@OdedRechavi It could be. Depends on what was in the training set.
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NimwegenLab
4.7K posts
NimwegenLab
@NimwegenLab
Gene regulatory networks and genome evolution. How do single cells make up their minds? @[email protected]
Basel City, Switzerland Katılım Şubat 2014
179 Takip Edilen3.5K Takipçiler
🥂(at least I'll know it's nothing personal)
Lior Pachter@lpachter
AI rejecting an Oded Rechavi paper using q.e.d Science.
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It’s astounding to me that a majority of people press the blue button. It’s like: either you swallow a placebo or deadly poison. And only if more than 50% of people swallow the poison, an antidote will be made available. Wtf? Just don’t swallow poison!
Tim Urban@waitbutwhy
Everyone in the world has to take a private vote by pressing a red or blue button. If more than 50% of people press the blue button, everyone survives. If less than 50% of people press the blue button, only people who pressed the red button survive. Which button would you press?
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This is such corrosive shit to say.
And it's simply not true. Yes, the higher up the ladder one goes, the more politics gets involved. But faculty hiring and tenure decisions, in my experience, are still largely based on a committee of peers trying to decide on academic merit.
Oded Rechavi@OdedRechavi
The fate of academic careers is decided in the dark, and the process is political, not based on merit or reason (“so vicious precisely because the stakes are so small”). AI is a black box? Don’t make me laugh. I’m a million times more afraid of humans than I am of AI (just look around you), and in academia that’s doubly true.
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NimwegenLab retweetledi
Officially out - very excited to share! “Emergent simplicity” in microbial ecosystems has long been an appealing idea—but meant different things to different people. As a result, the field hasn't agreed: is it real? surprising? useful? 1/3 doi.org/10.1126/scienc…
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@arjunrajlab @anshulkundaje Yes. I understand. We do too. But not median of 300 days.
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@NimwegenLab @anshulkundaje I can say for several of our papers, we have spent inordinate amounts of time waiting for reviewers. Experiences may vary of course…
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Yes after recent experiences, definitely plan to abandon Nature Genetics. And hopefully soon (within 2 years) all journals. I'm like so done with this shit.
Sasha Gusev@SashaGusevPosts
Monthly median Received to Accepted time (days) at Nature Genetics
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@arjunrajlab @anshulkundaje you are saying the increase from 100 to 400 day median is all due to the time looking for reviewers and the extension in the length of time reviewers take?
I call bullshit. I bet it's mainly in the vastly longer time needed to do all the demanded revisions.
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@anshulkundaje I actually don’t think it’s any journal in particular to blame. I think it’s really hard to find reviewers and reviewers take forever. So it’s a structural problem that we are all responsible for. I don’t really have a solution beyond paying reviewers for timely reviews.
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Remember KC complexity is only defined up to an additive constant that depends on the choice of the Turing machine. For LLMs the size of this machine is huge in comparison to the size of both inputs and outputs.
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No. LLMs have essentially memorized the internet in their weights. For LLMs the KC complexity is not in the prompts but in the size of the ‘Turing machine’ generating the output. If anything is surprising is that the internet can be compressed into an LLM.
Jonathan Gorard@getjonwithit
I think one of the conclusions we should draw from the tremendous success of LLMs is how much of human knowledge and society exists at very low levels of Kolmogorov complexity. We are entering an era where the minimal representation of a human cultural artifact... (1/12)
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NimwegenLab retweetledi
Protocells from three inorganic salts, some formaldehyde and water?
They grow? They synthesise organic molecules of core biomolecular classes: amino acids, sugars, lipid-like motifs?
And, there are similar structures in today's oceans?
Yes! Read on.
arxiv.org/abs/2601.11013
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@lpachter I think this is just mathematician trolling (although I admit even this physicist had to wince reading that).
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tl:dr this is an excerpt from a physics textbook.
Anthony Bonato@Anthony_Bonato
"Dad ‘Embarrassed’ To Be Struggling With Daughter’s Third-Grade Math Problem"
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NimwegenLab retweetledi
Research Associate (100%)
Starting from 1 November 2025 or as per agreement
@NimwegenLab
@biozentrum
@UniBasel_en
biozentrum.unibas.ch/open-positions…
#job #research #biology #microbiology #science #basel #recruiting #career
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Rash and premature, according to a spokesman of the Catholic Church .
Richard Sever@cshperspectives
Science finally retracts the Arsenic life paper science.org/content/articl…
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@mbeisen But they allow Americans to see some of BBC's greatest hits, no? And things like Inspector Montalbano.
At least that's what I remember from when I still lived in the US.
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It does nothing well. It’s news is soft-hitting. Its arts are middle brow. And its comedy is cringe-worthily unfunny.
John Collins@Logically_JC
Can someone explain to me why they hate NPR so much?
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Nice piece by Philip Ball on our new PRX Life publication
physics.aps.org/articles/v18/1…
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New paper! Concentrations of active transcription factors (TFs) can fluctuate on the same time scale as individual TF binding and unbinding events, causing 'non-equilibrium' regulatory responses in their targets. We believe this may be pervasive in bacterial gene regulation.
PRX Life@PRX_Life
Different target genes controlled by the same regulator respond to DNA damage with highly distinct expression responses when fluctuations in transcription factor levels match the timescale of their binding and unbindingfrom DNA. Read the paper: go.aps.org/3Iu2SnU
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@chemetrian @DucheneJohan For what it is worth, below is the ad hoc thing we did for the football player statistics. Even with that rather dumb processing, the results still look reasonable and informative to us.
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@chemetrian @DucheneJohan a good measure of their similarity. So it will depend on whether you can map small molecule structures to such a representation.
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Popular methods like UMAP & t-SNE are stochastic and distort data structure.
Bonsai - a novel method - builds trees to relate high-dimensional objects, accounting for measurement noise.
biorxiv.org/content/10.110…
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NimwegenLab retweetledi
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data biorxiv.org/content/10.110…
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