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<!DOCTYPE HTML>
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<head>
<title>A hackathon hosted by CMIC @ UCL</title>
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<h1> 10-11th November 2022 </h1>
<p>A hackathon hosted by CMIC @ UCL<br />
Organised by <a href="https://tobyUCL.github.io">Toby</a>, Snigdha</a>, <a href="https://sea-shunned.github.io/">Cameron</a>, <a href="https://iris.ucl.ac.uk/iris/browse/profile?upi=AJLEG92">Antoine</a>, <a href="http://manifold.cs.ucl.ac.uk/author/james-h-cole/">James</a>, and <a href="https://epanagiotaki.wordpress.com/">Laura</a>.</p>
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<ul>
<li><a href="#intro" class="active">What's a hackathon?</a></li>
<li><a href="#program">Program</a></li>
<li><a href="#projects">List of Projects</a></li>
<li><a href="#second">Location</a></li>
<li><a href="#cta">REGISTER!!!</a></li>
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<!-- Main -->
<div id="main">
<!-- What's a hackathon? -->
<section id="intro" class="main">
<div class="spotlight">
<div class="content">
<header class="major">
<h2>What's a hackathon?</h2>
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<p>A hackathon is an event, usually lasting a few days, during which participants are invited to use their programming skills to collaborate on one or more projects.</p>
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<span class="image"><img src="images/pic01.jpg" alt="" /></span>
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</section>
<section id="program" class="main">
<header class="major">
<h2>Program</h2>
</header>
<section class="main">
<div class="schedule" aria-labelledby="schedule-heading">
<span class="track-slot" aria-hidden="true" style="grid-column: track-1; grid-row: tracks;">Day 1 (10/11/2022)</span>
<span class="track-slot" aria-hidden="true" style="grid-column: track-2; grid-row: tracks;">Day 2 (11/11/2022)</span>
<h2 class="time-slot" style="grid-row: time-0900;">9:00</h2>
<h2 class="time-slot" style="grid-row: time-1000;">10:00</h2>
<h2 class="time-slot" style="grid-row: time-1100;">11:00</h2>
<h2 class="time-slot" style="grid-row: time-1200;">12:00</h2>
<h2 class="time-slot" style="grid-row: time-1300;">13:00</h2>
<h2 class="time-slot" style="grid-row: time-1400;">14:00</h2>
<h2 class="time-slot" style="grid-row: time-1500;">15:00</h2>
<h2 class="time-slot" style="grid-row: time-1600;">16:00</h2>
<h2 class="time-slot" style="grid-row: time-1700;">17:00</h2>
<h2 class="time-slot" style="grid-row: time-0930;">9:30</h2>
<h2 class="time-slot" style="grid-row: time-1030;">10:30</h2>
<h2 class="time-slot" style="grid-row: time-1130;">11:30</h2>
<h2 class="time-slot" style="grid-row: time-1230;">12:30</h2>
<h2 class="time-slot" style="grid-row: time-1330;">13:30</h2>
<h2 class="time-slot" style="grid-row: time-1430;">14:30</h2>
<h2 class="time-slot" style="grid-row: time-1530;">15:30</h2>
<h2 class="time-slot" style="grid-row: time-1630;">16:30</h2>
<div class="session session-1 track-1" style="grid-column: track-1; grid-row: time-1000 / time-1100;">
<h3 class="session-title"><a href="#">Welcome session + project leaders presentations</a></h3>
<span class="session-time">10:00 - 11:00</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-2 track-2" style="grid-column: track-1; grid-row: time-1100 / time-1200;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">11:00 - 12:00</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-3 track-2" style="grid-column: track-2; grid-row: time-0900 / time-1030;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">9:00 - 10:30</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-4 track-2" style="grid-column: track-2; grid-row: time-1045 / time-1200;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">10:45 - 12:00</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-5 track-all" style="grid-column: track-1; grid-row: time-1200 / time-1300;">
<h3 class="session-title">lunch break</h3>
</div>
<div class="session session-6 track-all" style="grid-column: track-2; grid-row: time-1200 / time-1300;">
<h3 class="session-title">lunch break</h3>
</div>
<div class="session session-7 track-2" style="grid-column: track-1; grid-row: time-1300 / time-1500;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">13:00 - 15:00</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-8 track-2" style="grid-column: track-1; grid-row: time-1515 / time-1700;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">15:15 - 17:00</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-9 track-2" style="grid-column: track-2; grid-row: time-1300 / time-1430;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">13:00 - 14:30</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-10 track-2" style="grid-column: track-2; grid-row: time-1445 / time-1630;">
<h3 class="session-title"><a href="#">Hacking</a></h3>
<span class="session-time">14:45 - 16:30</span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
<div class="session session-11 track-all" style="grid-column: track-1; grid-row: time-1500 / time-1515;">
<h3 class="session-title">coffee break</h3>
</div>
<div class="session session-12 track-all" style="grid-column: track-2; grid-row: time-1030 / time-1045;">
<h3 class="session-title">coffee break</h3>
</div>
<div class="session session-13 track-all" style="grid-column: track-2; grid-row: time-1430 / time-1445;">
<h3 class="session-title">coffee break</h3>
</div>
<div class="session session-14 track-4" style="grid-column: track-1; grid-row: time-1700 / time-1800;">
<h3 class="session-title"><a href="#">Socializing</a></h3>
<span class="session-time">17:00 - all night</span>
<span class="session-track">Function room - 90 High Holborn</span>
<span class="session-presenter"></span>
</div>
<div class="session session-15 track-4" style="grid-column: track-2; grid-row: time-1700 / time-1800;">
<h3 class="session-title"><a href="#">Socializing</a></h3>
<span class="session-time">17:00 - all night</span>
<span class="session-track">Function room - 90 High Holborn</span>
<span class="session-presenter"></span>
</div>
<div class="session session-15 track-3" style="grid-column: track-2; grid-row: time-1630 / time-1700;">
<h3 class="session-title"><a href="#">Closing session,   </a></h3>
<span class="session-time">16:30 - 17:00,   </span>
<span class="session-track">Jeremy Bentham room - UCL main campus</span>
<span class="session-presenter"></span>
</div>
</section>
</section>
<!-- Table -->
<section id="projects" class="main">
<header class="major">
<h2>List of Projects</h2>
</header>
<p>A list of currently proposed projects for the hackathon, along with links to the
proposer and the research group they're in for more background.</p>
<section class="main">
<div class="table-wrapper">
<table>
<colgroup>
<col span="1" style="width: 15%;">
<col span="1" style="width: 12%;">
<col span="1" style="width: 3%;">
<col span="1" style="width: 65%;">
</colgroup>
<thead>
<tr>
<th>Project Title</th>
<th>Project Leader</th>
<th>Research Group</th>
<th>Project Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>Lung and placenta united</td>
<td>Paddy Slator</td>
<td>MIG</td>
<td>This project will transfer knowledge, ideas, and techniques between the similar but different domains of lung and placenta imaging. We'll apply AirQuant to derive lower-dimensional representations of synthetic placental vascular trees, segment vessels in placental microCT with techniques designed for airways, calculate susceptibility maps from airway segmentations, and calculate flow and transport maps in the lungs.</td>
</tr>
<tr>
<td>Simulating diffusion microstructural models </td>
<td>Leevi Kerkela</td>
<td>??</td>
<td>An early version of a Python package that enables efficient simulations of microstructural models has been previously developed. The goal during the hackathon will be to turn it into a proper software package by adding features, fixing bugs, writing tests, writing documentation and use case examples. If the resulting software package is of sufficient quality, the hackathon can be followed by paper submission to, for example, JOSS like with my previous software package: https://doi.org/10.21105/joss.02527. To participate, it is required to know Python, git, and basic linear algebra. Used technologies include Python, NumPy, JAX, Sphinx, and PyTorch.</td>
</tr>
<tr>
<td>Comparing different Alzheimer's models </td>
<td>Cameron Shand</td>
<td><a href="https://ucl-pond.github.io/">POND</a></td>
<td>Are Alzheimer's disease progression models comparable? This hackathon project is part hacking, part research. Disease progression modelling has become increasingly popular with numerous different groups developing computational models and releasing the source code. The code can be challenging to run, which may explain why systematic comparison of selected models is yet to be conducted. This project will provide the code for multiple disease progression models, along with pre-prepared data from the Alzheimer's Disease Neuroimaging Initiative, among others. The challenge will be to get the code running, document the steps necessary for each, and perform a direct comparison of results from competing disease progression models.</td>
</tr>
<tr>
<td>Metrics Reloaded stress testing and GUI development</td>
<td>Neil Oxtoby</td>
<td><a href="https://ucl-pond.github.io/">POND</a></td>
<td>The Metrics Reloaded consortium has recently provided a list of reference metrics to use in the evaluation and validation of classification, object detection, instance segmentation and semantic segmentation. Adequate implementation of these evaluation processes and metrics is essential to ensure appropriate use and promote best practice. Most of the code for such an evaluation suite has already been developed but requires some stress-testing of edge cases. Another aspect of this project will be the creation of a GUI to help in the final choice of metrics to be employed in an evaluation setting.</td>
</tr>
<tr>
<td>Deploying Cloud ML Models Using Microsoft InnerEye</td>
<td>Tom Dowrick, <a href="https://www.haroonrchughtai.com/">Haroon Chugthai</a></td>
<td><a href="http://compass.cs.ucl.ac.uk/">COMPASS, </a><a href="https://cig-ucl.github.io/">ARC</a></td>
<td><a href="https://github.com/microsoft/InnerEye-DeepLearning">Microsoft InnerEye</a> provides a suite of tools for training and developing medical imaging algorithms either using local computing resources or Azure cloud services, and there are many algorithms/models developed within CMIC that would benefit from compatiblity with InnerEye, to allow for more widespread deployment. \n
During this hackathon project, participants will convert existing models developed within CMIC to use PyTorch Lightning, and then deploy them on the cloud using InnerEye. Pariticipants will also work to deploy a local InnerEye environment using existing CMIC computing resources, to provide a testing/development environment that can be used in the longer term, to prepare models before they are deployed on the cloud.</td>
</tr>
<tr>
<td>TBC</td>
<td><a href="https://csparker.github.io/about/">Chris Parker</a></td>
<td><a href="https://cig-ucl.github.io/">CIG</a></td>
<td>TBC.</td>
</tr>
</tbody>
</table>
</div>
</section>
</section>
<!-- Location -->
<section id="second" class="main special">
<header class="major">
<h2>Location</h2>
<p>The hackathon is a purely in person event which will take place in:<br />
Jeremy Bentham Room (JBR),
Wilkins Building (main building),<br />
UCL main campus, Gower St, London WC1E 6AE.</p>
</header>
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<p>At the end of day, participants are invited to socialize with food and drinks in:<br />
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