Sequences and consequences. @pp0196.bsky.social @bioinfhotep@genomic.social
Joined December 2009
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you see now, "curing all diseases" is the only non circular defensible argument for non capital owners of the trillions needed for gpt-10
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Bioinfhotep retweeted
Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses
hubs.li/Q04zq-Hl0
@HGGAdvances (@GeneticsSociety) highlight from the best of collection 2025-2026
Either the new astra is a big improvement or Neijuan for LLMs is coonfirmed in the vibesloping domain
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relearn this the hard way today mdr
the insanity made me want to puke, guess i can see better why people do not want to read code or prefer using languages they can t read for the vibeslop projects
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Bioinfhotep retweeted
Another thing: what you get from writing things yourself isn't just the code. It's an improved understanding of what the code does. That mental model is what lets you come up with further improvements, or invent a different way of doing things. You can't come up with ways to improve a blackbox you don't understand.
For most projects this doesn't really matter, because the code is the only thing you need. But if you're doing something novel, if you're doing research, the code is not the most important part. Understanding what the code does is the most important part.
When you hear Picard, you hear starwars, CollectMultipleMetrics is what I think about first
#Bioinformatics #GATK
#RIP Patrick Stewart
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Bioinfhotep retweeted
excited that this came out. congrats to everyone involved!
nature.com/articles/s41592-0…
@lh3lh Heng li's reply to some worker running llm loops on establish Bioinformatics software. Will Bioinformatics software also need the "digestion" stuff math people talk about ?
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Bioinfhotep retweeted
I have a truly marvelous Lean certificate for this proposition which this context-window is too narrow to contain.
Bioinfhotep retweeted
My thought on AI review: lh3.github.io/2026/10/27/let…
TL;DR: journals are banning fully AI-generated review and I think that is the right decision
dr-openai is the github handle of the openai/math commiter now :D
100% LLM connector pseudo. Imagine like Dumenil that your whole research program is sterilized by "dr-openai"
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The complaints in this thread are very funny, look like vibesloping still feels a bit dirty in some circles (but my guess is there is also some angst around IP lol)
We have origin and/or "ingredient" labeling for most kinds of consumer products. It is an anomaly that software has not been required to have such disclosures. I think it's very reasonable to require AI use to be disclosed, as well as other information that may be relevant.
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As we understand now, the php use after free was known pre cyber attack optimized LLM era and put on the back burner because it was unclear it was easy to exploit, so basically gpt 5.6 produced a poc convincing enough to get things moving.
Many other such cases I would guess
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"AI" And the Enclosure of the Scientific Commons
Capital advances, as same altman says "selling intelligence like an utility"
Bioinfhotep retweeted
🧬 New paper in Bioinformatics Advances: "DistPCA: Tera-scale genomic PCA via out-of-core distributed parallelism"
Read it here: doi.org/10.1093/bioadv/vbag3…
Bioinfhotep retweeted
If you’ve ever run a GWAS, chances are you've used COJO (Conditional and Joint analysis). Well, we've extended and improved (up to 100× faster 🚀) this essential tool in the GWAS toolkit to enable joint analyses across multiple ancestry groups.
Paper:
nature.com/articles/s41588-0…
Bioinfhotep retweeted
🦆 Announcing DuckDB 2.0.0 LTS “Cinnamon Teal”
We are proud to release DuckDB 2.0.0, named after the cinnamon teal (Spatula cyanoptera), a striking reddish-brown duck found in the western Americas. 🌎
DuckDB 2.0.0 is the biggest DuckDB feature release so far. It ships a polished version of the Quack protocol, which turns DuckDB into a full-fledged server. It improves performance and lowers costs through supporting asynchronous I/O, a first-class VARIANT type, and a dedicated “agent mode”. It also empowers extension developers with a new SQL parser that allows adding new statements, clauses, and keywords, a new API to build on, and a new mechanism to distribute extensions more easily.
In our announcement blog post, we summarize the highlights and then walk through the key changes and give guidance on how to migrate to 2.0. For the complete release notes, see the release page on GitHub.
duckdb.org/2026/10/21/announ…
#DuckDB
