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Sam Abbott

@seabbs.bsky.social

1.4K followers 690 following 620 posts

Real-time infectious disease modelling. Developing methods for outbreak response, surveillance, and pandemic preparedness. samabbott.co.uk Come join me on the epinowcast forum: https://community.epinowcast.org/latest

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Sam Abbott @seabbs.bsky.social · Dec 13

In 2022 @sbfnk.bsky.social and I wrote this blog on what it was like estimating the effective reproduction number daily for 2 years and if it was helpful

epiforecasts.io/posts/2022-0...

Reflections on two years estimating effective reproduction numbers – EpiForecasts

Over the last two years we have estimated reproduction numbers daily for several thousand locations, presented these estimates as a curated data set and visualised them at epiforecasts.io/covid. In th...

epiforecasts.io

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Reposted by Sam Abbott

Adam Kucharski @adamjkucharski.bsky.social · 11h

Want to build an interactive dashboard so others can explore epidemic scenarios? For COVID, @ngdavies.bsky.social spearheaded a great drag-and-drop approach, which made use of the JavaScript-based nature of RShiny... 1/

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Reposted by Sam Abbott

Jacob Schreiber @jmschreiber91.bsky.social · 1d

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

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Sam Abbott @seabbs.bsky.social · 1d

This is really encouraging as I thought my 6 month turn around time for email was just a little slow but clearly I am above average!

Sam Abbott @seabbs.bsky.social · 1d

One of the fun things about being in the redundancy process at LSHTM is they put you on the redeployment register.

Currently, I am getting a strong message I am suited to a project management role.

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Reposted by Sam Abbott

Aki Vehtari @avehtari.bsky.social · 2d

I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.

Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...

ELLIS PhD Program: Call for Applications 2025

The ELLIS mission is to create a diverse European network that promotes research excellence and advances breakthroughs in AI, as well as a pan-European PhD program to educate the next generation of AI...

ellis.eu

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Sam Abbott @seabbs.bsky.social · 2d

here I specifically mean in pandemic prep stuff etc that I work on

Sam Abbott @seabbs.bsky.social · 2d

For a long time I thought this would be a place where the "effective" funders would step in as the potential for massive leverage is so obvious but they really do not seem interested (probably need to rebrand to AI safety)

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Sam Abbott @seabbs.bsky.social · 2d

(why does no one fund software properly... cry whine sad face sit in the corner and sulk)

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Sam Abbott @seabbs.bsky.social · 2d

Reminded of this today:

xkcd.com/2347/

Dependency

xkcd.com

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Reposted by Sam Abbott

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 6d

Are we doing simulations wrong? This paper convinced me we are. doi.org/10.1098/rstb... Usually we run 2 sets of "worlds" w and w-out intervention. Gives large uncertainties that include negative (harm) effects of interventions that are actually always positive (beneficial)!

Figure 5. Time series showing cumulative number of cases averted at each time caused by the intervention calculated using our method (single-world) and a
standard method. Shaded regions denote 90% confidence intervals. Note that there is more variation in the middle of the epidemic, so it may seem as though the
number of cases averted is large during those times. (Online version in colour.)

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Reposted by Sam Abbott

David Hodgson @dchodge.bsky.social · 19d

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

Interactive Bayesian Epidemic Modelling

widget-bayesian-sir.davidhodgson.me

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Sam Abbott @seabbs.bsky.social · 6d

There is definitely a deployment of it somewhere they are using for teaching but you know Imperial

Sam Abbott @seabbs.bsky.social · 6d

Also either you or your LLM is much too cheery for me! I have been liking sonnet 4.5 its terse grumpiness is much more me

Sam Abbott @seabbs.bsky.social · 6d

Given their developer shake up I also don't know what the status of this project is

Sam Abbott @seabbs.bsky.social · 6d

No live version I can find. They have coded it to need a server for pulling the models form (i.e. so it can do any model) and then its in the browser but it feels like they missed a trick to make a self contained deployable one with static models like you have.

Sam Abbott @seabbs.bsky.social · 6d

Its: github.com/mrc-ide/wodin

and demo: github.com/mrc-ide/wodi...

GitHub - mrc-ide/wodin: odin on the web

odin on the web. Contribute to mrc-ide/wodin development by creating an account on GitHub.

github.com

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Sam Abbott @seabbs.bsky.social · 6d

Yes, using webR and a similar stack from what I can tell. I saw it at the workshop earlier this year - they have got great feedback using it for teaching so I definitely see the value especially for the serology stuff which is hard to get without playing.

Sam Abbott @seabbs.bsky.social · 6d

This is really cool @dchodge.bsky.social - how does it compare to the wasm stuff they have been doing with ODIN do you think? I would be keen to read a blog post along those lines...

Reposted by Sam Abbott

Cameron @cameron.pfiffer.org · 7d

Only an autistic person would make this so you know it's accurate

I got energy burnout like immediately. I was shooting for masking but I'm just too good at it 💅

autism-simulator.vercel.app

Autism Simulator - Workplace Experience Simulation

Experience the workplace through the lens of a high-masking autistic professional. An educational simulation exploring sensory overload, social navigation, and burnout in corporate environments.

autism-simulator.vercel.app

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Sam Abbott @seabbs.bsky.social · 7d

This is now

Sam Abbott @seabbs.bsky.social · 7d

This is today at 3pm uk time. As a change of pace I think there will be a fairly heavy #julialang component

Sam Abbott @seabbs.bsky.social · 9d

For this weeks #epinowcast seminar at 3pm UK time online we have Sandra Montes speaking about dynamic survival analysis and optimal control policy for infectious disease modelling.

www.epinowcast.org/seminars/202...

Sandra Montes - Optimisation and Dynamic Survival Analysis: Towards a Toolkit for Epidemic Preparedness – Epinowcast

Epinowcast community site

www.epinowcast.org

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Reposted by Sam Abbott

David Hodgson @dchodge.bsky.social · 8d

🚀 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-...

Dynamic Mixture Model Analysis

dchodge.github.io

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Reposted by Sam Abbott

Adrian Hill @adrianhill.de · 8d

Perfect timing! If you are in Paris for @juliacon.bsky.social on Friday, join us for our talk on Automatic Sparse Differentiation at 11:30.

If you can't make it, check out both the paper and our introductory ICLR blog post: iclr-blogposts.github.io/2025/blog/sp...

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Sam Abbott @seabbs.bsky.social · 8d

that I’m aware of

Sam Abbott @seabbs.bsky.social · 8d

This is mostly a joke I don’t have paywalled work.

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