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Jarno N. Alanko

@jnalanko.bsky.social
666 followers 294 following 103 posts

Postdoc in computer science and bioinformatics at the University of Helsinki. Website: jnalanko.net. Various writings in English and Finnish: blog.jnalanko.net. Also on Mastodon: genomic.social/@jnalanko

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Jarno N. Alanko @jnalanko.bsky.social · 29/09/2026
People say Claude Opus 5.5 is amazing. I find it infuriating. It constantly tries to be one step ahead of me. If I ask for some simple plot, it tries to infer what I *really* want and adds all sorts of things that I never asked for. I does not feel like I'm in charge.
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Jarno N. Alanko @jnalanko.bsky.social · 23/09/2026
www.anthropic.com/news/claude-... 950 Claude agents spent 21 hours looking at sequences encoding reverse transcriptases and noticed nearby spaced repeats like in CRISPR. It's cool but.... how come the string matching community had not found this before? Embarrassing.
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John Lovell @jotlovell.bsky.social · 19/05/2026
We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.
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Jarno N. Alanko @jnalanko.bsky.social · 23/09/2026
I'm starting to believe in the labor theory of value for TCS/math papers. That is, given equally skilled workers, with equal tools, and equally important problems, the value of a paper is roughly proportional to the amount of (human) labor that has gone into it.
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Jarno N. Alanko @jnalanko.bsky.social · 22/09/2026
It is really starting to feel like at least a decade worth of pure math/TCS results is going to be happening in Q4 2026. Human understanding, digestation and dissemination is going to take a while. But wow.
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Jarno N. Alanko @jnalanko.bsky.social · 21/09/2026
Exciting news regarding the SBWT rust API! We now have an implementation of the subset rank method in this preprint, written Anastasia Diseth. It takes the space down from 5 bits/kmer to 2.5 bits/kmer (double that if both strands are indexed). About 4-5 times slower. www.biorxiv.org/content/10.6...
biorxiv.org
New Space-Time Tradeoffs for Subset Rank and k-mer Lookup
Given a sequence S of subsets of symbols drawn from an alphabet of size σ , a subset rank query srank( i, c ) asks for the number of subsets before the i th subset that contain the symbol c . It was r...
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Ada Palmer @adapalmer.bsky.social · 20/09/2026
The world’s largest battery-electric aircraft flew for the first time on the 12th of August, a 27-minute test flight over upstate New York that cost about five dollars in electricity. Heart Aerospace’s 30-seat prototype is a big step toward a commercial version. buff.ly/i3f0PhR #ShareGoodNewsToo
techspot.com
The largest all-electric plane ever flew for 27 minutes, on $5 of electricity
Heart's X1 demonstrator flew for 27 minutes from a regional airport in upstate New York, running on battery power the entire time. The aircraft reached 1,100 feet...
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Jarno N. Alanko @jnalanko.bsky.social · 20/09/2026
3Blue1Brown posted a great exposition of the proof of problem 6 of IMO 2025. This problem is brilliant. It's insane that some contestants managed to solve it. www.youtube.com/watch?v=Nbwv...
youtube.com
The last IMO problem AI could not solve
YouTube video by 3Blue1Brown
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Jarno N. Alanko @jnalanko.bsky.social · 19/09/2026
This race to be the first to publish an AI-generated result is getting silly. If the answer is just a prompt away for anyone, why should *any* human get credit for it? The value is in the quality of the exposition. Racing to be the first to publish is detrimental to that.
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Jarno N. Alanko @jnalanko.bsky.social · 19/09/2026
www.anthropic.com/research/cla... Anthropic optimizes open-source models for protein design, gets a 4x speedup and a low-memory mode. That's actually... pretty underwhelming? With their resources I would have though they can do better than small constant speedups.
anthropic.com
How Claude is uplifting biomolecular modeling
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Jarno N. Alanko @jnalanko.bsky.social · 18/09/2026
developer.nvidia.com/blog/introdu... Native GPU programming support in Rust from Nvidia!
developer.nvidia.com
Introducing CUDA Rust: Two Tracks for Writing GPU Kernels | NVIDIA Technical Blog
In September 2026, NVIDIA announced it is leaning into native GPU programming in Rust. CUDA C++ and CUDA Python are mature, enterprise-grade toolchains, and NVIDIA will be growing and maturing CUDA…
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Jarno N. Alanko @jnalanko.bsky.social · 18/09/2026
STOC is fighting AI-generated submissions by requiring a proof-of-human 20-30 minute video explaining the work. Seems reasonable to me. Otherwise the PC will drown in submissions.
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Rust Language @rust-lang.org · 17/09/2026
⚠️ We believe that there is an ongoing campaign targeting owners of popular crates and rust-lang team members that is attempting to compromise devices and accounts in order to use them to publish malware. See our blog post for details: blog.rust-lang.org/2026/09/17/t...
blog.rust-lang.org
Be alert: targeted attacks on prominent Rustaceans | Rust Blog
Empowering everyone to build reliable and efficient software.
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Jarno N. Alanko @jnalanko.bsky.social · 16/09/2026
terrytao.wordpress.com/2026/09/16/l... >Since research papers are the standard currency in math, a currency that is being rapidly devalued by AI, perhaps we should find ways to inject more humanity into them. For instance, we could add a “backstory” section... Yes!! Do it! Make math human.
terrytao.wordpress.com
Let the Diners Into the Kitchen
[This is a guest post by Noah Giansiracusa. This blog post was initially written in a different file format and converted using AI. — T.] Imagine a tech company announces new robot workers th…
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Jarno N. Alanko @jnalanko.bsky.social · 16/09/2026
I think that the year of the Linux desktop is finally coming. AI is really good at debugging obscure issues that used to require lots of technical expertise to solve. It already fixed an issue with my Bluetooth headphones, and another one with my USB audio card.
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Jarno N. Alanko @jnalanko.bsky.social · 14/09/2026
People say that viral genomes are tiny. Not all! Today, I learned that this exists: en.wikipedia.org/wiki/Pandora.... It's a giant virus that spans 1 micrometer and has a genome with 2.5 million bases and 2500 genes. Discovered in 2013.
en.wikipedia.org
Pandoravirus - Wikipedia
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Jarno N. Alanko @jnalanko.bsky.social · 13/09/2026
terrytao.wordpress.com/2026/09/12/a... A thoughtful post about how to salvage math.
terrytao.wordpress.com
After Math
[This is a guest post by Silvia De Toffoli and Eamon Duede. This blog post was initially written in a different file format and converted using AI. — T.] Silvia De Toffoli (University School …
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Evgenii Protasov @evgenii-protasov.bsky.social · 11/09/2026
Alternative genetic codes in bacteria and archaea identified with a fast k-mer–based algorithm #microbiology #genetics #archaea #bacteria #MicroSky @pnas.org www.pnas.org/doi/10.1073/...
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Terence Tao @teorth.bsky.social · 11/09/2026
A group of 25 Fields Medalists, including myself, have made a joint declaration on Math and AI: mathandai.org . We welcome additional signatories. See also this article in the Economist announcing the declaration: www.economist.com/science-and-...
mathandai.org
Declaration — Math and AI
Read the declaration and add your name.
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Zamin Iqbal @zaminiqbal.bsky.social · 11/09/2026
2D billiards are Turing complete! "We show that, even in 2D, billiard trajectories can simulate arbitrary Turing machines...Our results place undecidability, alongside chaos, as a fundamental obstruction to long-term prediction even in low-dimensional classical dynamics" www.pnas.org/doi/abs/10.1...
pnas.org
Two-dimensional billiards are Turing complete | PNAS
We show that two-dimensional billiard systems can simulate universal Turing machines. Billiards serve as idealized models of particle motion with e...
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Jarno N. Alanko @jnalanko.bsky.social · 11/09/2026
2025 was a simpler time.
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Jarno N. Alanko @jnalanko.bsky.social · 11/09/2026
Navier-Stokes: I see people calling academics egoistical because they care so much about someone getting cited if someone else builds on their work. Why does it matter so much? (1/?)
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The Rust Foundation @rustfoundation.org · 09/09/2026
NVIDIA, our newest Platinum Member, launched CUDA Rust today. You can now write GPU kernels in Rust and compile them straight to PTX. Learn more on their blog: developer.nvidia.com/blog/introdu...
developer.nvidia.com
Introducing CUDA Rust: Two Tracks for Writing GPU Kernels | NVIDIA Technical Blog
In September 2026, NVIDIA announced it is leaning into native GPU programming in Rust. CUDA C++ and CUDA Python are mature, enterprise-grade toolchains, and NVIDIA will be growing and maturing CUDA…
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Jarno N. Alanko @jnalanko.bsky.social · 09/09/2026
How does one write a grant proposal concerning theoretical problems nowadays? By the time you have a solid and feasible plan, it's very possible that AI can already execute it in no time. It feels like I need to propose a meta-plan for coming up with a plan.
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Jarno N. Alanko @jnalanko.bsky.social · 25/08/2026
There are so many data centers planned in Finland that the electricity demand of the whole country could go up 40%. www.hs.fi/visio/art-20...
hs.fi
Energia | Fingrid: Suomen sähkönkulutus voi kasvaa pian jopa 40 prosenttia
Sähkönkulutuksen suuri kasvu mullistaa Suomen sähkömarkkinaa monin tavoin.
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Jarno N. Alanko @jnalanko.bsky.social · 13/08/2026
I used to use AI for math, and then check its work. Now I use AI to supervise *me* when I do math.
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Jarno N. Alanko @jnalanko.bsky.social · 30/05/2026
Mapping all 19k genes in the human genome into the space of... anime characters? This project is nuts. www.lesswrong.com/posts/BJ7AqX...
lesswrong.com
Mnemonic portraits for 19,023 human genes — LessWrong
Back in 2013, Scott Alexander wrote in Extreme mnemonics: …
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Jarno N. Alanko @jnalanko.bsky.social · 26/05/2026
One incredible thing about AI coding is how the AI has to learn the codebase again at the start of every session. It starts from a blank slate. Then it reads documentation and greps some source code and gets to work. It does this bootstrapping every time! And it takes just a few minutes. Superhuman.
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Floris Barthel @florisbarthel.bsky.social · 17/05/2026
The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...
KaryoScope karyotype of the HG002 diploid assembly. All 22 autosomes plus X and Y, each shown as paired haplotypes (h1, h2). Each chromosome has a full-length track colored by chromosome of origin, a centromere zoom panel showing satellite composition, and a subtelomere zoom panel. Legends map chromosomes, satellite families, and subtelomeric features to colors.
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Jarno N. Alanko @jnalanko.bsky.social · 16/05/2026
Today, I did some Rust coding. Claude could not implement a feature properly. It was complex. So I did it myself. I typed every character into the text editor myself! I had forgotten how laborious coding used to be. 2.5 hours later, it was done. 212 lines added and 71 lines deleted. Feels great!
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Jarno N. Alanko @jnalanko.bsky.social · 07/05/2026
What is this progress bar doing
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Jarno N. Alanko @jnalanko.bsky.social · 01/05/2026
www.war.gov/News/Release... "These agreements accelerate the transformation toward establishing the United States military as an AI-first fighting force". "AI-first fighting force".
war.gov
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Jarno N. Alanko @jnalanko.bsky.social · 20/04/2026
I redesigned my personal website: jnalanko.net.
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Jarno N. Alanko @jnalanko.bsky.social · 16/04/2026
Feels important. www.theguardian.com/environment/...
theguardian.com
Critical Atlantic current significantly more likely to collapse than thought
Scientists say finding is ‘very concerning’ as collapse would be catastrophic for Europe, Africa and the Americas
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Jarno N. Alanko @jnalanko.bsky.social · 15/04/2026
www.erdosproblems.com/forum/thread... AI apparently just provided a new insight into number theory. Terence Tao comments: "In any case, I would indeed say that this is a situation in which the AI-generated paper inadvertently highlighted a tighter connection between two areas of mathematics".
erdosproblems.com
Erdős Problem #1196 - Discussion thread
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Jarno N. Alanko @jnalanko.bsky.social · 13/04/2026
Finding the right level of abstraction in software engineering is hard. It's tempting to generalize things, but as we generalize, we lose opportunities to optimize for specific cases. 1/4
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Jarno N. Alanko @jnalanko.bsky.social · 07/04/2026
The latest Trump post makes me think: Is there anything Europeans could do to influence US politics to a less crazy and less genocidal direction? Would economic sanctions work? Support for resistance movements? Anything?
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Jarno N. Alanko @jnalanko.bsky.social · 07/04/2026
I regret to inform you but, you are, in fact, the bad guys. So sad.
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Jarno N. Alanko @jnalanko.bsky.social · 03/04/2026
Did Mastodon already fail? It's very quiet. People tell me to follow hashtags. But tags like #bioinformatics have only 8 people posting in the last 2 days, and a lot of those are bots. Even #rustlang has just 10 people in the last 2 days. The posts that get on my timeline are not very interesting.
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Jarno N. Alanko @jnalanko.bsky.social · 01/04/2026
Accepted to CPM 2026! In this paper, we consider the problem of k-mer counting in *graphs*. We show that it's #P-hard even in deterministic DAGs. But on Wheeler graphs, it's tractable -- easy in O(nk) time. We can also do O(poly(n) log k) but it gets complicated. #CPM2026 arxiv.org/abs/2509.22885
arxiv.org
Computing k-mers in Graphs
We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on...
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Jarno N. Alanko @jnalanko.bsky.social · 27/03/2026
Rust PSA: don't use serde + bincode for deserializing large things, like bitvec::Bitvectors. It seems to use a doubling buffer to load it instead of pre-allocating the space. So it can have up to 2x overhead. Loading a 130GB bit vector can take 256GB of RAM. #rust
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Jarno N. Alanko @jnalanko.bsky.social · 25/03/2026
There's some really nifty math in the analysis of this paper!
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Jarno N. Alanko @jnalanko.bsky.social · 22/03/2026
Dependency tree of a time-tracking app that I vibecoded in Rust.
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Jarno N. Alanko @jnalanko.bsky.social · 20/03/2026
I wanted to poke around the Gene Ontology database. Claude was immediately useful to get some basics statistics on the ontology graph. Then I asked it to make a visualization. In a few minutes, it gave me this really useful interactive browser. I keep getting blown away by these AI models.
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Jarno N. Alanko @jnalanko.bsky.social · 19/03/2026
New measure of software engineering ability: value-added-over-AI. This is what CS degrees will be about, and this is where the money is. Can you do a better code review than AI? If not, I could've just asked the AI myself -- no value added. AI is the new baseline.
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Jarno N. Alanko @jnalanko.bsky.social · 18/03/2026
Frustrations with Claude today. It generated some array indexing logic and added a comment that endpoints are inclusive. They weren't. The code worked though. But the comment wasn't helping! 1/2
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Jarno N. Alanko @jnalanko.bsky.social · 05/03/2026
ChatGPT5.4 (Extended Thinking) feels no better at math problem solving than 5.2 did. This is the first model that does not feel significantly better than the previous ones at this. Are we finally hitting a ceiling? My timeline to math research automation and AGI just got a bit longer.
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Jarno N. Alanko @jnalanko.bsky.social · 05/03/2026
64GB of DDR5 RAM costs... 1000 dollars now? Bullish for succinct data structures!
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Jarno N. Alanko @jnalanko.bsky.social · 03/03/2026
Donald Knuth is impressed by the creative problem solving capabilities of Claude.
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Jarno N. Alanko @jnalanko.bsky.social · 27/02/2026
The latest Claude seems to be able to synthesize small apps from a short description pretty much autonomously. I'm having hard time adjusting to this reality. I can now make small bespoke productivity apps just for myself. Computers just become a lot more useful for a lot of things.
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