Related papers: piBUSS: a parallel BEAST/BEAGLE utility for sequen…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
Large-scale numerical simulations underpin modern scientific discovery but remain constrained by prohibitive computational costs. AI surrogates offer acceleration, yet adoption in mission-critical settings is limited by concerns over…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…
In this paper, we propose the Parallel Elite Biased framework (PEB framework) for parallel trajectory-based metaheuristics. In the PEB framework, multiple search processes are executed concurrently. During the search, each process sends its…
Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a…
The rigorous safety verification of control systems in critical applications is essential, given their increasing complexity and integration into everyday life. Simulation-based falsification approaches play a pivotal role in the safety…
Variation in the evolutionary process across the sites of nucleotide sequence alignments is well established, and is an increasingly pervasive feature of datasets composed of gene regions sampled from multiple loci and/or different genomes.…
Bees display the remarkable ability to return home in a straight line after meandering excursions to their environment. Neurobiological imaging studies have revealed that this capability emerges from a path integration mechanism implemented…
Diffusion models have achieved remarkable success in high-fidelity image generation but remain computationally demanding due to their multi-step denoising process and large model sizes. Although prior work improves efficiency either by…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
A suitable piece of software is presented to connect Abaqus, a sophisticated finite element package, with Matlab, the most comprehensive program for mathematical analysis. This interface between these well-known codes not only benefits from…
In this study, we present a new module built for users interested in a programming language similar to BUGS to fit a Bayesian model based on the piecewise exponential (PE) distribution. The module is an extension to the open-source program…
LibBi is a software package for state-space modelling and Bayesian inference on modern computer hardware, including multi-core central processing units (CPUs), many-core graphics processing units (GPUs) and distributed-memory clusters of…
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural…
In this work, we introduce TUNeS (Temporal UNet emulator for Structure formation), a neural network framework for accelerating N-body simulations by predicting the nonlinear evolution of the matter density field from an initial particle…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
We present $\texttt{PyBird-JAX}$, a differentiable, $\texttt{JAX}$-based implementation of $\texttt{PyBird}$, using internal neural network emulators to accelerate computationally costly operations for rapid large-scale structure (LSS)…