Related papers: piBUSS: a parallel BEAST/BEAGLE utility for sequen…
We present robust high-performance implementations of signal-processing tasks performed by a high-throughput wildlife tracking system called ATLAS. The system tracks radio transmitters attached to wild animals by estimating the time of…
The complex and computationally expensive nature of landscape evolution models pose significant challenges in the inference and optimisation of unknown parameters. Bayesian inference provides a methodology for estimation and uncertainty…
The scaling up of deep neural networks has been demonstrated to be effective in improving model quality, but also encompasses several training challenges in terms of training efficiency, programmability, and resource adaptability. We…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within digital populations of computational agents. Consequently,…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…
During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…
The formalism of Bayesian model selection provides a very elegant way of ranking different physical models in terms of how compatible they are with a given set of observed data. However, its practical application is often hampered by the…
Bayesian multidimensional scaling (BMDS) is a probabilistic dimension reduction tool that allows one to model and visualize data consisting of dissimilarities between pairs of objects. Although BMDS has proven useful within, e.g., Bayesian…
This dissertation presents the design, implementation and evaluation of GPU-accelerated simulation frameworks for Evolutionary Spatial Cyclic Games (ESCGs), a class of agent-based models used to study ecological and evolutionary dynamics.…
The massively parallel nature of biological information processing plays an important role for its superiority to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits…
Neural Architecture Search (NAS) has emerged as a powerful framework for automatically discovering neural architectures that balance accuracy and efficiency. However, as AI transitions from static benchmarks to real-world deployment, the…
With the development of fast and massively parallel evaluations in many domains, Quality-Diversity (QD) algorithms, that already proved promising in a large range of applications, have seen their potential multiplied. However, we have yet…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
Recent advances in large language models (LLMs) have enabled multimodal foundation models to tackle both image understanding and generation within a unified framework. Despite these gains, unified models often underperform compared to…
We propose Hercules, a parallel tree-based technique for exact similarity search on massive disk-based data series collections. We present novel index construction and query answering algorithms that leverage different summarization…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
GoTools is a program which solves life & death problems in the game of Go. This paper describes experiments using a Genetic Algorithm to optimize heuristic weights used by GoTools' tree-search. The complete set of heuristic weights is…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…