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How to Transform Research Oriented Code into Machine Learning APIs with Python

How to Transform Research Oriented Code into Machine Learning APIs with Python

Pycon JP 2020

32aaa4ac3529ab1886190d7ed5acdcbc?s=128

tetsuya0617

August 29, 2020
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  1. How to Transform Research Oriented Code into Machine Learning APIs

    with Python @JesseTetsuya ———————————————————————————————————————————————————————————————————————————————— Software Engineer at an IT company specializing in education technology based in Tokyo. I mostly work in both data science and engineering. PyCon 2020 talk at !
  2. Background and Purpose - Recently, Python Engineers have more opportunities

    to work with data scientists and researchers than before. - Understanding the processes to develop ML APIs can help make AI / ML projects work more smoothly. @JesseTetsuya
  3. Premise 1: Educational Technologies Learning Contents / Functions Learning Management

    System (LMS) / Online Learning Platform Learning Contents / Functions - Online Quiz - Video Lesson - Discussion Forum - Contents Box - Information View / Notifications - Peer and self assessment - Integrated Badges - Personalized Dashboard - Recommend System - Intelligent Tutoring System - Authoring Tools etc…
  4. Premise 2: A Development Cycle in AI / ML projects

    Learning Log Data From Database LMS / Online Learning Platform 3FTFBSDI 0SJFOUFE $PEF .-"1*T Analyze learning log data and find optimal ml models / algorithms . Transform Research oriented code into ML APIs Integrate ML APIs into LMS / Online learning platform Data Scientists Engineers Periods: 2 - 3 months Periods: between 2 weeks and 2 months
  5. 3FTFBSDI 0SJFOUFE $PEF .-"1*T  Steps to transform Research Oriented

    Code into ML APIs   3FGBDUPS $IFDL 6OEFSTUBOE .PEVMBSJ[F  @JesseTetsuya
  6. 3FTFBSDI 0SJFOUFE $PEF .-"1*T  Steps to transform Research Oriented

    Code into ML APIs 6OEFSTUBOE 8IBUJT3FTFBSDI0SJFOUFE$PEF  8IBUBSF.-"1*T  )PXTIPVMEFOHJOFFSTIBOEMFSFTFBSDIPSJFOUFEDPEF @JesseTetsuya
  7. Definition Research oriented code in AI/ML projects is the code

    written mainly by data scientists or researchers for figuring out the most efficient and suitable machine learning model.
  8. 1.Preparation code for accessing data 2.Pre-processing code 3.Machine learning (ML)

    code Production code (Engineers) Research oriented code (Data Scientists/Researchers) Machine Learning APIs are composed of three elements Research oriented code is developed through an iterative process and integrated into production code.
  9. Data Pre-Processing code Visually trace the code from the top

    to the bottom Easily and quickly write it
  10. ML code (a part of whole code) Easily handle input

    data and trace output data with data frame
  11. Refactor both code in Pythonic way This code builds the

    model in a much faster and simpler way
  12. 3FTFBSDI0SJFOUFE$PEF 1SPEVDUJPO$PEF 4DPQFT 1SFQBSBUJPODPEF  1SFQSPDFTTJOHDPEF .-DPEF 1SFQBSBUJPODPEF 1SFQSPDFTTJOHDPEF .-DPEF

    $IBSBDUFSJTUJDT PG$PEJOH4UZMF &BTJMZIBOEMFE 7JTVBMMZUSBDFBCMF )JHIDBMDVMBUJPOTQFFE )JHISFBEBCJMJUZ 5FTUBCMFBOENPEVMBS 0CKFDUJWFTPG $PEJOH4UZMF 'JOEJOHUIFNPTUF⒏DJFOUBOE TVJUBCMFNBDIJOFMFBSOJOHNPEFM .BLJOHUIFDPEFXPSLPOUIFTFSWFS DPSSFDUMZBOESFMJBCMZ Three Differences between Research Oriented Code and Production Code
  13. What are Python Engineers supposed to do for Research Oriented

    Code?
  14. 3FTFBSDI0SJFOUFE$PEF 1SPEVDUJPO$PEF 4DPQFT 1SFQSPDFTTJOHDPEF .BDIJOFMFBSOJOHDPEF 1SFQBSBUJPODPEF 1SFQSPDFTTJOHDPEF .-DPEF $IBSBDUFSJTUJDT PG$PEJOH4UZMF

    &BTJMZIBOEMFE 7JTVBMMZUSBDFBCMF )JHIDBMDVMBUJPOTQFFE )JHISFBEBCJMJUZ 5FTUBCMFBOENPEVMBS 0CKFDUJWFTPG $PEJOH4UZMF 'JOEJOHUIFNPTUF⒏DJFOUBOE TVJUBCMFNBDIJOFMFBSOJOHNPEFM .BLJOHUIFDPEFXPSLPOUIFTFSWFS DPSSFDUMZBOESFMJBCMZ Three Differences between Research Oriented Code and Production Code 3FGBDUPS $IFDL .PEVMBSJ[F
  15. 3FTFBSDI 0SJFOUFE $PEF .-"1*T  Steps to Transform Research Oriented

    Code into ML APIs .PEVMBSJ[F   $BUFHPSJ[FSFTFBSDIPSJFOUFEDPEFJOUPQSFQBSBUJPODPEF  QSFQSPDFTTJOHDPEF BOE.-DPEF  #SFBLUIFNPVUJOUPGVODUJPOTBOENBLFUIFNUFTUBCMF  $MBSJGZJOQVUBOEPVUQVUPGUIFDPEF BOEEFpOF63* @JesseTetsuya
  16. This is a page of research oriented code written with

    jupyter notebook. This code is procedural and some of them are not classified. The research oriented code seems to be tightly coupled. 2.1. Categorize research oriented code into preparation code, preprocessing code, ML code
  17. Find the code to load input data or access database

    → preparation code Find the code to make, replace, filter, or delete input data → preprocessing code Find the code to execute calculation or train data → ML code 2.1. Categorize research oriented code into preparation code, preprocessing code, ML code
  18. Module name Functions Preparation code preparation.py - Access big query,

    execute query, and load input data - Rename columns Preprocessing code preprocessing.py - Replace categorical data with discrete numbers - Filter input data ML code prediction.py - Calculate icc parameters, logistic regression, and item response theory (IRT) The research oriented code became loosely coupled 2.2. Break them out into functions and make them testable
  19. app.py @app.route("/v1/probabilities", methods=['GET']) def probabilities(): return calc_results(), 200 return get_probs(),

    200 ← noun ← the same endpoint name ← verb (+ noun) INPUT OUTPUT *item means a question INPUT: results of student answers OUTPUT: probabilities to answer questions correctly 2.3. Clarify input and output of the whole code and define URI
  20. 3FTFBSDI 0SJFOUFE $PEF .-"1*T  Steps to transform Research Oriented

    Code into ML APIs  Refactor  1. Prepare for refactoring 2. Simplify I/O in preparation code 3. Pandas → Python in preprocessing code @JesseTetsuya
  21. The code to prepare and preprocess data tends to be

    ’Big Ball of Mud’ [1] -Redundant -Repetitive [1] Foote, Brian; Yoder, Joseph (26 June 1999). "Big Ball of Mud". laputan.org. Retrieved 14 April 2019.
  22. . ᵓᴷᴷ ml_api ᴹ ᵓᴷᴷ api ᴹ ᴹ ᵓᴷᴷ app.py

    ᴹ ᴹ ᵓᴷᴷ config ᴹ ᴹ ᵓᴷᴷ prediction.py ᴹ ᴹ ᵓᴷᴷ preparation.py ᴹ ᴹ ᵓᴷᴷ preprocessing.py ᴹ ᵓᴷᴷ requirements.txt ᴹ ᵓᴷᴷ run.py ᴹ ᵋᴷᴷ tests ᴹ ᵓᴷᴷ test_app.py ᴹ ᵓᴷᴷ test_prediction.py ᴹ ᵓᴷᴷ test_preparation.py ᴹ ᵋᴷᴷ test_preprocessing.py ᵋᴷᴷ setup.py 3.1 Prepare for refactoring Narrow down requirements of each code by writing test code and take notes about requirements on the comments for refactoring (or you can tell data scientist to write comments in advance) def func(arg1, arg2): """Summary line. Extended description of function. Args: arg1 (int): Description of arg1 arg2 (str): Description of arg2 Returns: bool: Description of return value """ return True ex) Google Style #comments out or doc strings (reStructuredText style /Numpy style/Google Style)
  23. CASE STUDY: Refactoring the redundant code to access BigQuery and

    GCS by using google cloud client libraries with Python 3.2 Simplify I/O in redundant preparation code
  24. from google.cloud import bigquery client = bigquery.Client() query = "SELECT

    column_1, column_2, column_3 FROM `data set name` where column_1 is not NULL query_job = client.query(query) results = [list(row.values()) for row in query_job.result()] OUTPUT: Two Dimensional Arrays + Filter Values + Drop Null OUTPUT: Two Dimensional Arrays from google.cloud import bigquery client = bigquery.Client() query = "SELECT * FROM `data set name` query_job = client.query(query) results = [list(row.values()) for row in query_job.result()] → Preprocess the data with query as much as possible → It is faster and lower-cost than preprocess data with python Code B Code A 3.2. Simplify I/O in preparation code ex) Big Query with Python
  25. import io, csv, gzip from google.cloud import storage storage_client =

    storage.Client() bucket = storage_client.get_bucket(‘bucket name’) with io.StringIO() as csv_obj: writer = csv.writer(csv_obj, quotechar='"', quoting=csv.QUOTE_ALL, lineterminator="\n") writer.writerows(two_dimentional_arrays) result = csv_obj.getvalue() with io.BytesIO() as gzip_obj: with gzip.GzipFile(fileobj=gzip_obj, mode="wb") as gzip_file: bytes_f = result.encode() gzip_file.write(bytes_f) blob = bucket.blob(‘storage_path’) blob.upload_from_file(gzip_obj, rewind=True, content_type='application/gzip') Make bytes object and upload it from memory to GCS with Python 3.2 Simplify I/O in preparation code ex) Google Cloud Storage with Python
  26. import gcp_accessor bq = gcp_accessor.BigQueryAccessor() query = "SELECT * FROM

    `data set name` bq.execute_query(query) gcs = gcp_accessor.GoogleCloudStorageAccessor() gcs.upload_csv_gzip( ‘bucket name', ‘full path on gcs', ‘input data’) 3.2. Simplify I/O more by using wrapper import io, csv, gzip from google.cloud import storage storage_client = storage.Client() bucket = storage_client.get_bucket(‘bucket name’) with io.StringIO() as csv_obj: writer = csv.writer(csv_obj, quotechar='"', quoting=csv.QUOTE_ALL, lineterminator="\n") writer.writerows(two_dimentional_arrays) result = csv_obj.getvalue() with io.BytesIO() as gzip_obj: with gzip.GzipFile(fileobj=gzip_obj, mode="wb") as gzip_file: bytes_f = result.encode() gzip_file.write(bytes_f) blob = bucket.blob(storage_path) blob.upload_from_file(gzip_obj, rewind=True, content_type='application/gzip') from google.cloud import bigquery client = bigquery.Client() query = "SELECT * FROM `data set name` query_job = client.query(query) results = [list(row.values()) for row in query_job.result()] google-cloud-bigquery google-cloud-storage gcp-accessor (wrapper library) (https://pypi.org/project/gcp-accessor/)
  27. 3.3. Pandas → Python in preprocessing code All data in

    the api is processed using the same data type. This improves readability and maintainability as opposed to prioritizing coding speed.
  28. One day, I wondered why I struggled so much with

    refactoring of the repetitive code of preprocessing in research oriented code that I wrote a previous week. 3.3. Pandas → Python in preprocessing code
  29. 3.3. Pandas → Python in preprocessing code Code Styles/ Preprocessing

    Functions Pandas Python Filter dataframe.where(.query) dataframe.groupby() dataframe[[“”, “”, ‘“]] dataframe.loc[] dataframe.iloc[] if - else + for +.append() [[v1, v2, v3] for value in values] Replace dataframe.fillna() dic = {“key1”: value1, “key2”: value, …} dataframe['column1'].replace(dic, inplace=True) dic = {“key1”: value1, “key2”: value, …} [[dic.get(v, v) for v in value] for value in values] De-duplicate /Be unique duplicated() / drop_duplicates() dataframe['column1'].unique()
 (outuput: array([v1, v2, v3])) set(list) list({v1, v2, v2, …}) list({value[0] for value in values}) Delete/Drop dataframe.dropna() dataframe.drop() dataframe.drop(index=index list) if - else + for +.append() [[v1, v2, v3] for value in values]
  30. 3FTFBSDI 0SJFOUFE $PEF .-"1*T  Steps to transform Research Oriented

    Code into ML APIs   $IFDL  1. Write decorators to check parameters 2. Set up production-like environments @JesseTetsuya
  31. 4.1. Write decorators to check parameters Error handling Request parameter

    check Access token check Image of Decorators in APIs 3FRVFTU $MJFOU URIs preparation preprocessing calculation
  32. 4.1. Write decorators to check parameters Error handling Request parameter

    check Access token check Image of Decorators in APIs 3FRVFTU $MJFOU URIs preparation preprocessing calculation
  33. { "$schema": "http://json-schema.org/draft-04/schema#", "student_name": { "type": "string", "required": "True" },

    "student_grade": { "type": "string", "required": "True", "maximum": 120, "minimum": 1 } } curl http://localhost:5000/ -X POST -H "Content-Type: application/json" -d '{"student_name": "test_name", "student_grade": “forth-grade"}' make_name_grade.json request curl command 4.1. Write decorators to check parameters ex) Request parameter check with JSON Schema
  34. def validate_json(f): @wraps(f) def wrapper(*args, **kw): try: request.json except BadRequest

    as e: msg = “ This is an invalid json" return jsonify({"error": msg}), 400 return f(*args, **kw) return wrapper def validate_schema(schema_name): def decorator(f): @wraps(f) def wrapper(*args, **kw): try: validate(request.json, current_app.config[schema_name]) except ValidationError as e: return jsonify({"error": e.message}), 400 return f(*args, **kw) return wrapper return decorator @app.route('/', methods=['POST']) @validate_json @validate_schema('make_name_grade') def index(): if request.is_post: data = json.loads(request.data) print(data["student_name"]) print(data["student_grade"]) return "Hi! " + data["student_name"] else: return "Hi!" app.py json_validate.py 4.1. Write decorators to check parameters ex) Request parameter check with JSON Schema
  35. Automate Continuous Integration Visualize data (Load Test) Deploy on GCP

    'MBTL"QQ #VJMEFS %BTI 4.2. Set up production-like environments with Flask Monitor the accuracy of the ML model $MPVE.POJUPSJOH 4UBDLESJWFS
  36. Resources LOCUST: https://www.youtube.com/watch?v=XQ4hrbgVysk (Pycon Korea 2015) Refactoring: https://www.youtube.com/watch?v=D_6ybDcU5gc (Pycon US

    2016)
 Pytest: https://www.youtube.com/watch?v=G-MAMrJ-CSA (Pycon US 2019) Flask workshop: https://www.youtube.com/watch?v=DIcpEg77gdE (Pycon US 2015) Dash: https://www.youtube.com/watch?v=WLbQYFZc-YY (Pycon Jp 2019) google-cloud-bigquery: https://pypi.org/project/google-cloud-bigquery/ google-cloud-storage: https://pypi.org/project/google-cloud-storage/ gcp-accessor: https://pypi.org/project/gcp-accessor/0.0.1/ Flask-AppBuilder: https://flask-appbuilder.readthedocs.io/en/latest/ Python Tools that I mentioned in this talk Python Packages that I mentioned in this talk
  37. Summary 3FTFBSDI 0SJFOUFE $PEF .-"1*T    3FGBDUPS $IFDL

    6OEFSTUBOE .PEVMBSJ[F  - What is Research Oriented Code ? - What are ML APIs - How should engineers handle research oriented code ? - Categorize research oriented code into preparation code, preprocessing code, ML code - Break them out into functions and make them testable - Clarify input and output of the code, and define URI - Prepare for refactoring - Simplify I/O in preparation code - Pandas → Python in preprocessing code - Write decorators to check parameters - Set up production-like environments @JesseTetsuya
  38. @JesseTetsuya ———————————————————————————————————————————————————————————————————————————————— Software Engineer at an IT company specializing in

    education industry based in Tokyo. I mostly work in both data science and engineering. If you have an interest in the education and technology domain, feel free to contact with me !!
  39. @JesseTetsuya ———————————————————————————————————————————————————————————————————————————————— Software Engineer at an IT company specializing in

    education industry based in Tokyo. I mostly work in both data science and engineering. Q & A