Bioinfhotep (@pp0196) profile picture

Sequences and consequences. @pp0196.bsky.social @bioinfhotep@genomic.social

Joined December 2009
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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
read your code before it's too late
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Bioinfhotep retweeted
Replying to @VictorTaelin
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.
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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
Soon we will have symbolic proofs whose full verification can take days on a cpu cluster or even weeks. It's only a matter of time before AI-generated mathematics converges to full blown theology.
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@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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I have a truly marvelous Lean certificate for this proposition which this context-window is too narrow to contain.
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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
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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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Bioinfhotep retweeted
Mathematics is 100% dead 🪦 A cause for celebration 🎉 Read my eulogy and weap 😭 Link👇
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Bioinfhotep retweeted
Replying to @chrisalbon
Because you’re giving examples of ingredients, not recipe, the “recipe” token in your input doesn’t have a match. So the system will try and complete that given the ingredients. 1/
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"AI" And the Enclosure of the Scientific Commons Capital advances, as same altman says "selling intelligence like an utility"
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🧬 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…
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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…
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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
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“The ultimate hidden truth of the world is that it is something we make, and could just as easily make differently” — David Graeber (1961-2020) Link: tinyurl.com/y9a24tv9
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Bioinfhotep retweeted
recommended reading. i like the term "coherence" over "taste". historically, simplified, a human would approach a software writing human, asking them to build a thing. that's an iterative process, until software writing human truely understands what the other human needs and wants. which is also why we moved away from waterfall. you often can't know what you want before you've build a first shitty solution you can feel out. and your wants might change. in this scenario, the outcome is what matters, not the program structure itself, unless that makes the outcome worse/impossible (bugs, perf, ease of adding features). the software writing human's skill is not so much programming itself, but understanding the other humans wants, pulling out domain knowledge from the other human, asking questions, and ultimately translating the other human's wants into programs, while ensuring the program structure is fit to be modified for future needs. now, can you replace the software writing human with an agent? for simple one-off stuff, yes. if the human with a want is technically minded that extends to more complex programs. most humans suuuuuck at this iterative colab with agents tho, as they are bad at structuring and communicating their wants. and agents currently still suck at the software writing human skill of colaborating with another human to understand their wants and translate them to a program. my gut tells me that this is because the training data and RL for coding agent tasks is largely composed of trajectories where a software writing human and an agent colaborate. that missed the other half of the problem: the human with a want and software writing human interaction. and until we can encode that agents for writing programs will likely only be effective in the hands of software writing humans, or very technically minded humans. another thing agents currently suck ar is translating software writing human shallow instructions into architecture that's not a house of cards. i think this too is a consequence of the lack of training data/RL-able trajectories that encode the process a team of software writing humans go through when building a thing. we do have digitized artifacts (design docs, commits/PRs, issue trackers) that capture some but not all of that. i think this will improve, as we all are now doing design sessions with our agents, so labs could in theory train on that. however, even if this data were available and becomes part of training, the pretraining data still has tons of shit code from around the internet in it, ehich posttraining would have to combat. welcome to my morning word salad.
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