22 papers · ranked by Valyu relevance
Eduardo Guerra, Everaldo Mariano Gomes, Jeferson Ferreira, Igor Wiese + 3 more
'Igor Wiese' 'Phyllipe Lima' 'Marco Aurélio Gerosa' 'Paulo Meirelles'] Context: Code annotations have gained widespread popularity in programming languages, offering developers the ability to attach metadata to code elements to define custom behaviors. Many modern frameworks and APIs use annotations to keep integration…
Edward Misback, Erik Vank, Zachary Tatlock, Steven Tanimoto
When annotation data is stored along with code in the repository, teams immediately gain shared context, and annotations naturally follow version control history. However, such sharing also means that annotations become part of the codebase's footprint and could become a source of merge conflicts. This decision also…
Phyllipe Lima, Jorge Melegati, Everaldo Gomes, Nathalya Stefhany Pereira + 2 more
'Nathalya Stefhany Pereira' 'Eduardo Guerra' 'Paulo Meirelles'] Context: Code annotations is a widely used feature in Java systems to configure custom metadata on programming elements. Their increasing presence creates the need for approaches to assess and comprehend their usage and distribution. In this context…
Anastasia Drozdova, Ekaterina Trofimova, Polina Guseva, Anna Scherbakova + 2 more
The use of program code as a data source is increasingly expanding among data scientists. The purpose of the usage varies from the semantic classification of code to the automatic generation of programs. However, the machine learning model application is somewhat limited without annotating the code snippets. To address…
Jian Wang, Tao Lin, Rongsen Zhao, Huiling Zhao + 1 more
The deep natural language translation models have been used for automatic code error correction and have demonstrated outstanding potential. However, a large and accurately annotated training dataset is essential for these models to perform well. The key to improving the performance of these models lies in…
Zhongxing Yu, Chenggang Bai, Lionel Seinturier, Martin Monperrus
—Annotations have been formally introduced into Java since Java 5. Since then, annotations have been widely used by the Java community for different purposes, such as compiler guidance and runtime processing. Despite the ever-growing use, there is still limited empirical knowledge about the actual usage of annotations…
Kevin M Livingston, Michael Bada, Lawrence E Hunter, Karin Verspoor
Background Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures…
Matúš Sulír, Jaroslav Porubän, Ondrej Zoricak
—Traditionally, we have two possibilities to design tools for program comprehension and analysis. The first option is to create a standalone program, independent of any source code editor. This way, the act of source code editing is separated from the act of viewing the code analysis results. The second option is to…
Ehsan Abdekhodaie, Javad Hatami, Hadi Bahrami Ehsan, Reza Kormi-Nouri
'Reza Kormi-Nouri'] There is a lack of free software that provides a professional and smooth experience in text editing and markup for qualitative data analysis. Word processing software like Microsoft Word provides a good editing experience, allowing the researcher to effortlessly add comments to text portions.…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Christian O'Reilly, Elisabetta Iavarone, Sean L. Hill
Large models of complex neuronal circuits require specifying numerous parameters, with values that often need to be extracted from the literature, a tedious and error-prone process. To help establishing shareable curated corpora of annotations, we have developed a literature curation framework comprising an annotation…
Nicolaï Hoffmann, Aurore Besson, Edouard Cadieu, Matthias Lorthiois + 6 more
With the advent of complete genome assemblies, genome annotation has become essential for the functional interpretation of genomic data. Long-read RNA sequencing (LR-RNAseq) technologies have significantly improved transcriptome annotation by enabling full-length transcript reconstruction for both coding and non-coding…
Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan
The integration of genome annotations and reference databases is critical to identifying genetic variants that may be of interest in studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. We have developed vcfanno as a flexible toolset…
Alex R. Van Dam, Francisco Hita Garcia
The accelerating biodiversity crisis demands new approaches to taxonomic description that can scale beyond the capacity of professional taxonomists alone. We present the Descriptron-GBIF Annotator, a zero-installation, browser-based tool for morphological annotation of biodiversity specimen images retrieved directly…
Authors not listed
Computational models predicting the sites of metabolism (SOM) of small or- ganic molecules have become invaluable tools for studying and optimizing the metabolic properties of xenobiotics. However, the performance of SOM predic- tors has shown signs of plateauing in recent years, primarily due to the limited…
Kathleen Bates, Shen Jiang, Ruth Bates, Shivesh Chaudhary + 5 more
We report a generic smartphone app for quantitative annotation of complex images. The app is simple enough to be used by children, and annotation tasks are distributed across app users, contributing to efficient annotation. We demonstrate its flexibility and speed by annotating >30,000 images, including features of…
Fabio Giachelle, Ornella Irrera, Gianmaria Silvello
Background Semantic annotators and Natural Language Processing (NLP) methods for Named Entity Recognition and Linking (NER+L) require plenty of training and test data, especially in the biomedical domain. Despite the abundance of unstructured biomedical data, the lack of richly annotated biomedical datasets poses…
Nicolaï Hoffmann, Aurore Besson, Edouard Cadieu, Matthias Lorthiois + 6 more
With the advent of complete genome assemblies, genome annotation has become essential for the functional interpretation of genomic data. Long-read RNA sequencing (LR-RNAseq) technologies have significantly improved transcriptome annotation by enabling full-length transcript reconstruction for both coding and non-coding…
Marcelo Cicconet
The Python Bioimage Computing Toolkit (PuBliCiTy) is an evolving set of functions, scripts, and classes, written primarily in Python, to facilitate the analysis of biological images, of two or more dimensions, from electron or light microscopes. While the early development was guided by the goal of replacing an…
Andrea Ghelfi, Kenta Shirasawa, Sachiko Isobe
The rapid growth of next-generation sequencing (NGS) technology has led to a surge in the determination of whole genome sequences in plants. This has created a need for functional annotation of newly predicted gene sequences in the assembled genomes. To address this, “Hayai-Annotation Plants” was developed as a gene…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…