Related papers: Rust-Bio - a fast and safe bioinformatics library

Historically, Fortran and C have been the default programming languages in High-Performance Computing (HPC). In both, programmers have primitives and functions available that allow manipulating system memory and interacting directly with…

Translating legacy C codebases to Rust is increasingly demanded for building safety-critical systems. While various approaches have emerged for this task, they face inherent trade-offs: rule-based methods often struggle to satisfy code…

The Rust programming language is increasingly being considered for safety-critical system development. However, established safety standards such as ISO 26262 require the use of coding guidelines that do not yet exist for Rust. This paper…

Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…

BioSig is an open source software library for biomedical signal processing. Most users in the field are using Matlab; however, significant effort was undertaken to provide compatibility to Octave, too. This effort has been widely…

Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…

We introduce Retrieval-Based Speculative Decoding (REST), a novel algorithm designed to speed up language model generation. The key insight driving the development of REST is the observation that the process of text generation often…

The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…

This paper complements "Writing R Extensions," the official guide for writing R extensions, for those interested in developing R packages using Rust. It highlights idiosyncrasies of R and Rust that must be addressed by any integration and…

The Rust programming language enforces three basic Rust principles, namely ownership, borrowing, and AXM (Aliasing Xor Mutability) to prevent security bugs such as memory safety violations and data races. However, Rust projects often have…

Summary: R and Matlab are two high-level scientific programming languages which are frequently applied in computational biology. To extend the wide variety of available and approved implementations, we present the Rcall interface which runs…

Ownership and borrowing systems, designed to enforce safe memory management without the need for garbage collection, have been brought to the fore by the Rust programming language. Rust also aims to bring some guarantees offered by…

We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…

Dancing Links connotes an optimization to a circular doubly-linked list data structure implementation which provides for fast list element removal and restoration. The Dancing Links optimization is used primarily in fast algorithms to find…

We introduce Rambrain, a user space library that manages memory consumption of your code. Using Rambrain you can overcommit memory over the size of physical memory present in the system. Rambrain takes care of temporarily swapping out data…

Rust's novel type system has proved an attractive target for verification and program analysis tools, due to the rich guarantees it provides for controlling aliasing and mutability. However, fully understanding, extracting and exploiting…

Numerical simulations are ubiquitous in mathematics and computational science. Several industrial and clinical applications entail modeling complex multiphysics systems that evolve over a variety of spatial and temporal scales. This study…

In this work, we investigate improving the runtime performance of key computational kernels in the Python Tensor Toolbox (pyttb), a package for analyzing tensor data across a wide variety of applications. Recent runtime performance…

This paper provides the description of a novel, multi-purpose spline library. In accordance with the increasingly diverse modes of usage of splines, it is multi-purpose in the sense that it supports geometry representation, finite element…

Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software…