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We present POTATO, the Portable text annotation tool, a free, fully open-sourced annotation system that 1) supports labeling many types of text and multimodal data; 2) offers easy-to-configure features to maximize the productivity of both…

Computation and Language · Computer Science 2023-03-27 Jiaxin Pei , Aparna Ananthasubramaniam , Xingyao Wang , Naitian Zhou , Jackson Sargent , Apostolos Dedeloudis , David Jurgens

Single-cell RNA-seq (scRNA-seq) technology is a powerful tool for unraveling the complexity of biological systems. One of essential and fundamental tasks in scRNA-seq data analysis is Cell Type Annotation (CTA). In spite of tremendous…

Genomics · Quantitative Biology 2024-11-04 Chaochen Wu , Meiyun Zuo , Lei Xie

The Linked Open Data (LOD) cloud diagram is a picture that helps us grasp the contents and the links of globally available data sets. Such diagram has been a powerful dissemination method for the Linked Data movement, allowing people to…

Databases · Computer Science 2014-08-29 Luca Matteis

In managed languages, serialization of objects is typically done in bespoke binary formats such as Protobuf, or markup languages such as XML or JSON. The major limitation of these formats is readability. Human developers cannot read binary…

Software Engineering · Computer Science 2025-12-16 Julian Wachter , Deepika Tiwari , Martin Monperrus , Benoit Baudry

Sonification as a complement of visualization is been under research for decades as a new ways of data deployment. ICAD conferences, gather together specialists from different disciplines to discuss about sonification. Different tools as…

Instrumentation and Methods for Astrophysics · Physics 2023-02-02 Gonzalo De La Vega , Leonardo Martin Exequiel Dominguez , Johanna Casado , Beatriz García

We introduce giotto-tda, a Python library that integrates high-performance topological data analysis with machine learning via a scikit-learn-compatible API and state-of-the-art C++ implementations. The library's ability to handle various…

Saada transforms a set of heterogeneous FITS files or VOTables of various categories (images, tables, spectra ...) in a database without writing code. Databases created with Saada come with a rich Web interface and an Application…

Instrumentation and Methods for Astrophysics · Physics 2014-09-02 Laurent Michel , Christian Motch , Hoan Ngoc Nguyen , François-Xavier Pineau

Annotations are a critical component of visualizations, helping viewers interpret the visual representation and highlighting critical data insights. Despite their significant role, we lack an understanding of how annotations can be…

Human-Computer Interaction · Computer Science 2024-08-09 Rhys Sorenson-Graff , S. Sandra Bae , Jordan Wirfs-Brock

Even relatively simple code analysis can be a daunting task for many first year students. Perceived complexity, coupled with foreign and harsh syntax, often outstrips the ability for students to take in what they are seeing in terms of…

Human-Computer Interaction · Computer Science 2008-03-05 Christopher Pearson , Celina Gibbs , Yvonne Coady

We introduce SODA, a self-supervised diffusion model, designed for representation learning. The model incorporates an image encoder, which distills a source view into a compact representation, that, in turn, guides the generation of related…

Computer Vision and Pattern Recognition · Computer Science 2023-11-30 Drew A. Hudson , Daniel Zoran , Mateusz Malinowski , Andrew K. Lampinen , Andrew Jaegle , James L. McClelland , Loic Matthey , Felix Hill , Alexander Lerchner

Live coding is a performance and creative technique based on improvised and interactive coding. Many recent endeavors have focused in live coding both because of aesthetics and as a way to alleviate performance drawbacks when the musical…

The best way to understand complex data structures or algorithm is to see them in action. The present work presents a new tool, especially useful for students and lecturers in computer science. It is written in Java and developed at…

Computers and Society · Computer Science 2014-03-19 Kaninda Musumbu

The multidimensional, heterogeneous, and temporal nature of speech databases raises interesting challenges for representation and query. Recently, annotation graphs have been proposed as a general-purpose representational framework for…

Computation and Language · Computer Science 2007-05-23 Steven Bird , Peter Buneman , Wang-Chiew Tan

Diagrams often appear as node-link representations in many contexts, such as taxonomies, mind maps and networks in textbooks. Despite their pervasiveness, they present significant accessibility challenges for blind and low-vision people. To…

Human-Computer Interaction · Computer Science 2024-05-08 Yichun Zhao , Miguel A. Nacenta , Mahadeo A. Sukhai , Sowmya Somanath

Software visualization seeks to represent software artifacts graphical-ly in two or three dimensions, with the goal of enhancing comprehension, anal-ysis, maintenance, and evolution of the source code. In this context, visualiza-tions…

Software Engineering · Computer Science 2025-09-30 Anthony Savidis , Christos Vasilopoulos

Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that…

Genomics · Quantitative Biology 2016-02-24 Fran Supek , Nives Škunca

Interactive visualization can support fluid exploration but is often limited to predetermined tasks. Scripting can support a vast range of queries but may be more cumbersome for free-form exploration. Embedding interactive visualization in…

Dialogue systems have the potential to change how people interact with machines but are highly dependent on the quality of the data used to train them. It is therefore important to develop good dialogue annotation tools which can improve…

Computation and Language · Computer Science 2019-11-06 Edward Collins , Nikolai Rozanov , Bingbing Zhang

This paper introduces a new web-based software tool for annotating text, Text Annotation Graphs, or TAG. It provides functionality for representing complex relationships between words and word phrases that are not available in other…

Computation and Language · Computer Science 2018-03-02 Angus G. Forbes , Kristine Lee , Gus Hahn-Powell , Marco A. Valenzuela-Escárcega , Mihai Surdeanu

We propose Stepwise cOnditional likelihood variable selection for Discriminant Analysis (SODA) to detect both main and quadratic interaction effects in logistic regression and quadratic discriminant analysis (QDA) models. In the forward…

Methodology · Statistics 2017-05-31 Yang Li , Jun S. Liu