Related papers: CGAL Made More Accessible
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its perceivable advantages have been impeded by the long-standing lack of a robust open-source graphical user interface (GUI) that…
We introduce AutoGluon-Tabular, an open-source AutoML framework that requires only a single line of Python to train highly accurate machine learning models on an unprocessed tabular dataset such as a CSV file. Unlike existing AutoML…
E-graphs have emerged as a versatile data structure with applications in synthesis, optimization, and verification through techniques such as equality saturation. This paper introduces Python bindings for the experimental egglog library…
A C++ software design is presented that can be used to interpolate data in any number of dimensions. The design is based on a combination of templates of functional collections of elements and so-called type lists. The design allows for…
Effective relaxation methods are necessary for good multigrid convergence. For many equations, standard Jacobi and Gau{\ss}-Seidel are inadequate, and more sophisticated space decompositions are required; examples include problems with…
Control flow graphs (CFGs) are essential tools for understanding program behavior, yet the size of real-world CFGs makes them difficult to interpret. With thousands of nodes and edges, sophisticated graph drawing algorithms are required to…
Program synthesis with Genetic Programming searches for a correct program that satisfies the input specification, which is usually provided as input-output examples. One particular challenge is how to effectively handle loops and recursion…
We introduce the Bandicoot C++ library for linear algebra and scientific computing on GPUs, overviewing its user interface and performance characteristics, as well as the technical details of its internal design. Bandicoot is the…
For configurations of point-sets that are pairwise constrained by distance intervals, the EASAL software implements a suite of algorithms that characterize the structure and geometric properties of the configuration space. The algorithms…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
A visual programming language uses pictorial tools such as diagrams to represent its structural units and control stream. It is useful for enhancing understanding, maintenance, verification, testing, and parallelism. This paper proposes a…
Standard transformer-based language models, while powerful for general text, often struggle with the fine-grained syntax and entity relationships in complex technical, engineering documents. To address this, we propose the Contextual Graph…
Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative…
Interval computation is widely used to certify computations that use floating point operations to avoid pitfalls related to rounding error introduced by inaccurate operations. Despite its popularity and practical benefits, support for…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Over recent years heterogeneous systems have become more prevalent across HPC systems, with over 100 supercomputers in the TOP500 incorporating GPUs or other accelerators. These hardware platforms have different performance characteristics…
The C Object System (Cos) is a small C library which implements high-level concepts available in Clos, Objc and other object-oriented programming languages: uniform object model (class, meta-class and property-metaclass), generic functions,…
Testing is one of the most indispensable tasks in software engineering. The role of testing in software development has grown significantly because testing is able to reveal defects in the code in an early stage of development. Many unit…
Complementary-label learning (CLL) is a weakly supervised learning paradigm for multiclass classification, where only complementary labels -- indicating classes an instance does not belong to -- are provided to the learning algorithm.…
Here practical aspects of conducting research via computer simulations are discussed. The following issues are addressed: software engineering, object-oriented software development, programming style, macros, make files, scripts, libraries,…