Joined February 2014
215 Photos and videos
Speak for yourself. I’m so sick of this cynicism. EVEN if it were true that people just copy lists and that it’s all politics (which not isn’t). Those lists wouldn’t include hallucinations. That shit is entirely due to AIs.
I'll tell you why so many people upset about the "no hallucinated citations" ban on the arxiv: because they've all been copying citation lists from each other without checking them since the beginning of time. And why did they do this? Because half of the citations in scientific papers are politics and not to the benefit of the reader. If you don't list the right papers, your paper doesn't look 'right' and reviewers will complain that you didn't cite this-and-that other unrelated work. For what I am concerned, these are all bullshit citations that shouldn't be in the papers in the first place. They can easily be automated by "related papers" links, that are (wait for it) provided by... AI...
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I’m so terrified by this cynical race to the bottom. Yes, science is done by fallible people that can do all kinds of bullshit. But that’s not a fucking argument for just letting go of any and all standards.
At my doctoral defense one of the members of my committee was outraged that I quoted a scholar they had a personal beef with. It was a single citation for a minor establishment of fact not in question. I quoted nothing else by this author. Still, they refused to approve my dissertation until I agreed to remove it. I replaced it with a citation of the committee member instead. That was the only requested change by anyone on the committee for the entire dissertation.
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NimwegenLab retweeted
on the whole @arxiv flap about hallucinated references etc you don't see the stuff we reject... some of it is really really egregious the decision to impose additional consequences is largely to throttle that stuff so n00bs and bad actors don't trash us trying repeatedly
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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!
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.
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 retweeted
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/science.adr1…
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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.
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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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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NimwegenLab retweeted
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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NimwegenLab retweeted
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Rash and premature, according to a spokesman of the Catholic Church .
Science finally retracts the Arsenic life paper science.org/content/article/…
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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.
18 Jul 2025
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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NimwegenLab retweeted
10 May 2025
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data biorxiv.org/content/10.1101/…
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NimwegenLab retweeted
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/10.1101/…
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NimwegenLab retweeted
Radical approach to the UMAP debate: offering an actual alternative
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/10.1101/…
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Here it is! Bonsai. No more excuse to use t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Absolutely incredible work of @dhdegroot.bsky.social. I'm so excited about this. biorxiv.org/content/10.1101/…
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Remarkably, famous players show up as outliers on the Bonsai tree, e.g. Messi is on the longest branch! Try it on your own data! Our webserver allows you to upload UMI count tables after which all analysis is performed automatically. youtube.com/watch?v=9h7GUkRj…
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Or play with the visualizations of example datasets. A full Bonsai-scout tutorial is available at: youtube.com/watch?v=JDHZ... Single-cell omics data are amazing and deserve more reliable tools for visualization and exploratory analysis. We hope to have made a difference here!

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