkit/master/MLToolkit/image/MLTKServing.png" height="300">

Define ETL Function
```python
def ETL(DataFrame, variables_setup_dict=None):
    # Add ID column
    DataFrame = mltk.add_identity_column(DataFrame, id_label='ID', start=1, increment=1)

    # Clean column names
    DataFrame = mltk.clean_column_names(DataFrame, replace='')
    input_columns = list(DataFrame.columns)

	if variables_setup_dict==None:
		variables_setup_dict = """   
		{
			"setting":"score",

			"variables": {            
					"category_variables" : ["sex", "race", "occupation", "workclass", "maritalstatus", "relationship"],
					"binary_variables": [],
					"target_variable":"HighIncome"
			},

			"preprocess_tasks": [
				{
					"type": "transform",
					"out_type":"cnt",
					"include": false,
					"operation": "normalize",
					"variables": {
						"source": "age",
						"destination": "normalizedage"
					},
					"parameters": {
						"method": "zscore"
					}
				},
				{
					"type": "category_merge",
					"out_type":"cat",
					"include": true,
					"operation": "catmerge",
					"variables": {
						"source": "maritalstatus",
						"destination": "maritalstatus"
					},
					"parameters": {
						"group_value": "Married",
						"values": [ "Married-civ-spouse", "Married-spouse-absent", "Married-AF-spouse" ]
					}
				},
				{
					"type": "entity",
					"out_type":"cat",
					"include": true,
					"operation": "dictionary",
					"variables": {
						"source": "nativecountry",
						"destination": "nativecountryGRP"
					},
					"parameters": {
						"match_type": null,
						"dictionary": [
							{
								"entity": "USA",
								"values": [ "United-States" ],
								"case": true
							},
							{
								"entity": "Canada",
								"values": [ "Canada" ],
								"case": true
							},
							{
								"entity": "OtherAmericas",
								"values": [ "South", "Mexico", "Trinadad&Tobago", "Jamaica", "Peru", "Nicaragua", "Dominican-Republic", "Haiti", "Ecuador", "El-Salvador", "Columbia", "Honduras", "Guatemala", "Puerto-Rico", "Cuba", "Outlying-US(Guam-USVI-etc)"],
								"case": true
							},
							{
								"entity": "Europe-Med",
								"values": [ "Greece", "Holand-Netherlands", "Poland", "Iran", "England", "Germany", "Italy", "Ireland", "Hungary", "France", "Yugoslavia", "Scotland", "Portugal" ],
								"case": true
							},
							{
								"entity": "Asia",
								"values": [ "Vietnam", "China", "Taiwan", "India", "Philippines", "Japan", "Hong", "Cambodia", "Laos", "Thailand" ],
								"case": true
							},
							{
								"entity": "Other",
								"values": [ "?" ],
								"case": true
							}
						],
						"null": "NA",
						"default": "OTHER"
					}
				},
				{
					"type": "category",
					"out_type":"cat",
					"include": true,
					"operation": "bucket",
					"variables": {
						"source": "age",
						"destination": null
					},
					"parameters": {
						"labels_str": [ "0", "20", "30", "40", "50", "60", "INF" ],
						"right_inclusive": true,
						"default": "OTHER",
						"null": "NA"
					}
				},
				{
					"type": "category",
					"out_type":"cat",
					"include": true,
					"operation": "bucket",
					"variables": {
						"source": "educationnum",
						"destination": null
					},
					"parameters": {
						"labels_str": [ "1", "5", "8", "9", "12", "16" ],
						"right_inclusive": true,
						"default": "OTHER",
						"null": "NA"
					}
				},
				{
					"type": "category",
					"out_type":"cat",
					"include": true,
					"operation": "bucket",
					"variables": {
						"source": "hoursperweek",
						"destination": null
					},
					"parameters": {
						"labels_str": [ "0", "20", "35", "40", "60", "INF" ],
						"right_inclusive": true,
						"default": "OTHER",
						"null": "NA"
					}
				}
			]
		}
		"""

    DataFrame, categoryVariables, binaryVariables, targetVariable = mltk.setup_variables_task(DataFrame, variables_setup_dict)

    # Create One Hot Encoded Variables
    DataFrame, featureVariables, targetVariable = mltk.to_one_hot_encode(DataFrame, category_variables=categoryVariables, binary_variables=binaryVariables, target_variable=targetVariable)

    return DataFrame, input_columns
```

Scoring/Ranking
```python
MLModelObject = mltk.load_model(saveFilePath)
SampleDataset = pd.read_csv(r'test.csv')
SampleDataset = ETL(SampleDataset)

SampleDataset = mltk.score_processed_dataset(SampleDataset, MLModelObject, edges=None, score_label=None, fill_missing=0)
Robustnesstable1 = mltk.robustness_table(ResultsSet=SampleDataset, class_variable=targetVariable, score_variable=score_variable,  score_label=score_label, show_plot=True)
```

```python
MLModelObject = mltk.load_model(saveFilePath)

TestInput = """
{
      "ID": "A001",
      "age": 32,
      "workclass": "Private",
      "education": "Doctorate",
      "education-num": 16,
      "marital-status": "Married-civ-spouse",
      "occupation": "Prof-specialty",
      "relationship": "Husband",
      "race": "Asian-Pac-Islander",
      "sex": "Male",
      "capital-gain": 0,
      "capital-loss": 0,
      "hours-per-week": 40,
      "native-country": "?"
}
"""
output = mltk.score_records(TestInput, MLModelObject, edges=None, ETL=ETL, return_type='dict') # Other options for return_type, {'json', 'frame'}
```
Output
```python
[{'ID': 'A001',
 'age': 32,
 'capitalgain': 0,
 'capitalloss': 0,
 'education': 'Doctorate',
 'educationnum': 16,
 'hoursperweek': 40,
 'maritalstatus': 'Married',
 'nativecountry': '?',
 'occupation': 'Prof-specialty',
 'race': 'Asian-Pac-Islander',
 'relationship': 'Husband',
 'sex': 'Male',
 'workclass': 'Private',
 'Probability': 0.6790258814478549,
 'Score': 7}]
```

### Model Output Explanation (Using SHAP and LIME Python libraries)
```python
# Create Explainer
Explainer = mltk.build_explainer(MLModelObject, explainer_config={'IdColumns':['ID'], 'Method':'shap', 'ClassNumber':1, 'FillMissing':0})

save_file_path = '{}_Explainer.pkl'.format(MLModelObject.get_model_id())
mltk.save_explainer(Explainer, save_file_path)

Explainer = mltk.load_explainer(save_file_path)
```
```python
# Calculate Impact Values
ImpactValues, VariableValues = mltk.get_explainer_values_task(DataFrame, Explainer=Explainer, verbose=False)

# Plot Variable Impact
# force_plot
explainer_visual = mltk.get_explainer_visual(ImpactValues, VariableValues, Explainer, visual_config={'figsize':[20,4], 'text_rotation':90})

# Generate Explain Summary
explainer_summary = mltk.get_shap_impact_summary(ImpactValues, VariableValues, Explainer.get_model_variables(), iloc=0, top_n=5, show_plot=True)

explainer_report, explain_plot = mltk.get_explainer_report(DataFrame, Explainer, top_n=10, show_plot=True, return_type='frame')
```

### JSON Input for scoring

Records Format for single or fewer number of records
```json
[{
	"ID": "A001",
	"age": 32,
	"workclass": "Private",
	"education": "Doctorate",
	"occupation": "Prof-specialty",
	"sex": "Female",
	"hoursperweek": 40,
	"nativecountry": "USA"
}]
```

Split Format for mulltiple records
```json
{
	"columns":["ID","age","education","hoursperweek","nativecountry","occupation","sex","workclass"],
	"data":[["A001",32,"Doctorate",40,"USA","Prof-specialty","Female","Private"]]
}
```

Using Model Chest to Deploy Models
```python
MyModelChest = mltk.ModelChest()
MyModelChest.add_model(model_key='test', model_file=None, model_object=MLModelObject, replace=False)
MyModelChest.save_model_chest()
MyModelChest.get_model_chest_json()
```

load Models from Model Chest
```python
lodedModel = MyModelChest.get_model_object('test')
lodedModel.get_model_manifest()
```

## Working with Image Data
```python
size=(96, 64)
file_folder_path = r'C:\Projects\Data\images\train'
ImagesDataFrame = mltk.read_image_folder(file_folder_path, size=size, show_image=False)
```

```python
ImagesDataFrame, input_shape = mltk.prepare_image_dataset_to_model(ImagesDataFrame, 
                                                             image_column='Image', 
                                                             processed_image_column='ImageToModel',
                                                             label_column='Label',
                                                             image_data_format='channels_last', 
                                                             size=size)

```
### Building CNN Model
```python
sample_attributes = {'SampleDescription':'Image CLassification Example',
                    'NumClasses':NClasses,
                    'ClassLabels':ClassLabels,
                    'DataFormat':'image',
                    'RecordIdentifiers':identifierColumns,
                    'ModelDataStats':modelDataStats
                    }                        

score_parameters = {'Edges':[0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
                    'Percentiles':[0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0],
                    'Threshold':0.5,
                   'Quantiles':10,
                   'ScoreVariable':'Probability',
                   'ScoreLabel':'Score',
                   'QuantileLabel':'Quantile',
                   'PredictedLabel':'Predicted'
                   }

model_attributes = {
                    'ModelID': None,   
                    'ModelType':'classification',
                    'EnumerationType': 'multi', # 'binary' 'mono' None
                    'ModelName': 'ImageTest',
                    'Version':'0.1',
                    'TrainingMethod': 'supervised' 
                   }

architecture = {'layers': [
        {'name':'Conv2D1', 'type':'Conv2D', 'position':'input', 'config':{'filters':32, 'kernel_size':(3,3), 'strides':None, 'padding':'same', 'activation':'relu', 'input_shape':input_shape, 'data_format':'channels_last'}},
        {'name':'MaxPooling2D1', 'type':'MaxPooling2D', 'position':'hidden', 'config':{'pool_size':(2,2), 'strides':None, 'padding':'same', 'data_format':'channels_last'}},      
        {'name':'Conv2D2', 'type':'Conv2D', 'position':'hidden', 'config':{'filters': 64, 'kernel_size': (3,3), 'strides':None, 'padding':'same', 'activation':'relu', 'data_format':'channels_last'}},
        {'name':'MaxPooling2D2', 'type':'MaxPooling2D', 'position':'hidden', 'config':{'pool_size':(2,2), 'strides':None, 'padding':'same', 'data_format':'channels_last'}},       
        {'name':'Dropout1', 'type':'Dropout', 'position':'hidden', 'config':{'rate':0.5, 'noise_shape':None, 'seed':None}},
        {'name':'Flatten1', 'type':'Flatten', 'position':'hidden', 'config':{'data_format':'channels_last'}},
        {'name': 'Dense1', 'type':'Dense', 'position':'output',  'config':{'units': 256, 'activation':'relu', 'kernel_regularizer':None}}, 
        {'name':'Dropout2', 'type':'Dropout', 'position':'hidden', 'config':{'rate':0.5, 'noise_shape':None, 'seed':None}},
        {'name': 'Dense2', 'type':'Dense', 'position':'output',  'config':{'units':n_classes, 'activation':'softmax'}}
    ]}	

model_parameters = {'MLAlgorithm':'CNN',
                    'BatchSize':128,
                   'InputShape':inputShape,
                   'NumClasses':NClasses,
                   'Epochs':50,
                   'EvalMatrics':['accuracy'],
                   'Architecture':architecture} 

CNNModel = mltk.build_ml_model(TrainDataset, ValidateDataset, TestDataset, 
                                  model_variables=modelVariables,
                                  variable_setup = None,
                                  target_variable=targetVariable,
                                  model_attributes=model_attributes, 
                                  sample_attributes=sample_attributes, 
                                  model_parameters=model_parameters, 
                                  score_parameters=score_parameters, 
                                  return_model_object=True, 
                                  show_results=False, 
                                  show_plot=True
                                  )

CNNModel.plot_eval_matrics()						  
```

## License
```
Copyright 2019-2020 Sumudu Tennakoon

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
```

## Cite as
```
@misc{mltk2019,
  author =  "Sumudu Tennakoon",
  title = "MLToolKit(mltk): A Simplified Toolkit for Unifying End-To-End Machine Learning Projects",
  year = 2019,
  publisher = "GitHub",
  howpublished = {\url{https://mltoolkit.github.io/mltk/}},
  version = "0.1.11",
  doi = "https://doi.org/10.5281/zenodo.3596163"
}
```

## MLToolKit Project Timeline
- 2018-07-02 [v0.0.1]: Initial set of functions for data exploration, model building and model evaluation was published to Github. (https://github.com/sptennak/MachineLearning).
- 2018-01-03 [v0.0.2]: Created more functions for data exploration including web scraping and geo spacial data analysis for for IBM Coursera Data Science Capstone Project was published to Github. (https://github.com/sptennak/Coursera_Capstone).
- 2019-03-20 [v0.1.0]: Developed and published initial version of model building and serving framework for IBM Coursera Advanced Data Science Professional Certificate Capstone Project. (https://github.com/sptennak/IBM-Coursera-Advanced-Data-Science-Capstone).
- 2019-07-02 [v0.1.2]: First release of the PyMLToolkit Python package, a collection of clases and functions facilitating end-to-end machine learning model building and serving over RESTful API.
- 2019-07-04 [v0.1.3]: Minor bug fixes.
- 2019-07-14 [v0.1.4]: Improved documentation, Integrated TensorFlow Models, Enhancements and Minor bug fixes.
- 2019-07-28 [v0.1.5]: Integrated CatBoost Models, Improved model building and serving frameework, text analytics functions, support JSON input/output to the ML model bulding and scoring processes, Enhancements and bug fixes.
- 2019-08-12 [v0.1.6]: Improved Features, Bug Fixes, Enhanced JSON input/output to the ML model bulding and scoring processes (JSON-MLS) and bug fixes.
- 2019-08-31 [v0.1.7] : Added more data processing functions, Enhanced output formats, Enhanced model deployment, Overall improvements and bug fixes.
- 2019-09-28 [v0.1.8] : Improved Documentation, Enhancements and bug fixes.
- 2019-12-07 [v0.1.9] : Added model explainability, Integrate image classification model Deployment, Enhancements and bug fixes.
- 2019-12-31 [v0.1.10] : Improved data read write functions, Enhancements and bug fixes, Improved Documentation.
- 2020-02-12 [v0.1.11] : Enhanced Support to Gradient Boosting and Neural Network algorithms, Bug fixes, Improved Documentation.

## Future Release Plan
- TBD [v0.1.x1] : Support multi-class classification, Improved Data Pre-processing, EDA/Data Profiling and Vizualization functions, Enhancements and bug fixes.
- TBD [v0.1.x2] : Working with Imbalanced Samples, Integrate Cross-validation, Post additional tutorials and examples, Improve Documentation, Enhancements and bug fixes.
- TBD [v0.1.x3] : Building Ensamble Models, UI Preview, Improved Feature Selection, Cross-validation and Hyper parameter tuning functionality, Enhancements and bug fixes.
- TBD [v0.1.X5]: ML Model Building Projects, Enhancements and bug fixes.
- 2019-12-31 [v0.1.x6]:Comprehensive documentation, Post implementation evaluation functions, Enhanced Data Input and Output functios, Major bug-fix version of the initial release with finalized enhancements.
- TBD [v0.2.0]: Imporved model building and serving frameework and UI, Support more machine learning algorithms, Improved multi-class classification and enhanced text analytics functions.
- TBD [v0.3.0]: Imporved scalability and performance, Automated Machine Learning, Integrate GUI.
- TBD [v0.4.0]: Building continious learning models.

## Acknowledgement and Remarks
Some functions of MLToolKit depends on number of Open Source Python Libraries such as
- Data Manipulation : Pandas
- Machine Learning: Statsmodels, Scikit-learn, Catboost, XGBoost, LightGBM
- Deep Learning: Tensorflow, 
- Model Interpretability: Shap, Lime
- Server Framework: Flask
- Text Processing: BeautifulSoup, TextLab
- Database Connectivity: SQLAlchemy, PyODBC
MLToolkit Project acknowledge the creators and contributors of the above libraries for their contribution to the Open Source Community.

MLToolKit library and some novel concepts introduced with original ideas of the author implemented as an effort of putting together the lifetime learning and experience working on multiple data science projects to a good use and as a contribution back to the Open Source Community. 

Author would like to thank number of content creators in the data science and machine learning topics not limited to online learning platforms and blogs for making aviable insightful resources to explore and learn the subject. A complete reference list will be published with a future version...

As a Free and Open Source initiative and a independent R&D project, author has no conflict of interest or, financial interest to the MLToolKit library. However, proper mention of the source abiding the License Terms is highly appreciated when the library itself or any useful concepts or parts are used. 

MLToolKit is set to evolve with adding more features and functionality, and interoperability with more standard data science and machine learning libraries. MLToolKit will always be available as Free and Open Source Python library in the future.

## References
- https://pandas.pydata.org
- https://scikit-learn.org
- https://www.tensorflow.org
- https://keras.io
- https://www.numpy.org
- https://docs.python.org/3.6/library/re.html
- https://www.statsmodels.org
- https://matplotlib.org
- http://flask.pocoo.org
- https://catboost.ai
- https://xgboost.readthedocs.io
- https://lightgbm.readthedocs.io
- https://github.com/slundberg/shap
- https://github.com/marcotcr/lime
- http://json.org
- https://pillow.readthedocs.io