iiinova — where your digital self keeps evolving

It serves as a nice reminder to me that some of the most elegant solutions in machine learning and statistics aren't always the newest deep learning architectures. Sometimes, good old Bayesian inference with smart sampling strategies can create something really cool!

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This visualises how modern statistical inference actually works. RJMCMC explores spaces where we don't even know how many parameters we need, perfect for art, where we don't know in advance how many strokes capture an image.

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- Proposals are accepted/rejected based on how well they reconstruct your image - The final painting emerges from thousands of probabilistic decisions - It's not deterministic, run it twice -> get two different artworks

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Upload an image, and the algorithms "paints", one probabilistic brushstroke at a time. Each brushstroke represents a "birth" or "death" jump in the model space: - The algorithm proposes adding new strokes or removing existing ones

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David Hodgson @dchodge.bsky.social · 12/10/2025

I built an MCMC painter! I'm excited to share this project I've been working on for a long time, which sits at the intersection of computational statistics and generative art; mcmcPainter! Link here: mcmcpainter.davidhodgson.me

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Getting started on Substack, just some rambling on Yoga Philosophy and a academia. Give me a follow if interested and share yours too! Open to reading anything 😊 open.substack.com/pub/themindf...

open.substack.com

Three Paths to Freedom (And Why Academia Needs All of Them)

On Trimārga, the three yoga paths from the Bhagavad Gita, and what they mean for researchers

David Hodgson @dchodge.bsky.social · 09/10/2025

Want to understand serological data better? We've compiled a suite of tools which can help you out 🔗 seroanalytics.org These tools are free, open source, peer reviewed and have comprehensive documentation. Big thanks to @alexlizhill.com, @jameshay.bsky.social and others for their contributions!

seroanalytics.org

Seroanalytics

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David Hodgson @dchodge.bsky.social · 05/10/2025

New blog post on Correlates of Protection! I try and give an overview of this very confusing concept: davidhodgson.me/post/sm3_cop1/ I think it's good ID modellers try and get a solid understanding of this as it's going become increasingly important for vaccine development over the next few years.

davidhodgson.me

CORRELATES OF PROTECTION: FUMBLING THROUGH THE TERMINOLOGY | David Hodgson

Long ago, Edward Jenner made medical history by inoculating a young boy with cowpox and demonstrating protection against smallpox. Jenner had no idea why it worked, he just rolled with it, and thus in...

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David Hodgson @dchodge.bsky.social · 02/10/2025

Haha I actually switched to Claude this week so terse bluesky posts incoming.....

David Hodgson @dchodge.bsky.social · 02/10/2025

AHH cool! I'll have a play with this, doesn't seem active currently tho

David Hodgson @dchodge.bsky.social · 02/10/2025

Cheers Sam! I've not seen this have you got a link? They are fitting ODIN models with monty these days right?

David Hodgson @dchodge.bsky.social · 30/09/2025

Yeah it's actually great, converting the c++ to JavaScript is actually not too bad with a little help from AI !

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David Hodgson @dchodge.bsky.social · 30/09/2025

Watch RJMC explore different model dimensions in real-time, use sample data or upload your own CSV. No installation, just open and experiment. Great for teaching/learning Bayesian model selection! Package/vignette: dchodge.github.io/rjmc/article... #statistics #bayesian #MCMC #datascience

dchodge.github.io

Example 1: Mixture model

David Hodgson @dchodge.bsky.social · 30/09/2025

🚀 New tool: Reversible Jump MCMC running in your browser! Built an interactive widget for fitting mixture distributions when you don't know how many components you need. Check it out: dchodge.github.io/rjmc-widget-...

dchodge.github.io

Dynamic Mixture Model Analysis

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David Hodgson @dchodge.bsky.social · 27/09/2025

🔬 New to serological data? You’re not alone When I first saw spreadsheets full of columns labelled ELISA_OD, PRNT50, HI_titre, and PVNT_ID50, I had no idea what they really meant. That confusion inspired me to write a new blog post, “A Dummy’s Guide to Serological Assays” 👉 tinyurl.com/586dsy77

lnkd.in

This link will take you to a page that’s not on LinkedIn

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David Hodgson @dchodge.bsky.social · 26/09/2025

Sure, wanna drop me an email to sort out deets?

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David Hodgson @dchodge.bsky.social · 24/09/2025

"2.1. Overview of inference framework" in the methods gives an overview. But basically if you infer an infection you also need to infer an infection time (an extra parameter), no infection then infection time isn't in the framework anymore. Hence need to jump between different dimensions

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Thanks to everyone who worked on this: @jameshay.bsky.social, Sheikh Jarju, Dawda Jobe, Rhys Wenlock, @adamjkucharski.bsky.social, and @thushan-desilva.bsky.social!

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Interactive widget for serojump

It uses reversible jump MCMC to infer missed infections, to help understanding I made a little widget to show you how the fitting process works for simulated data: seroanalytics.org/serojump-widget

seroanalytics.org

✨ What we did: - Made a Bayesian model to infer who was infected, when, and how their antibody levels changed - Validated on both simulations and real-world SARS-CoV-2 data from The Gambia. - Showed that serojump detects more infections (including sub-threshold ones) and provides richer insights

A serological inference package using reversible jump mcmc

🚨 New paper out in PLOS Computational Biology! 🚨 We're excited to share our new paper, serojump, a new probabilistic framework and R package for inferring infections and antibody kinetics from longitudinal serological data. 📄 Full paper: tinyurl.com/re7du3t2 R package: seroanalytics.org/serojump

seroanalytics.org

The `serojump` package provides tools for fitting serological models to antibody kinetics data using reversible-jump Markov Chain Monte Carlo (RJ-MCMC). It enables researchers to model the dynamics of...

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Thanks to every who worked on this! @jameshay.bsky.social, Sheikh Jarju, Dawda Jobe, Rhys Wnelock, @adamjkucharski.bsky.social and @thushan-desilva.bsky.social

This link will take you to a page that’s not on LinkedIn

serojump was designed to be a flexible and pathogen-agnostic solution that can be applied to a wide range of pathogens. Heres an interactive widget to help with understanding of them reversible jump mcmc methods: lnkd.in/eWGJ39PG

lnkd.in

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What we did: - Made a Bayesian model to infer who was infected, when, and how antibody levels changed over time. - Validated on both simulations and real-world SARS-CoV-2 data from The Gambia. - Showed that serojump detects more infections (including sub-threshold ones) and provides richer insights

David Hodgson @dchodge.bsky.social · 19/09/2025

Key features: - WebAssembly-powered performance (10-50x faster than JS) - Adaptive MCMC for Bayesian inference - Vaccine intervention analysis with waning immunity - Real-time convergence diagnostics - Export data and plots for further analysis

David Hodgson @dchodge.bsky.social · 19/09/2025

Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser! No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation. >> widget-bayesian-sir.davidhodgson.me

widget-bayesian-sir.davidhodgson.me

Interactive Bayesian Epidemic Modelling

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David Hodgson @dchodge.bsky.social · 17/09/2025

What does it really mean to be “infected”? PCR? Symptoms? Antibodies? Being able to pass it on? I’ve written a blog digging into why infection isn’t a simple on/off switch, and why the definition you choose matters for modelling, vaccines, & public health. davidhodgson.me/post/sm1_wha...

davidhodgson.me

WHAT DOES IT MEAN TO BE INFECTED? | David Hodgson

Defining infection is like reading tarot cards - the interpretation depends on who’s asking and what they’re looking for. You wake up with a sore throat. You take a lateral flow...

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David Hodgson @dchodge.bsky.social · 15/09/2025

🚨 New vignette: reversible-jump MCMC for epidemic change-points Used RJMCMC to infer piecewise attack rates in an SEIR model — the sampler figures out how many change-points there are and where they happen. Code + walkthrough 👉 dchodge.github.io/rjmc/article... #R #Bayesian #Epidemiology #RJMCMC

dchodge.github.io

Example 2: SEIR change-point attack rate

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Reposted by David Hodgson

Adam Kucharski @adamjkucharski.bsky.social · 09/04/2025

We've got a new pre-print (spearheaded by @dchodge.bsky.social) on how to reconstruct unobserved antibody kinetics and infections - and use these to estimate correlates of protection: www.medrxiv.org/content/10.1... And here's the accompanying {serojump} R package: seroanalytics.org/serojump/

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Adam Kucharski @adamjkucharski.bsky.social · 31/03/2025

Why did neutralising antibody responses vary between the Oxford-AZ and Pfizer-BioNTech SARS-CoV-2 vaccines? And how did changing the duration between first and second dose affect the underlying biological processes? Our new paper, spearheaded by @dchodge.bsky.social had a look.... 1/

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Alex Hill @alexlizhill.com · 06/03/2025

@dchodge.bsky.social and I developed an app using WebR and React, to see how this stack compares to RShiny. Looks quite promising I think! The app wraps the SeroSim R package by @jameshay.bsky.social for simulating serosurvey data: serosim.seroanalytics.org

serosim.seroanalytics.org

SeroSim

Web interface for serosurvey data simulation

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Reposted by David Hodgson

Khoa @khoavuumn.bsky.social · 02/01/2025

Researcher: "We let the data speak for itself." Earlier that day:

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David Hodgson @dchodge.bsky.social · 22/12/2024

🎅🌟 CHRISTMAS PRESENT 🌟🎅 Got a flexible reversible jump mcmc R packaged up for those who are keen to explore trans-dimensional spaces when fitting; cmmid.github.io/rjmc, with application to a mixture model here; cmmid.github.io/rjmc/article.... More theory and vignettes in 2025!!

cmmid.github.io

A general-purpose package to run reversible-jump mcmc

What the package does (one paragraph).

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Reposted by David Hodgson

Marcel Salathé @marcelsalathe.bsky.social · 19/12/2024

Academic writing is getting harder to read - the humanities most of all www.economist.com/science-and-techn…

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Gwen Knight @gmknght.bsky.social · 11/12/2024

Many, many thanks to colleagues, collaborators, students, friends and family for being with me on this awesome journey to Professor @lshtm.bsky.social! It has involved lots of hard but fun work as well as the usual dose of luck. Onwards and upwards to trying to tackle more challenges in #AMR!

Prof Gwen Knight and some members of her group outside LSHTM

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Saloni @scientificdiscovery.dev · 11/12/2024

Scientists: *develop a once-every-two-months HIV antiviral injection* Scientists: Hold my beer. *develop a once-every-six-months antiviral* Scientists: Hold my beer.

statnews.com

Gilead to test once-a-year HIV prevention shot

Gilead is going to start testing a drug it believes could prevent HIV infection with just a single shot every year.

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David Hodgson @dchodge.bsky.social · 12/12/2024

🚨 Exciting PhD Opportunity with me and @adamjkucharski.bsky.social at LSHTM (MRC LID)! 🚨 Dive into cutting-edge in-host immunological modeling: ✨ Explore immune responses to SARS-CoV-2 & Influenza. ✨ Develop Bayesian models to analyse immune dynamics. more info: mrc-lid.lshtm.ac.uk/2025-26-proj...

mrc-lid.lshtm.ac.uk

2025-26 Project (Hodgson & Kucharski) - MRC London Intercollegiate Doctoral Training Partnership Studentships

Modelling the kinetics of immunity to influenza and SARS-CoV-2 in different populations SUPERVISORY TEAM Supervisor...

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Adam Kucharski @adamjkucharski.bsky.social · 09/12/2024

Have enjoyed early version of seroviz.seroanalytics.org to explore and discuss data - great work by @alexlizhill.com @dchodge.bsky.social And if you're interested in immunological kinetics for SARS-CoV-2 and influenza, we're currently advertising a PhD project: mrc-lid.lshtm.ac.uk/2025-26-proj...

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Edward Nirenberg @enirenberg.bsky.social · 07/12/2024

For those wondering why we seem to be so behind when it comes to effective mucosal vaccines against respiratory viruses, this really excellent overview from leaders in the field offers a great summary: www.nature.com/articles/s41... few additional points for those who want a bit more detail🧵:

nature.com

Challenges for developing broad-based mucosal vaccines for respiratory viruses - Nature Biotechnology

Nature Biotechnology - Challenges for developing broad-based mucosal vaccines for respiratory viruses

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Neil Renic @ncrenic.bsky.social · 04/12/2024

Two stages of writing: 1) This shouldn't take too long 2) Oh no

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David Hodgson @dchodge.bsky.social · 05/12/2024

8/ We hope this sparks new ideas for exploring how host factors shape immune responses in infectious disease dynamics! 🚀