Related papers: Modernizing PHCpack through phcpy
Scientific computing requires handling large linear models, which are often composed of structured matrices. With increasing model size, dense representations quickly become infeasible to compute or store. Matrix-free implementations are…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
High Performance Computing~(HPC) software stacks have become complex, with the dependencies of some applications numbering in the hundreds. Packaging, distributing, and administering software stacks of that scale is a complex undertaking…
In resent years, the software ecosystem for numerical simulation still remains fragmented, with different algorithms and discretization methods often implemented in isolation, each with distinct data structures and programming conventions.…
Fourier transforms are an often necessary component in many computational tasks, and can be computed efficiently through the fast Fourier transform (FFT) algorithm. However, many applications involve an underlying continuous signal, and a…
SnapVX is a high-performance Python solver for convex optimization problems defined on networks. For these problems, it provides a fast and scalable solution with guaranteed global convergence. SnapVX combines the capabilities of two open…
Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based…
LiteEFG is an efficient library with easy-to-use Python bindings, which can solve multiplayer extensive-form games (EFGs). LiteEFG enables the user to express computation graphs in Python to define updates on the game tree structure. The…
High-Content Digital Microscopy enhances user comfort, data storage and analysis throughput, paving the way to new researches and medical diagnostics. A digital microscopy platform aims at capturing an image of a cover slip, at storing…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
Programming Computable Functions (PCF) is a simplified programming language which provides the theoretical basis of modern functional programming languages. Answer set programming (ASP) is a programming paradigm focused on solving search…
Flaky tests obstruct software development, and studying and proposing mitigations against them has therefore become an important focus of software engineering research. To conduct sound investigations on test flakiness, it is crucial to…
Control system middle layers act as a co-ordination and communication bridge between end users, including operators, system experts, scientists, and experimental users, and the low-level control system interface. This article describes a…
Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…
We are interested in the fast computation of the exact value of integrals of polynomial functions over convex polyhedra. We present speed ups and extensions of the algorithms presented in previous work. We present the new software…
In the realm of scientific computing, both Julia and Python have established themselves as powerful tools. Within the context of High Energy Physics (HEP) data analysis, Python has been traditionally favored, yet there exists a compelling…
Modern HPC architectures consist of heterogeneous multi-core, many-node systems with deep memory hierarchies. Modern applications employ ever more advanced discretisation methods to study multi-physics problems. Developing such applications…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
This paper presents PIQP, a high-performance toolkit for solving generic sparse quadratic programs (QP). Combining an infeasible Interior Point Method (IPM) with the Proximal Method of Multipliers (PMM), the algorithm can handle…
Python libraries are widely used for machine learning and scientific computing tasks today. APIs in Python libraries are deprecated due to feature enhancements and bug fixes in the same way as in other languages. These deprecated APIs are…