Related papers: LabPipe: an extensible informatics platform to str…
Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…
Digital pathology plays a crucial role in the development of artificial intelligence in the medical field. The digital pathology platform can make the pathological resources digital and networked, and realize the permanent storage of visual…
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…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
Good research data management is essential in modern-day lab work. Various solutions exist that are either highly specific or need a significant effort to be customized appropriately. This paper presents an integrated solution for…
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
The MIMIC-IV dataset is a large, publicly available electronic health record (EHR) resource widely used for clinical machine learning research. It comprises multiple modalities, including structured data, clinical notes, waveforms, and…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
MeTime is an opensource R package for reproducible analysis of longitudinal metabolomics data. It builds upon a central S4 container, metime_analyser, that stores multiple datasets, associated metadata and analysis outputs, enabling unified…
With large volumes of health care data comes the research area of computational phenotyping, making use of techniques such as machine learning to describe illnesses and other clinical concepts from the data itself. The "traditional"…
The increasing demand for intelligent mobile applications has made multi-agent collaboration with Transformer-based large language models (LLMs) essential in mobile edge computing (MEC) networks. However, training LLMs in such environments…
This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across…
Background: Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot studies are rarely…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
Liquid Chromatography Mass Spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be…
Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…
PubMed is a freely accessible system for searching the biomedical literature, with approximately 2.5 million users worldwide on an average workday. We have recently developed PubMed Labs (www.pubmed.gov/labs), an experimental platform for…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
The metaphor studies community has developed numerous valuable labelled corpora in various languages over the years. Many of these resources are not only unknown to the NLP community, but are also often not easily shared among the…