iiinova — where your digital self keeps evolving

Reposted by Sam Abbott

Andrei R. Akhmetzhanov (吳亞克) @aakhmetz.bsky.social · 29/09/2026

Data, code and all Stan models are on GitHub, with a link to the full model output: github.com/aakhmetz/Bun...

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IDDjobs @iddjobs.org · 25/09/2026

Postdoc (London, UK) Develop new methods for pathogen genomic epidemiology with @ceciletk.bsky.social at Imperial College London @mrc-outbreak.bsky.social More details: iddjobs.org/jobs/2596

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Stephen Kissler @skissler.bsky.social · 29/07/2026

I'm excited to share a preprint that's been years in the making: the idea took shape during the COVID pandemic. Anecdotally, people would sometimes spread COVID at work but not at home, and vice versa. Why? One explanation would be if infectiousness is fleeting...

medrxiv.org

How bursty infectiousness shapes epidemic dynamics

An epidemic’s expected course is determined by the magnitude and timing of a typical person’s infectiousness — captured, in turn, by the basic reproduction number and the generation-time distribution....

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Sam Abbott @seabbs.bsky.social · 25/09/2026

So would it be crazy to have a auto diff library in the future that uses a tool using LLM to find and write custom rules for pain points in your code on the fly (with ideally some kind of backed local cache and way to share with the community).

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Eloise Newman @eloisenewman.bsky.social · 21/09/2026

Fantastic to have attended “Modelling Epidemics with Julia” at the LSHTM run by Simon Frost, Sandra Montes and @seabbs.bsky.social My first formal foray into #julia and gosh! How powerful it is for modelling. Exciting to see the toolkit available for modelling outbreaks! Will be using in the PhD!

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James Hay @jameshay.bsky.social · 18/09/2026

Are you interested in using serology to detect hidden infections, model immune responses, and estimate epidemic dynamics? You may be interested in the new 1.2.0 release of the R package, serosolver: seroanalytics.org/serosolver/i...

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Leo Bastos @leosbastos.bsky.social · 18/09/2026

I am pleased to share that our nowcasting R package {nowcaster} is finally on CRAN! The package wraps statistical models to estimate not yet reported data using an empirical delay distribution, either from individual-level data or from the differences of aggregated time series of cases.

Nowcaster package logos in blue and white. They display a time series of Covid-19 cases during the pandemic in a city in Brazil.

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Joe Bak-Coleman @jbakcoleman.bsky.social · 18/09/2026

Setting aside all the absurdity of thinking we need to have scientific papers with risks of hallucination, I'm flabbergasted this was taken as sufficiently novel to warrant publication in Nature. It's just sort of stitching things together with MCP...

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Billy Quilty @bquilty.bsky.social · 17/09/2026

A nice concept but seems a bit... obvious...? to be in Nature? Ah, it was first up on arxiv a year ago. Perhaps says a lot about how quickly things are progressing in the field that this seems less than revolutionary - like in COVID, journals will struggle to keep up arxiv.org/abs/2509.06917

arxiv.org

Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents

We introduce Paper2Agent, an automated framework that converts research papers into AI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate dow...

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IDDjobs @iddjobs.org · 14/09/2026

CLOSING SOON: Non academic (Bilthoven-Utrecht, The Netherlands) Infectious disease modeller (sexually transmitted infections) at National Institute for Public Health and the Environment (RIVM) More details: iddjobs.org/jobs/2582

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Sam Abbott @seabbs.bsky.social · 13/09/2026

Looking forward to AI and infectious disease modelling workshop in Brussels tomorrow! I am giving a bit of an overview of my takes on ID and AI as well as on communicating in the age of AI. samabbott.co.uk/AIandIDVUB/

samabbott.co.uk

Modelling and AI, Brussels 2026

Two talks, a panel, and a research exchange on infectious disease modelling and AI

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Reposted by Sam Abbott

austin @aparker.io · 12/09/2026

some thoughts - there’s a fucking cambrian explosion of software but it’s invisible because it’s personal. github isn’t getting hugged every other week for nothin’

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Sam Abbott @seabbs.bsky.social · 11/09/2026

New primarycensored release. Main additions are a double censoring and right truncation adjusted set of "non-parametric" methods which I don't advise using but are at least bias adjusted and support for analytical solutions for the generalised Gamma primarycensored.epinowcast.org/news/index.h...

primarycensored.epinowcast.org

Changelog

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Reposted by Sam Abbott

JUNIPER @juniper-network.bsky.social · 07/09/2026

We've recently introduced our new JUNIPER Fellows – but what does being a Fellow involve? 2025 Fellow @joebhilton.bsky.social joined our friends at @plusmaths.bsky.social to discuss health economics, mathematical modelling and how evidence becomes NHS policy. Listen: plus.maths.org/joe-hilton-s...

plus.maths.org

Joe Hilton: Striking the balance with health economics

Should a life-saving, but expensive, cancer drug be made available on the NHS even though it only benefits very few people? We spoke to Joe Hilton, a health economist, to understand more about how dif...

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Sam Abbott @seabbs.bsky.social · 02/09/2026

This is now and should be great!

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Sam Abbott @seabbs.bsky.social · 27/08/2026

I have a slightly updated thought on this which is in the past we would see complete reimplementations to add one smallish feature and once done no one with the time to reimplement into established packages. LLMs have made this reimplementation fairly trivial (with some time and sufficient tokens).

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Reposted by Sam Abbott

Andrei R. Akhmetzhanov (吳亞克) @aakhmetz.bsky.social · 25/08/2026

"Recent analyses indicate a median interval of eight days from symptom onset to death, with almost half of deaths occurring within the first week of illness" -> Yes, indeed, if the median is 8 days, than almost half would be within the first week... reliefweb.int/report/democ...

reliefweb.int

Ebola Bundibugyo virus disease outbreak: Democratic Republic of the Congo | Uganda Weekly External Situation Report 12, Data as of 02 August 2026 - Democratic Republic of the Congo

Situation Report in English on Democratic Republic of the Congo about Health and Epidemic; published on 6 Aug 2026 by WHO

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Sam Abbott @seabbs.bsky.social · 19/08/2026

It's been really sad to see the complete death of community open-source work in infectious disease modelling due to the rise of LLMs helping to empower individual/small team contributors (not that this in itself is a bad thing).

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Reposted by Sam Abbott

Aki Vehtari @avehtari.bsky.social · 18/08/2026

@mjskay.com starting the StanCon 2026 talks with "Systematic uncertainty visualization design (and its foundation in probabilistic models)" All talks are recorded and will be made available after the conference

Photo of a person in front of a lecture hall

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Sam Abbott @seabbs.bsky.social · 14/08/2026

I've been quite surprised by the absence of both stats and inference work at #juliacon2026. Lots of lots of engineering (including lots on closed source stuff built on Julia) and mechanistic physics modelling.

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Sam Abbott @seabbs.bsky.social · 13/08/2026

Just got through some 😡 at 🤖 to get the first deck in shape. samabbott.co.uk/JuliaCon2026... on to the next ones.

samabbott.co.uk

Building a composable Julia ecosystem for infectious disease modelling – JuliaCon 2026

A roadmap, challenges, and questions

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Reposted by Sam Abbott

Alice Schwarze @aliceschwarze.bsky.social · 12/08/2026

Using AI to revise a document based on feedback received from test readers, I am noticing a pattern: Without AI assistance, I strategize how to address comments with minimal changes. But AI generates text with ease, so its response to each reviewer comment is to add 1-2 new paragraphs of text

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Sam Abbott @seabbs.bsky.social · 11/08/2026

Been surprised to see and hear this a lot from ECRs recent - maybe losing some ground? “Too much of the open science system, even today, thinks of open science as a retrospective process that begins upon publication.” To be fair to them I am not clear doing these practices properly is rewarded.

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Sam Abbott @seabbs.bsky.social · 11/08/2026

Looking forward to attending my first @juliacon.org #juliacon tomorrow! Based on the keynote first I might have learnt the wrong language though and need to pick up Haskell 😅

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Reposted by Sam Abbott

CMMID @cmmid-lshtm.bsky.social · 06/08/2026

📊 Working in #InfectiousDisease modelling? It’s your last chance to apply for our @lshtm.bsky.social short course: Model Fitting and Inference for Infectious Disease Dynamics Running from 7-10 Sept 2026 #PublicHealth Apply by 23:59 BST on 7 August 🔽 www.lshtm.ac.uk/study/course...

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Sam Abbott @seabbs.bsky.social · 06/08/2026

Buring many tokens at the EpiAware.org shrine (i.e my terminal) ahead of #juliacon next week both approaches are starting to take shape, but boy does driving a lot of LLMs take work. Some vague ranting about this here: community.epinowcast.org/t/epiaware-n...

epiaware.org

EpiAware, composable tools for infectious disease modelling

A composable Julia ecosystem for infectious disease modelling.

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Sam Abbott @seabbs.bsky.social · 05/08/2026

Some times when I read code for papers I find it hard to believe that people care so little for the craft of their work. I have to constantly remind myself that its lack of aesthetic sense doesn't always mean it is bad.

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Thomas House @tah-sci.com · 31/07/2026

With various things in the news and maybe time passing, COVID discourse seems to be coming around again and the main thing I can share as a specialist is how different pandemic preparedness is from standard politics or almost all the other things in the Opinion columns. Primarily, a lot of >

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Sam Abbott @seabbs.bsky.social · 31/07/2026

Had a nice time reading arxiv.org/pdf/2607.058... which develops a new (I think) deconvolution approach and then takes the popular spline approach to Rt estimation.

arxiv.org

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Reposted by Sam Abbott

Dan Simpson @danpsimpson.bsky.social · 30/07/2026

I really think the solution has to be open source but not open contributor projects. A small barrier to being allowed to open a PR goes a long way.

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Sam Abbott @seabbs.bsky.social · 30/07/2026

Thought this claude generated documents my slide into LLM madness quite well

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Sam Abbott @seabbs.bsky.social · 30/07/2026

Just gave a talk to the @cmmid-lshtm.bsky.social ECR group on how I llm (of course as is fitting written by an llm hoard) samabbott.co.uk/how-I-llm/

samabbott.co.uk

How I am LLM

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The Ferrari Lab @theferrarilab.bsky.social · 28/07/2026

In 2017, while working at Epicentre/Medecins Sans Frontieres I helped to develop the Urgepi program in southeast DRC. What started as measles surveillance program has matured into a prioritization scheme for outbreak prevention and response that serves 15m people (land area ~Spain).

medrxiv.org

Risk-targeted interventions for measles control- Lessons from an emergency response project in the Katanga Region, Democratic Republic of the Congo (2021-2023)

The Urgepi project is a measles emergency initiative implemented by Medecins Sans Frontieres Operational Centre Paris (MSF-OCP) in the Katanga region of the Democratic Republic of Congo, a setting cha...

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Reposted by Sam Abbott

John Lees @johnlees.bacpop.org · 27/07/2026

What is an 'everyday task' and what is a 'complex problem' in bioinformatics software engineering? Feels more important use the right model now they're not so heavily subsidised! I did a small comparison on an optimisation task: johnlees.me/posts/ska2-c... Small/cheap model wasn't good enough

johnlees.me

Credit use of AI models for bioinformatics: a tiny benchmark

Agentic coding models such as codex and claude code are really useful for software engineering tasks. We sadly (and unsurprisingly) seem to be exiting the era of highly subsidised costs to get us hook...

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Reposted by Sam Abbott

Kai Kupferschmidt @kakape.bsky.social · 16/07/2026

Yesterday marked two months since the DRC declared the ongoing Ebola outbreak, @drtedros.who.int says in presser. "It's now the third largest Ebola outbreak on record, and in the past months, it has expanded faster than any previous outbreak."

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Sam Abbott @seabbs.bsky.social · 13/07/2026

Looking forward to teaching the nowcasting half of our nowcasting and forecast course at SISMID starting today! Some nice (I hope) new content on modelling workflows vibing on the Bayesian workflow book from @avehtari.bsky.social et al. and new session on complex reporting processes.

nfidd.github.io

Nowcasting infectious disease dynamics - SISMID – SISMID: Nowcasting

Nowcasting infectious disease dynamics - SISMID

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Sam Abbott @seabbs.bsky.social · 11/07/2026

New #epinowcast release including support for ARIMA latent processes. New contribution from Nick Davies fixing an issue they found whilst doing some response work github.com/epinowcast/e...

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Reposted by Sam Abbott

Dr Edward Hill @edmhill.bsky.social · 10/07/2026

1/ For those attending @ecmtb2026.org, I will be presenting three talks during the conference. #IDsky #EpiSky 🧪 🔗 ECMTB 2026: ecmtb2026.org 👇 See thread for further talk details and associated papers.

ecmtb2026.org

European Conference on Mathematical & Theoretical Biology 2026 | ECMTB 2026

Join us in Graz, Austria, from July 13–17, 2026, for the 14th European Conference on Mathematical and Theoretical Biology (ECMTB'26)!

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Sam Abbott @seabbs.bsky.social · 07/07/2026

Really enjoyed giving a short workshop on what is a forecast and is it any good at #iddconf. I lasted attended (I think) 8 years ago as Phd student and loved it so looking forward to the talks and community. Our workshop material is here: nfidd.github.io/iddconf2026/

nfidd.github.io

What is a forecast, and is it any good?

A hands-on workshop on visualising, evaluating and combining infectious disease forecasts (IDDconf 2026)

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Reposted by Sam Abbott

IDDjobs @iddjobs.org · 03/07/2026

PhD position (Melbourne, Australia) Mechanistic modelling of the epidemic dynamics of vector-borne zoonotic diseases in Australia with Oliver Eales, Freya Shearer, Marya Potorek at University of Melbourne More details: iddjobs.org/jobs/2561

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Sam Abbott @seabbs.bsky.social · 01/07/2026

epinowcast seminar now on infectious disease modelling crossed over with survival analysis.

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Sam Abbott @seabbs.bsky.social · 30/06/2026

Looking forward to this tomorrow at 3pm uk time. The workshop was great.

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