SPARK (Sprint AI Training for African Medical Imaging Knowledge Translation) Academy

Training for Change, from Science to Practice

2023 Program Guide

Program Platform: https://event.fourwaves.com/spark/pages

Overview: The SPARK Academy is designed to train a new generation of African AI experts in medical imaging who can train others.
Participants will be selected from a collective intelligence from various related fields (medical physics, computer science, radiology,
oncology, and neurology/neurosurgery) to rapidly turn knowledge into action.

The first SPARK Academy is in collaboration with McMedHacks and endorsed by the Medical Image Computing and Computer
Assisted Interventions (MICCAI) Society. This first SPARK Academy event is planned to coincide with the release of the AfNiA (The
African Neuroimaging Archive) brain tumor data (Africa-BraTS) in May 2023, ahead of the 2023 MICCAI Brain Tumor Segmentation
(BraTS) Challenge. Seventy-three trainees from various African nations will participate in the first SPARK Academy and trained to
create state-of-the-art AI methods for brain tumor diagnostics. This first cohort will work together to produce 10 AI methods for the
2023 MICCAI BraTS, with top ranked methods eligible for The Lacuna Fund monetary prize (up to $5000).

For more details on the program vision, mission and approach see program platform.

Program Objectives:
1. Build an interdisciplinary network of AI experts in medical imaging across Africa
2. Provide transferable research skills in study design, execution, and dissemination including publications and science
communication
3. Create a collaborative culture of developing innovative medical solutions across Africa
4. Contribute to the open science efforts of the global AI imaging community
5. Train and Retain experts to advance medical research across Africa

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 6. Win Medical or Health Care Grand Challenges.

Program Format:
● All training will be delivered through the SPARK Academy Fourwaves program platform.
○ Review the Platform overview and how to use the platform and the Live APP, Here.
● Program guide, tutorial materials are in the Program Google Drive.
● Fourwaves and Google Drive require unique login and single access and cannot be shared.

Program Structure:
● Training is completed in 3 blocks (see below)
● Training is completed as a team not as an individual.
○ Each candidate is enrolled as part of a team (see team composition in program guide folder)
○ The McMedHacks foundation block is self-paced and is intended to be completed individually.
○ All tutorial assignments including during the foundation block are completed as a team.
○ Each candidate participates in the hackathon and MICCAI BraTS Challenge as a team.
○ Teams comprise of 1 site director, 1 team supervisor, 1 team captain and 6-7 members
○ Each team has at least 3 members from the same country.
○ To foster cross-regional and cross-discipline collaborations, each team includes ≥2 members from outside the country
and at least 2 clinicians.
○ Team roles and assignments are in the Team Composition documentation in the program guide folder

Program Expectations and Code of Conduct:

1. All candidates are expected to be active team players.
2. All candidates are expected to participate in all program activities including live lectures and tutorials.
3. All candidates are expected to complete all reading and lecture materials, assignments, milestones and deliverables.
4. All candidates are expected to attend and participate in the hackathon, daily.

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 5. All participants of the SPARK Academy are expected to behave professionally and responsibly towards everyone both
in-person and online during all formal and informal activities, regardless of location.
6. All participants are expected to review and understand the SPARK Academy code of conduct appended below, as well as on
the SPARK program platform.

Program Contact information:

● General program information is in the FAQ section of the program platform.
● General program inquiry: SPARK Academy Team at spark@mailab.io
● Project specific inquiry including questions related to team assignment, hackathon project, or team BraTS project, contact
Team Supervisor.
● Follow SPARK Academy social channels for program updates; Twitter (CAMERA and MAI Lab) and LinkedIn.

Program Blocks (TTU):

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 1. Teach - Six-weeks McMedHacks Virtual Foundation Course. (April 3rd to May 13th, 2023)

Learn the basics. Engage our self-paced online learning platform and live tutorials on Saturdays and discover
fundamentals in imaging and computational science relevant to building advanced AI applications for medical
imaging in six weeks.

2. Try - One Week Hybrid Africa-BraTS BrainHack 2023 (May 22nd to May 26th, 2023)

Charge your creative adrenaline. Join six regional participants for a one-week (M-F) hybrid hackathon where we
deconstruct and reconstruct top AI glioma diagnostic methods as well as engage in daily seminars, networking
opportunities, and team building capstone projects.

3. Use - Six weeks BraTS Practicum (May 29th to July 31st, 2023)

GO for the win. Apply skills gained and create winning AI models for the MICCAI BraTS challenge. There is a 50%
chance of winning a monetary prize as the top African winning model and another chance to win even more as the
top ranked method from around the world.

Tutorial and Assignment Submissions

● Each team submits one assignment/tutorial exercise/Capstone project or BraTS practicum exercises through the Team
Captain.
● Submissions are uploaded to the program google drive or where directed to the program platform.
● No late submission will be considered or reviewed.

Program Schedule
● Each block is outlined below.
● All tutorials and live events including hackathon are in East Africa Time
● To complete each course or attend live training events, log into your Fourwaves account to access the program content.

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SPARK Virtual Foundational Course Schedule - Week of April 3 to May 13th (Tutorials - Sat 4 to 6 pm, East Africa Time)
Week Activities Weekend Tutorial

1 Introduction to Python and Machine Learning April 9

● Review of Python Basics
● Object-oriented-programming and data science workflow in Python
● Scientific Programming in Python
● Introduction to Classical Machine Learning
● Classical Machine Learning: A Case Study in XGBoost

2 Fundamentals of Image Processing April 16

● Introduction to Image Processing: Image IO and Transformation
● Medical image (pre-)processing

3 Fundamentals of Deep Learning April 23

● Introduction to PyTorch
● Deep Learning Framework (PyTorch): Tensors and Autograd
● Introduction to AI: Definitions, Strengths, Limitations & Misconceptions
● Introduction to AI: Machine Learning Models

4 Deep Learning Framework (PyTorch): Model Training and Evaluation April 30

● Deep Learning Framework (PyTorch): Implement your own Image Classifier
● Code saving and versioning
● Introduction to AI: Convolutional and Neural Networks

5 Fully Supervised Medical Image Segmentation May 7

● Medical Image Segmentation
● Deep Learning Framework (PyTorch): Tensorboard & Pytorch Lightning

6 Deep Learning Framework (PyTorch): Implement U-Net May 14

● Model Validation
Adapted from McMedHacks 2022 Program
Every Week ends with a virtual 2-hour tutorial on Saturday (1 hr Review talk and 1hr Q&A)

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SPARK Hackathon Schedule - May 22 to May 26th (East Africa Time)
Monday Tuesday Wednesday Thursday Friday

7:00 am Morning Coffee

7:30 – 8:30 am Neuropathology of Neurooncology Imaging Physics – MRI State of AI in Brain Bioinformatics &
AM Seminar Gliomas Treatment of Gliomas of Gliomas Tumor Radiomics of Gliomas

8:30 – 10:30 am Code Hack Code Hack Code Hack Code Hack Code Hack
DeCode

10:30 -11:30 am Lunch Break

11:30-12:30 pm Team Exercise, Recode Team Exercise, Recode Team Exercise, Recode Team Exercise, Recode Team Exercise, Recode
Ubuntu

12:30 – 2:30 pm Neuroradiology of Neurosurgery of Radiation Physics & Big Data, FAIR & Open
PM Seminar Gliomas Gliomas Radiobiology of Science
Gliomas

AI imaging in LMICs

2:30 pm Afternoon Tea

3:00 – 4:00 pm Image Processing & Intro to BraTS Data Science ELSI How to Write MICCAI Capstone Project
Umoja Analysis (Ethics, Legal & Social Papers Presentations
Implications)

Intro to Africa-BraTS MICCAI 2022 Paper

Challenge Presentation

4:00pm Closing Plenary

5:00pm Group Dinner

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SPARK Practicum Weekly Schedule (Tutorials - Sat 4 to 6 pm, East Africa Time)
Week Weekend Tutorial Deliverable

1 June 3 Project planning and data acquisition

● Complete a two page summary of BraTS review
● Outline the aims and objective
● Describe data sources and data

2 June 10 Data Exploration and Preprocessing

● Perform exploratory data analysis.
● Preprocess data for deep learning (DL) model training.

3 June 17 Model Selection and Training

● Outline the DL architecture for the 2023 BraTS challenge.

4 June 24 Model Selection and Training

● Train DL model on 2023 BraTS data & report preliminary results.
● Participate in the SANO AI Neuro Summer school

5 July 1 No Tutorial – Canada Holiday

6 July 8th Hyperparameter Tuning and Validation

● Fine-tune DL model to optimize performance.
● Validate model performance on 2023 BraTS validation data.

7 July 15th Model Evaluation and Optimization

● Identify model deficiencies & outline strategies to address them.
● Optimize model and the training process.
● Submit a 1-page description of DL model & architecture

8 July 22 Model Evaluation and Optimization

● Evaluate model performance using 2023 BraTS validation data.
● Compare result with previous BraTS methods (leaderboard)
● Submit Draft of MICCAI paper

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 9 July 29th Model Publication and Reporting
● Submit MICCAI Short Paper to MICCAI Submission site.
● Group Presentation of MICCAI paper
● Group Presentation Radiology AI: Bits & Bytes
Each week ends with a 2hr virtual weekend tutorial on Saturday (30 min overview & 1.5hr Q&A / review of exercises).

SPARK Timeline: Road to 2023 MICCAI BraTS Challenge

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Code of Conduct
SPARK Academy is dedicated to providing a harassment-free experience and safe environment for all, regardless of race, cultural affiliations,
gender, nationality, beliefs, age, or disability. Indecent imagery is not appropriate at any of the Academy’s events including virtual and in-person
events.

All attendees, speakers, and volunteers are expected to comply with this code of conduct and violations of its standards may result in sanctions
or expulsion from participating in events, at the discretion of the Academy Team. Upholding the standards of behavior is mandatory to maintain
SPARK's integrity and create a positive environment.

Expected behavior
All attendees, speakers, and volunteers at SPARK events must:
1. Behave professionally and responsibly towards each other, both in-person and online, during all formal and informal social activities,
regardless of location.
2. Respect each other and avoid making judgments based on race, gender, nationality, beliefs, age, or disability.
3. Refrain from any forms of harassment, bullying, or discrimination towards fellow participants.
4. Adhere to the guidelines and instructions given by SPARK organizers and staff during events.
5. Maintain confidentiality of any sensitive information shared during events.
6. Avoid engaging in any illegal or unethical behavior.

Unexpected behavior
1. Behaving in a manner that is disruptive or disrespectful towards other participants, staff, or the event itself.
2. Using language that is inappropriate, disrespectful, or offensive towards other participants, staff, or the event itself.
3. Engaging in any illegal or unethical behavior, such as theft, plagiarism, vandalism, or fraud.
4. Disobeying or ignoring the guidelines and instructions given by SPARK organizers and staff during the event.
5. Engaging in any behavior that may pose a threat to the safety or security of other participants, staff, or the event itself.
6. Intentionally causing damage to the event venue, equipment, or other property.
7. Engaging in any form of inappropriate or unwanted physical contact towards other participants or staff.
8. Violating the confidentiality of any sensitive information shared during the event.
9. Using SPARK events or platforms for personal or commercial gain without prior authorization from the organizers.

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Recording Policy: Online events may be recorded or live streamed, but only with express written permission from SPARK Academy and the
authors/owners of the content. Any unauthorized recordings will violate ethical and legal standards.

Reporting Process: To report any concerns regarding the violation of the aforementioned guidelines, please email the SPARK Academy organizers
at spark@mailab.io.

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