discovery-transition-ds 3.4.18

Advanced data cleaning, data wrangling and feature extraction tools for ML engineers

Contents

• 1 Filling the Gap - Project Hadron

• 2 Main features

• 3 Background

• 4 Getting Started

• 5 Installation

• 6 Building a Component

  • 6.1 Getting Started

  • 6.2 Run Component Pipeline

  • 6.3 Reloading and Extending our Component

  • 6.4 Environment Variables

• 7 Building a Pipeline

  • 7.1 Setting Up

  • 7.2 Adding Select Actions

  • 7.3 Featutres of Interest

  • 7.4 Run Component Pipeline

  • 7.5 Ordering the Actions of a Component

  • 7.6 Component Pipeline

  • 7.7 Run Books

• 8 Reference

  • 8.1 Python version

  • 8.2 Pandas version

  • 8.3 GitHub Project

  • 8.4 Change log

  • 8.5 Licence

  • 8.6 Authors

1 Filling the Gap - Project Hadron

Project Hadron has been built to bridge the gap between data scientists and data engineers. More specifically between machine learning business outcomes and the final product.

Project Hadron is a core set of abstractions that are the foundation of the three key elements that represent data science, those being: (1) feature engineering, (2) the construction of synthetic data with simulators, and generators (3) and statistics and machine learning algorithms for discovery and creating models. Project Hadron uniquely sees data as ‘all the same’ (lazyprogrammer (2020) https://lazyprogrammer.me/all-data-is-the-same/) , by which we mean its origin, shape and size stay independent throughout the disciplines so its content, form and structure can be removed as a factor in the design and implementation of the components built.

Project Hadron has been designed to place data scientists in the familiar environment of machine learning and statistical tools, extracting their ideas and translating them automagicially into production ready solutions familiar to data engineers and Subject Matter Experts (SME’s).

Project Hadron provides a clear Separation of Concerns, whilst maintaining the original intentions of the data scientist, that can be passed to a production team. It offers trust between the data scientists teams and product teams. It brings with it transparency and traceability, dealing with bias, fairness, and knowledge. The resulting outcome provides the product engineers with adaptability, robustness, and reuse; fitting seamlessly into a microservices solution that can be language agnostic.

At the heart of Project Hardon is a multi-tenant, NoSQL, singleton, in memory data store that has minimal code and functionality and has been custom built specifically for Hadron tasks in mind. Abstracted from this is the component store which allows us to build a reusable set of methods that define each tenanted component that sits separately from the store itself. In addition, a dynamic key value class provides labeling so that each tenant is not tied to a fixed set of reference values unless by specificity. Each of the classes, the data store, the component property manager, and the key value pairs that make up the component are all independent, giving complete flexibility and minimum code footprint to the build process of new components.

This is what gives us the Domain Contract for each tennant which sits at the heart of what makes the contracts reusable, translatable, transferable and brings the data scientist closer to the production engineer along with building a production ready component solution.

2 Main features

• Data Preparation

• Feature Selection

• Feature Engineering

• Feature Cataloguing

• Augmented Knowledge

• Synthetic Feature Build

3 Background

Born out of the frustration of time constraints and the inability to show business value within a business expectation, this project aims to provide a set of tools to quickly build production ready data science disciplines within a component based solution demonstrating coupling and cohesion between each disipline, providing a separation of concerns between components.

It also aims to improve the communication outputs needed by ML delivery to talk to Pre-Sales, Stakholders, Business SME’s, Data SME’s product coders and tooling engineers while still remaining within familiar code paradigms.

4 Getting Started

The discovery-transition-ds package is a set of python components that are focussed on Data Science. They are a concrete implementation of the Project Hadron abstract core. It is build to be very light weight in terms of package dependencies requiring nothing beyond what would be found in an basic Data Science environment. Its designed to be used easily within multiple python based interfaces such as Jupyter, IDE or command-line python.

5 Installation

package install

The best way to install AI-STAC component packages is directly from the Python Package Index repository using pip. All AI-STAC components are based on a pure python foundation package aistac-foundation

$ pip install aistac-foundation

The AI-STAC component package for the Transition is discovery-transition-ds and pip installed with:

$ pip install discovery-transition-ds

if you want to upgrade your current version then using pip install upgrade with:

$ pip install --upgrade discovery-transition-ds

6 Building a Component

This tutorial shows the fundamentals of how to run a basic Project Hadron component. It is the simpliest form of running a task demonstrating the input, throughput and output of a dataset. Each instance of the component is given a unique reference name whereby the Domain Contract uses that name as its unique identifier and thus can be used to reference the said Domain Contract for the purposes of referencing and reloading. Though this may seem complicated at this early stage it is important to understand the relationship between a named component and its Domain Contract.

6.1 Getting Started

Firstly we have imported a component from the Project Hadron library for this demonstration. It should be noted, the choice of component is arbritary for this demonstration, as even though each component has its own unique set of tasks it also has methods shared across all components. In this demonstration we only use these common tasks, this is why our choice of component is arbitrary.

from ds_discovery import Transition

To create a Domain Contract instance of the component we have used the Factory method from_env and given it a referenceable name hello_comp, and as this is the first instantiation, we have used the one off parameter call has_contract that by default is set to True and is used to avoid the accidential loading of a Domain Contract instance of the same task name. As common practice we capture the instance of this specific componant transition as tr.

tr = Transition.from_env('hello_comp', has_contract=False)

We have set where the data is coming from and where the resulting data is going to. The source identifies a URI (URL) from which the data will be collected and in this case persistance uses the default settings, more on this later.

tr.set_source_uri('https://www.openml.org/data/get_csv/16826755/phpMYEkMl.csv')
tr.set_persist()

6.2 Run Component Pipeline

To run a component we use the common method run_component_pipeline which loads the source data, executes the component task then persists the results. This is the only method you can use to run the tasks of a component and produce its results and should be a familiarized method.

tr.run_component_pipeline()

This concludes building a component and though the component doesn’t change the throughput, it shows the core steps to building any component.

6.3 Reloading and Extending our Component

Though this is a single notebook, one of the powers of Project Hadron is the ability to reload componant state across new notebooks, not just locally but even across locations and teams. To load our componant state we use the same factory method from_env passing the unique component name hello_comp which reloads the Domain Contract. We have now reinstated our origional component state and can continue to work on this component.

tr = Transition.from_env('hello_comp')

Lets look at a sample of some commonly used features that allow us to peek inside our components. These features are extremely useful to navigate the component and should become familiar.

The first and probably most useful method call is to be able to retrieve the results of run_component_pipeline. We do this using the component method load_persist_canonical. Because of the retained state the component already knows the location of the results, and in this instance returns a report.

Note: All the components from a package internally work with a canonical data set. With this package of components, because they are data science based, use Pandas Dataframes as their canonical, therefore wherever you see the word canonical this will relate to a Pandas Dataframe.

df = tr.load_persist_canonical()

The second most used feature is the reporting tool for the canonical. It allows us to look at the results of the run as an informative dictionary, this gives a deeper insight into the canonical results. Though unlike other reports it requests the canonical of interest, this means it can be used on a wider trajectory of circumstances such as looking at source or other data that is being injested by the task.

Below we have an example of the processed canonical where we can see the results of the pipeline that was persisted. The report has a wealth of information and is worth taking time to explore as it is likely to speed up your data discovery and the understanding of the dataset.

tr.canonical_report(df)

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When we set up the source and persist we use something called Connector contracts, these act like brokers between external data and the internal canonical. These are powerful tools that we will talk more about in a dedicated tutorial but for now consider them as the means to talk data to different data storage solutions. In this instance we are only using a local connection and thus a Connector contract that manages this type of connectivity.

In order to report on where the source and persist are located, along with any other data we have connected to, we can use report_connectors which gives us, in part, the name of the connector and the location of the data.

tr.report_connectors()

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This gives a flavour of the tools available to look inside a component and time should be taken viewing the different reports a component offers.

6.4 Environment Variables

To this point we have using the default settings of where to store the Domain Contract and the persisted dataset. These are in general local and within your working directory. The use of environment variables frees us up to use an extensive list of connector contracts to store the data to a location of the choice or requirements.

Hadron provides an extensive list of environment variables to tailor how your components retrieve and persist their information, this is beyond the scope of this tutorial and tend to be for specialist use, therefore we are going to focus on the two most commonly used for the majority of projects.

We initially import Python’s os package.

import os

In general and as good practice, most notebooks would run a set up file that contains imports and environment variables that are common across all notebooks. In this case, for visibility, because this is a tutorial, we will import the packages and set up the two environment variables within each notebook.

The first environment variable we set up is for the location of the Domain Contract, this is critical to the components and the other components that rely on it (more of this later). In this case we are setting the Domain Contract location to be in a common local directory of our naming.

os.environ['HADRON_PM_PATH'] = '0_hello_meta/demo/contracts'

The second environment variable is for the location of where the data is to be persisted. This allows us to place data away from the working files and have a common directory where data can be sourced or persisted. This is also used internally within the component to avoid having to remember where data is located.

os.environ['HADRON_DEFAULT_PATH'] = '0_hello_meta/demo/data'

As a tip we can see where the default path environment variable is set by using report_connectors. By passing the parameter inc_template=True to the report_connectors method, showing us the connector names. By each name is the location path (uri) where, by default, the component will source or persist the data set, this is taken from the environment variable set. Likewise we can see where the Domain Contract is being persisted by including the parameter inc_pm giving the location path (uri) given by the environment variable.

tr.report_connectors(inc_template=True)

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Because we have now changed the location of where the Domain Contract can be found we need to reset things from the start giving the source location and using the default persist location which we now know has been set by the environment variable.

tr = Transition.from_env('hello_tr,', has_contract=False)

tr.set_source_uri('https://www.openml.org/data/get_csv/16826755/phpMYEkMl.csv')
tr.set_persist()

Finally we run the pipeline with the new environemt variables in place and check everything runs okay.

tr.run_component_pipeline()

And we are there! We now know how to build a component and set its environment variables. The next step is to build a real pipeline and join that with other pipelines to construct our complete master Domain Contract.

7 Building a Pipeline

Now we know what a component looks like we can start to build the pipeline adding in actions that gives the component purpose.

The first component we will build as part of the pipeline is the data selection component with the class name Transition. This component provides a set of actions that focuses on tidying raw data by removing data columns that are not useful to the final feature set. These may include null columns, single value columns, duplicate columns and noise etc. We can also ensure the data is properly canonicalised through enforcing data typing.

Project Hadron Canonicalizes data following the canonical model pattern so that every component speaks the same data language. In this case and with this package all components use Pandas DataFrame format. This is common format used by data scientists and statisticians to manipulate and visualise large data sets.

7.1 Setting Up

Before we do that, and as shown in the previous section, we now use the environment variables to define the location of the Domain Contract and datastore.

import os

os.environ['HADRON_PM_PATH'] = '0_hello_meta/demo/contracts'
os.environ['HADRON_DEFAULT_PATH'] = '0_hello_meta/demo/data'

For the feature selection we are using the Transition component with the ability to select the correct columns from raw data, potentially reducing the column count. In addition the Transistioning component extends the common reporting tools and provides additional functionality for identifying quality, quantity, veracity and availability.

It should be worth noting we are creating a new component and as such must set up the input and the output of the component.

from ds_discovery import Transition

# get the instance
tr = Transition.from_env('hello_tr', has_contract=False)

tr.set_source_uri('https://www.openml.org/data/get_csv/16826755/phpMYEkMl.csv')
tr.set_persist()

7.2 Adding Select Actions

At the core of a component is its tasks, in other words how it changes incoming data into a different data outcome. To achieve this we use the actions that are set up specificially for this Component. These actions are the intensions of the specific component also know as the components intent. The components intent is a finate set of methods, unique to each component, that can be applied to the raw data in order to change it in a way that is useful to the outcome of the task.

In order to get a list of a component’s intent, in this case feature selection, you can use the Python method __dir__(). In this case with the transition component tr we would use the comand tr.tools.__dir__()to produce the directory of the components select intent. Remember this method call can be used in any components intent tools.

Now we have added where the raw data is situated we can load the canonical, called, df…

df = tr.load_source_canonical()

…and produce the report on the raw data so we can observe the features of interest.

tr.canonical_report(df)

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7.3 Featutres of Interest

The components intent methods are not first class methods but part of the intent_model_class. Therefore to access the intent specify the controller instance name, in this case tr, and then reference the intent_model_class to access the components intent. To make this easier to remember with an abbreviated form we have overloaded the intent_model name with the name tools. You can see with all reference to the intent actions they start with tr.tools.

When looking for features of interest, through observation, it appears, within some columns space has been repalaced by a question mark ?. In this instance we would use the auto_reinstate_nulls to replace all the obfusacted cells with nulls. In addition we can immediately observe columns that are inappropriate for our needs. In this case we do not need the column name and it is removed using to_remove passing the name of the attribute.

# returns obfusacted nulls
df = tr.tools.auto_reinstate_nulls(df, nulls_list=['?'])
# removes data columns of no interest
df = tr.tools.to_remove(df, headers=['name'])

7.4 Run Component Pipeline

To run a component we use the common method run_component_pipeline which loads the source data, executes the component task then persists the results. This is the only method you can use to run the tasks of a component and produce its results and should be a familiarized method.

We can now run the run_component_pipeline and use the canonical report to observe the outcome. From it we can see the nulls column now indicates the number of nulls in each column correctly so we can deal with them later. We have also removed the column name.

tr.run_component_pipeline()
tr.canonical_report(tr.load_persist_canonical())

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As we continue the observations we see more columns that are of limited interest and need to be removed as part of the selection process. Because the components intent action is mutable we can re-implement the to_remove including the new headers within the list. As this overwrites the original component intent we must make sure to include the name Column.

df = tr.tools.to_remove(df, headers=['name', 'boat', 'body', 'home.dest'])

As the target is a cluster algorithm we can use the auto_to_category to ensure the data typing is appropriate to the column type.

df = tr.tools.auto_to_category(df, unique_max=20)

Finally we ensure the two contigious columns are set to numeric type. It is worth noting though age is an interger, Python does not recognise nulls within an interger type and automaticially choses it as a float type.

df = tr.tools.to_numeric_type(df, headers=['age', 'fare'])

Using the Intent reporting tool to check the work and see what the Intent currently looks like all together.

tr.report_intent()

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Adding these actions or the components intent is a process of looking at the raw data and the observer making decisions on the selection of the features of interest. Therefore component selection is potentially an iterative task where we would add component intent, observe the changes and then repeat until the process is complete.

7.5 Ordering the Actions of a Component

With the component intent now defined the run pipeline does its best to guess the best order of that Intent but sometimes we want to ensure things run in a certain order due to dependancies or other challenges. Though not necessary, we will clear the previous Intent and write it again, this time in order.

tr.remove_intent()

This time when we add the Intent we include the parameter intent_level to indicate the different order or level of execution.

We load the source canonical and repeat the Intent, this time including the new intent level.

df = tr.load_source_canonical()

df = tr.tools.auto_reinstate_nulls(df, nulls_list=['?'], intent_level='reinstate')
df = tr.tools.to_remove(df, headers=['name', 'boat', 'body', 'home.dest'], intent_level='remove')
df = tr.tools.auto_to_category(df, unique_max=20, intent_level='auto_category')
df = tr.tools.to_numeric_type(df, headers=['age', 'fare'], intent_level='to_dtype')
df = tr.tools.to_str_type(df, headers=['cabin', 'ticket'],use_string_type=True , intent_level='to_dtype')

In addition, and as an introduction to a new feature, we will add in the column description that describes the reasoning behind why an Intent was added.

tr.add_column_description('reinstate', description="reinstate nulls that where obfuscated with '?'")
tr.add_column_description('remove', description="remove column of no value")
tr.add_column_description('auto_category', description="auto fit features to categories where their uniqueness is 20 or less")
tr.add_column_description('to_dtype', description="ensure all other columns of interest are appropriately typed")

Using the report we can see the addition of the numbers, in the level column, which helps the run component run the tasks in the order given. It is worth noting that the tasks can be given the same level if the order is not important and the run component will deal with it using its ordering algorithm.

tr.report_intent()

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As we have taken the time to capture the reasoning to include the compoment Intent we can use the reports to produce a view of the Intent column comments that are invaluable when interrogating a component and understanding why decisions were made.

tr.report_column_catalog()

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7.6 Component Pipeline

As usual we can now run the Compant pipeline to apply the components tasks.

tr.run_component_pipeline()

As an extension of the default, run_component_pipeline provides useful tools to help manage the outcome. In this case we’ve specificially defined the Intent order we wanted to run.

tr.run_component_pipeline(intent_levels=['remove', 'reinstate', 'auto_category', 'to_dtype'])

7.7 Run Books

A challenge faced with the component intent is its order, as you have seen. The solution thus far only applies at run time and is therefore not repeatable. We introduced the idea of Run Books as a repeatable set of instructions which contain the order in which to run the components intent. Run Books also provide the ability to particially implement component intent actions, meaning we can replay subsets of a fuller list of a components intent. For example through experimentation we have created a number of additional component intents, that are not pertinent to a production ready selection. By setting up two Run Books we can select which component intent is appropriate to their objectives and run_component_pipeline to produce the appropriate outcome.

In the example we add our list of intent to a book in the order needed. In this case we have not specified a book name so this book is allocated to the primary Run Book. Now each time we run pipeline, it is set to run the primary Run Book.

tr.add_run_book(run_levels=['remove', 'reinstate', 'auto_category', 'to_dtype'])

Here we had a book by name where we select only the intent that cleans the raw data. The Run book report Now what are shows us the two run books;

tr.add_run_book(book_name='cleaner', run_levels=['remove', 'reinstate'])

tr.report_run_book()

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In this next example we add an additional Run Book that is a subset of the tasks to only clean the data. By passing this named Run Book to the run pipeline it is obliged to only run this subset and only clean the data. We can see the results of this in our canonical report below.

tr.run_component_pipeline(run_book='cleaner')

tr.canonical_report(tr.load_persist_canonical())

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As a contrast to the above we can run the pipeline without providing a Run Book name and it will automatically default to the primary run book, assuming this has been set up. In this case running the full component Intent the resulting outcome is shown below in the canonical report.

tr.run_component_pipeline()

tr.canonical_report(tr.load_persist_canonical())

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8 Reference

8.1 Python version

Python 3.7 or less is not supported. Although it is recommended to install discovery-transition-ds against the latest Python version or greater whenever possible.

8.2 Pandas version

Pandas 0.25.x and above are supported but It is highly recommended to use the latest 1.0.x release as the first major release of Pandas.

8.3 GitHub Project

discovery-transition-ds: https://github.com/Gigas64/discovery-transition-ds.

8.4 Change log

See CHANGELOG.

8.5 Licence

BSD-3-Clause: LICENSE.

8.6 Authors

Gigas64 (@gigas64) created discovery-transition-ds.