Data Science Fundamentals with Python for Healthcare


Course Number: PYTH-218

Duration: 5 days (32.5 hours)

Format: Live, hands-on

Python for Healthcare Training Overview

This Data Science Fundamentals with Python for Healthcare training course teaches quantitative professionals (engineers, statisticians, analysts, and others) how to successfully apply data science methods to analyze and visualize real-world problems in healthcare data.

Location and Pricing

Accelebrate offers instructor-led enterprise training for groups of 3 or more online or at your site. Most Accelebrate classes can be flexibly scheduled for your group, including delivery in half-day segments across a week or set of weeks. To receive a customized proposal and price quote for private corporate training on-site or online, please contact us.

In addition, some Programming courses are available as live, online classes for individuals.

Objectives

  • Understand and implement key Python concepts (data types, functions)
  • Use libraries to import dynamic EHR (Electronic Health Record) data and static data
  • Parse unstructured clinical text data into structured data
  • Apply functions in Pandas and NumPy to quickly clean and explore data
  • Understand techniques to assess missingness in patient data
  • Extend cleaning techniques to reshaping data for use in advanced analytics
  • Explore and clean clinical text data
  • Apply regular expressions to manipulate and extract data from text
  • Understand rules-based Natural Language Processing (NLP) approaches for information extraction, such as diagnoses or medications
  • Identify tests for group differences using inferential statistics
  • Implement linear regression to model and forecast clinically relevant data
  • Using non-linear terms, as well as understanding confounding and interaction terms for more advanced system modeling
  • Apply logistic regressions to model non-numeric outcomes, such as patient follow-up

Prerequisites

All attendees should have prior programming experience and an understanding of basic statistics.

Outline

Expand All | Collapse All

Overview of Data Science in Healthcare
  • Limitations of EHR data
  • Importance of NLP methods
  • Overview of advanced data science work in healthcare (image recognition and temporospatial modeling)
An Accelerated Introduction and Overview to Python for Data Science
  • Review of course and computing environment
  • Explanation of Integrated Development Environments (IDEs) Jupyter and Spyder
  • Python syntax essentials
    • Primitive data types
    • Collection variable types
    • Control flow operations
    • Function syntax
    • Error handling
    • Managing libraries
Reading and Manipulating Datasets with Libraries (NumPy and Pandas)
  • Overview of NumPy
    • Data types in NumPy
    • Array masks
    • Manipulation and broadcasting
    • Random number generation
  • Data processing methods with Pandas
    • Using DataFrames and Series
    • Creating calculated columns
    • Discretizing data
    • Filtering and indexing syntax
    • Merging datasets
    • Melting/pivoting DataFrames
Exploratory Data Analysis (EDA) and Graphics Fundamentals
  • Statistical summaries, and outlier detection for both univariate and multivariate variables using graphical and numeric methods
  • Visualization crash course with Seaborn and Matplotlib
  • Generating publication-quality documents with Jupyter
Applied NLP Techniques for Clinical Text
  • Unstructured data fundamentals
  • Implementing regular expressions for basic information extraction
  • Applying MedSpaCy for advanced processing of clinical text
  • Measuring accuracy and limitations in rules-based methods
  • Using Term Frequency Inverse Document Frequency (TF-IDF) techniques for term importance
Applying Statistical Models for Analysis in Python
  • Explanation of statsmodels library of functions
  • Inferential and descriptive statistics refresher
  • Implementing A/B tests for detecting group differences
  • Applying linear regressions
  • Overview of generalized linear models (GLMs) and the link function
  • Applying logistic regression
  • Discussion of confounding, interaction terms and model building approaches
Conclusion

Training Materials

All attendees receive comprehensive courseware.

Software Requirements

  • Anaconda Python 3.6 or later
  • Spyder IDE and Jupyter notebook (comes with Anaconda)


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