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Brendan J. Kelly

@bjklab.bsky.social
2.7K followers 1.6K following 31 posts

infectious diseases / epidemiology / microbial ecology motionlab.site Philadelphia, PA, USA

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Reposted by Brendan J. Kelly
Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 10/09/2026
Modeling non-response is an example I like to use when arguing that "descriptive" statistics also require causal inference. To describe the population, you have to model what causes the sample. Similar to occupancy modeling in ecology in many ways.
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Stephanie Farr @farfarraway.bsky.social · 01/09/2026
We need to protect the Franklin Institute and Giant Heart at all costs. It's sad to see such a storied Philly institution go, especially one dedicated to science, which we need more than ever right now. www.inquirer.com/education/ac...
inquirer.com
The Academy of Natural Sciences is closing its museum after nearly two centuries
The closure does not affect the rest of the institution, which builds and maintains the collections and conducts research through departments such as the Patrick Center for Environmental Research.
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The New Yorker @newyorker.com · 26/08/2026
Metagenomic testing was able to help identify the hantavirus aboard the M.V. Hondius cruise ship, and determine the strain of Ebola infecting patients in the Democratic Republic of the Congo. How else can it help us solve medical mysteries? newyorkermag.visitlink.me/Xs8As0
newyorkermag.visitlink.me
Stumped by a Medical Mystery? Try Metagenomics
When doctors can’t figure out what’s ailing us, they can search our bodies for snippets of genetic material from viruses, bacteria, and fungi.
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Andrew Gelman et al. @statmodeling.bsky.social · 25/08/2026
Bayesian Workflow free pdf! statmodeling.stat.columbia.edu/2026/08/25/b...
statmodeling.stat.columbia.edu
Bayesian Workflow free pdf! | Statistical Modeling, Causal Inference, and Social Science
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Andrew Heiss @andrew.heiss.phd · 25/08/2026
hey hey hey I got Positron Server working through JupyterHub running on a DigitalOcean droplet thanks to Posit's Positron for Education license positron.posit.co/education.html - I have a few iPad-only students this semester and now they can use Positron like the rest of the class #rstats
Screenshot of Positron, but in a browser
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Vincent Arel-Bundock @vincentab.bsky.social · 23/08/2026
The 𝚝𝚒𝚗𝚢𝚝𝚊𝚋𝚕𝚎 0.18.0 📦 for #RStats is out! The new version is faster, has lots of bug fixes, and some beat new features. Check it out if you need a dead simple, ultra-flexible, and dep-free package to draw tables: (interactive) html, typ, tex, pdf, and png. vincentarelbundock.github.io/tinytable
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MC Stan @mc-stan.org · 20/08/2026
StanCon 2026 conference part is over and all the talks are available at StanCon 2026 playlist!
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MC Stan @mc-stan.org · 18/08/2026
There is now StanCon 2026 Uppsala playlist www.youtube.com/playlist?lis... At the moment talks by @mjskay.com, @aseyboldt.bsky.social, @paulbuerkner.com, @charlesm993.bsky.social are up, and we'll keep uploading more during the week
youtube.com
StanCon 2026 Uppsala - YouTube
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Aki Vehtari @avehtari.bsky.social · 13/08/2026
All four books I've co-authored are freely available online for non-commercial use: - Bayesian Workflow at avehtari.github.io/Bayesian-Wor... Links to other three books are in the quoted post 👇 (too many books to fit in one post!)
avehtari.github.io
Bayesian Workflow book: Website – Bayesian Workflow book
Website for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 14/08/2026
For enjoyers of this thread on reasons not use ratio outcome variables in statistical analysis, I have a short blog post from 2022 about why dividing an outcome by something like population density doesn't always control for population density: elevanth.org/blog/2022/09...
elevanth.org
There Are No Magic Outcome Variables
I'm very sorry but I am going to write about statistics and causal inference again. I'd much rather be doing science. I'll make it brief. I was reading a preprint about the relationship between kinsh...
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Andrew Gelman et al. @statmodeling.bsky.social · 07/08/2026
The blessing of dimensionality statmodeling.stat.columbia.edu/2026/08/06/t...
statmodeling.stat.columbia.edu
The blessing of dimensionality | Statistical Modeling, Causal Inference, and Social Science
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Reposted by Brendan J. Kelly
Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 29/07/2026
For examples of the priorsense package in use, see e.g. chapter 17 case study ("sleep study") from the Bayesian Workflow website: avehtari.github.io/Bayesian-Wor...
figure 10 from the linked page, showing prior sensitivity checks for three parameters
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SILVA @arb-silva.bsky.social · 13/07/2026
Public Service Announcement: SILVA has joined the Bluesky community! 

📢🎉 SILVA is part of the the DSMZ Digital Diversity consortium, a Global Core Biodata Resource and an ELIXIR Core Data Resource. www.arb-silva.de Follow for the latest information and announcements 🦠🔬👩‍🔬
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ESCMID @escmid.bsky.social · 13/07/2026
📢 Last call: ESCMID is seeking an Associate Programme Director for ESCMID Global! This is a unique opportunity to help shape the scientific programme of ESCMID’s flagship congress, working closely w/ the Programme Director & Executive Committee. 💡Info: ow.ly/ZzJv50ZebVQ #IDSky #clinmicro
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BayesFlow @bayesflow.org · 12/06/2026
Check out the new baygent skill @alex-andorra.bsky.social and I wrote to automate your amortized workflows! 🚀 learnbayesstats.com/blog-posts/a...
learnbayesstats.com
Train Once, Infer a Million Times: Bayesian Inference That's (Finally) Cheap at Query Time
MCMC re-runs from scratch on every new dataset. Amortized Bayesian inference pays the cost once -- then gives you a posterior in milliseconds, forever. Stefan Radev (BayesFlow creator) and I built an ...
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Reposted by Brendan J. Kelly
Charles Margossian @charlesm993.bsky.social · 26/06/2026
📘 With the release of our textbook "Bayesian Workflow" (avehtari.github.io/Bayesian-Wor...), I figured I'd also share the content of my graduate course on the topic at UBC. 🌎 charlesm93.github.io/stat547/ The course contains overlapping and complementary material, homeworks and reading.
avehtari.github.io
Bayesian Workflow book: Website – Bayesian Workflow book
Website for the Bayesian Workflow book by Gelman, Vehtari, McElreath, et al. — case studies, code, and exercises in R and Stan.
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Nature Medicine @natmed.nature.com · 28/05/2026
Moritz Kramer & colleagues discuss global approaches to infectious disease analysis and modelling, emphasizing federated approaches and addressing challenges in data interoperability, equity, & trust. Part of our Focus issue on #infectiousdiseases.
dlvr.it
Global approaches to infectious disease surveillance and modeling - Nature Medicine
This Review discusses global approaches to infectious disease analysis and modeling, focusing on federated methods and addressing long-standing challenges in data interoperability, equity and trust.
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 28/05/2026
Thinking about how this might go Listener: My chains aren't converging Andrew: Your model is bad Aki: Your parameterization is bad Richard: The Buddha teaches us that numerical integration is suffering
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Steven Tong @steventong.bsky.social · 14/05/2026
ESCMID 2026 highlights COBRA Trial – One day is enough Dutch RCT: 1 day of antibiotics after ERCP drainage for cholangitis was non‑inferior to 4–7 days. Bottom line: Antibiotic durations can safely be much shorter once source control is achieved. #IDSky clarityinitiative.org/escmid-2026-...
clarityinitiative.org
Clarity Initiative
Clinical Literature Appraisal and Research education in InfecTious diseases
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The Lancet Microbe @lancetmicrobe.bsky.social · 13/05/2026
New research article Emergence of carbapenemase-producing #Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey) www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #Ecoli #OpenAccess #OA
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Chengkun Li @chengkunli.bsky.social · 30/04/2026
😀 Enter the amortized Bayesian workflow from here 👉 pipme.github.io/amortized-Ba... Huge thanks to my great collaborators: @avehtari.bsky.social, @paulbuerkner.com, @stefanradev.bsky.social, @lacerbi.bsky.social, @marvin-schmitt.com!
pipme.github.io
Amortized Bayesian Workflow
Adaptive Bayesian workflow combining amortized inference with PSIS and MCMC diagnostics.
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Andrew Gelman et al. @statmodeling.bsky.social · 04/05/2026
Expanding the Stan User’s Guide statmodeling.stat.columbia.edu/2026/05/04/e...
statmodeling.stat.columbia.edu
Expanding the Stan User’s Guide | Statistical Modeling, Causal Inference, and Social Science
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Brendan J. Kelly @bjklab.bsky.social · 05/05/2026
Maybe we shouldn't let a black-box AI product decide who gets to become a board-certified physician... ?
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Nicola Low @nicolamlow.bsky.social · 04/05/2026
🧪 #IDsky #immunology #GlobalHealth This obituary and tribute to #mensch Barry Bloom is uplifting and beautiful - an extraordinarily complete scientist and person Thank you @yhgrad.bsky.social and Marc Lipsitch This link is #FreeToRead via @archive.org archive.ph/LfUO3
archive.ph
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Mizrahi Lab @mizrahilab.bsky.social · 26/04/2026
"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule! Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other. www.nature.com/articles/s41...
nature.com
Community context reshapes microbial proteomes and reduces functional overlap - Nature Microbiology
Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.
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Angus O’Ferrall @angusoferrall.bsky.social · 28/03/2026
Very pleased to see this work published. We analysed the oral microbiomes of children with noma and found that previously uncharacterised Treponema bacteria were both prevalent and highly abundant. journals.plos.org/plosntds/art...
journals.plos.org
Shotgun metagenomic analysis of the oral microbiomes of children with noma
Author summary Noma is a rapidly progressing necrotic disease that destroys the tissues of the mouth and face, mainly affecting children living in abject poverty. Although antibiotic treatment can be ...
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Andrew Gelman et al. @statmodeling.bsky.social · 16/04/2026
The Bayesian Workflow book is coming! statmodeling.stat.columbia.edu/2026/04/16/t...
statmodeling.stat.columbia.edu
The Bayesian Workflow book is coming! | Statistical Modeling, Causal Inference, and Social Science
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Michael Flynn @flynnpolsci.bsky.social · 13/04/2026
Finally finished up a blog post on estimating Bradley–Terry models using brms. www.m-flynn.com/posts/2025-1...
m-flynn.com
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TMLR Published Papers @tmlr-pub.bsky.social · 09/04/2026
Amortized Bayesian Workflow Chengkun LI, Aki Vehtari, Paul-Christian Bürkner et al. Action editor: Tom Rainforth openreview.net/forum?id=osV7adJlKD #mcmc #generative #amortized
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Brendan J. Kelly @bjklab.bsky.social · 14/04/2026
"Here's a Health to the Company" - Moya Brennan and Kevin Conneff: youtu.be/IdIJP3-pzy0 Clannad (and The Chieftains) were the soundtrack of my Irish-American childhood.
youtu.be
Here's A Health To The Company - Kevin Conneff & Moya Brennan
YouTube video by CR's Video Vaults
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Reposted by Brendan J. Kelly
Joe Zackular @joeyzacks.bsky.social · 12/04/2026
Tomorrow is the last day to submit an abstract for @keystonesymposia.bsky.social meeting Beyond Antibiotics: Emerging Strategies Combating Bacterial Infections. It is going to be an amazing meeting and we have a few slots left! keysym.us/KSBeyondAntibiotics26 #KSBeyondAntibiotics26
keysym.us
Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection | Keystone Symposia
Join us at the Keystone Symposia on Beyond Antibiotics: Emerging Strategies for Combating Bacterial Infection, May 2026, in Breckenridge, with field leaders!
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Aki Vehtari @avehtari.bsky.social · 07/04/2026
More details about the Bayesian Workflow book and case studies now available on the book web site avehtari.github.io/Bayesian-Wor... (but you still need to wait a bit for the book)
avehtari.github.io
Bayesian Workflow book: Website – Bayesian Workflow book
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Daan Speth @daanspeth.bsky.social · 25/03/2026
We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵
Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories
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Steve Fleming @smfleming.bsky.social · 22/03/2026
Scientific publishing: Rethinking how research is reviewed and published Review of how the loss of impact factor affected submissions at eLife - uneven drop across countries, but generally holding up remarkably well and shows a new model is possible elifesciences.org/articles/110...
elifesciences.org
Scientific Publishing: Rethinking how research is reviewed and published
Taking a radical new approach to the publication process resulted in eLife losing its impact factor, but authors, reviewers, editors and funders support the journal and its efforts to reform scientifi...
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Frank Harrell @f2harrell.bsky.social · 24/03/2026
Celebrating the draft FDA Bayesian guidance document with our perspective in @jama.com. Honored to co-author w/Jack Lee (MD Anderson), Lisa LaVange (past director of Office of Biostatistics FDA CDER&president of ASA),& my Bayesian inspiration Sir David Spiegelhalter jamanetwork.com/journals/jam...
jamanetwork.com
Embracing Bayesian Methods in Clinical Trials
This Perspective discusses the importance of the US Food and Drug Administration’s draft guidance on the use of bayesian methods in clinical trials because it underscores its commitment to modernizing...
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Bill McKibben @billmckibben.bsky.social · 18/03/2026
The drone is to warfare as the solar panel is to energy: small, cheap, harder to centralize and control. We're seeing the sudden rise of both technologies www.newyorker.com/news/the-led...
newyorker.com
The Iran War Is Another Reason to Quit Oil
What if the drone is to warfare as the solar panel is to energy?
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ArviZ @arviz.bsky.social · 20/03/2026
New paper out in JOSS: “ArviZ: a modular and flexible library for exploratory analysis of Bayesian models” It covers the design principles behind ArviZ and the motivation for the refactoring in 1.0. joss.theoj.org/papers/10.21...
joss.theoj.org
ArviZ: a modular and flexible library for exploratory analysis of Bayesian models
Martin et al., (2026). ArviZ: a modular and flexible library for exploratory analysis of Bayesian models. Journal of Open Source Software, 11(119), 9889, https://doi.org/10.21105/joss.09889
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 22/03/2026
Statistical Rethinking 2026 is done: 20 new lectures emphasizing logical and critical statistical workflow, from basics of probability theory to causal inference to reliable computation to sensitivity. It's all free, made just for you. Lecture list and links: github.com/rmcelreath/s...
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UW Infectious Disease Fellowship Program @uwidfellowship.bsky.social · 13/03/2026
UW’s diagnostics guru, Dr Alex Greninger, interviewed by Axios for for this story on measles in WA state… www.axios.com/local/seattl... #IDSky
axios.com
Washington measles cases expected to rise this summer
Cruises, summer trips and World Cup crowds could accelerate measles spread, experts say.
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James Lind Library @jameslindlibrary.bsky.social · 13/03/2026
2/2 The paper was so well reported that it has a special place in the history of #statistics providing data for Student's famous paper ‘The probable error of a mean’ a few years later. www.jameslindlibrary.org/articles/cus... #HistoryOfMedicine #ClinicalTrials
jameslindlibrary.org
Cushny and Peebles, optical isomers, and the birth of modern statistics. - The James Lind Library
Arthur Cushny was born in Fochabers, Scotland in 1866 and died in Edinburgh in 1926. He had a varied career that included periods in Switzerland, Alsace, America and England. Between ...
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Andrew Gelman et al. @statmodeling.bsky.social · 12/03/2026
SparseNUTS: Preconditioning hierarchical models in HMC with a sparse “Laplace approximation” at the marginal mode statmodeling.stat.columbia.edu/2026/03/12/s...
statmodeling.stat.columbia.edu
SparseNUTS: Preconditioning hierarchical models in HMC with a sparse “Laplace approximation” at the marginal mode | Statistical Modeling, Causal Inference, and Social Science
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Eric R. Scott @leafyericscott.hachyderm.io.ap.brid.gy · 02/03/2026
Very cool example of spatial GAMs by @drxeo.eu on bsky (not bridged, as far as I can tell): dominicroye.github.io/blog/canary-g… #gam #statistics #rstats #rspatial
dominicroye.github.io
Downscaling daily solar radiation in the Canary Islands with GAM
Researcher in climate science at MBG-CSIC
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Andrew Heiss @andrew.heiss.phd · 06/03/2026
Finally got around to adding fancy links to my different interactive teaching websites for showing things like p-hacking, p-value interpretations, and (still-in-draft-form) DAGs at www.andrewheiss.com/teaching/ #rstats #QuartoPub #statsky
Interactive resources

With the power of OJS and Quarto, I’ve created a few interactive websites to illustrate trickier statistical concepts when teaching. Check them out (and adapt and copy as much as you want!)

With links to three different websites (accessible at the main link in the post)
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Brendan J. Kelly @bjklab.bsky.social · 04/03/2026
Love this South Jersey accent deep dive. A great watch... after you're done your homework. Thanks, @evanedinger.bsky.social
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Måns Magnusson @mansmag.bsky.social · 17/02/2026
🔥 StanCon 2026 third keynote announced 🔥 Kaitlyn Johnson, London School of Hygiene & Tropical Medicine More information here discourse.mc-stan.org/t/announcing... @mc-stan.org
discourse.mc-stan.org
Announcing the third keynote speaker for StanCon 2026
We’re happy to share the third keynote speaker for StanCon 2026! StanCon 2026 will take place 17–21 August 2026 in Uppsala, Sweden. Kaitlyn Johnson, London School of Hygiene and Tropical Medicine Jo...
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UW Infectious Disease Fellowship Program @uwidfellowship.bsky.social · 26/02/2026
New review of Group B strep from the NEJM… www.nejm.org/doi/full/10.... #IDSky
nejm.org
Group B Streptococcal Disease | NEJM
Group B streptococcus commonly colonizes the human gastrointestinal and genitourinary tracts and is the single most common bacterial cause of invasive infection among newborns in the United States....
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The Lancet Microbe @lancetmicrobe.bsky.social · 23/02/2026
New research article Serotype-specific pneumococcal invasiveness: a global meta-analysis of paired estimates of disease incidence and carriage prevalence www.thelancet.com/journals/lan... #IDSky #ClinMicro #Streptococcus #IPD #OpenAccess #OA
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BayesFlow @bayesflow.org · 02/01/2026
Diffusion models & flow matching are reshaping simulation-based inference. Thus, we wrote the first tutorial review on diffusion-based SBI. For an overview or a deep dive, check it out and let us know what you think: arXiv: arxiv.org/abs/2512.20685 Web: bayesflow-org.github.io/diffusion-ex...
arxiv.org
Diffusion Models in Simulation-Based Inference: A Tutorial Review
Diffusion models have recently emerged as powerful learners for simulation-based inference (SBI), enabling fast and accurate estimation of latent parameters from simulated and real data. Their score-b...
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Andrew Gelman et al. @statmodeling.bsky.social · 19/02/2026
The 80% power lie statmodeling.stat.columbia.edu/2026/02/19/t...
statmodeling.stat.columbia.edu
The 80% power lie | Statistical Modeling, Causal Inference, and Social Science
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Sam Abbott @seabbs.bsky.social · 16/02/2026
I had a great time talking at the Juniper seminar series last week about composable infectious disease models. Some very good discussion after the talk. The recording is now up! youtu.be/FQYOqGnbJWA?...
youtu.be
Sam Abbott (LSHTM): Composable probabilistic models can lower barriers to rigorous ID modelling
YouTube video by Juniper Consortium Seminars
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