Build a Fully Automated Data Drift Detection Pipeline

Motivation

Data drift occurs when the distribution of input features in the production environment differs from the training data, leading to potential inaccuracies and decreased model performance.

To mitigate the impact of data drift on model performance, we can design a workflow that detects drift, notifies the data team, and triggers model retraining.

Workflows

The workflow comprises the following tasks:

Fetch reference data from the Postgres database.
Get the current production data from the web.
Detect data drift by comparing the reference and current data.
Append the current data to the existing Postgres database.
When there is data drift, the following actions are taken:
- Send a Slack message to alert the data team.
- Retrain the model to update its performance.
- Push the updated model to S3 for storage.

This workflow is scheduled to run at specific times, such as 11:00 AM every Monday.

Overall, the workflow includes two types of tasks: data science and data engineering tasks.

Data science tasks, represented by pink boxes, are performed by data scientists and involve data drift detection, data processing, and model training.

Data engineering tasks, represented by blue and purple boxes, are performed by data engineers and involve tasks related to data movement and sending notifications.

Data Science Tasks

Detect Data Drift

To detect data drift, we will create a Python script that takes two CSV files “data/reference.csv” (reference data) and “data/current.csv” (current data).

We will use Evidently, an open-source ML observability platform, to compare the reference data, serving as a baseline, with the current production data. If dataset drift is detected, the “drift_detected” output will be True; otherwise, it will be False.

from evidently.metric_preset import DataDriftPreset
from evidently.report import Report
from kestra import Kestra
data_drift_report = Report(metrics=[DataDriftPreset()])
data_drift_report.run(reference_data=reference, current_data=current)
report = data_drift_report.as_dict()
drift_detected = report["metrics"][0]["result"]["dataset_drift"]
if drift_detected:
    print("Detect dataset drift")
else:
    print("Detect no dataset drift")
Kestra.outputs({"drift_detected": drift_detected})

Full code.

Retrain the Model

Next, we will create a Python script responsible for model training. This script takes the combined past and current data as input and saves the trained model as a “model.pkl” file.

def train_model(X_train: pd.DataFrame, y_train: pd.Series, model_params: DictConfig):
    y_train_log = np.log1p(y_train)
    model = Ridge()
    scorer = metrics.make_scorer(rmsle, greater_is_better=True)
    params = dict(model_params)
    grid = GridSearchCV(model, params, scoring=scorer, cv=3, verbose=3)
    grid.fit(X_train, y_train_log)
    return grid
model = train_model(X_train, y_train, config.model.params)
joblib.dump(model, "model.pkl")

Full code.

Push to GitHub

After finishing developing these two scripts, data scientists can push them to GitHub, allowing data engineers to use them in creating workflows.

View the GitHub repository for these files here:

View on GitHub

Data Engineering Tasks

Popular orchestration libraries such as Airflow, Prefect, and Dagster require modifications to the Python code to use their functionalities.

When Python scripts are tightly integrated into the data workflows, the overall codebase can become more complex and harder to maintain. Without independent Python script development, data engineers may need to modify the data science code to add orchestration logic.

On the other hand, Kestra, an open-source library, allows you to develop your Python scripts independently and then seamlessly incorporate them into data workflows using YAML files.

This way, data scientists can focus on model processing and training, while data engineers can focus on handling orchestration.

Thus, we will use Kestra to design a more modular and efficient workflow.

Clone the detect-data-drift-pipeline repository to get the docker-compose file for Kestra, then run:

docker compose up -d

Navigate to localhost:8080 to access and explore the Kestra UI.

Follow these instructions to configure the required environment for this tutorial.

Before developing the target flows, let’s get familiar with Kestra by creating some simple flows.

Access Postgres Tables From a Python Script

We will create a flow that includes the following tasks:

getReferenceTable: Exports a CSV file from a Postgres table.
saveReferenceToCSV: Creates a local CSV file that can be accessed by the Python task.
runPythonScript: Reads the local CSV file with Python.

To enable data passing between the saveReferenceToCSV and runPythonScript tasks, we will place these two tasks in the same working directory by enclosing them inside the wdir task.

id: get-reference-table
namespace: dev
tasks:
  - id: getReferenceTable
    type: io.kestra.plugin.jdbc.postgresql.CopyOut
    url: jdbc:postgresql://host.docker.internal:5432/
    username: "{{secret('POSTGRES_USERNAME')}}"
    password: "{{secret('POSTGRES_PASSWORD')}}"
    format: CSV
    sql: SELECT * FROM reference
    header: true
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
    - id: saveReferenceToCSV
      type: io.kestra.core.tasks.storages.LocalFiles
      inputs:
        data/reference.csv: "{{outputs.getReferenceTable.uri}}"
    - id: runPythonScript
      type: io.kestra.plugin.scripts.python.Script
      beforeCommands:
        - pip install pandas
      script: | 
        import pandas as pd
        df = pd.read_csv("data/reference.csv")
        print(df.head(10))

Executing the flow will show the following logs:

Parameterize Flow with Inputs

Let’s create another flow that can be parameterized with inputs. This flow will have the following inputs: startDate, endDate, and dataURL.

The getCurrentCSV task can access these inputs using the {{inputs.name}} notation.

id: get-current-table
namespace: dev
inputs:
  - name: startDate
    type: STRING
    defaults: "2011-03-01"
  - name: endDate
    type: STRING
    defaults: "2011-03-31"
  - name: dataURL
    type: STRING 
    defaults: "https://raw.githubusercontent.com/khuyentran1401/detect-data-drift-pipeline/main/data/bikeride.csv"
tasks:
  - id: getCurrentCSV
    type: io.kestra.plugin.scripts.python.Script
    beforeCommands:
      - pip install pandas
    script: |
      import pandas as pd
      df = pd.read_csv("{{inputs.dataURL}}", parse_dates=["dteday"])
      print(f"Getting data from {{inputs.startDate}} to {{inputs.endDate}}")
      df = df.loc[df.dteday.between("{{inputs.startDate}}", "{{inputs.endDate}}")]
      df.to_csv("current.csv", index=False)

The values of these inputs can be specified in each flow execution.

Load a CSV File into a Postgres Table

The following flow does the following tasks:

getCurrentCSV: Runs a Python script to create a CSV file in the working directory.
saveFiles: Sends the CSV file from the working directory to Kestra’s internal storage.
saveToCurrentTable: Loads the CSV file into a Postgres table.

id: save-current-table
namespace: dev
tasks:
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
    - id: getCurrentCSV
      type: io.kestra.plugin.scripts.python.Script
      beforeCommands:
        - pip install pandas
      script: |
        import pandas as pd
        data_url = "https://raw.githubusercontent.com/khuyentran1401/detect-data-drift-pipeline/main/data/bikeride.csv"
        df = pd.read_csv(data_url, parse_dates=["dteday"])
        df.to_csv("current.csv", index=False)
    - id: saveFiles
      type: io.kestra.core.tasks.storages.LocalFiles
      outputs:
        - current.csv
  - id: saveToCurrentTable
    type: io.kestra.plugin.jdbc.postgresql.CopyIn
    url: jdbc:postgresql://host.docker.internal:5432/
    username: "{{secret('POSTGRES_USERNAME')}}"
    password: "{{secret('POSTGRES_PASSWORD')}}"
    from: "{{outputs.saveFiles.uris['current.csv']}}"
    table: current
    format: CSV
    header: true
    delimiter: ","

After running this flow, you will see the resulting data in the “current” table within your Postgres database.

Run a File From a GitHub Repository

This flow includes the following tasks:

cloneRepository: Clones a public GitHub repository
runPythonCommand: Executes a Python script from a CLI

Both of these tasks will operate within the same working directory.

id: clone-repository
namespace: dev
tasks:
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
      - id: cloneRepository
        type: io.kestra.plugin.git.Clone
        url: https://github.com/khuyentran1401/detect-data-drift-pipeline
        branch: main
      - id: runPythonCommand
        type: io.kestra.plugin.scripts.python.Commands
        commands:
          - python src/example.py

After running the flow, you will see the following logs:

Run a Flow on Schedule

We will create another flow that runs a flow based on a specific schedule. The following flow runs at 11:00 AM every Monday.

id: triggered-flow
namespace: dev
tasks:
  - id: hello
    type: io.kestra.core.tasks.log.Log
    message: Hello world
triggers:
  - id: schedule
    type: io.kestra.core.models.triggers.types.Schedule
    cron: "0 11 * * MON"

Upload to S3

This flow includes the following tasks:

createPickle: Generates a pickle file in Python
savetoPickle: Transfers the pickle file to Kestra’s internal storage
upload: Uploads the pickle file to an S3 bucket

id: upload-to-S3
namespace: dev
tasks:
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
    - id: createPickle
      type: io.kestra.plugin.scripts.python.Script
      script: |
        import pickle
        data = [1, 2, 3]
        with open('data.pkl', 'wb') as f:
          pickle.dump(data, f)
    - id: saveToPickle
      type: io.kestra.core.tasks.storages.LocalFiles
      outputs:
        - data.pkl  
  - id: upload
    type: io.kestra.plugin.aws.s3.Upload
    accessKeyId: "{{secret('AWS_ACCESS_KEY_ID')}}"
    secretKeyId: "{{secret('AWS_SECRET_ACCESS_KEY_ID')}}"
    region: us-east-2
    from: '{{outputs.saveToPickle.uris["data.pkl"]}}'
    bucket: bike-sharing
    key: data.pkl

After running this flow, the data.pkl file will be uploaded to the “bike-sharing” bucket.

Put Everything Together

Build a Flow to Detect Data Drift

Now, let’s combine what we have learned to create a flow to detect data drift. At 11:0 AM every Monday, this flow executes the following tasks:

Fetches reference data from the Postgres database.
Runs a Python script to get the current production data from the web.
Clones the GitHub repository containing the drift detection code
Runs a Python script to data drift by comparing the reference and current data.
Appends the current data to the existing Postgres database.

id: detect-data-drift
namespace: dev
inputs:
  - name: startDate
    type: STRING
    defaults: "2011-03-01"
  - name: endDate
    type: STRING
    defaults: "2011-03-31"
  - name: data_url
    type: STRING 
    defaults: "https://raw.githubusercontent.com/khuyentran1401/detect-data-drift-pipeline/main/data/bikeride.csv"
tasks:
  - id: getReferenceTable
    type: io.kestra.plugin.jdbc.postgresql.CopyOut
    url: jdbc:postgresql://host.docker.internal:5432/
    username: "{{secret('POSTGRES_USERNAME')}}"
    password: "{{secret('POSTGRES_PASSWORD')}}"
    format: CSV
    sql: SELECT * FROM reference
    header: true
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
      - id: cloneRepository
        type: io.kestra.plugin.git.Clone
        url: https://github.com/khuyentran1401/detect-data-drift-pipeline
        branch: main
      - id: saveReferenceToCSV
        type: io.kestra.core.tasks.storages.LocalFiles
        inputs:
          data/reference.csv: "{{outputs.getReferenceTable.uri}}"
      - id: getCurrentCSV
        type: io.kestra.plugin.scripts.python.Script
        beforeCommands:
          - pip install pandas
        script: |
          import pandas as pd
          df = pd.read_csv("{{inputs.data_url}}", parse_dates=["dteday"])
          print(f"Getting data from {{inputs.startDate}} to {{inputs.endDate}}")
          df = df.loc[df.dteday.between("{{inputs.startDate}}", "{{inputs.endDate}}")]
          df.to_csv("data/current.csv", index=False)
      - id: detectDataDrift
        type: io.kestra.plugin.scripts.python.Commands
        beforeCommands:
          - pip install -r src/detect/requirements.txt
        commands:
          - python src/detect/detect_data_drift.py
      - id: saveFileInStorage
        type: io.kestra.core.tasks.storages.LocalFiles
        outputs:
          - data/current.csv
  - id: saveToCurrentTable
    type: io.kestra.plugin.jdbc.postgresql.CopyIn
    url: jdbc:postgresql://host.docker.internal:5432/
    username: "{{secret('POSTGRES_USERNAME')}}"
    password: "{{secret('POSTGRES_PASSWORD')}}"
    from: "{{outputs.saveFileInStorage.uris['data/current.csv']}}"
    table: current
    format: CSV
    header: true
    delimiter: ","
triggers:
  - id: schedule
    type: io.kestra.core.models.triggers.types.Schedule
    cron: "0 11 * * MON"

Build a Flow to Send Slack Messages

Next, we will create a flow to send Slack messages via a Slack Webhook URL when the detectDataDrift task inside the detect-data-drift flow returns drift_detected=true.

id: send-slack-message
namespace: dev
tasks:
  - id: send
    type: io.kestra.plugin.notifications.slack.SlackExecution
    url: "{{secret('SLACK_WEBHOOK')}}"
    customMessage: Detect data drift
triggers:
  - id: listen
    type: io.kestra.core.models.triggers.types.Flow
    conditions:
    - type: io.kestra.core.models.conditions.types.ExecutionFlowCondition
      namespace: dev
      flowId: detect-data-drift
    - type: io.kestra.core.models.conditions.types.VariableCondition
      expression: "{{outputs.detectDataDrift.vars.drift_detected}} == true"

After running the detect-data-drift flow, the send-slack-message flow will send a message on Slack.

Build a Flow to Retrain the Model

Lastly, we will create a flow to retrain the model. This flow executes the following tasks:

Exports a CSV file from the current table in the Postgres database
Clones the GitHub repository containing the model training code
Runs a Python script to train the model and generates a pickle file
Uploads the pickle file to S3

id: train-model
namespace: dev
tasks:
  - id: getCurrentTable
    type: io.kestra.plugin.jdbc.postgresql.CopyOut
    url: jdbc:postgresql://host.docker.internal:5432/
    username: "{{secret('POSTGRES_USERNAME')}}"
    password: "{{secret('POSTGRES_PASSWORD')}}"
    format: CSV
    sql: SELECT * FROM current
    header: true
  - id: wdir
    type: io.kestra.core.tasks.flows.WorkingDirectory
    tasks:
      - id: cloneRepository
        type: io.kestra.plugin.git.Clone
        url: https://github.com/khuyentran1401/detect-data-drift-pipeline
        branch: main
      - id: saveCurrentToCSV
        type: io.kestra.core.tasks.storages.LocalFiles
        inputs:
          data/current.csv: "{{outputs.getCurrentTable.uri}}"
      - id: trainModel
        type: io.kestra.plugin.scripts.python.Commands
        beforeCommands:
          - pip install -r src/train/requirements.txt
        commands:
          - python src/train/train_model.py
      - id: saveToPickle
        type: io.kestra.core.tasks.storages.LocalFiles
        outputs:
          - model.pkl
  - id: upload
    type: io.kestra.plugin.aws.s3.Upload
    accessKeyId: "{{secret('AWS_ACCESS_KEY_ID')}}"
    secretKeyId: "{{secret('AWS_SECRET_ACCESS_KEY_ID')}}"
    region: us-east-2
    from: '{{outputs.saveToPickle.uris["model.pkl"]}}'
    bucket: bike-sharing
    key: model.pkl
triggers:
  - id: listenFlow
    type: io.kestra.core.models.triggers.types.Flow
    conditions:
      - type: io.kestra.core.models.conditions.types.ExecutionFlowCondition
        namespace: dev
        flowId: detect-data-drift
      - type: io.kestra.core.models.conditions.types.VariableCondition
        expression: "{{outputs.detectDataDrift.vars.drift_detected}} == true"

After running this flow, the model.pkl file will be uploaded to the “bike-sharing” bucket.

Ideas to Extend This Workflow

Rather than relying on scheduled data pulls to identify data drift, we can leverage Grafana’s outgoing webhook and Kestra’s inbound webhook to establish real-time data monitoring and trigger a flow instantly when data drift occurs. This approach enables the detection of data drift as soon as it happens, eliminating the need to wait for a scheduled script to run.

Let me know in the comments how you think this workflow could be extended and what other use cases you would like to see in future content.

I love writing about data science concepts and playing with different data science tools. You can stay up-to-date with my latest posts by:

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Article

3 thoughts on “Build a Fully Automated Data Drift Detection Pipeline”

Kiran Narahari
August 14, 2023 at 11:27 am

Hey Khuyen, just a small correction to your blog. The first flowchart (above workflows) has “yes” and “no” labels mixed up. They need to be interchanged. 😊
1. Khuyen Tran
  August 15, 2023 at 10:10 am
  
  Yes you are right. Thanks for correcting it. I’ll fix it.
2. Khuyen Tran
  August 15, 2023 at 10:15 am
  
  It’s done. Thank you!

Comments are closed.

Jupyter Notebook

Build a Fully Automated Data Drift Detection Pipeline

Motivation

Workflows

Data Science Tasks

Detect Data Drift

Retrain the Model

Push to GitHub

Data Engineering Tasks

Access Postgres Tables From a Python Script

Parameterize Flow with Inputs

Load a CSV File into a Postgres Table

Run a File From a GitHub Repository

Run a Flow on Schedule

Upload to S3

Put Everything Together

Build a Flow to Detect Data Drift

Build a Flow to Send Slack Messages

Build a Flow to Retrain the Model

Ideas to Extend This Workflow

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6 Common Mistakes to Avoid in Data Science Code

3 thoughts on “Build a Fully Automated Data Drift Detection Pipeline”

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Build a Fully Automated Data Drift Detection Pipeline

Motivation

Workflows

Data Science Tasks

Detect Data Drift

Retrain the Model

Push to GitHub

Data Engineering Tasks

Access Postgres Tables From a Python Script

Parameterize Flow with Inputs

Load a CSV File into a Postgres Table

Run a File From a GitHub Repository

Run a Flow on Schedule

Upload to S3

Put Everything Together

Build a Flow to Detect Data Drift

Build a Flow to Send Slack Messages

Build a Flow to Retrain the Model

Ideas to Extend This Workflow

Related Posts

3 Tools to Track and Visualize the Execution of your Python Code

Setting Up Automated Model Training Workflows with AWS S3

6 Common Mistakes to Avoid in Data Science Code

3 thoughts on “Build a Fully Automated Data Drift Detection Pipeline”

Related Posts

Automate Jupyter Notebooks with Papermill

Automate SQL Formatting with SQLFluff

Simplify Custom Object Operations with Python Magic Methods

Get Started

Follow Us

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