Bioinfhotep

31.2K posts

Bioinfhotep

Bioinfhotep

@pp0196

Sequences and consequences. @pp0196.bsky.social @[email protected]

Katılım Aralık 2009
2.2K Takip Edilen1.2K Takipçiler
Richárd
Richárd@krichard121212·
What I'm not sure about is whether general on the fly learning is possible(see the lack of a positive manifold even in humans)
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Richárd
Richárd@krichard121212·
I hereby preregister my prediction: This will happen again and again. Everytime a new thing gets invented, LLMs will have to get retrained. I mean it's kinda obvious if you don't drink the "LLMs will reach agi" koolaid.
François Chollet@fchollet

This is more evidence that current frontier models remain completely reliant on content-level memorization, as opposed to higher-level generalizable knowledge (such as metalearning knowledge, problem-solving strategies...)

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Bioinfhotep
Bioinfhotep@pp0196·
@ohmypy Indeed this might be a way to make go a "better C" for language bindings since it would not involve copying the whole runtime into host programs
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Anton Zhiyanov
Anton Zhiyanov@ohmypy·
Could Go be a better C? I think so! Meet Solod — a strict subset of Go that translates to C, without hidden memory allocations and with source-level interop. antonz.org/solod
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Quanquan Gu
Quanquan Gu@QuanquanGu·
Actually not just math, this is happening across almost every field. AI is collapsing the barrier to entry for research. What once required a PhD and years of training can now start much easier. We are moving toward a world where there is no “hard research”, but just unsolved problems. Big things are coming!
Andrew Curran@AndrewCurran_

Terence Tao responding to a question on what advice he would give someone considering a career in math in 2026: 'Yeah, so we live in a time of change. It is, as I said, we live in a particularly unpredictable era. And I think things that we've taken for granted for centuries may not hold anymore. So, yeah, the way we... do everything, not just mathematics, will change. In many ways, I would prefer the much more boring, quiet era where things are much the same as they were 10 years ago, 20 years ago. But I think one just has to embrace that there's going to be a lot of change and that, you know, the things that you study, some of them may become obsolete or revolutionized, but some things will be retained. There'll be a lot of opportunities for things that you wouldn't be able to do before. So, I mean, in math, you previously had to basically go through years and years of education to be a math PhD before you could contribute to the frontier of math research. But now it's quite possible at the high school level or whatever, that you could get involved in a math project and actually make a real contribution because of all these AI tools and lean and everything else. So there'll be a lot of non-traditional opportunities to learn. So you need a very adaptable mindset. There'll be one for pursuing things just for curiosity, for playing around. And I mean, you still need to get your credentials. I mean, I think for a while it would still be important to sort of still go through traditional education and learn math and science and so forth the old-fashioned way for a while. Yeah, but you should also be open to very, very different ways of doing science, some of which don't exist yet. Yeah, so it's a scary time, but also very exciting.'

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delaniac 🌹🌱
delaniac 🌹🌱@ChadNotChud·
I have a million scripts that wind up looking like set -e some_command || true some_command2 || true fascinating
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delaniac 🌹🌱
delaniac 🌹🌱@ChadNotChud·
Claude loves to write bash scripts by putting “set -e” at the top (make the entire script fail if any command fails) and then silently suppress any error it encounters, thereby defeating the purpose
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Sauers
Sauers@Sauers_·
Closed-source software in a peer-reviewed journal (government funded research too)! You have to email the authors to get a self-destructing binary (I asked for the source code). LOL
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Bioinfhotep
Bioinfhotep@pp0196·
@olcan @fchollet x.com/lossfunk/statu… this is suggesting that the LLMs loops opted for transpilation route. One can make an argument (unconvincingly) that is about an extreme version of the non idiomatic code a java coder would do when solving a problem in C
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Lossfunk@lossfunk

@ShriKaranHanda After the paper was done, we tried modern agentic tools like claude code, gave them tools and instructed them to explore/learn We found it actually wrote something like this by itself (without instructing) Stay tuned for this update.

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Olcan
Olcan@olcan·
@pp0196 @fchollet presumably to generate examples, because otherwise there is no human-like learning as they are claiming
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François Chollet
François Chollet@fchollet·
This is more evidence that current frontier models remain completely reliant on content-level memorization, as opposed to higher-level generalizable knowledge (such as metalearning knowledge, problem-solving strategies...)
Lossfunk@lossfunk

🚨 Shocking: Frontier LLMs score 85-95% on standard coding benchmarks. We gave them equivalent problems in languages they couldn't have memorized. They collapsed to 0-11%. Presenting EsoLang-Bench. Accepted to the Logical Reasoning and ICBINB workshops at ICLR 2026 🧵

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Bioinfhotep
Bioinfhotep@pp0196·
@olcan @fchollet the author says in the comments that one of the strategy employed by the LLMs is to literally transpile python into the language or something
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Bioinfhotep retweetledi
Francesco Bertolotti
Francesco Bertolotti@f14bertolotti·
This is a simple alternative to low-dimensional embedding methods such as tSNE, UMAP, and PCA. It trains an autoencoder to match the distances of the reference space. The results quite good. 🔗arxiv.org/abs/2603.16568
Francesco Bertolotti tweet mediaFrancesco Bertolotti tweet mediaFrancesco Bertolotti tweet mediaFrancesco Bertolotti tweet media
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Greg Medlock
Greg Medlock@MedlockGreg·
Hopefully this experiment shows other folks how peer review and collaborative work are going to evolve with AI... you can just "do the thing" now. I came away with a much better understanding and appreciation of GPU-kallisto! cc @lpachter
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Greg Medlock
Greg Medlock@MedlockGreg·
I was curious how @pmelsted's new GPU-kallisto implementation affects compute costs. Given the massive (50X!) improvement in speed, this wasn't straightforward. Instead of just asking "ackchyually, is it cheaper", my friend Claude and I did the analysis!
Pall Melsted@pmelsted

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv biorxiv.org/content/10.648… Figure 1 shows they key result

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Grigory Sapunov
Grigory Sapunov@che_shr_cat·
1/ @jeremyphoward recently made a point that resonates: coding ≠ engineering. LLMs can write functions, but real software work is about understanding systems — architecture, dependencies, constraints. We built a benchmark to measure exactly that gap. Some early findings👇
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Bioinfhotep
Bioinfhotep@pp0196·
@Sauers_ By simulation here I mind here take simulated genomes under realistic demographics and generate the weights given some assumptions and run plink2 (forget ref of that project that released ~1M simulated pgen file under OOA models)
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Sauers
Sauers@Sauers_·
Look at that Z_norm2 plot: there's not really kurtosis or higher-order skew visible. I suspect any gain is very negligible in practice. I could simulate but not worth the effort for likely super small difference. I implemented it with Clauodex anyway though. Popgen sim to produce score distribution skew would require some non-standard setup, and simpler sim of the math would probably require unrealistic setup to see effect. If I had to guess when it could be relevant, perhaps combo monogenic / polygenic arch (creating the distributional weirdness)
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Soynade Research
Soynade Research@soynade·
4e publication du mois de l'open-source de Soynade. Oolel-Embed: un modèle permettant de récupérer des documents directement à partir de la parole, sans passer par des étapes intermédiaires coûteuses de reconnaissance vocale et de traduction. Model: huggingface.co/soynade-resear…
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le big y
le big y@seygalare·
We scaled crazy on pseudo-labeling and synthetic data for training a cross-lingual speech-to-document retrieval model. We make this efficient with Matryoshka Representation Learning (MRL), but a key finding is that MRL doesn’t achieve optimal sparsity since
le big y tweet media
Soynade Research@soynade

4e publication du mois de l'open-source de Soynade. Oolel-Embed: un modèle permettant de récupérer des documents directement à partir de la parole, sans passer par des étapes intermédiaires coûteuses de reconnaissance vocale et de traduction. Model: huggingface.co/soynade-resear…

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Bioinfhotep
Bioinfhotep@pp0196·
@nomad421 @konst_int_i @OpenAI Good news for the oxydization of Bioinformatics tooling. Will be looking forward to make R bindings of the Rust crates coming out of it
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𝕐
𝕐@nomad421·
Amazing! Thank you @konst_int_i & @OpenAI, for recognizing the importance of Open Source Scientific software. We may not have as many ⭐️s as the latest NPM package, but we still provide important value to the open science community & this will help us build more, better & faster!
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Konsti@konst_int_i

@nomad421 Loving the push for better single-cell OS libraries - would love to give you some free @OpenAI Codex @nomad421. DM me to sort the logistics.

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Bioinfhotep
Bioinfhotep@pp0196·
@Sauers_ I do this and related stuff full time, open to some part time and interesting GIG tough
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Sauers
Sauers@Sauers_·
@pp0196 I'm doing the hard way (all four that you mentioned) and more. I'm impressed that you mentioned absolute scale since everyone misses that lol. What do you do for work? How do you know this? Are you hirable part-time?
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Bioinfhotep
Bioinfhotep@pp0196·
@halting_river At one point zionism (or part of it) conceptualized itself as a colonial, civilization mission too (including the socialist brand of this at some point). So I would try to differentiate accommodation to dominant justifying narratives and the "intrinsic" tendencies
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Miara Sung
Miara Sung@halting_river·
Very interesting how Zionism sees itself as decolonial and what this means for deoclonial nationalism writ large
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