I redesigned my personal website: jnalanko.net.

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

Feels important.

www.theguardian.com/environment/...

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".

A solution would be to write the software in the most generic terms, but compile separate versions for the specific use cases. But this can be a nightmare to develop and maintain. There is a sweet spot somewhere. 4/4

On the other it's tempting to assume that we have an alphabet of size 4: {A,C,G,T}. It can make things super fast and convenient! But what about ambiguous bases? methylated nucleotides? The amino-acid alphabet? 3/4

For example, in my field of k-mer data structures, pretty much everything we do could be modeled with relational databases and SQL queries. But that does not exploit the special properties of genomic k-mers, so the performance is far from what it could be 2/4.

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

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?

I regret to inform you but, you are, in fact, the bad guys. So sad.

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.

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...

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

I'll check it out.

Not sure. I might just roll my own and serialize the length and the bytes myself.

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

There's some really nifty math in the analysis of this paper!

Dependency tree of a time-tracking app that I vibecoded in Rust.

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.

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.

Then, it wanted to compute floor(log(x)) for an integer x by storing a lookup table. NO! Why waste space and take a cache miss for that? I told it that it could be done with leading zeros instead. So it inlined that to every place. NO! Just make it a function... or actually, just use the std lib.

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

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.

The main file is called CMakeLists.txt. I mean, already off to a bad start. Good names are important, and this is not that. And it only gets worse from there.

I hate CMake with a burning passion. It is the worst thing ever. An unmitigated disaster. A throwback to the 90s. Which is impressive as it was released in the 00s.

Castles in the sky.

64GB of DDR5 RAM costs... 1000 dollars now? Bullish for succinct data structures!

Donald Knuth is impressed by the creative problem solving capabilities of Claude.

Kuva means "picture" in Finnish. Is that where the name is from?

Something that used to be a weekend project is now a 15-minute project. This unlocks so much that wasn't worth doing before.

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.

Once you see it, you cannot unsee it.