amanjeetsahu / AI-for-Healthcare-Nanodegree

Learn to build, evaluate, and integrate predictive models that have the power to transform patient outcomes. Begin by classifying and segmenting 2D and 3D medical images to augment diagnosis and then move on to modeling patient outcomes with electronic health records to optimize clinical trial testing decisions. Finally, build an algorithm that uses data collected from wearable devices to estimate the wearer’s pulse rate in the presence of motion.

AI for Healthcare

NANODEGREE PROGRAM SYLLABUS

Overview

Play a critical role in enhancing clinical decision-making with machine learning to build the treatments of
the future. Learn to build, evaluate, and integrate predictive models that have the power to transform
patient outcomes. Begin by classifying and segmenting 2D and 3D medical images to augment diagnosis
and then move on to modeling patient outcomes with electronic health records to optimize clinical trial
testing decisions. Finally, build an algorithm that uses data collected from wearable devices to estimate the
wearer’s pulse rate in the presence of motion.

A graduate of this program will be able to:

• Recommend appropriate imaging modalities for common clinical applications of 2D medical imaging
• Perform exploratory data analysis (EDA) on 2D medical imaging data to inform model training and explain model performance
• Establish the appropriate ‘ground truth’ methodologies for training algorithms to label medical images
• Extract images from a DICOM dataset
• Train common CNN architectures to classify 2D medical images
• Translate outputs of medical imaging models for use by a clinician
• Plan necessary validations to prepare a medical imaging model for regulatory approval
• Detect major clinical abnormalities in a DICOM dataset
• Train machine learning models for classification tasks using real-world 3D medical imaging data
• Integrate models into a clinician’s workflow and troubleshoot deployments
• Build machine learning models in a manner that is compliant with U.S. healthcare data security and privacy standards
• Use the TensorFlow Dataset API to scalably extract, transform, and load datasets that are aggregated at the line, encounter, and longitudinal (patient) data levels
• Analyze EHR datasets to check for common issues (data leakage, statistical properties, missing values, high cardinality) by performing exploratory data analysis with TensorFlow Data Analysis and Validation library
• Create categorical features from Key Industry Code Sets (ICD, CPT, NDC) and reduce dimensionality for high cardinality features
• Use TensorFlow feature columns on both continuous and categorical input features to create derived features (bucketing, cross-features, embeddings)
• Use Shapley values to select features for a model and identify the marginal contribution for each selected feature
• Analyze and determine biases for a model for key demographic groups
• Use the TensorFlow Probability library to train a model that provides uncertainty range predictions in order to allow for risk adjustment/prioritization and triaging of predictions
• Preprocess data (eliminate “noise”) collected by IMU, PPG, and ECG sensors based on mechanical, physiology and environmental effects on the signal.
• Create an activity classification algorithm using signal processing and machine learning techniques
• Detect QRS complexes using one-dimensional time series processing techniques
• Evaluate algorithm performance without ground truth labels
• Generate a pulse rate algorithm that combines information from the PPG and IMU sensor streams

Prerequisites :
Intermediate
Python, and
Experience with
Machine Learning

Flexible Learning : Self-paced, so you can learn on the schedule that works best for you.

Estimated Time : 4 Months at 15 hours / week

Need Help?
udacity.com/advisor
Discuss this program
with an enrollment
advisor.

Course 1: Applying AI to 2D Medical Imaging

Data

2D imaging, such as X-ray, is widely used when making critical decisions about patient care and accessible by most healthcare centers around the world. With the advent of deep learning for non-medical imaging data over the past half decade, the world has quickly turned its attention to how AI could be specifically applied to medical imaging to improve clinical decision-making and to optimize workflows. Learn the fundamental skills needed to work with 2D medical imaging data and how to use AI to derive clinically-relevant insights from data gathered via different types of 2D medical imaging such as x-ray, mammography, and digital pathology. Extract 2D images from DICOM files and apply the appropriate tools to perform exploratory data analysis on them. Build different AI models for different clinical scenarios that involve 2D images and learn how to position AI tools for regulatory approval.

Course Project

Pneumonia Detection

from Chest X-Rays

Chest X-ray exams are one of the most frequent and cost-effective
types of medical imaging examinations. Deriving clinical diagnoses
from chest X-rays can be challenging, however, even by skilled
radiologists. When it comes to pneumonia, chest X-rays are the best
available method for point-of-care diagnosis. More than 1 million
adults are hospitalized with pneumonia and around 50,000 die
from the disease every year in the US alone. The high prevalence
of pneumonia makes it a good candidate for the development of a
deep learning application for two reasons: 1) Data availability in a
high enough quantity for training deep learning models for image
classification 2) Opportunity for clinical aid by providing higher
accuracy image reads of a difficult-to-diagnose disease and/or reduce
clinical burnout by performing automated reads of very common
scans. In this project, you will analyze data from the NIH Chest
X-ray dataset and train a CNN to classify a given chest X-ray for the
presence or absence of pneumonia. First, you’ll curate training and
testing sets that are appropriate for the clinical question at hand from
a large collection of medical images. Then, you will create a pipeline
to extract images from DICOM files that can be fed into the CNN for
model training. Lastly, you’ll write an FDA 501(k) validation plan that
formally describes your model, the data that it was trained on, and a
validation plan that meets FDA criteria in order to obtain clearance of
the software being used as a medical device.

LEARNING OUTCOMES

LESSON ONE

Introduction to
AI for 2D Medical
Imaging

• Explain what AI for 2D medical imaging is and why it is relevant.

LESSON TWO

Clinical
Foundations of 2D
Medical Imaging

• Learn about different 2D medical imaging modalities and their clinical applications
• Understand how different types of machine learning algorithms can be applied to 2D medical imaging
• Learn how to statistically assess an algorithm’s performance
• Understand the key stakeholders in the 2D medical imaging space.

LESSON THREE

2D Medical Imaging
Exploratory Data
Analysis

• Learn what the DICOM standard it is and why it exists
• Use Python tools to explore images extracted from DICOM files
• Apply Python tools to explore DICOM header data
• Prepare a DICOM dataset for machine learning
• Explore a dataset in preparation for machine learning

LESSON FOUR

Classification
Models of 2D
Medical Images

• Understand architectures of different machine learning and deep learning models, and the differences between them
• Split a dataset for training and testing an algorithm
• Learn how to define a gold standard
• Apply common image pre-processing and augmentation techniques to data
• Fine-tune an existing CNN architecture for transfer learning with 2D medical imaging applications
• Evaluate a model’s performance and optimize its parameters

LESSON FIVE

Translating AI
Algorithms for
Clinical Settings
with the FDA

• Learn about the FDA’s risk categorization for medical devices and how to define an Intended Use statement
• Identify and describe algorithmic limitations for the FDA
• Translate algorithm performance statistics into clinically meaningful information that can trusted by professionals
• Learn how to create an FDA validation plan

Course 2: Applying AI to 3D Medical Imaging

Data

3D medical imaging exams such as CT and MRI serve as critical decision-making tools in the clinician’s everyday diagnostic armamentarium. These modalities provide a detailed view of the patient’s anatomy and potential diseases, and are a challenging though highly promising data type for AI applications. Learn the fundamental skills needed to work with 3D medical imaging datasets and frame insights derived from the data in a clinically relevant context. Understand how these images are acquired, stored in clinical archives, and subsequently read and analyzed. Discover how clinicians use 3D medical images in practice and where AI holds most potential in their work with these images. Design and apply machine learning algorithms to solve the challenging problems in 3D medical imaging and how to integrate the algorithms into the clinical workflow.

LEARNING OUTCOMES

LESSON ONE Introduction to
AI for 3D Medical
Imaging

• Explain what AI for 3D medical imaging is and why it is relevant

Course Project

Hippocampal Volume

Quantification in

Alzheimer’s Progression

Hippocampus is one of the major structures of the human brain
with functions that are primarily connected to learning and
memory. The volume of the hippocampus may change over time,
with age, or as a result of disease. In order to measure hippocampal
volume, a 3D imaging technique with good soft tissue contrast is
required. MRI provides such imaging characteristics, but manual
volume measurement still requires careful and time consuming
delineation of the hippocampal boundary. In this project, you will
go through the steps that will have you create an algorithm that will
help clinicians assess hippocampal volume in an automated way
and integrate this algorithm into a clinician’s working environment.
First, you’ll prepare a hippocampal image dataset to train the U-net
based segmentation model, and capture performance on the test
data. Then, you will connect the machine learning execution code
into a clinical network, create code that will generate reports based
on the algorithm output, and inspect results in a medical image
viewer. Lastly, you’ll write up a validation plan that would help
collect clinical evidence of the algorithm performance, similar to
that required by regulatory authorities.

LESSON TWO

3D Medical
Imaging - Clinical
Fundamentals

• Identify medical imaging modalities that generate 3D images
• List clinical specialties who use 3D images to influence clinical decision making
• Describe use cases for 3D medical images
• Explain the principles of clinical decision making
• Articulate the basic principles of CT and MR scanner operation
• Perform some of the common 3D medical image analysis tasks such as windowing, MPR and 3D reconstruction

LESSON THREE

3D Medical
Imaging
Exploratory Data
Analysis

• Describe and use DICOM and NIFTI representations of 3D medical imaging data
• Explain specifics of spatial and dimensional encoding of 3D medical images
• Use Python-based software packages to load and inspect 3D medical imaging volumes
• Use Python-based software packages to explore datasets of 3D medical images and prepare it for machine learning pipelines
• Visualize 3D medical images using open software packages

LESSON FOUR

3D Medical
Imaging - Deep
Learning Methods

• Distinguish between classification and segmentation problems as they apply to 3D imaging
• Apply 2D, 2.5D and 3D convolutions to a medical imaging volume
• Apply U-net algorithm to train an automatic segmentation model of a real-world CT dataset using PyTorch
• Interpret results of training, measure efficiency using Dice and Jaccard performance metrics

LESSON FIVE

Deploying AI
Algorithms in the
Real World

• Identify the components of a clinical medical imaging network and integration points as well as DICOM protocol for medical image exchange
• Define the requirements for integration of AI algorithms
• Use tools for modeling of clinical environments so that it is possible to emulate and troubleshoot real-world AI deployments
• Describe regulatory requirements such as FDA medical device framework and HIPAA required for operating AI for clinical care
• Provide input into regulatory process, as a data scientist

Course 3: Applying AI to EHR Data

With the transition to electronic health records (EHR) over the last decade, the amount of EHR data has increased
exponentially, providing an incredible opportunity to unlock this data with AI to benefit the healthcare system.
Learn the fundamental skills of working with EHR data in order to build and evaluate compliant, interpretable
machine learning models that account for bias and uncertainty using cutting-edge libraries and tools including
TensorFlow Probability, Aequitas, and Shapley. Understand the implications of key data privacy and security
standards in healthcare. Apply industry code sets (ICD10-CM, CPT, HCPCS, NDC), transform datasets at different
EHR data levels, and use TensorFlow to engineer features.

LEARNING OUTCOMES

LESSON ONE

EHR Data Security
and Analysis

• Understand U.S. healthcare data security and privacy best practices (e.g. HIPAA, HITECH) and how they affect utilizing protected health information (PHI) data and building models
• Analyze EHR datasets to check for common issues (data leakage, statistical properties, missing values, high cardinality) by performing exploratory data analysis

LESSON TWO EHR Code Sets

• Understand the usage and structure of key industry code sets (ICD, CPT, NDC).
• Group and categorize data within EHR datasets using code sets.

Course Project

Patient Selection for

Diabetes Drug Testing

EHR data is becoming a key source of real-world evidence (RWE)
for the pharmaceutical industry and regulators to make decisions
on clinical trials. In this project, you will act as a data scientist
for an exciting unicorn healthcare startup that has created a
groundbreaking diabetes drug that is ready for clinical trial
testing. Your task will be to build a regression model to predict the
estimated hospitalization time for a patient in order to help select/
filter patients for your study. First, you will perform exploratory
data analysis in order to identify the dataset level and perform
feature selection. Next, you will build necessary categorical and
numerical feature transformations with TensorFlow. Lastly, you will
build a model and apply various analysis frameworks, including
TensorFlow Probability and Aequitas, to evaluate model bias and
uncertainty.

LESSON THREE

EHR Transformations
& Feature
Engineering

• Use the TensorFlow Dataset API to scalably extract, transform, and load datasets
• Build datasets aggregated at the line, encounter, and longitudinal(patient) data levels
• Create derived features (bucketing, cross-features, embeddings) utilizing TensorFlow feature columns on both continuous and categorical input features

LESSON FOUR

Building, Evaluating,
and Interpreting
Models

• Analyze and determine biases for a model for key demographic groups by evaluating performance metrics across groups by using the Aequitas framework.
• Train a model that provides an uncertainty range with the TensorFlow Probability library
• Use Shapley values to select features for a model and identify the marginal contribution for each selected feature

Course 4: Applying AI to Wearable Device Data

Wearable devices are an emerging source of physical health data. With continuous, unobtrusive monitoring they hold the promise to add richness to a patient’s health information in remarkable ways. Understand the functional mechanisms of three sensors (IMU, PPG, and ECG) that are common to most wearable devices and the foundational signal processing knowledge critical for success in this domain. Attribute physiology and environmental context’s effect on the sensor signal. Build algorithms that process the data collected by multiple sensor streams from wearable devices to surface insights about the wearer’s health.

LEARNING OUTCOMES

LESSON ONE

Intro to Digital
Sampling & Signal
Processing

• Describe how to digitally sample analog signals
• Apply signal processing techniques (eg. filtering, resampling, interpolation) to time series signals.
• Apply frequency domain techniques (eg. FFT, STFT, spectrogram) to time series signals
• Use matplotlib’s plotting functionality to visualize signals

LESSON TWO

Introduction to
Sensors

• Describe how sensors convert a physical phenomenon into an electrical one.
• Understand the signal and noise characteristics of the IMU and PPG signals

Course Project

Motion Compensated

Pulse Rate Estimation

Wearable devices have multiple sensors all collecting information
about the same person at the same time. Combining these
data streams allows us to accomplish many tasks that would be
impossible from a single sensor. In this project, you will build an
algorithm which combines information from two of the sensors
that are covered in this course -- the IMU and PPG sensors -- that
can estimate the wearer’s pulse rate in the presence of motion.
First, you’ll create and evaluate an activity classification algorithm
by building signal processing features and a random forest model.
Then, you will build a pulse rate algorithm that uses the activity
classifier and frequency domain techniques, and also produces
an associated confidence metric that estimates the accuracy
of the pulse rate estimate. Lastly, you will evaluate algorithm
performance and iterate on design until the desired accuracy is
achieved.

LESSON THREE Activity Classification

• Perform exploratory data analysis to understand class imbalance and subject imbalance
• Gain an intuitive understanding signal characteristics and potential feature performance
• Write code to implement features from literature
• Recognize the danger overfitting of technique (esp. on small datasets), not simply of model parameters or hyperparameters

LESSON FOUR ECG Signal Processing

• Understand the electrophysiology of the heart at a basic level
• Understand the signal and noise characteristics of the ECG
• Understand how atrial fibrillation manifests in the ECG
• Build a QRS complex detection algorithm
• Build an arrhythmia detection algorithm from a wearable ECG signal
• Understand how models can be cascaded together to achieve higher-order functionality

Our Classroom Experience

REAL-WORLD PROJECTS

Build your skills through industry-relevant projects. Get
personalized feedback from our network of 900+ project
reviewers. Our simple interface makes it easy to submit
your projects as often as you need and receive unlimited
feedback on your work.

KNOWLEDGE

Find answers to your questions with Knowledge, our
proprietary wiki. Search questions asked by other students,
connect with technical mentors, and discover in real-time
how to solve the challenges that you encounter.

STUDENT HUB

Leverage the power of community through a simple, yet
powerful chat interface built within the classroom. Use
Student Hub to connect with your fellow students in your
Executive Program.

WORKSPACES

See your code in action. Check the output and quality of
your code by running them on workspaces that are a part
of our classroom.

QUIZZES

Check your understanding of concepts learned in the
program by answering simple and auto-graded quizzes.
Easily go back to the lessons to brush up on concepts
anytime you get an answer wrong.

CUSTOM STUDY PLANS

Preschedule your study times and save them to your
personal calendar to create a custom study plan. Program
regular reminders to keep track of your progress toward
your goals and completion of your program.

PROGRESS TRACKER

Stay on track to complete your Nanodegree program with
useful milestone reminders.

Learn with the Best

Nikhil Bikhchandani

DATA SCIENTIST
AT VERILY LIFE SCIENCES
Nikhil spent five years working with
wearable devices at Google and Verily Life
Sciences. His work with wearables spans
many domains including cardiovascular
disease, neurodegenerative diseases, and
diabetes. Before Alphabet, he earned a
B.S. and M.S. in Electrical Engineering and
Computer Science at Carnegie Mellon.

Mazen Zawaideh

RADIOLOGIST
AT UNIVERSITY OF WASHINGTON
Mazen Zawaideh is a Neuroradiology
Fellow at the University of Washington,
where he focuses on advanced diagnostic
imaging and minimally invasive
therapeutics. He also served as a Radiology
Consultant for Microsoft Research for AI
applications in oncologic imaging.

Emily Lindemer

DIRECTOR OF DATA SCIENCE &
ANALYTICS AT WELLFRAME
Emily is an expert in AI for both medical
imaging and digital healthcare. She holds
a PhD from Harvard-MIT’s Health Sciences
& Technology division and founded her
own digital health company in the opioid
space. She now runs the data science
division of a digital healthcare company in
Boston called Wellframe.

Ivan Tarapov

SR. PROGRAM MANAGER
AT MICROSOFT RESEARCH
At Microsoft Research, Ivan works on robust
auto-segmentation algorithms for MRI and CT
images. He has worked with Physio-Control,
Stryker, Medtronic, and Abbott, where he
helped develop external and internal cardiac
defibrillators, insulin pumps, telemedicine,
and medical imaging systems.

Learn with the Best

Michael Dandrea

PRINCIPAL DATA SCIENTIST
AT GENENTECH

Michael is on the Pharma Development
Informatics team at Genentech (part of
the Roche Group), where he works on
improving clinical trials and developing
safer, personalized treatments with
clinical and EHR data. Previously, he was
a Lead Data Scientist on the AI team at
McKesson’s Change Healthcare.

All Our Nanodegree Programs Include:

EXPERIENCED PROJECT REVIEWERS

REVIEWER SERVICES

• Personalized feedback & line by line code reviews
• 1600+ Reviewers with a 4.85/5 average rating
• 3 hour average project review turnaround time
• Unlimited submissions and feedback loops
• Practical tips and industry best practices
• Additional suggested resources to improve

TECHNICAL MENTOR SUPPORT

MENTORSHIP SERVICES

• Questions answered quickly by our team of technical mentors
• 1000+ Mentors with a 4.7/5 average rating
• Support for all your technical questions

PERSONAL CAREER SERVICES

CAREER COACHING

• Personal assistance in your job search
• Monthly 1-on-1 calls
• Personalized feedback and career guidance
• Interview preparation
• Resume services
• Github portfolio review
• LinkedIn profile optimization

Frequently Asked Questions

PROGRAM OVERVIEW

WHY SHOULD I ENROLL? Artificial Intelligence has revolutionized many industries in the past decade, and healthcare is no exception. In fact, the amount of data in healthcare has grown 20x in the past 7 years , causing an expected surge in the Healthcare AI market from $2.1 to $36.1 billion by 2025 at an annual growth rate of 50.4%. AI in Healthcare is transforming the way patient care is delivered, and is impacting all aspects of the medical industry, including early detection, more accurate diagnosis, advanced treatment, health monitoring, robotics, training, research and much more.

By leveraging the power of AI, providers can deploy more precise, efficient, and impactful interventions at exactly the right moment in a patient’s care. In light of the worldwide COVID-19 pandemic, there has never been a better time to understand the possibilities of artificial intelligence within the healthcare industry and learn how you can make an impact to better the world’s healthcare infrastructure.

WHAT JOBS WILL THIS PROGRAM PREPARE ME FOR?

This program will help you apply your Data Science and Machine Learning expertise in roles including Physician Data Scientist; Healthcare Data Scientist; Healthcare Data Scientist, Machine Learning; Healthcare Machine Learning Engineer, Research Scientist, Machine Learning, and more roles in the healthcare and health tech industries that necessitate knowledge of AI and machine learning techniques.

HOW DO I KNOW IF THIS PROGRAM IS RIGHT FOR ME?

If you are interested in applying your data science and machine learning experience in the healthcare industry, then this program is right for you.

Additional job titles and backgrounds that could be helpful include Data Scientist, Machine Learning Engineer, AI Specialist, Deep Learning Research Engineer, and AI Scientist. This program is also a good fit for Researchers, Scientists, and Engineers who want to make an impact in the medical field.

ENROLLMENT AND ADMISSION

DO I NEED TO APPLY? WHAT ARE THE ADMISSION CRITERIA?

There is no application. This Nanodegree program accepts everyone, regardless of experience and specific background.

FAQs Continued

WHAT ARE THE PREREQUISITES FOR ENROLLMENT?

To be best prepared to succeed in this program, students should be able to:

Intermediate Python:

• Read, understand, and write code in Python, including language constructs such as functions and classes.
• Read code using vectorized operations with the NumPy library.

Machine Learning:

• Build a machine learning model for a supervised learning problem and understand basic methods to represent categorical and numerical features as inputs for this model
• Perform simple machine learning tasks, such as classification and regression, from a set of features
• Apply basic knowledge of Python data and machine learning frameworks (Pandas, NumPy, TensorFlow, PyTorch) to manipulate and clean data for consumption by different estimators/algorithms (e.g. CNNs, RNNs, tree- based models).

IF I DO NOT MEET THE REQUIREMENTS TO ENROLL, WHAT SHOULD I DO? To best prepare for this program, we recommend the AI Programming with Python Nanodegree program and the Deep Learning Nanodegree program or the Intro to Machine Learning with PyTorch Nanodegree program or the Intro to Machine Learning with TensorFlow Nanodegree program.

TUITION AND TERM OF PROGRAM

HOW IS THIS NANODEGREE PROGRAM STRUCTURED? The AI for Healthcare Nanodegree program is comprised of content and curriculum to support four projects. Once you subscribe to a Nanodegree program, you will have access to the content and services for the length of time specified by your subscription. We estimate that students can complete the program in four months, working 15 hours per week.

Each project will be reviewed by the Udacity reviewer network. Feedback will be provided and if you do not pass the project, you will be asked to resubmit the project until it passes.

HOW LONG IS THIS NANODEGREE PROGRAM? Access to this Nanodegree program runs for the length of time specified in the payment card on the Nanodegree program overview page. If you do not graduate within that time period, you will continue learning with month to month payments. See the Terms of Use for other policies around the terms of access to our Nanodegree programs.

FAQs Continued

CAN I SWITCH MY START DATE? CAN I GET A REFUND?

Please see the Udacity Program Terms of Use and FAQs for policies on enrollment in our programs.

SOFTWARE AND HARDWARE

WHAT SOFTWARE AND VERSIONS WILL I NEED IN THIS PROGRAM? For this Nanodegree program, you will need a desktop or laptop computer running recent versions of Windows, Mac OS X, or Linux and an unmetered broadband Internet connection. For an ideal learning experience, a computer with Mac or Linux OS is recommended.

You will use Python, PyTorch, TensorFlow, and Aequitas in this Nanodegree program.