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Progress in Prognostics and Health Management (PHM) is hindered by the lack of standardized and reusable evaluation practices across tasks, datasets, and application domains. Reported results are often difficult to reproduce and compare, as…
We present zea (pronounced ze-yah), a Python package for cognitive ultrasound imaging that offers a flexible, modular, and differentiable pipeline for ultrasound data processing. Additionally, it includes a collection of pre-defined models…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…
The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…
The Electronic Health Record (EHR) is an essential part of the modern medical system and impacts healthcare delivery, operations, and research. Unstructured text is attracting much attention despite structured information in the EHRs and…
Digital twin technology has is anticipated to transform healthcare, enabling personalized medicines and support, earlier diagnoses, simulated treatment outcomes, and optimized surgical plans. Digital twins are readily gaining traction in…
The Herschel Common Science System (HCSS) (Ott et al. 2006) (Ott & Science Ground Segment Consortium 2010) is a substantial Java software package, accompanying the development of the Herschel Mission (Pilbratt et al. 2010), supporting all…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
Spatial join is a fundamental operation in spatial databases. With the rapid growth of 3D data in applications such as LiDAR-based object detection and 3D digital pathology, there is an increasing need to support spatial join over 3D…
Personal health record (PHR) management is under new scrutiny as private companies move into the market and government agencies actively address perceived health care distribution inequalities and inefficiencies. Current systems are…
Data quality is fundamental to modern data science workflows, where data continuously flows as unbounded streams feeding critical downstream tasks, from elementary analytics to advanced artificial intelligence models. Existing data quality…
Scientific applications in HPC environment are more com-plex and more data-intensive nowadays. Scientists usually rely on workflow system to manage the complexity: simply define multiple processing steps into a single script and let the…
The widespread development and adoption of open-source software have built an ecosystem for open development and collaboration. In this ecosystem, individuals and organizations collaborate to create high-quality software that can be used by…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Multi-institutional electronic health record (Multi-EHR) data have emerged as a powerful resource for developing predictive models to support clinical decisions and for generating reliable real-world evidence. By aggregating information…
We developed a software pipeline for quality control (QC) of histopathology whole slide images (WSIs) that segments various regions, such as blurs of different levels, tissue regions, tissue folds, and pen marks. Given the necessity and…
The last 15 years have seen a surge of new multi-chip optical and near-IR imagers. While some of them are accompanied by specific reduction pipelines, user-friendly and generic reduction tools are uncommon. In this paper I introduce THELI,…
We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii)…
The personalized health care service utilizes the relational patient data and big data analytics to tailor the medication recommendations. However, most of the health care data are in unstructured form and it consumes a lot of time and…