Relative positional embeddings with RoPE
In language models, the order of tokens is of critical importance. This post explains RoPE: a technique that ensures that the pairwise token attention weights only depend on their relative position.
Lucas van Dijk
I'm a bioinformatics scientist and software engineer with expertise ranging from analyzing multi-omic datasets to implementing high-performance sequence alignment algorithms in C++ or Rust. I currently work at PacBio as Bioinformatics Software Engineer, working on the instrument software that turns raw sensor data into highly accurate DNA reads.
Selected Publications
Blog
Using locality sensitive hashing to compactly represent k-mers
K-mers are frequently used in bioinformatics to profile and compare genomes. This article describes a technique for compactly representing long k-mers with locality-sensitive hashing.
Visualizing the height of the Netherlands
The Netherlands is very flat country, with most area lying below sea level. So how flat is it really, and how to we keep the water at bay? Let's visualize the official "height" dataset of the Netherlands to find out!
Drawing arbitrary shapes with OpenGL points
Through some clever mathematical definitions, we can use OpenGL "point" primitives to draw any kind of vector shapes. This article explains how that's done and how it applies to my Google Summer of Code 2015 project.
Controlling a servo with an AVR microcontroller
Servos are useful small motors with applications in robotics, RC cars, and others. Here, we describe how to use an ATTiny44 to control its position.
Multithreading with C++11: protecting data
Introduction to threads with C++11
Experience
- Senior Software Engineer, BioinformaticsNov 2025 — PresentPacific Biosciences, Remote
- Computational Scientist II, Data Sciences PlatformSep 2024 — Jul 2025Broad Institute of MIT and Harvard, Cambridge, MA
Developed interpretable machine learning models for integrating multi-omic (genomic, transcriptomic, and proteomic) data from 10,000 participants in the "All of Us" biobank.
- Computational Associate II, Bacterial Genomics LabNov 2017 — Aug 2024Broad Institute of MIT and Harvard, Cambridge, MA
Led development of strain-level human microbiome analysis tools that enabled new insights into the role of the gut microbiome and recurrent UTIs. My work here contributed to my PhD at Delft University of Technology.
- Software EngineerMay 2013 — Jun 2016Studio bereikbaar, Rotterdam, The Netherlands
Developed web-based geographic information systems (GIS) tools using Django and PostgreSQL, securing multi-million euro infrastructure contracts with the government through improved collaborative project planning and design.