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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">A toolkit for the infectious disease modeller</h1>
<p class="subtitle">the odin, dust, mcstate and orderly suite of R packages</p>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
Marc Baguelin
</div>
</div>
</div>
<p class="date">4/24/24</p>
</section>
<section>
<section id="our-raison-dêtre-why" class="title-slide slide level1 center" data-background-color="#153E70">
<h1>Our Raison d’être (why?)</h1>
</section>
<section id="from-1946-to-2024" class="slide level2 smaller">
<h2>From 1946 to 2024</h2>
<div class="columns">
<div class="column" style="width:50%;">
<ul>
<li>Scarcity</li>
<li>Not powerful by today’s standards</li>
<li>Technical skills needed to operate</li>
<li>Complete knowledge possible</li>
</ul>
</div><div class="column" style="width:50%;">
<ul>
<li>Widely available</li>
<li>Incredibly more powerful</li>
<li>No technical skills needed</li>
<li>No one understands 100% how it works</li>
</ul>
</div>
</div>
<p><img data-src="images/Screenshot%202024-04-24%20at%2006.55.27.png" class="absolute" style="top: 320px; left: 20px; width: 435px; height: 338px; "></p>
<p><img data-src="images/photo_sip.jpg" class="absolute" style="top: 320px; left: 520px; width: 489px; height: 338px; "></p>
</section>
<section id="expectations-for-ml-in-gp-health" class="slide level2">
<h2>Expectations for ML in G/P Health?</h2>
<ul>
<li>Availability of access: large access to computing ressources</li>
<li>Computing power/complexity: Model (and data associated) are expected to be big and complex</li>
<li>Technical skills: Low entry point</li>
<li>Control: Not so much discussed, but relies on expert committee/peer review, emphasizes reproducible and transparent evidence</li>
</ul>
</section>
<section id="what-did-happen-during-covid" class="slide level2">
<h2>What did happen during Covid ?</h2>
<ul>
<li>Availability: large access to computing ressources but disparities for e.g. HPC</li>
<li>Complexity: More models and on average much more complex than before</li>
<li>Technical skills: People with low experience in epi modelling did initiate models</li>
<li>Control: Very variable in space and time, definitely not full transparency, explosion of pre-prints</li>
</ul>
</section>
<section id="how-do-we-get-1-2-3-with-4" class="slide level2">
<h2>How do we get 1-2-3 with 4?</h2>
<ul>
<li>We want (1) widely available (2) complex model with (3) low technical entry point BUT (4) reproducible and truly transparent</li>
<li>Many ML tools have (1*), (2) and (3) but not (4)</li>
<li>Our response to the “black box” problem : modularity (and open source!)</li>
<li>When pipelines get complex, no single person person can control everything but each module can be trusted</li>
<li>Experts can confidently focus on their bit</li>
</ul>
</section>
<section id="core-components" class="slide level2 smaller">
<h2>Core Components</h2>
<ul>
<li><strong>odin:</strong> A domain-specific modelling language for generating systems of ordinary differential equations and deterministic and stochastic difference equations</li>
<li><strong>dust:</strong> Facilitates high-performance parallel computation</li>
<li><strong>mcstate:</strong> Integrates efficient Bayesian inference algorithms</li>
<li><strong>orderly:</strong> Simplifies and enhances reproducibility of collaborative data analyses</li>
</ul>
<p><img data-src="images/logo_odin.png" class="absolute" style="top: 420px; left: 320px; width: 120px; height: 139px; "> <img data-src="images/logo_dust.png" class="absolute" style="top: 420px; left: 520px; width: 120px; height: 139px; "> <img data-src="images/logo_mcstate.png" class="absolute" style="top: 420px; left: 720px; width: 120px; height: 139px; "></p>
</section>
<section id="a-flavour-of-odin" class="slide level2">
<h2>A flavour of odin</h2>
<ul>
<li>Simple ‘R-like’ language to write models in R</li>
<li>Intuitive mapping with mathematical objects</li>
</ul>
<div class="columns">
<div class="column" style="width:60%;">
<div class="sourceCode" id="cb1"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">deriv</span>(S) <span class="ot"><-</span> <span class="sc">-</span>beta <span class="sc">*</span> S <span class="sc">*</span> I <span class="sc">/</span> N</span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="fu">deriv</span>(I) <span class="ot"><-</span> beta <span class="sc">*</span> S <span class="sc">*</span> I <span class="sc">/</span> N <span class="sc">-</span> sigma <span class="sc">*</span> I</span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="fu">deriv</span>(R) <span class="ot"><-</span> sigma <span class="sc">*</span> I</span>
<span id="cb1-4"><a href="#cb1-4"></a></span>
<span id="cb1-5"><a href="#cb1-5"></a><span class="fu">initial</span>(S) <span class="ot"><-</span> N <span class="sc">-</span> I0</span>
<span id="cb1-6"><a href="#cb1-6"></a><span class="fu">initial</span>(I) <span class="ot"><-</span> I0</span>
<span id="cb1-7"><a href="#cb1-7"></a><span class="fu">initial</span>(R) <span class="ot"><-</span> <span class="dv">0</span></span>
<span id="cb1-8"><a href="#cb1-8"></a></span>
<span id="cb1-9"><a href="#cb1-9"></a>N <span class="ot"><-</span> <span class="fu">user</span>(<span class="fl">1e6</span>)</span>
<span id="cb1-10"><a href="#cb1-10"></a>I0 <span class="ot"><-</span> <span class="fu">user</span>(<span class="dv">1</span>)</span>
<span id="cb1-11"><a href="#cb1-11"></a>beta <span class="ot"><-</span> <span class="fu">user</span>(<span class="dv">4</span>)</span>
<span id="cb1-12"><a href="#cb1-12"></a>sigma <span class="ot"><-</span> <span class="fu">user</span>(<span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:5%;">
</div><div class="column" style="width:35%;">
<span class="math display">\[\begin{align}
\frac{dS}{dt} &= -\beta S \frac{I}{N}\\
\frac{dI}{dt} &= \beta S \frac{I}{N} - \sigma I\\
\frac{dR}{dt} &= \sigma I
\end{align}\]</span>
</div>
</div>
</section></section>
<section>
<section id="whats-there-now-and-beyond" class="title-slide slide level1 center" data-background-color="#153E70">
<h1>What’s there now (and beyond)</h1>
</section>
<section id="history-of-project" class="slide level2">
<h2>History of project</h2>
<ul>
<li>odin and orderly pre-existed the COVID pandemic</li>
<li>Decision to use odin and build Imperial UK real model “from scratch”</li>
<li>Decision based on discussion with our research software engineer team</li>
<li>Ambition to build tools with “legacy”</li>
<li>Creating mcstate (inference) dust (efficient parallelisation)</li>
<li>The process has created a huge technical debt</li>
</ul>
</section>
<section id="application-during-covid-19" class="slide level2">
<h2>Application during COVID-19</h2>
<ul>
<li>Huge impact, informing critical government decisions in the UK through SPI-M and SAGE, from April 2020 to May 2022, while ensuring constant public access to our model code</li>
<li>Despite no real advertisement of the tools (and lack of documentation), the toolkit has been adopted by several groups worldwide</li>
</ul>
</section>
<section id="publications" class="slide level2">
<h2>Publications</h2>
<img data-src="images/Papers.png" class="r-stretch"></section>
<section id="an-inclusive-tool" class="slide level2">
<h2>An inclusive tool</h2>
<ul>
<li>Empowering researchers to efficiently utilize the toolkit for policy scenarios by the lowering entry ticket to (complex) modelling pipelines</li>
<li>Accelerating uptake and adoption in academic (incl. teaching) and operational settings</li>
<li>Supporting computation from web browser to HPC and GPUs</li>
</ul>
</section>
<section id="web-app" class="slide level2">
<h2>Web app</h2>
<p>We can use the wodin web interface for odin to fit to <a href="https://epimodels.dide.ic.ac.uk/demo/files/fit/influenza_data.csv">data</a></p>
<p><a href="https://epimodels.dide.ic.ac.uk/demo/apps/fit/" class="uri">https://epimodels.dide.ic.ac.uk/demo/apps/fit/</a></p>
<img data-src="MLGH_talk_2024_files/figure-revealjs/unnamed-chunk-1-1.png" width="960" class="r-stretch"><div class="cell">
</div>
</section>
<section id="harnessing-contemporary-approach" class="slide level2">
<h2>Harnessing contemporary approach</h2>
<ul>
<li>Inference tools (mcstate) developed during the pandemic focused on PMCMC and MCMC</li>
<li>Developping mcstate2 including support for:
<ul>
<li>Automatic differentiation for odin models</li>
<li>Gradient descent, HMC and NUTS</li>
<li>Parallel tempering</li>
<li>Efficient hierarchical modelling of large models</li>
</ul></li>
<li>Modular approach where “models” talk to “samplers”</li>
</ul>
</section>
<section id="a-flavour-of-mcstate2" class="slide level2">
<h2>A flavour of mcstate2</h2>
<img data-src="images/samplers.png" class="r-stretch"></section>
<section id="creating-a-community" class="slide level2">
<h2>Creating a community</h2>
<ul>
<li>Organizing a workshop in the autumn to gather user feedback for interface and API improvement and resource development</li>
<li>User input is crucial in enhancing toolkit usability and effectiveness</li>
<li>Need to build a community</li>
<li>Contact me if interested [email protected]</li>
</ul>
</section>
<section id="summary" class="slide level2">
<h2>Summary</h2>
<ul>
<li>COVID-19 pandemic highlighted the critical need for rapid, reproducible pipelines for the modelling of epidemics</li>
<li>odin, dust, dcstate, and orderly developed to enhance teaching, understanding, production, and reproducibility of population-dynamic models</li>
<li>Some modelling groups worldwide have already embraced these packages</li>
<li>We are working on reimbursing the technical debt contracted during the pandemic</li>
</ul>
</section>
<section id="our-ambition" class="slide level2">
<h2>Our ambition</h2>
<ul>
<li>Improving efficiency and reproducibility of infectious disease modelling</li>
<li>Positioning the toolkit as a key global resource for population dynamic modelling</li>
<li>Transforming how infectious diseases and epidemic threats are modelled, leading to better public health outcomes worldwide</li>
</ul>
</section></section>
<section id="the-end" class="title-slide slide level1 center" data-background-color="#153E70">
<h1>The End</h1>
<p>Thank you for your attention. I’m happy to take any questions you may have.</p>
<img src="_extensions/tickle_ext/logo_modelling_hpru.png" class="slide-logo r-stretch"><div class="footer footer-default">
<p>MLGH day | odin, dust, mcstate and orderly | <a href="https://www.imperial.ac.uk/people/m.baguelin">Marc Baguelin</a></p>
</div>
</section>
</div>
</div>
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