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Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…

In this paper we combine many of the standard and more recent algebraic techniques for testing isomorphism of finite groups (GpI) with combinatorial techniques that have typically been applied to Graph Isomorphism. In particular, we show…

Software Product Lines (SPL) are inherently difficult to test due to the combinatorial explosion of the number of products to consider. To reduce the number of products to test, sampling techniques such as combinatorial interaction testing…

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…

Scientific optimization problems are usually concerned with balancing multiple competing objectives, which come as preferences over both the outcomes of an experiment (e.g. maximize the reaction yield) and the corresponding input parameters…

Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…

Flow cytometry (FC) is a single-cell profiling platform for measuring the phenotypes of individual cells from millions of cells in biological samples. FC employs high-throughput technologies and generates high-dimensional data, and hence…

Polymer composite materials require softening to reduce their glass transition temperature and improve processability. To this end, plasticizers, which are small organic molecules, are added to the polymer matrix. The miscibility of these…

pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…

Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…

We present a novel algebraic combinatorial view on low-rank matrix completion based on studying relations between a few entries with tools from algebraic geometry and matroid theory. The intrinsic locality of the approach allows for the…

The advancement of AI technologies has greatly increased the complexity of AI pipelines as they include many stages such as data collection, pre-processing, training, evaluation and visualisation. To provide effective and accessible AI…

Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…

We propose a new approach for metric learning by framing it as learning a sparse combination of locally discriminative metrics that are inexpensive to generate from the training data. This flexible framework allows us to naturally derive…

This paper presents an automated tool called Morphy for datamorphic testing. It classifies software test artefacts into test entities and test morphisms, which are mappings on testing entities. In addition to datamorphisms, metamorphisms…

Computational materials science increasingly benefits from data management, automation, and algorithm-based decision-making for the simulation of material properties and behavior. Experimental materials science also changes rapidly by…

Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for…

This paper develops new combinatorial approaches to analyze and compute special set partitions, called complementary set partitions, which are fundamental in the study of generalized cumulants. Moving away from traditional graph-based and…

Offload of MPI collectives to network devices, e.g., NICs and switches, is being implemented as an effective mechanism to improve application performance by reducing inter- and intra-node communication and bypassing MPI software layers.…

Process mining offers techniques to exploit event data by providing insights and recommendations to improve business processes. The growing amount of algorithms for process discovery has raised the question of which algorithms perform best…