Tal Korem
@tkorem.bsky.social
Microbiome, metagenomics, ML, and reproductive health. All views are mine. So are all your base
I'm hiring a #postdoc 🥳 and applications are open 🤩 Candidates with interests in EITHER statistical methodology or microbial ecology / microbiome are welcome to apply. The position / projects will be tailored to the candidate 🌟📈🎤 Thank you for sharing widely! apply.interfolio.com/188571
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How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...
Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study
The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
merenlab.org
Absolute banger: "find that metaSPAdes consistently outperforms MEGAHIT" "Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance" "We further show that CheckM2 systematically overestimates completeness and underestimates contamination"
Sebastian Schmidt@tsbschm.bsky.social · 4mo agoThis simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...
This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...
biorxiv.org
i've yet to see evidence that this man is anything other than the fucking coolest to ever do it
Steve Mullis@stevemullis.net · 4mo agoTravel writer Rick Steves on Washington's newly signed "Millionaires Tax"
The truly visionary thing for Simons to do would be to map the collaboration graph of submitted proposals, find the bridges between large connected components, and offer them unrestricted awards
Michael Baym@baym.lol · 6mo agoCondolences to nearly everyone in ecology and evolution today on your grant rejection!
Pollution dropping by that much likely means a whole bunch of people are alive who otherwise wouldn’t be. Incredible stuff.
Mark D. Levine@marklevinenyc.bsky.social · 8mo agoYear 1 data on congestion pricing in Manhattan… * Vehicle traffic: -11% * Foot traffic: +3.4% * Storefront vacancy: -0.9% * Pollution: -22% * Revenue for mass transit: $548M So YES this has been a huge success.
We just published in @molsystbiol.org with the Mugler lab (UPitt) on bacterial population dynamics during tumor colonization (mouse model). Our study was guided by a Luria–Delbrück-style idea: infer mechanism from statistics (1/7) 🧪🦠 doi.org/10.1038/s443...
Out after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.
Distributional bias compromises leave-one-out cross-validation
Leave-one-out cross-validation, a common machine learning evaluation method, has a pernicious flaw; a practical fix is presented.
science.org
Tal Korem@tkorem.bsky.social · 2y agoNew preprint! In a few words: we don't think you should use leave-one-out cross-validation (LOOCV). In a lot of words (+RebalancedCV, a LOOCV alternative): arxiv.org/abs/2406.01652 In a thread:
Using leave-one-out cross-validation to calculate metrics such as AUC and R^2 creates bias! This can be fixed by removing one of each class in the meanwhile to maintain the training data distribution - great work by Tal and his team 🧪🧬🖥️
Tal Korem@tkorem.bsky.social · 8mo agoOut after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.
Back when we hid beer in the cold room in a box labeled “yeast embryos.”
Out after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.
Distributional bias compromises leave-one-out cross-validation
Leave-one-out cross-validation, a common machine learning evaluation method, has a pernicious flaw; a practical fix is presented.
science.org
Tal Korem@tkorem.bsky.social · 2y agoNew preprint! In a few words: we don't think you should use leave-one-out cross-validation (LOOCV). In a lot of words (+RebalancedCV, a LOOCV alternative): arxiv.org/abs/2406.01652 In a thread:
"This could take down Democrats, too." I know. And I frankly wouldn't give even an itty bitty damn if it implicated every Democratic man in Congress, every Democratic hopeful for 2028 and every Democrat who has even thought about running for office. Down with the sex predators, wherever they are.
White paper: github.com/aqlaboratory... GitHub Repo: github.com/aqlaboratory... Huggingface: huggingface.co/OpenFold/Ope... Testimonials: openfold.ghost.io/openfold3-co...
github.com
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Just to be super clear, if you’re phoning in your peer review to ai you should quit your job so someone else who actually likes science can have it.
Oded Rechavi@odedrechavi.bsky.social · 10mo agoHere's the link to the system, try it! qedscience.com @qedscience.bsky.social
We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health! Message or email me if interested. 🖥️ 🧬
Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA
We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...
koremlab.science
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Garud Lab
garud.eeb.ucla.edu
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...
rdcu.be
Not getting much attention, except in a recent NYTimes story, is a provision to increase the tax on university endowments and those of other nonprofits.
New paper in Genome Biology! genomebiology.biomedcentral.com/articles/10.... We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization - Genome Biology
Statistical normalizations are used in differential analyses to address sample-to-sample variation in sequencing depth. Yet normalizations make strong, implicit assumptions about the scale of biologic...
genomebiology.biomedcentral.com
as a resident of syracuse, ny, a rust belt town that used to be an economic epicenter for the nation: syracuse university is our largest local employer now and if it goes under, so does my town, which has the largest concentration of child poverty in the nation.
Evan Torner@guyintheblackhat.bsky.social · last yr.There is a false dichotomy drawn between "the ivory tower" and "the real world," and I'm here to report that in a post-industrial society, your real-world economy absolutely hinges on the university. University towns are factory towns. Universities drive economic activity, not the other way around.
"I'm still in shock. I know that there have been political issues around Harvard in recent weeks, but antibiotic resistance isn't one of them." My conversation with Harvard microbiologist @baym.lol, one of many researchers there who just lost millions in fed. grants. www.wbur.org/news/2025/05...
Antibiotic research at Harvard lab threatened by federal funding cuts
Microbiologist Michael Baym studies antibiotic resistance at Harvard Medical School. He lost millions in federal funding this week.
wbur.org