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Table of Contents Input data Electricity cost and coal usage Energy to GPUs Agents per GPU Tokens per second Extrapolating Putting things in perspective Conclusion As they1 say, a mathematician is a machine for turning coffee into theorems.

Table of Contents 1 A history independent quickheap 1.1 History independent data structures 1.2 History independent list labeling 1.3 History independent quickheap 1.4 Duplicate elements and randomized weights 1.5 Stronger quickheaps 1.6 Order of elements…

Minimizer schemes Link to heading Input: a window \(W\in \Sigma^{w+k-1}\) Minimizer scheme: Sample the \(k\)-mer with the one with smallest hash: \[f(W) = \mathrm{argmin}_{0\leq i\lt w\ \ } h(W_{i\dots i+k}).\] Sampling scheme: Arbitrary function \(f: \Si…

Table of Contents Johnson (1977): Efficient special-purpose priority queues This is a collection of some PDFs of hard-to-find papers.

Table of Contents Quick introduction A new strategy Inverse operation Some more variants TODO Repeated applications of \(f\) Collisions TODO Consecutive small values \[ \newcommand{\rot}{\mathsf{rot}} \newcommand{\shift}{\mathsf{shift}} \] This is the thi…

For a pangenome deduplication tool I’m working on (pandedup), I’m using 128-bit hashes as “unique” identifiers of substrings.

Table of Contents The Route Prep Day 0 Day 1: Engure river to lake Day 2: Lake + Rinda river to Rinda Day 3: Rinda to middle of Irbe river + walk to ghost town Day 4: Irbe river to the sea Countryside Logistics Boats Water / drinks Food supplies Packing A…

Previously Link to heading Previously Link to heading Long-read global alignment is just not a problem people have… Link to heading … Sassy: 100bp semi-global alignment Link to heading Takeaway 1: Math yay, Bio nay Link to heading Takeaway 2: Do simple st…

Table of Contents 1 Why should you care?

FM-index et al.: LF cache-miss per character :( Link to heading I/O-efficient pattern matching using suffix tries Link to heading Suffix trees are in text space and I/O efficient!

Text indexing: Locate all matches of a pattern Link to heading Focus: Locate leftmost match of a pattern Link to heading FM/r-index: cache miss per character Link to heading Suffix trees of repetitive text are repetitive too!

Blackboard: Binary Heap Link to heading Blackboard: QuickHeap Link to heading

Bioinformatics software Link to heading Bioinformatics theory Link to heading Algorithm engineering Link to heading Misc Link to heading

Table of Contents Abstract 1 Introduction 2 Preliminaries 2.1 Minimizer, sampling, and selection schemes 2.2 Bidirectional string anchors 2.3 Maximal suffixes 3 Character-based orders 4 Smallest unique substring anchors 4.1 Properties 4.2 Computing SUS-an…

Table of Contents 1 Naive 1.1 Compute on-the-fly 1.2 Precompute everything 2 Space lower bounds 3 Sparse Table: \(O(1)\) queries, \(O(n \log_2 n)\) words 4 Segment Tree: \(O(\log n)\) queries, \(O(n)\) words 5 Blocks: \(O(s)\) queries, \(O(n/s \log n)\) w…

Table of Contents April 2026: The fall of the theorem economy - David Bessis These are some links to interesting posts around the web, with some quick quotes/notes.

Previous slides: Rank & Select, Elias-Fano Link to heading Rank: counting 1 bits 2 levels of blocks of length \(\log^2 n\) and \(\log n\) Select: finding 1 bits 2 levels of blocks with \(\log^2 n\) 1-bits and \(\sqrt{\log n}\) 1-bits.

My background Link to heading International co-authors in bioinformatics Link to heading Theory KIT, Venice, Halifax Bioinformatics Venice, Lille, Helsinki, Maryland Practice Birmingham, Utrecht (de-facto PhD “supervisor”) Background Link to heading DNA s…

Last week: Models of computation Link to heading Big-O notation Word RAM model Applications & limitations Today Link to heading Bit vectors storing bits Rank counting 1-bits Select finding 1-bits Engineering Rank making it fast Elias-Fano coding storing i…

Previous slides: Bit vectors, Rank & Select Link to heading Bit vector: storing bits Rank: counting 1 bits Select: finding 1 bits Goal: Storing lists of integers Link to heading How do we efficiently store a list of integers \[ 0\leq x_0 \leq x_1 \leq \do…

Today Link to heading Why do we care about models?

Organizational matters Link to heading Lectures: In English Monday 14:00 - 15:30 Building 50.34, room 236 Grade: 80% oral exam, 20 minutes 20% programming project Details coming a few weeks Requires registration Materials Link to heading This year’s mater…

Tl;dr: if you want to refund your NordVPN payment, go to my.nordaccount.com/billing/billing-history?

Table of Contents 1 Problem Statement: Customizable Route Planning (CRP) 2 Contraction Hierarchies (CH) 2.1 Classic Contraction Hierarchies 2.2 Customizable Contraction Hierarchies (CCH) 3 Analogy with trees 4 Shortest Paths in CHs 5 Parents: Faster Short…

Table of Contents 1 Deterministic Finite Automaton (DFA) 2 Wheeler-DFA 3 Linear graphs: Prefix array 4 De Bruijn graphs are Wheeler 5 Not all DFAs are Wheeler 6 Locating patterns via binary search 7 Locating patterns via the BOSS table These are some notes

Binary Rank: Problem statement Link to heading Input: a many-GB text \(T = t_0\dots t_{n-1}\) of \(n\) bits.

My blog: curiouscoding.nl Link to heading Pairwise alignment: finding differences between strings Link to heading Covid – \(\alpha\), December 2020 Link to heading Covid – \(\omicron\), December 2021 Link to heading Pairwise alignment Link to heading Find…

1 File formats Link to heading This stuff is all insanely confusing.

Table of Contents Abstract 1 Introduction 2 Background 2.1 Further implementations 3 BiRank 3.1 Variants 4 QuadRank 4.1 Variants 5 Results 5.1 BiRank 5.2 QuadRank 6 Conclusion 7 Acknowledgements 8 Code snippets 9 Pairing superblocks 10 Additional results…

Table of Contents 1 Types of hash tables 2 Metrics 3 Lower bounds 4 Iceberg hashing (2023) 5 IcebergHT (2023) 6 Tight Bounds for Classical Open Addressing (2024) 7 Optimal Non-oblivious Open Addressing (2025) 8 Optimal Bounds for Open Addressing Without R…

Table of Contents 1 Testing 2 Releasing libraries 2.1 Changelog 2.2 cargo release 2.3 crates.io 3 Releasing binaries 3.1 Crates.io 3.2 The pain of AVX2 3.2.1 ensure_simd 3.3 Profile selection 3.4 GitHub 3.5 cargo binstall 3.6 PyPI 3.7 Bioconda 4 Conclusion

Table of Contents 1 Questions 2 A load of articles/blogs/pages to read 2.1 Wikipedia articles 2.2 More posts 2.3 Notes 2.4 My own RAM 2.5 Continued notes 2.6 Address mapping notation 2.7 Intel spec 2.8 Rank interleaving 2.9 Nontemporal reads/writes 3 reMa…

These are some nice quotes from “The Evolution of Mathematical Software”, Turing Lecture by the 2021 Turing Award winner Jack J.

The Movi 2 paper (Zakeri et al. 2025) builds a fast index on HPRCv2 (Human Pangenome Reference Consortium 2025), a collection of 466 human genomes.

I was listening to an episode of the well there’s your problem podcast about pencil towers (youtube), and it had a section on how elevators are a problem because they require a lot of space.

Table of Contents 1 Classification of static data structures 2 Space lower bounds and practical approaches 2.1 Rank 2.2 Rank + Select 2.3 Minimal perfect hash function (MPHF) 2.4 TODO Monotone MPHF 2.5 TODO Order-preserving MPHF 2.6 Static retrieval: Stat…

This is a short note on setting up Doom emacs for very fast typst previews. typst-ts-mode provides typst-ts-watch-mode via C-c C-w, which runs typst watch in the background, as well as typst-ts-preview via C-c C-p which opens the current pdf file.

Table of Contents 1 What’s inside 2 Compile-time feature detection 2.1 Other solutions 3 Rust’s default target-cpu 3.1 cargo build vs cargo install 4 Hardware support 5 Distributing binaries 5.1 GitHub Releases 5.2 Bioconda 5.3 Pypi 6 Open questions Many…

This is a quick post summarizing the idea of “Singletrack: An Algorithm for Improving Memory Consumption and Performance of Gap-Affine Sequence Alignment” by López-Villellas, Iñiguez, Jiménez-Blanco, Aguado-Puig, Moretó, Alastruey-Benedé, Ibáñez, and Marc…

Table of Contents 1 Problem definitions 2 Optimal solutions 3 Why an overhead is necessary 4 Augmented Retrieval These are some summarizing notes and thoughts on “Static Retrieval Revisited: To Optimality and beyond” by Hu, Kuszmaul, Liang, Yu, Zhang, and…

Table of Contents Dormant Long term plans Abandoned Some not-up-to-date lists of ongoing work to keep things organized for myself.

A rating system for theoretical computer scientists.

Table of Contents 1 Background Priority queue Binary heap D-ary heaps Other heaps 2 Literature on Quickheaps Optimal incremental sorting Quickheap Randomized quickheaps 3 Bucket-based implementation Data structure Push Pop Partition 4 Results Libraries Da…

Table of Contents 1 Minimizing critical sections 2 RabbitFx: chunking 3 Different chunking 4 Experiments 5 Outlook 6 Some helicase benchmarks This is a quick note on some thoughts & experiments on fasta parsing, alongside github:RagnarGrootKoerkamp/fasta-…

Ragnar {Groot Koerkamp} Link to heading Did IMO & ICPC; currently head-of-jury for NWERC.

Minimal Perfect Hash Functions Link to heading A set of \(n\) keys Link to heading A hash function Link to heading A hash function: collisions!

Ragnar {Groot Koerkamp} Link to heading Did IMO & ICPC; currently head-of-jury for NWERC.

For all my projects, feel free to create issues and/or reach out for help in using them.

Table of Contents GreedyMini Results A first look Comparison with optimal ILP values Large alphabets Analysing GreedyMini at \(w=3\) \(w=3\), \(k=3\) \(w=7\), \(k=3\) \(w=3\), \(k=4\) \(w=3\), \(k=5\) \(w=3\), \(k=6\) \(w=3\), \(k=7\) Looking at fixed \(k…

Table of Contents Abstract 1 Introduction 1.1 Part 1: Pairwise Alignment 1.2 Part 2: Low Density Minimizers 1.3 Part 3: High Throughput Bioinformatics 2 Discussion 2.1 Pairwise Alignment 2.2 Low Density Minimizers 2.3 High Throughput Bioinformatics 2.4 Pr…