Leo Lahti
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antagomir.bsky.social
Leo Lahti
@antagomir.bsky.social
620 followers 690 following 49 posts
Prof. in Data Science, Turku, Finland. Analysis and modeling of complex natural and social systems. Open X.
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Reposted by Leo Lahti
martinscheinin.bsky.social
Sisäministeri Rantanen saa oman ICE:n? Ei säännöksiä eduskunnan osallistumisesta, oikeasuhtaisuudesta, välttämättömyydestä. Ei tarvittaisi edes hallituksen päätöstä vaan sisäministeri päättäisi itse. Poliisilakiin ehdotetun uuden 15k §:n 3 mom. antaisi avoimen harkintavallan lähettää ICE kaduille
November 11, 2025 at 10:40 AM
Reposted by Leo Lahti
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Leo Lahti
jsantoyo.bsky.social
Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Orchestrating Microbiome Analysis with Bioconductor
The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous…
www.biorxiv.org
November 9, 2025 at 11:31 AM
Reposted by Leo Lahti
biorxiv-bioinfo.bsky.social
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
October 30, 2025 at 8:54 PM
antagomir.bsky.social
Greetings from Brisbane, Int'l Data Week #IDW2025, SciDataCon25 & CODATA ExComm this week - -

Looking fwd to catch up! Also check this one:

"Open data science and responsible research" summarizing the national policy work on open methods in #Finland (Wed 2pm) lnkd.in/d7zBrNNn
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
October 14, 2025 at 4:57 AM
Reposted by Leo Lahti
drannecarpenter.bsky.social
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
mitochondria from bipolar patients are closer to the nucleus in these images; control patients' are spread out further
October 10, 2025 at 4:47 PM
Reposted by Leo Lahti
robert.bio
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
Reposted by Leo Lahti
nordic-compbio.org
🎉 The Nordic CompBio Conference is coming soon to Tallinn, Estonia 🇪🇪
📅 Thursday-Friday 23-24th of October (10:30-17:15 EEST)
📢 Abstract submissions and registration are open
🔗 nordic-compbio.org/ncb-week

#NordicCompBio #ComputationalBiology #Bioinformatics #Nordics
October 6, 2025 at 2:47 PM
Reposted by Leo Lahti
halllab.bsky.social
Come join us 2-4th March 2026 for a cracking #microbiome conference in Hinxton UK! Speaker line up is AMAZING and lots of opportunities for ECRs for selected talks, flash talks and posters.

Bursaries are also available!

See details below 👇
eventswcs.bsky.social Wellcome Connecting Science Learning and Training @eventswcs.bsky.social · Sep 30
Showcase your microbiome research at our 2026 conference! #Microbiome26

Demonstrate how #genomics tools and technologies are contributing to a deeper understanding of the microbiome.

🗓️ 2-4 March
Submit an abstract by 24 November ✍🏼

📎 bit.ly/4kttBOX
#MicrobiomeSky #AcademicSky
Wellcome Connecting Science hybrid conference Microbiome Interactions in Health and Disease Conference dates: 2-4 March 2026 Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online Bursary and abstract deadline: 24 November 2025 Registration deadline In person: 2 February Virtual: 14 February
September 30, 2025 at 7:22 AM
Reposted by Leo Lahti
zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
September 25, 2025 at 9:29 PM
Reposted by Leo Lahti
craigmaclean.bsky.social
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:31 PM
Reposted by Leo Lahti
jukkasuomela.fi
New fun stuff for those applying for RCF funding:
www.aka.fi/en/research-...
Research security
All applicants must include an appendix with their application that contains a self-assessment of research security issues and, if necessary, a more detailed description of the risks and a risk manage...
www.aka.fi
September 25, 2025 at 3:16 PM
Reposted by Leo Lahti
mcopelov.bsky.social
Nothing is inevitable. In either direction. Hope and work.
scottlgreer.bsky.social Scott L Greer @scottlgreer.bsky.social · Sep 20
“52% of all autocratization episodes become U-Turns, which increases to 73% when focusing on the last 30 years. The vast majority of U-Turns (90%) lead to restored or even improved levels of democracy”

V-Dem data
When autocratization is reversed: episodes of U-Turns since 1900
The world is in a “wave of autocratization.” Yet, recent events in Brazil, the Maldives, and Zambia demonstrate that autocratization can be halted and reversed. This article introduces “U-Turn” as ...
www.tandfonline.com
September 20, 2025 at 7:22 PM
Reposted by Leo Lahti
physaliacourses.bsky.social
🌱 New course: Orchestrating Microbiome Analysis with @bioconductor.bsky.social (2–6 Feb 2026, online). Learn from @antagomir.bsky.social & Toumas Borman how to analyse microbiome & multi-omics data in R/Bioconductor.

www.physalia-courses.org/courses-work...
Orchestrating Microbiome Analysis with Bioconductor
2–6 February 2026
www.physalia-courses.org
September 16, 2025 at 4:53 PM
Reposted by Leo Lahti
sabinaleonelli.bsky.social
A quick reminder to all those who care about open research to consider joining us for the FOR2026 Conference in the Future of Open Research at the Technical University of Munich in May 4-6, 2026! Deadline for paper and poster proposals: 30 September

opensciencestudies.eu/for-2026-con...
FOR 2026 Conference – A Philosophy of Open Science for Diverse Research Environments
opensciencestudies.eu
September 12, 2025 at 10:20 AM
Reposted by Leo Lahti
professoriliitto.bsky.social
TIA Seed 2025 -rahoitushaku avautuu 15.9. Rahoitusta voivat hakea professorit, jotka ovat olleet palkattuna suomalaisessa korkeakoulussa tai tutkimuslaitoksessa enintään kolme vuotta ja jotka ovat asuneet vähintään viisi vuotta yhtäjaksoisesti Suomen ulkopuolella ennen Suomeen tuloaan.
TIA Seed 2025 -rahoitushaku avautuu 15.9. – ilmoittaudu info-webinaariin! - www.vaikuttavuussaatio.fi
Vaikuttavuussäätiö avaa tänä syksynä Tandem Industry Academia (TIA) Seed -rahoitushaun, joka on suunnattu hiljattain suomalaisen tutkimusrahoitusjärjestelmän piiriin tulleille professoritasoisille tut...
www.vaikuttavuussaatio.fi
August 21, 2025 at 5:49 AM
Reposted by Leo Lahti
w-joel-schneider.bsky.social
Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other.
wjschne.github.io/ggdiagram/ar...
An arrow with a LaTeX equation Trigonometric functions and a unit circle A bivariate change model with structured residuals A hierarchical model of cognitive abilities
August 20, 2025 at 10:43 AM
Reposted by Leo Lahti
evolvedbiofilm.bsky.social
Race by other names: critiquing population categories in microbiome research

#mSystems MiniReview by Marta Scaglioni

journals.asm.org/doi/10.1128/...
Race by other names: critiquing population categories in microbiome research | mSystems
Behind the façade of scientific objectivity, race continues to haunt modern science. Contemporary biomedical research often employs categories of human difference that have recently come under critici...
journals.asm.org
August 17, 2025 at 9:04 AM
antagomir.bsky.social
Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis www.nature.com/articles/s42...
Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis - Communications Biology
An interpretable Transformer-based model accurately predicts chronological age across body site and identifies key microbial signatures of aging.
www.nature.com
August 10, 2025 at 8:19 AM
Reposted by Leo Lahti
ewcspottesmith.bsky.social
The Journal of Open Source Software (@joss-openjournals.bsky.social‬) is looking for editors. Come join our team!

I've only been an editor for a few months, but I love working with JOSS. Our peer review process is actually collaborative, and we're Diamond Open Access.

#AcademicSky 🧪 ⚗️ #CompChem
Call for editors | Journal of Open Source Software Blog
Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>
blog.joss.theoj.org
August 8, 2025 at 1:02 PM
Reposted by Leo Lahti
mikeinouye.bsky.social
IMHO green computing & green software engineering are becoming even very important.

Check out our Green Algorithms Initiative for more tools and information www.green-algorithms.org

And the GREENER Principles which lay the foundation for a sustainability roadmap www.nature.com/articles/s43...
Green Algorithms
Towards environmentally sustainable computational science
www.green-algorithms.org
August 4, 2025 at 3:44 PM
Reposted by Leo Lahti
const-ae.bsky.social
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline. Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
August 4, 2025 at 1:52 PM
Reposted by Leo Lahti
jbgruber.bsky.social
The next version of the #rstats 📦 {atrrr} will likely contain a function to stream from the Bluesky Firehose! Looking for people to test and comment now:

github.com/JBGruber/atr...
support firehose · Issue #23 · JBGruber/atrrr
See: https://docs.bsky.app/docs/advanced-guides/firehose I tried it at some point and the socket part works fine. However, decoding the CBOR event data is a bigger challenge. The Python package use...
github.com
August 3, 2025 at 12:40 PM
Reposted by Leo Lahti
gibbological.bsky.social
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...
journals.asm.org
July 31, 2025 at 3:33 PM
Reposted by Leo Lahti
euripsconf.bsky.social
EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅

EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu

eurips.cc
July 16, 2025 at 10:01 PM