Related papers: PSDF: Particle Stream Data Format for N-Body Simul…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
Digital sensors are increasingly being used to monitor the change over time of physiological processes in biological health and disease, often using wearable devices. This generates very large amounts of digital sensor data, for which, a…
Multimodal biosignal acquisition is facilitated by recently introduced software solutions such as LabStreaming Layer (LSL) and its associated data format XDF (Extensible Data Format). However, there are no stand-alone applications that can…
Point-spread-function (PSF) engineering is a powerful computational imaging techniques wherein a custom phase mask is integrated into an optical system to encode additional information into captured images. Used in combination with deep…
Medical image segmentation plays an important role in accurately identifying and isolating regions of interest within medical images. Generative approaches are particularly effective in modeling the statistical properties of segmentation…
We introduce Simulation Streams, a programming paradigm designed to efficiently control and leverage Large Language Models (LLMs) for complex, dynamic simulations and agentic workflows. Our primary goal is to create a minimally interfering…
Process mining extends far beyond process discovery and conformance checking, and also provides techniques for bottleneck analysis and organizational mining. However, these techniques are mostly backward-looking. PMSD is a web application…
Polysomnography (PSG) data is recorded and stored in various formats depending on the recording software. Although the PSG data can usually be exported to open formats, such as the European Data Format (EDF), they are limited in data types,…
Standardization of data formats in a scientific discipline brings a range of benefits to researchers, as it enables the sharing of workflows and solutions to common problems, provides the foundation for generically useful tools that can be…
We propose a novel 3D spatial representation for data fusion and scene reconstruction. Probabilistic Signed Distance Function (Probabilistic SDF, PSDF) is proposed to depict uncertainties in the 3D space. It is modeled by a joint…
Advancements in theoretical and algorithmic approaches, workflow engines, and an ever-increasing computational power have enabled a novel paradigm for materials discovery through first-principles high-throughput simulations. A major…
First, a meshless simulation method is presented for multiphase fluid-particle flows with a two-way coupled Smoothed Particle Hydrodynamics (SPH) for the fluid and the Discrete Element Method (DEM) for the solid phase. The unresolved fluid…
We present the first public release (v0.1) of the open-source GADGET Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
We study the Single File Diffusion (SFD) of a cyclic chain of particles that cannot cross each other, in a thermal bath, with long ranged interactions, and arbitrary damping. We present simulations that exhibit new behaviors specifically…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Stenting is among the most common transcatheter interventions for congenital heart disease (CHD). Patient-specific computational fluid dynamics (CFD) simulations can predict hemodynamic outcomes of intervention scenarios but require…
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,…
In this document and the accompanying documents we describe a data model (Simulation Data Model) describing numerical computer simulations of astrophysical systems. The primary goal of this standard is to support discovery of simulations by…
Biomedical signals are stored in many different data formats. Most formats have been developed for a specific purpose of a specialized community for ECG research, EEG analysis, sleep research, etc. So far none of the existing formats can be…