Objectives

The main objective of this phase is to prepare the Project Proposal and the Phase II report. The new report will serve as the literature review for your final report.

During this phase you should:

  • Meet with your teammates and guidance mentor(s) to discuss and refine project background, proposal, and timeline
  • Find and review literature related to relevant data, findings, and analysis methods
  • Make revisions to your Phase I report
  • Write up your Phase II report, Project Proposal, and Timeline
  • Solicit feedback on these documents from your guidance mentor(s)
  • Submit the Phase II report as a team through the [Phase II Report Submission Form]
  • Submit your Project Proposal as a team through the [Proposal and Timeline Form]

After submitting the report, you also be assigned to review other proposals

  • Submit [Phase II Evaluation] for each proposal reviewed, your mentors will formally evaluate your submission

Timeline and Key Dates

  • [30 Points] Each team submits the Phase II Report by July 1, 2022
    • [Phase II Report Submission Link]
    • PDF with an updated Phase I section (5 Points) and the new literature review section (25 Points)
    • Please read the detailed requirements below
  • [10 Points] Each team submits the [Proposal and Timeline Form] by July 1, 2022
  • [10 Points] Submit the [Phase II Evaluation] for all projects you are assigned to review by July 15, 2022.

Phase II Report Requirements

Report Format

At this point, you should consider formatting your report in a formal paper submission style. You will gradually add additional components to it in later phases and it will eventually become your final report. In terms of the structure of this report, most medical journal templates are acceptable. For example, you can consider this collection of science/medical journal templates provided by nextgenediting.com. NEJM also has these manuscript requirements, which you should read and use as a general guideline for writing your report.

Overall, your combined report at this phase should be submitted as a pdf that is not longer than 4 pages (excluding any figures, tables, and references). The name of the submitted pdf should contain a short title of the project followed by the last names of the medical student team members (e.g. “Being President - Washington, Adams.pdf”).

Phase II Report Contents

The Phase II Report mainly consists of your (revised) Phase I report and the new comprehensive literature review. Consider this new component as the introduction section in a journal paper. It should be well-organized and should

  • Summarize the current literature on your chosen topic and closely related topics
  • Give proper references formatted in the style of a journal paper
  • Highlight the limitations of the current literature
  • Highlight the importance of your proposed work

The literature review should consider and cover answers to questions such as:

  • Metric Selections: What is the best metric/measure for answering your specific clinical question? What are alternative metrics? What are the advantages and shortcomings of the best metric?
  • Method Details: What statistical or machine learning data analysis methods are typically applied to the data? What are some advantages and shortcomings of those analysis types? What makes them best suited for the data and the research questions? What assumptions do these analysis models make? especially about the number of training samples and features? (Volume)
  • Results History: What has been previously shown with this data? What performance benchmarks have been previously achieved in its analysis?

Phase I Report Update

When you receive your Phase I feedback, many of you will discover that you missed an important component in your report of providing summary statistics on your dataset. For example, consider Table 1 from this recent NEJM paper [Creech, et al. (2022)]. An important part of characterizing a dataset is describing to your audience how that data breaks down. If your have demographic or other important categorical variables, they should be summarized in a format similar to the example. If you have image data, you may also want to present a few images as examples. When doing your literature survey, examine similar medical journal articles and observe how they summarize the data in their studies. Remember, improvements and revisions to the Phase I report are encouraged, should be clearly indicated, and are scored during Phase II.

Phase II Report Submission

When you submit your Phase II report, you will need to answer additional questions in the Google form that:

  • Reaffirm your team membership and project title
  • Highlight changes made to the Phase I report
  • Describe your interaction with your mentors

Grading Criteria Considerations (Final Report)

We would like to provide our grading criteria of the final report early. It will be graded in consideration of the following items. This list should give you an idea on what considerations to make while writing up your report.

  • [Content] Content is thorough, accurate, and supported by citation of relevant literature. There is no redundancy or unnecessary minutia. Shows ability to summarize essential points of a large body of information. The report has an appropriate number of words. The targeted page limit is 8 with 12 point font. There is no page limit for the appendix.
  • [Data Analytics] Data collection, pre-processing and analysis are described clearly. Figures/tables are used to support the arguments and conclusion. Additional information should be presented in the appendix.
  • [Reasoning and Clarity of Summary] The topic is introduced, and groundwork is laid as to the direction of the report. Conclusions logically rely on prior information.
  • [Format & Organization] Clear organization. Paragraphs are complete yet concise, with strong topic sentences indicating the focus of each paragraph. Transitions tie sections together, as well as adjacent paragraphs. Formatting consistent throughout.
  • [Audience] Written at the appropriate level for an audience of medical researchers and data scientists, with no or well-defined jargon. Concepts should be explained when necessary in a formal tone.
  • [Clarity of Language and Writing Technique] Writing is crisp, clear, and concise. Use active voice, complete sentences, and grammatically correct subject-verb constructions with no spelling errors.
  • [Citations / References] Cites appropriate references in the body of the paper, using proper format. The bibliography is complete, appropriately formatted, and matches in-text references.

Project Proposals

The project proposal is an opportunity to receive feedback from your mentors and your peers about the analysis topic you have decided to focus on and your plan for completing your data analysis. The information of the project proposal will be submitted as answers to individual questions within a Google form. The questions cover:

  • Project Title
  • Project Abstract: Provide a succinct description of your project’s overall goals, clinical relevance, and data analysis deliverables. Limit 1500 characters (approximately 250 words).
  • Data Source: Provide a succinct description of the data that you are using. Consider this as a summary of your updated version of the Phase I report.
  • Analysis Plan: Please provide a description of your analysis plan moving forward. Please note that this question is asking about the analysis beyond what you have ready done in the Phase II report. For example, what type of model you want to consider, what computational resources you want to try, how they are going to answer your clinical questions, etc.
  • Timeline Details: Please provide a tentative completion time for the key items/steps in the previous analysis plan question.
  • Challenges: Moving forward, what are some of the biggest challenges you anticipate?
  • Risk Analysis: Moving forward, what are some of the risks inherent in completing this project? What sort of contingency plans have you considered to address these potential pitfalls?

Project Proposal Evaluations

Your mentors and randomly assigned peers with evaluate your Project Proposal and Phase II Report. They will assigned scores based on the following criteria:

  • Proposal addresses an important issue relevant to clinical practice
  • Report provides background information on the relevant data sets, analysis methods, and previous findings
  • Proposal articulates a clear, well-formulated research question
  • Dataset(s) is appropriate for addressing the proposed problem (relevant with sufficient size and quality)
  • Project contains sufficient difficulty in the acquisition, processing, and management of data
  • Analysis method(s) are appropriate for addressing the proposed problem (relevant and matching current literature)
  • Project contains sufficient difficulty in its described, iterative analysis
  • Report and Proposal were well-written in a professional, concise, understandable manner
  • The estimated amount of time the proposed project will take per team member on average
  • The likelihood that this project can be successfully completed as proposed
  • If the project is carried out as planned, its likely impact