Related papers: Rust-Bio - a fast and safe bioinformatics library
We introduce dro, an open-source Python library for distributionally robust optimization (DRO) for regression and classification problems. The library implements 14 DRO formulations and 9 backbone models, enabling 79 distinct DRO methods.…
Applications with safety requirements have become ubiquitous nowadays and can be found in edge devices of all kinds. However, microcontrollers in those devices, despite offering moderate performance by implementing multicores and cache…
This paper proposes a set of techniques to develop correctly rounded math libraries for 32-bit float and posit types. It enhances our RLibm approach that frames the problem of generating correctly rounded libraries as a linear programming…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
Command-line bioinformatics tools remain essential for genomic analysis, yet their diversity in syntax and parameterization presents a persistent barrier to productive research. We present oxo-call, a Rust-based command-line assistant that…
We present Aeneas, a new verification toolchain for Rust programs based on a lightweight functional translation. We leverage Rust's rich region-based type system to eliminate memory reasoning for many Rust programs, as long as they do not…
Distinct HEP workflows have distinct I/O needs; while ROOT I/O excels at serializing complex C++ objects common to reconstruction, analysis workflows typically have simpler objects and can sustain higher event rates. To meet these…
Rust supports type conversions and safe Rust guarantees the security of these conversions through robust static type checking and strict ownership guidelines. However, there are instances where programmers need to use unsafe Rust for…
Bioinformatics research depends on high-quality databases to provide accurate results. In silico experiments, correctly performed, may prospect novel discoveries and elucidates pathways for biological experiments through data analysis in…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinformatics is phylogenetics -- the study of hereditary…
Quantum++ is a modern general-purpose multi-threaded quantum computing library written in C++11 and composed solely of header files. The library is not restricted to qubit systems or specific quantum information processing tasks, being…
Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the…
Modern high-assurance software systems development favors memory safe languages such as SPARK (ADA) or Rust. However, developers often encounter non-memory safe code (e.g., C) in legacy systems and libraries which would be prohibitively…
Black-box optimization (BBO) has a broad range of applications, including automatic machine learning, engineering, physics, and experimental design. However, it remains a challenge for users to apply BBO methods to their problems at hand…
RustMC is a stateless model checker that enables verification of concurrent Rust programs. As both Rust and C/C++ compile to LLVM IR, RustMC builds on GenMC which provides a verification framework for LLVM IR. This enables the automatic…
An invitation to simulation is made into a realizable challenge: the reader is taken from scratch to games with words, to mathematical models, to statistical analysis, to simulation of evolution. No special requirements are needed: we work…
The current bulk materials discovery cycle has several inefficiencies from initial computational predictions through fabrication and analyses. Materials are generally evaluated in a singular fashion, relying largely on human-driven…
Refactoring tools are central to modern development, with extract-function refactorings used heavily in day-to-day work. For Rust, however, ownership, borrowing, and advanced type features make automated extract-function refactoring…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…