iiinova — where your digital self keeps evolving

Ragnar {Groot Koerkamp} @curiouscoding.nl · 29/09/2026

Randomly browsing crates.io, when suddenly... Can LLM-generated testimonials be part of academic CVs already?

This module is a derivative work; the algorithm — the cache-line-sized
implicit S(+)-tree, the branchless SIMD node compare, and the software-pipelined/prefetched batch traversal that hides memory latency — is entirely Ragnar's. **Thank you, Ragnar Groot Koerkamp**, for the design and the beautifully written explanation; every fast path here traces back to your work, including the B-factor and batching trade-offs we re-measured for i64.

1130

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/09/2026

Woke up at 2500m this morning 🤩

Picture of a rugged mountain ridge with a perfectly clear blue lake in front. The ridge is reflected in the lake. The foreground shows rocks at the bottom of the (shallow) lake, while the shoreline on the back shows a red upside down tent drying in the sun.

0140

Ragnar {Groot Koerkamp} @curiouscoding.nl · 16/09/2026

LLMs turn coal into theorems. Or, more precisely: OpenAI turns one panamax bulk carrier of coal into Navier-Stokes.

380

Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/09/2026

good times when you go back far enough that references turn French :)

Algebres de Lie Libres et Monoides Libres
by Gerard Viennot

250

Ragnar {Groot Koerkamp} @curiouscoding.nl · 28/08/2026

Dear people at Microsoft, Will you please not only show the trash icon on hover? I click on a row, and suddenly a wild trashcan appears under my mouse. WTF is this?!?!?!? Does anybody even care anymore??? (Did I say I'm sick and tired of software and in a bad mood today...)

Screenshot of a row in the emails table, showing the 'attachment' icon.

Screenshot of the same row, now with a mouse hovering it (unfortunately mouse not shown). Suddenly there is a trash icon as well as others.

120

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/08/2026

After never having seen any work on the quality of linear hashing, here's two 1-day-apart papers proving very similar results 🤔 arxiv.org/abs/2608.23502 arxiv.org/abs/2608.24866

left half: the abstract of Linear hashing is not that awesome, by Or Zamir
right half: the abstract of Lower bounds for linear hashing via arithmetic kakeya, by Bakshi, Conway, Komlos, Kuszmaul, and Westover.

030

Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/08/2026

Got my first hallucinated citation 🎉🎉🎉 Lots of k-mer papers being attributed to NeurIPS, and our minimizers paper definitely doesn't belong here at all.

B. Kille et al. A near-tight lower bound on the density of forward sampling schemes, in NuerIPS, 2025.

081

Ragnar {Groot Koerkamp} @curiouscoding.nl · 19/08/2026

OMG! SimdQuickHeap got best paper for ESA track E 🥰 Many thanks and congrats to my coauthors Marvin Williams and Johannes Breitling!

ESA TRACK E BEST PAPER
SimdQuickHeap: The QuickHeap Reconsidered
Johannes Breitling, Ragnar Groot Koerkamp and Marvin Williams

2191

Ragnar {Groot Koerkamp} @curiouscoding.nl · 05/08/2026

Travis has been cooking something up since IGGSy ;) A fast algorithm for SMEM finding in haplotype panels that uses space proportional to the number of 1s in the (sparse) matrix, inspired by the jump index [13].

[13] Ragnar Groot Koerkamp. Personal communication, 2026.

031

Ragnar {Groot Koerkamp} @curiouscoding.nl · 28/07/2026

Something different: a little report of kayaking in Latvia curiouscoding.nl/posts/latvia...

4 kajaks lying on a beach next to where the river meets the sea. They're packed with bags.

031

Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/07/2026

The main k-PHF-set speedup figure, with our results in blue. On my laptop (top row), the k-PHF allows throughput very close to the maximal memory throughput up to n=2^28, whereas previous methods only reached that up to 2^24. Also, it performs equally well for both positive and negative queries.

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/07/2026

So now, a non-minimal 8-PHF suffices, which only needs 0.08 bits/key at load factor 80%, compared to 0.86 bits/key for k=1 at load factor 80% or 1.44 bits/key for k=1 and a minimal PHF with load factor 1. Since it's 10x smaller, it fits in a lower cache and supports faster queries or larger inputs.

Table of space lowerbounds for various bucket sizes k and load factors alpha.

120

Ragnar {Groot Koerkamp} @curiouscoding.nl · 06/07/2026

Some heated debate at the #iggsy poster session between Andre - Metagraph - Kahles and Evo - Barbell - Garrison!

Evo, a kid, wields the rolled-up Barbell poster in a fight against Andre with the metagraph poster rolled and folded up.

160

Ragnar {Groot Koerkamp} @curiouscoding.nl · 24/06/2026

In other news: Great SEA talk by Nathaniel Brown on Orbit, an efficient implementation of the move structure for run-length encoded permutations. Also, congrats on winning a best paper award with this work!

Nathaniel standing in front of his title slide at the start of the presentation.

2104

Ragnar {Groot Koerkamp} @curiouscoding.nl · 21/06/2026

On the way to SEA! Might be my longest train trip so far, and will for sure be if we don't make the 30 min transfer in Hamburg.

DB app screenshot: train from Kilchberg (Zurich) to Copenhagen, leaving 4:25 and arriving 20:16.

170

Ragnar {Groot Koerkamp} @curiouscoding.nl · 11/06/2026

OUCH This assertion does not do what you think it does...

A screenshot of Rust code:

const BIST: u32 = 31;
assert!(pos < (1 << BITS) as usize);

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 08/06/2026

First thing I see on reddit after reading this post 🤔 Anyway: big-pan does not want you to know this one simple trick!

Reddit add for r/castiron writing "One pan to rule them all"

010

Ragnar {Groot Koerkamp} @curiouscoding.nl · 03/06/2026

We get a figure like this, where the sweep line goes from left to right and the coloured regions indicate the best preceding anchor for each position. Most of the work is in maintaining the shapes of these regions, which we do with predecessor structures on the horizontal and diagonal boundaries.

Figure showing a 2D edit-graph with diagonal segments showing anchors, and red diagonal segments showing an optimal chain of anchors.
A coloured background of overlapping triangular-shaped regions with a horizontal top and diagonal bottom, with one colour per anchor, show the best anchor to use in each position.

020

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/05/2026

So Gonzalo Navarro used 'diagonal transition' in his '01 ASM survey. Some digging by him now found that it (first???) appears in Chang & Lampe '92. In fact, the 'transition' is not between adjacent diagonals (as I thought), but *along* a diagonal where the cost increments. doi.org/10.1007/3-54...

$Navarro'01: Ukkonen (1983). In 1983, Ukkonen [1985a] presented an algorithm able to compute the edit distance between two strings x and y in O(ed(x, y)^2) time, or to check in time O(k^2) whether that distance was ≤k or not. This is the first member of what has been called “diagonal transition algorithms,” since it is based on the fact that the diagonals of the dynamic programming matrix (running from the upper-left to the lower-right cells) are monotonically increasing (more than that, C[i+1, j+1] ∈{C[i, j], C[i, j +1]}). The algorithm is based on computing in constant time the positions where the values along the diagonals are incremented. Only O(k^2) such positions are computed to reach the lower-right decisive cell.$ Chang & Lampe '92:
Diagonal Transition Algorithms:
Diagonal monotonicity implies the locations of the first k + 1 transitions along each diagonal are sufficient to characterize D for the solution to the k differences problem [20]. A key ingredient is the "jump" J(j, i) = length of the longest exact match P[j,...] = T[i,...].

Chang & Lampe '92:
Diagonal Transition Algorithms:
Diagonal monotonicity implies the locations of the first k + 1 transitions along each diagonal are sufficient to characterize D for the solution to the k differences problem [20]. A key ingredient is the "jump" J(j, i) = length of the longest exact match P[j,...] = T[i,...].

011

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/05/2026

Turns out I presented Sassy yesterday without realising it has been published! Finally officially a coauthor with @rickbitloo.bsky.social 😆 doi.org/10.1093/bioi...

4177

Ragnar {Groot Koerkamp} @curiouscoding.nl · 22/05/2026

My WABI submission: anti-lexicographic SUS-anchors. For sigma=4, this selection scheme (a k=1 sampling scheme) has density within 1% of the lower bound! The idea: find the smallest* substring that does not have a 2nd occurrence, and sample its start pos. curiouscoding.nl/posts/sus-an...

Plots with the density of the sus-anchor for sigma in 2, 4, 32 as a function of w. For sigma=4, they have an overhead over the lowerbound of <1%, while other schemes have >15% overhead.

142

Ragnar {Groot Koerkamp} @curiouscoding.nl · 20/05/2026

Just tried it. So ChatGTP shows some pretty small bubbles. There's additional sources in the hover-popup, but hovering doesn't work on mobile... There's also a 'sources' button at the bottom, but on phone that's _also_ broken. On PC it actually shows also some sources that are never in a bubble :/

Screenshot of ChatGTP answering a question about the 'diagonal transition' algorithm, with a low-contrast bubble saying 'CuriousCoding' and +1.

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 12/05/2026

Barbell: Fast & Accurate nanopore demultiplexing github.com/rickbeeloo/b...

Example of a barbell command showing the flanks and barcodes being searched.

The top 10 most common patterns are shown. 8000 reads are as intended, but many (>1000) have multiple matches of the flanks and/or barcodes.

040

Ragnar {Groot Koerkamp} @curiouscoding.nl · 12/05/2026

Sassy: Fast approximate string matching. Aka: A fuzzy grep for fasta files. Available as both CLI and library. github.com/RagnarGrootK...

Sassy's grep-like output, with matches in green, and indels coloured red/blue.

161

Ragnar {Groot Koerkamp} @curiouscoding.nl · 29/04/2026

With AVX-512, the SimdQuickHeap is consistently 2x faster than the radix heap and other engineered heaps that are I/O-efficient, and up to 10x faster than the binary heap and other tree-based heaps.

Log-log time-per-operation plots for different workloads. The x-ax has increasing input sizes, and the y-ax has the normalized time per push-pop pair of operations divided by lg n.
The binary heap, d-ary heap, and weak heap all slow down as n increases, while the I/O-efficient heaps all get faster. The SimdQuickHeap is 2x faster than the radix heap and up to 10x faster than the binary heap.

120

Ragnar {Groot Koerkamp} @curiouscoding.nl · 29/04/2026

The data structure has some similarities to QuickSelect and is pretty simple: repeatedly partition the list of values using random pivots until the smallest is left, and store each part in its own array. New elements are compared to the pivots and pushed to the right layer.

Overview of the SimdQuickHeap data structure: a list (vector) of pivots is stored, and the elements between consecutive pivots are stored in their own bucket (also a vector). The elements in a bucket are in between the two pivots surrounding it.

100

Ragnar {Groot Koerkamp} @curiouscoding.nl · 19/04/2026

It's 5:20 am, but look what I can do now 😊 Now fingers crossed that it's possible at all to write lecture notes that also work on slides.

140

Ragnar {Groot Koerkamp} @curiouscoding.nl · 14/04/2026

Jeez... 6 in a day... this is gonna be so bad for the ecosystem long term. Even if none of these gains any traction, the name squatting and confusion/bloat that others will have to deal with just to figure out which crates are/are not serious is a pain.

crates.io screenshot showin 6 crates, most of which *-rs, all created 2 days ago

3122

Ragnar {Groot Koerkamp} @curiouscoding.nl · 07/04/2026

Once should be enough when not in meetings ;) But well; 7 newly uploaded crates in the last 2 days does not inspire confidence. Probably not worth my time to make a PR until it has credible maintenance and users?

crates.io screenshot showing 7 *-rs crates created in the last 2 days, like blast-rs, hmmer-pure-rs, and minimap2-pure-rs.

120

Ragnar {Groot Koerkamp} @curiouscoding.nl · 04/04/2026

Have I advertised perfcnt yet? It's awesome! Super easy to add fine-grained perf counters benchmarks, for eg branch misses and last-level cache misses. (These things are otherwise annoying to get from `perf stat`, because that includes benchmark setup and such.) crates.io/crates/perfcnt

Screenshot showing the initialization of a perf counter that counts last-level cache misses. It then starts the counter, executes the function to be benchmarked, stops the counter, and reads its value.

1111

Ragnar {Groot Koerkamp} @curiouscoding.nl · 19/03/2026

More like: remove line numbers, remove stuff like the un-filled header fields below. And OUP footer. And stuff like [PROCEEDINGS] in the title that I now see presumably because of the Recomb-Seq submissions (as opposed to [OVERLAY]). Basically, preprints deserve to be pretty and properly typeset.

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 19/03/2026

Cute new idea in here: Existing ABB+ (green) minimizers prefer kmers starting with 1 and then as many 0 as possible (in the binary case). "Spacers" (orange) instead prefer kmers starting with 10 that have maximum distance to the next occurrence of 10. (For DNA, A maps to 1 and CTG map to 0.)

Plot of minimizer density for DNA alphabet for w=12 and increasing k.
The new "spacers" perform well for k=5..7 in this case.

140

Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/03/2026

Lastly, regions that pass this suffix-filter with cost <=k are verified fully in a 2nd full-width stage that uses SIMD with fewer but larger lanes. The result: throughput that is independent of text length, 2-4x higher than v1 (with AVX2/512) for many patterns and long texts, up to 13x for 150bp.

100

Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/03/2026

In v2, we filp the SIMD tiling and bitpacking direction: Each lane represents a separate *pattern*, and the bits are adjacent *rows* of the matrix. Basically the original 'pack multiple patterns in a word' of Hyyrö 2005, but on an AVX-512 SIMD level. So now we can search 16 32bp patterns at once!

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/03/2026

Just for reference, the tiling strategy in v1: the text is split into 4 chunks that are processed in parallel with 1 chunk per 64 bit SIMD lane. Each lane represents 64 adjacent *columns* of the DP matrix.

Fig. 1: The tiling strategy used by Sassy. The text is first split into word-size blocks of 64 bases. Then, the list of blocks is split into 4 chunks that are processed in parallel, with one SIMD lane per chunk. The text is implicitly padded as needed. Within a chunk, filling the matrix proceeds block-by-block. For each block, all (up to, see Section 2.3 and Figure 3) m = |P | rows are computed before proceeding to the next block. Each chunk is extended into the succeeding chunk as long as there is a sufficiently good “in progress” alignment (not shown).

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/03/2026

That's on top of ~10x speedup over Edlib that we got in v1, (which also has a slightly updated preprint)! Specifically, v1 splits the text into 4 chunks and uses SIMD in the text direction, but this is inefficient when the text is only ~W=256 long, which v2 fixes. www.biorxiv.org/content/10.1...

A plot, with caption:

Fig. 5: Throughput of searching texts of varying length. We search a pattern of length m = 100 against texts with length varying from n = 150 to n = 128 000 bp, with k ∈{3, 20}. All points are computed by averaging over 1000 random texts and then converting to throughput. Note that this does not include searching the reverse-complement strand. While Sassy is consistently faster than Edlib, its relative advantage is smaller for shorter texts.

The plot shows that Sassy is consistently ~4-8x faster than Edlib, and that both are relatively slow for short sequences and converge only for sequences of length >8kbp or so.

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 06/03/2026

Are people actually using A*PA? It suddenly got 4 stars in the last 2 days and appears to be growing steadily either way, but I'm getting issues maybe twice a year, which can either mean nobody uses it, or that it just works (but the UX is really not so great).

start-history.com graph of A*PA github stars, with bumps at time of preprint and publication, and steady growth since then.

220

Ragnar {Groot Koerkamp} @curiouscoding.nl · 02/03/2026

Some notes on Nicola Prezza and group's work on Wheeler DFAs after finally properly understanding them at DSB. It's pretty cool how the LF-mapping of the FM-index translates nearly directly to Wheeler DFAs. curiouscoding.nl/posts/wheele...

A DFA of a variation graph, a tree representation of it, and the corresponding minimal Wheeler-DFA.

140

Ragnar {Groot Koerkamp} @curiouscoding.nl · 25/02/2026

If (big IF) the hardware and software logistics work out, I'm going to try to do a YouTube livestream on implementing QuadRank from scratch, following the DSB slides. Today/tomorrow Wednesday 5pm CET. Will put a link in this thread. curiouscoding.nl/posts/quadra...

Schematic overview of the QuadRank data layout.

1111

Ragnar {Groot Koerkamp} @curiouscoding.nl · 06/02/2026

Indeed! Bins of size 100k instead of 10k now, because at 10k it's too noisy. The BWT is super spikey! So there are regions of length 100k with >70% just one symbol. For 10k-long regions basically the entire figure is full of spikes.

We see that AT and GC have strong local correlation in density in the human genome.

In the BWT, we see very spiky data: here are 100k long regions consisting nearly only of one character!

100

Ragnar {Groot Koerkamp} @curiouscoding.nl · 06/02/2026

But if we now do the same for the BWT, it turns out there _is_ stuff going on! Each line is slightly steeper in it's 'own' quarter, indicating that AA, CC, TT, and GG are relatively common. Importantly, the C line is nearly flat in the last (slightly less than??) quarter! Because GC is rare!

A plot like before, but now all lines are different. In particular, the orange line for C is nearly flat in the last quarter?!?!

220

Ragnar {Groot Koerkamp} @curiouscoding.nl · 06/02/2026

The human genome is so boring! Cumulative character counts show that if you fix the AT and CG percentages, then the rest is basically just uniform random. 1/

Plot of the cumulative character count for each of ACTG in a human genome. 2 exactly straight lines are visible, with A and T overlapping, and C and G overlapping. They are at different slopes because they have different frequencies.

100

Ragnar {Groot Koerkamp} @curiouscoding.nl · 29/01/2026

The braces will remain a bit longer 😅 KGKMLT? (but I'm just 1 person) KGkMLT? (weird?believe) KG-KMLT? (weird) KGMLT? (wrong) Is there precedent for this? I have explicitly avoided the issue in PtrHash... Some citation styles do the first, eg it's [KGKM+24] in my thesis. (@yarono.bsky.social )

000

Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/01/2026

Getting to the hardware part of software engineering here... Unfortunately, It looks like the tool I'm using for measuring RAM properties doesn't work anymore with only 1 stick remaining. Maybe timings are somehow different now.

Picture of my laptop showing the startup menu, with next to it a set of tiny screwdrivers and a 32GB SO-DIMM ramstick.

140

Ragnar {Groot Koerkamp} @curiouscoding.nl · 10/01/2026

What's it called when you subtweet but it's the first sentence of a paper? (The footnote goes to Rank9 and Dijkstra)

Opening sentence of my rank paper, stating that rank queries are right exclusive.

100

Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/01/2026

When you fight the borrow checker for an hour, only to realize you shouldn't have been fighting it in the first place :sob:

120

Ragnar {Groot Koerkamp} @curiouscoding.nl · 03/01/2026

Yes, quote with replies disabled ... Anyway anyone who knows me knows I'm a Linux fan and unable to touch windows, but that I'm also a) into shitposting and b) do fuck up my Linux installation from time to time.

Screenshot of quote tweet claiming 'you're probably just a Microsoft-paid troll'

110

Ragnar {Groot Koerkamp} @curiouscoding.nl · 26/12/2025

Quick table with some back-of-the-envelope statistics on HPRC v1 and v2, extrapolating from the average run-lengths stated in the movi 2 preprint. curiouscoding.nl/posts/hprc-v...

Table comparing a random 3.2Gbp string against a human genome, HPRCv1, and HPRCv2. HPRCv1 has 94 copies and an estimated 33M mutations, while HPRCv2 has 466 copies and an estimated 68M mutations in total.

210

Ragnar {Groot Koerkamp} @curiouscoding.nl · 21/12/2025

curiouscoding.nl just migrated from the living room to the storage room 😆 Still better uptime than AWS.

Photo of a shoerack with in it a nuc server and a HDD.

Downnotifier screenshot: in 2025 I had 2 outages and 99.94% update.

040