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With increasing complexity of hardwares, systems with different memory nodes are ubiquitous in High Performance Computing (HPC). It is paramount to develop strategies to overlap the data transfers between memory nodes with computations in…
Labelling data is expensive and time consuming especially for domains such as medical imaging that contain volumetric imaging data and require expert knowledge. Exploiting a larger pool of labeled data available across multiple centers,…
Heliophysics image data largely relies on a forty-year-old ecosystem built on the venerable Flexible Image Transport System (FITS) data standard. While many in situ measurements use newer standards, they are difficult to integrate with…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
Accurate modeling of the complex dynamics of fluid flows is a fundamental challenge in computational physics and engineering. This study presents an innovative integration of High-Order Singular Value Decomposition (HOSVD) with Long…
Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount…
The fusion of complementary multimodal information is crucial in computational pathology for accurate diagnostics. However, existing multimodal learning approaches necessitate access to users' raw data, posing substantial privacy risks.…
Multimodal survival prediction, a crucial yet challenging task, demands the integration of multimodal medical data (\eg Whole Slide Images (WSIs) and Genomic Profiles) to achieve accurate prognostic modeling. Given the inherent…
Hyperdimensional Computing (HDC) is a bio-inspired computing framework that has gained increasing attention, especially as a more efficient approach to machine learning (ML). This work introduces the \name{} compiler, the first open-source…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
FleCSPH is a smoothed particle hydrodynamics simulation tool, based on the compile-time configurable framework FleCSI. The asynchronous distributed tree topology combined with a fast multipole method allows FleCSPH to efficiently compute…
Virtual screening is a technique used in drug discovery to select the most promising molecules to test in a lab. To perform virtual screening, we need a large set of molecules as input, and storing these molecules can become an issue. In…
Extracting quantitative phenotypic information from whole-slide images presents significant challenges for investigators who are not experienced in developing image analysis algorithms. We present new software that enables rapid…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Data management applications store their data using structured files in which data are usually sorted to serve indexing and queries. However, in-place insertions and removals of data are not naturally supported in a file's address space. To…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…