Machine Learning Model Training .

 

Assignment 2 B: Machine Learning Model Training 

• Two multi-part, multiple-choice questions, and short-answer questions.

•  2B HTML Scenario file link 

•  Q1 & Q2 m/c questions and short answers questions are shown in the attached question sheet.

• Lecture notes on Machine Learning in Healthcare for your reference

Assignment 2 Model Training Scenario file ( from HTML file)

Link to HTML FILE for Assignment 2

Please copy and paste the following link for access to the HTML file to answer the questions in this assignment.

https://d3c33hcgiwev3.cloudfront.net/LCgAs51KTA2oALOdSswN1g_cbba05960f9c4fd1b9c17ef732f2189f_PHASE_2.html?Expires=1674777600&Signature=VTr6QJzYC1utN7670sR4PC5LmuAhqzBtScgCNjZsp~gz1dgOiCwdCIuBHJHxOH5-nTmvic9JiiicDDEuNdCDithG0yBB7b8P6nygJcynv2SW6mPaMqKnHZWRFBsNp~XSYPY8CwwlKeYafsOt1aruFgU0bd1c1F1fsJJFnieDjwU_&Key-Pair-Id=APKAJLTNE6QMUY6HBC5A

Phase II Model Training Question Sheet

Copy the link provided in the
2B HTML scenario file to the HTML file, and open the link to read the scenario. After reading through the case, please review the parts of the two questions and short answer questions.

Keep the HTML file open so that it is easier for you to look for the information questioned in the quiz/exercise. Check all the correct answers boldfaced size 14 with an explanation in 2 or 3 sentences. For the short answer questions, keep the answers in 5 sentences or less

Q1

Part 1.

The team split the data into two partitions: the training set and the test set. It is considered best practice to have a third partition– the validation set. What added utility is there in having a validation set?
Check all that apply.

The validation set can be used for tuning hyperparameters

The validation set can be used for early stopping

The test set should be used for final evaluation only

The validation set can be used for updating the model directly

Part 2.

The team split the data randomly, without accounting for the patient to whom each exam belongs. Why would this be a problem?
Recall: “The COVID dataset consists of 30,000 exams across 21,000 patients (some patients may be associated with multiple exams)”

Patient overlap between the training and test sets may lead to problems with model convergence due to exposure to the test set

Patient overlap between the training and test sets may lead to problems with model bias because of the underrepresentation of certain patient demographics in the training set

Patient overlap between the training and test sets may lead to the leakage of PHI or other sensitive data

Patient overlap between the training and test sets may lead to inflated model performance due to unrealistic evaluation conditions

Part 3.

The team downsized the images to 224 by 224 pixels. Why might this lead to worse model performance?

The discriminative features in the image may be too small to identify without a higher resolution

Many publicly available models use 224 by 224 pixel images

Memory constraints may limit the model’s ability to process high-resolution images

224 by 224 pixel chest x-rays are easier to classify than 3000 by 3000 pixel chest x-rays

Part 4.

Why are Convolutional Neural Networks (CNN) particularly well suited for image classification tasks?
Check all that apply.

CNN architectures take advantage of feature locality through the use of filters

CNN architectures leverage multiple decision trees in order to make their predictions more robust

CNN architectures are parameter-efficient because they use the same set of weights on each region of the image

CNN architectures can condition on previous timesteps, which it takes as input in addition to the images themselves

Part 5.

What learning phenomena is the team observing?

Convergence

Overfitting

Underfitting

Generalization

Part 6

(i)

A colleague approaches you and suggests that it would be better if you created a model that relied only on observable features and exam metadata (patient age, gender, ethnicity, etc.). What trade-offs must be considered when using lab values as features?

Answer in 5 sentences or less

(ii)

Before using the new public COVID dataset, you want to verify that there is no PHI in the data. What are some privacy issues that could come into play with imaging data?

Answer in 5 sentences or less

Q 2 Part 1

The D-DIMER values are highly concentrated <1k, but there are many samples that are several orders of magnitude apart from the rest of the samples. What is the most likely explanation for this? (Hint: look at the data samples, particularly the exam metadata.)

There is a large disparity in D-DIMER lab values across patient gender

There is a large disparity in D-DIMER lab values across patient age

The data collected from one the clinics may use different units

The data was collected from two cohorts from two different time periods

Part 2.

Which of the following strategies can be used in order to accommodate for the missing values in the EHR dataset?
Check all that apply.

A logistic regression model can be trained after the missing values are synthetically generated, using a process known as

imputation

A tree-based model, such as random forest, can be trained directly on the data with missing values

A tree-based model, such as random forest, can be trained after the missing values are synthetically generated, using a process known as

imputation

A logistic regression model can be trained directly on the data with missing values

Part 3.

Which of the following is FALSE regarding logistic regression models?

Logistic regression uses the sigmoid activation function

Logistic regression can take unstructured inputs, such as images or text

Logistic regression produces values between 0 and 1, regardless of the scale of the features

Logistic regression is commonly used for classification problems

Part 4.

Which of the following is FALSE regarding random forest models?

Random forest models are a type of decision tree algorithm

Random forest models are highly interpretable

Random forest models learn multiple decision trees that each learn on a subset of the available features

Random forest models require feature normalization (i.e. scaling the features such that they are between 0 and 1) in order to work effectively

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Class notes on Machine Learning and AI in a healthcare setting

Artificial intelligence (AI) has transformed industries around the world, and has the potential to radically alter the field of healthcare. Imagine being able to analyze data on patient visits to the clinic, medications prescribed, lab tests, and procedures performed, as well as data outside the health system — such as social media, purchases made using credit cards, census records, Internet search activity logs that contain valuable health information, and you’ll get a sense of how AI could transform patient care and diagnoses.

In this course, we’ll discuss the current and future applications of AI in healthcare with the goal of learning to bring AI technologies into the clinic safely and ethically. Here is a list of the learning objectives for a quick reference.

1) Solving the problems and challenges within the U.S. healthcare system requires a deep understanding of how the system works. Successful solutions and strategies must take into account the realities of the current system.

This course explores the fundamentals of the U.S. healthcare system. It will introduce the principal institutions and participants in healthcare systems, explain what they do, and discuss the interactions between them. The course will cover physician practices, hospitals, pharmaceuticals, and insurance and financing arrangements. We will also discuss the challenges of healthcare cost management, quality of care, and access to care. While the course focuses on the U.S. healthcare system, we will also refer to healthcare systems in other developed countries.

AI in healthcare use case: Natural language processing

When subject matter experts help train AI algorithms to detect and categorize certain data patterns that reflect how language is actually used in their part of the health industry, this natural language processing (NLP) enables the algorithm to isolate meaningful data. This helps decision-makers with the information they need to make informed care or business decisions quickly.

Healthcare payers

For healthcare payers, this NLP capability can take the form of a virtual agent using conversational AI to help connect health plan members with personalized answers at scale. 

View the resource

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Government health and human service professionals

For government health and human service professionals, a case worker can use AI solutions to quickly mine case notes for key concepts and concerns to support an individual’s care.

Clinical operations and data managers

Clinical operations and data managers executing clinical trials can use AI functionality to accelerate searches and validation of medical coding, which can help reduce the cycle time to start, amend, and manage clinical studies.

2) This course introduces you to a framework for successful and ethical medical data mining. We will explore the variety of clinical data collected during the delivery of healthcare. You will learn to construct analysis-ready datasets and apply computational procedures to answer clinical questions. We will also explore issues of fairness and bias that may arise when we leverage healthcare data to make decisions about patient care.Only by training AI to correctly perceive information and make accurate decisions based on the information provided, can you ensure your AI will perform the way it’s intended.

3 Machine learning and artificial intelligence hold the potential to transform healthcare and open up a world of incredible promise. But we will never realize the potential of these technologies unless all stakeholders have basic competencies in both healthcare and machine learning concepts and principles.

This course will introduce the fundamental concepts and principles of machine learning as it applies to medicine and healthcare. We will explore machine learning approaches, medical use cases, metrics unique to healthcare, as well as best practices for designing, building, and evaluating machine learning applications in healthcare. The course will empower those with non-engineering backgrounds in healthcare, health policy, pharmaceutical development, as well as data science with the knowledge to critically evaluate and use these technologies.

4 With artificial intelligence applications proliferating throughout the healthcare system, stakeholders are faced with both opportunities and challenges of these evolving technologies. This course explores the principles of AI deployment in healthcare and the framework used to evaluate downstream effects of AI healthcare solutions.

5 This last course includes a project that takes you on a guided tour exploring all the concepts we have covered in the different classes up till now. We have organized this experience around the journey of a patient who develops some respiratory symptoms and given the concerns around COVID19 seeks care with a primary care provider. We will follow the patient’s journey from the lens of the data that are created at each encounter, which will bring us to a unique de-identified dataset created specially for this specialization. The data set spans EHR as well as image data and using this dataset, we will build models that enable risk-stratification decisions for our patient. We will review how the different choices you make — such as those around feature construction, the data types to use, how the model evaluation is set up and how you handle the patient timeline — affect the care that would be recommended by the model. During this exploration, we will also discuss the regulatory as well as ethical issues that come up as we attempt to use AI to help us make better care decisions for our patient. This course will be a hands-on experience in the day of a medical data miner.

6 How does AI training work?

AI training starts with data. While the actual size of the dataset needed is dependent on the project, all machine learning projects require high-quality, well-annotated data in order to be successful. It’s the old GIGO rule of computer science — garbage in, garbage out. If you train your AI using poor-quality or incorrectly tagged data, you’ll end up with poor-quality AI.

Once the quality assurance phase is complete, the AI training process has three key stages:

1. Training

2. Validation

3. Testing

Keys to successful AI training

You need three ingredients to train AI well: high-quality data, accurate data annotation, and a culture of experimentation.

High-quality data

Bad data skews AI’s judgment and produces undesirable results. It can even create AI that is biased.

Accurate data annotation

Not only do you need to have plenty of high-quality data, but you must also accurately annotate it. Otherwise, your AI will have no contextual guidance to help it properly interpret the data, let alone learn from it. For example, correctly annotated images can help teach AI programs to tell the difference between suspected skin cancer and benign birthmarks.

A culture of experimentation

7 Why is it important to evaluate your machine learning algorithm?

Evaluating your machine learning algorithm is an essential part of any project. Your model may give you satisfying results when evaluated using a metric say accuracy score but may give poor results when evaluated against other metrics such as logarithmic loss or any other such metric.

Choose an evaluation metric depending on your use case. Different metrics work better for different purposes. Selecting the appropriate metrics also allows you to be more confident in your model when presenting your data and findings to others. On the flip side, using the wrong evaluation metric can be detrimental to a machine learning use case. A common example is focusing on accuracy, with an imbalanced dataset.

Healthcare privacy is a central ethical concern involving the use of big data in healthcare, with vast amounts of personal information widely accessible electronically.

Medical records and prescription data are being used, and even sold, for a variety of purposes. As long as it’s de-identified, patients’ permission isn’t needed. However, some medical ethicist argues, “There is a need for sound regulation to guide and oversee this brave new world of algorithmic-based healthcare.”