Related papers: Ovopub: Modular data publication with minimal prov…
Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…
Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, RCR has the capacity to…
Provenance refers to the documentation of an object's lifecycle. This documentation (often represented as a graph) should include all the information necessary to reproduce a certain piece of data or the process that led to it. In a dynamic…
Generative retrieval represents a novel approach to information retrieval. It uses an encoder-decoder architecture to directly produce relevant document identifiers (docids) for queries. While this method offers benefits, current approaches…
Data provenance has numerous applications in the context of data preparation pipelines. It can be used for debugging faulty pipelines, interpreting results, verifying fairness, and identifying data quality issues, which may affect the…
Most of data on the Web are still stored in relational databases. Therefore, it is more important to make the correspondence between relational databases (RDB) and ontologies for storing the Web data. In this paper, we present an new…
The Paraphrase Database (PPDB; Ganitkevitch et al., 2013) is an extensive semantic resource, consisting of a list of phrase pairs with (heuristic) confidence estimates. However, it is still unclear how it can best be used, due to the…
Science depends on collaboration, result reproduction, and the development of supporting software tools. Each of these requires careful management of software versions. We present a unified model for installing, managing, and publishing…
We introduce 3DB: an extendable, unified framework for testing and debugging vision models using photorealistic simulation. We demonstrate, through a wide range of use cases, that 3DB allows users to discover vulnerabilities in computer…
Tabular data constitute a dominant form of information in modern data lakes and repositories, yet discovering the relevant tables to answer user questions remains challenging. Existing data discovery systems assume that each question can be…
The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain an RDF graph with a low amount of errors and internal redundancy, the chosen ontology must be consistently applied.…
The vast body of scientific publications presents an increasing challenge of finding those that are relevant to a given research question, and making informed decisions on their basis. This becomes extremely difficult without the use of…
Reproducibility is increasingly important to statistical research, but many details are often omitted from the published version of complex statistical analyses. A reader's comprehension is limited to what the author concludes, without…
The production, shipping, usage, and disposal of consumer goods have a substantial impact on greenhouse gas emissions and the depletion of resources. Machine Learning (ML) can help to foster sustainable consumption patterns by accounting…
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed--the CEDAR Workbench--is a suite of Web-based tools and…
This paper presents a creativity support tool, called FreePub, to collect and organize scientific material using mindmaps. Mindmaps are visual, graph-based represenations of concepts, ideas, notes, tasks, etc. They generally take a…
Over the past years, substantial numbers of microbial species' genomes have been deposited outside of conventional INSDC databases. The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Semantic occupancy prediction aims to infer dense geometry and semantics of surroundings for an autonomous agent to operate safely in the 3D environment. Existing occupancy prediction methods are almost entirely trained on human-annotated…
Many real-world planning domains involve diverse information sources, external entities, and variable-reliability agents, all of which may impact the confidence, risk, and sensitivity of plans. Humans reviewing a plan may lack context about…