Really neat bit on Rt confidence (also loving the blog write-up, more edible than skimming the full paper)

Sam Abbott@seabbs.bsky.social · 9mo ago

Is it a problem that common Reproduction number estimators produce overconfident results? New blog post from Barbora Němcová and Johannes Bracher summarising there recent preprint: www.epinowcast.org/posts/2026-0...

NHSN and other epi datasources back again. I imagine there is quite some work under the scene, thanks CDC folks we've been missing you.

#epinowcast 0.4.0 is out! This release has been a long time coming and contains work from many contributors. It includdes new features, better better and clearer documentation. package.epinowcast.org/news/index.h...

Changelog

package.epinowcast.org

just learnt that vs code recently added native git blame decorations with setting: "git.blame.editorDecoration.enabled": true good bye complex extensions, goodbye gitlens 👋

I've been sneaking on that course (by Sam Abbott, Thomas Robacker, Nick Reich) for the past few days on github (did not see the deployed version) and it is really good learning material for learning epi forecasting: nfidd.github.io/sismid/

Sam Abbott@seabbs.bsky.social · last yr.

Currently waiting to board a plane headed to Atlanta to teach Nowcasting and forecasting infectious disease dynamics w/ Nick Reich and Thomas Robacker. It's been a pleasure developing course material with them both and I think it should be a pretty fun time: Thomas Robacker.

James does really great science ! This is a great job

James Hay@jameshay.bsky.social · last yr.

We're hiring a modelling postdoc at PSI Oxford for two exciting projects: 1) modelling the early immune responses to Nipah vaccination, and 2) joining the PRESTO team working on immunobridging in vaccine evaluation studies. tinyurl.com/5abbxrjh Get in touch for more info! Deadline 4th August.

Wow. This is an amazing project with a huge amount of work behind it. Even if you aren't into drosophila, it's worth a look

Mark A. Hanson@hansonmark.bsky.social · last yr.

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

But in fact, fly immunity is highly reproducible! 🎊 ~80% of claims could be verified. Moreover, some challenged claims just reflect the field advancing its knowledge/tools. The lesson: if the tools are good and the research largely exempt from direct translation pressures, science works. 3.5/n

When everything is considered together (w/ caveats), the most prestigious institutes are the most likely to produce irreproducible work. Journal tier was a more minor effect, and in fact, "high-impact" but not "trophy" journals publish the most reproducible science. But, many caveats (cont.) 4.3/n

more than that but right order of magnitude. I always say $10^1 for preprint; $10^3 for journal article; $10^5 for research. most costs are staff not tech because of responsible screening, customer service, etc.

This opinion (LLMs have no world model) is repeated at every AI track in IDD conferences, and while it's true for a narrow definition of world model, I am sure it does not square with audience experience. Contrary to what Gary says, LLMs play good (1'800 ELO) chess: dynomight.net/more-chess/.

Onisillos@onisillos.bsky.social · last yr.

"It is not just that LLM’s fail to induce proper world models of chess. It’s that they never induce proper worlds of anything. Everything that they do is through mimicry, rather than abstracted cognition across proper world models." garymarcus.substack.com/p/generative...

Not sure how I missed this, but Dijkstra's algorithm has been beaten on sparse graphs 😮 arxiv.org/abs/2504.17033 (Unsurprisingly, this got a STOC'25 best paper award.)

Breaking the Sorting Barrier for Directed Single-Source Shortest Paths

We give a deterministic $O(m\log^{2/3}n)$-time algorithm for single-source shortest paths (SSSP) on directed graphs with real non-negative edge weights in the comparison-addition model. This is the fi...

arxiv.org

Which academic communities have a good record of sharing domain-specific open source tools? Bioinformatics and geospatial analysis comes to mind. I am trying to think about if they are examples to follow or if there is some difference in the domain (to Infectious disease modelling).

Earlier this month I gave a workshop on Bayesian methods in epidemiology. With my hosts I developed a pretty elaborate, demonstrative analysis for the workshop which I am happy to share publicly here. HTML: betanalpha.github.io/assets/chapt... PDF: betanalpha.github.io/assets/chapt...

Great news today for note-taking: logseq database feature branch got merged into master after two year of limbo. Very excited to stop using obsidian for notes and switch back to it! github.com/logseq/logseq

GitHub - logseq/logseq: A privacy-first, open-source platform for knowledge management and collaboration. Download link: http://github.com/logseq/logseq/releases. roadmap: http://trello.com/b/8txSM12...

A privacy-first, open-source platform for knowledge management and collaboration. Download link: http://github.com/logseq/logseq/releases. roadmap: http://trello.com/b/8txSM12G/roadmap - logseq/lo...

github.com

Sam Abbott@seabbs.bsky.social · 2y ago

Looking for something fun to do on a Friday night? Love maths but want to help out in applied infectious disease modelling? Have I got a fun time for you (solving some more special cases distribution combinations as discussed here). primarycensored.epinowcast.org/articles/ana...

Note that one of these projects is about delay estimation (described by one 5 year old as double extra boring) but critical to get right for most/all downstream modelling use cases.

Anne Cori@anne-cori.bsky.social · 2y ago

Amazing opportunity: a few PhD positions in Health Analytics, Epidemic Modelling and Health Economics available with myself and colleagues from @mrc-outbreak.bsky.social, @ccmid.bsky.social and @ukhsa.bsky.social. Please apply/circulate widely!

For a few years, I have been paying out of pocket for the epinowcast forum as I thought it was important to have a venue for people to collab. There is some great stuff kicking off at the moment which is lovely to see. community.epinowcast.org/t/include-a-...

Include a simple reference model

Baselines considered: no correction baseline (naïve but not realistically what epi colleagues would expect) cut off last few weeks and repeat the previous week(s) (i.e. thinking that the data will b...

community.epinowcast.org

This is a very interesting talk by @scarpino.bsky.social continuing the exploration of the predictability of an influenza season using fundamental and practical methods www.youtube.com/live/8RslYIn...

The deadline for the Epidemics special issue on Artificial Intelligence for Infectious Disease Dynamics has been extended to 30 April 2025, so there is still time to submit your paper 📝 Feel free to contact me or another guest editor for more information 😊 www.sciencedirect.com/journal/epid...

The studies informing stratified parameters in IDD models often have partitions (e.g age group) different from the model partitions. Most papers takes the median/mean estimates, but a correct solution exists: see this great paper/R pkg (C. Pearson, @lucygoodfellow.bsky.social @mert0248.bsky.social)

Justin Lessler@justinlessler.bsky.social · 2y ago

Congrats to team member Carl Pearson and his co-authors @lucygoodfellow.bsky.social and @mert0248.bsky.social. An important tool for a pervasive problem in modeling infectious disease data www.medrxiv.org/content/10.1...

Very interesting write up on OWD pandemic work. In general, it’s always surprising how small most teams doing important thing are.

Our World in Data@ourworldindata.org · 2y ago

When COVID-19 spread worldwide, our small team at Our World in Data — only 8 people at the start of 2020! — pivoted to compiling daily data of global importance. This is the behind-the-scenes story of how it happened: https://ourworldindata.org/owid-covid-history

Our framework for combining standard epi models with an economic dynamic decision model is up on medRxiv! super flexible and excited to see where this project goes next www.medrxiv.org/content/10.1...

Modeling dynamic disease-behavior feedbacks for improved epidemic prediction and response

Human behavior significantly influences infectious disease transmission, yet traditional models often overlook this factor, limiting predictions of disease and the associated socioeconomic impacts. We...

medrxiv.org

Just discovered this excellent book on genomics from Tanja Stadler et al. Free pdf offered here: decodinggenomes.org. The chapters I've read hit a biology/statistics sweet spot for me and probably other IDD researchers.