About me
I'm a PhD student in computer science supervised by Camille Marchet and Jean-Stéphane Varré in the Bonsai team at Univ Lille. I was previously a student at ENS Rennes, I completed a Master's degree in theoretical computer science in the MPRI and also spent a semester at EPFL. (More details in my resume, French version)
I'm interested in algorithmic bioinformatics, with a focus on randomized algorithms and space-efficient data structures. I'm currently working on representations of k-mer sets that preserve locality.
News
- [01/2025] New preprint on simd-minimizers, a SIMD-accelerated library to compute random minimizers!
- [12/2024] Our paper on hyper-k-mers has been accepted to RECOMB!
- [11/2024] New preprint on hyper-k-mers, a more efficient alternative to super-k-mers!
- [07/2024] Talk at ISMB 2024 in Montreal on CBL, a dynamic index for k-mer sets
- [06/2024] New preprint on constrained enumeration of k-mers using CBL!
More
- [03/2024] Talk at DSB 2024 in Montpellier about CBL, a dynamic k-mer index
- [01/2024] New preprint on fully dynamic sets of k-mers with high locality!
- [12/2023] Talk at the seminar on Lyndon words (as part of the Lyndex project) at Univ Rouen about using necklaces to build a locality-preserving k-mer index
- [11/2023] Talk at the SeqBIM days in Lille about a dynamic and locality-preserving data structure for k-mer sets
- [11/2023] Talk at the RT MIA workshop on dimensionality reduction at ENS Lyon about locality-preserving representation of sparse k-mer sets
- [10/2023] I'm starting my PhD in the Bonsai team!
- [09/2023] Talk at WABI 2023 in Houston about fractional hitting sets
- [06/2023] Our paper on fractional hitting sets has been accepted to WABI!
- [03/2023] I'm joining Camille Marchet and Antoine Limasset to work on locality-preserving representation of k-mer sets!
- [06/2022] I did a semester project supervised by Ola Svensson on the forest augmentation problem. [slides]
- [12/2021] I did a semester project with Erwan Le Merrer and Gilles Trédan on the indistinguishability of black-box recommenders outputs.
- [07/2021] I did my first research internship with Dominique Lavenier in the GenScale team. I've been working on a new algorithm for aligning long genomic sequences in the consensus problem. [report] [slides]
Publications
- Hyper-k-mers: efficient streaming k-mers representation, with Lucas Robidou, Yoshihiro Shibuya & Antoine Limasset, RECOMB 2025
[preprint] - Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets, with Bastien Cazaux, Antoine Limasset & Camille Marchet, ISMB 2024
[paper] [slides] [preprint] - Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching, with Timothé Rouzé, Camille Marchet & Antoine Limasset, WABI 2023
[paper] [slides] [poster]
Preprints
- SimdMinimizers: Computing random minimizers, fast, with Ragnar Groot Koerkamp
[preprint] - Brisk: Exact resource-efficient dictionary for k-mers, with Caleb Smith, Antoine Limasset & Yoann Dufresne
[preprint] - Constrained enumeration of k-mers from a collection of references with metadata, with Florian Ingels, Mikaël Salson & Camille Marchet
[preprint]
Teaching
- [2024-2025] Teaching assistant: Algorithms & Complexity
- [2023-2024] Teaching assistant: Information theory
- [2023-2024] Teaching assistant: Javascript
Recent projects
Some of the things I've been developing lately:
- a Rust library to iterate over (mod) minimizers in a DNA sequence
- a Rust library providing fast set operations on sorted iterators
- a Rust library providing a flat hashmap that supports multiple entries per key
- a Rust library providing fully dynamic sets of k-mers with high locality
- a Rust tool for correcting long reads with k-mers
- a Python library to reconstruct the social graph of Mastodon
More
- a LaTeX theme for scientific posters
- a fast sudoku solver based on dancing links
- an algorithm for the alignment of long genomic sequences
- two oracle attacks targeting AES and RSA encryption