Annotation

About: Annotation is a research topic. Over the lifetime, 6719 publications have been published within this topic receiving 203463 citations. The topic is also known as: note & markup.

Image Annotation by Propagating Labels from Semantic Neighbourhoods

Abstract: Automatic image annotation aims at predicting a set of semantic labels for an image. Because of large annotation vocabulary, there exist large variations in the number of images corresponding to different labels ("class-imbalance"). Additionally, due to the limitations of human annotation, several images are not annotated with all the relevant labels ("incomplete-labelling"). These two issues affect the performance of most of the existing image annotation models. In this work, we propose 2-pass k-nearest neighbour (2PKNN) algorithm. It is a two-step variant of the classical k-nearest neighbour algorithm, that tries to address these issues in the image annotation task. The first step of 2PKNN uses "image-to-label" similarities, while the second step uses "image-to-image" similarities, thus combining the benefits of both. We also propose a metric learning framework over 2PKNN. This is done in a large margin set-up by generalizing a well-known (single-label) classification metric learning algorithm for multi-label data. In addition to the features provided by Guillaumin et al. (2009) that are used by almost all the recent image annotation methods, we benchmark using new features that include features extracted from a generic convolutional neural network model and those computed using modern encoding techniques. We also learn linear and kernelized cross-modal embeddings over different feature combinations to reduce semantic gap between visual features and textual labels. Extensive evaluations on four image annotation datasets (Corel-5K, ESP-Game, IAPR-TC12 and MIRFlickr-25K) demonstrate that our method achieves promising results, and establishes a new state-of-the-art on the prevailing image annotation datasets.

Inter-annotator agreement on a multilingual semantic annotation task

Abstract: Six sites participated in the Interlingual Annotation of Multilingual Text Corpora (IAMTC) project (Dorr et al., 2004; Farwell et al., 2004; Mitamura et al., 2004). Parsed versions of English translations of news articles in Arabic, French, Hindi, Japanese, Korean and Spanish were annotated by up to ten annotators. Their task was to match open-class lexical items (nouns, verbs, adjectives, adverbs) to one or more concepts taken from the Omega ontology (Philpot et al., 2003), and to identify theta roles for verb arguments. The annotated corpus is intended to be a resource for meaning-based approaches to machine translation. Here we discuss inter-annotator agreement for the corpus. The annotation task is characterized by annotators’ freedom to select multiple concepts or roles per lexical item. As a result, the annotation categories are sets, the number of which is bounded only by the number of distinct annotator-lexical item pairs. We use a reliability metric designed to handle partial agreement between sets. The best results pertain to the part of the ontology derived from WordNet. We examine change over the course of the project, differences among annotators, and differences across parts of speech. Our results suggest a strong learning effect early in the project.

CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

Abstract: Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision of consistent, clinically applicable variant annotation of NGS data has proved difficult, particularly of indels, an important variant class in clinical genomics. Annotation in relation to a reference genome sequence, the DNA strand of coding transcripts and potential alternative variant representations has not been well addressed. Here we present tools that address these challenges to provide rapid, standardized, clinically appropriate annotation of NGS data in line with existing clinical standards. We developed a clinical sequencing nomenclature (CSN), a fixed variant annotation consistent with the principles of the Human Genome Variation Society (HGVS) guidelines, optimized for automated variant annotation of NGS data. To deliver high-throughput CSN annotation we created CAVA (Clinical Annotation of VAriants), a fast, lightweight tool designed for easy incorporation into NGS pipelines. CAVA allows transcript specification, appropriately accommodates the strand of a gene transcript and flags variants with alternative annotations to facilitate clinical interpretation and comparison with other datasets. We evaluated CAVA in exome data and a clinical BRCA1/BRCA2 gene testing pipeline. CAVA generated CSN calls for 10,313,034 variants in the ExAC database in 13.44 hours, and annotated the ICR1000 exome series in 6.5 hours. Evaluation of 731 different indels from a single individual revealed 92 % had alternative representations in left aligned and right aligned data. Annotation of left aligned data, as performed by many annotation tools, would thus give clinically discrepant annotation for the 339 (46 %) indels in genes transcribed from the forward DNA strand. By contrast, CAVA provides the correct clinical annotation for all indels. CAVA also flagged the 370 indels with alternative representations of a different functional class, which may profoundly influence clinical interpretation. CAVA annotation of 50 BRCA1/BRCA2 gene mutations from a clinical pipeline gave 100 % concordance with Sanger data; only 8/25 BRCA2 mutations were correctly clinically annotated by other tools. CAVA is a freely available tool that provides rapid, robust, high-throughput clinical annotation of NGS data, using a standardized clinical sequencing nomenclature.

Introduction to Linguistic Annotation and Text Analytics

Abstract: Linguistic annotation and text analytics are active areas of research and development, with academic conferences and industry events such as the Linguistic Annotation Workshops and the annual Text Analytics Summits. This book provides a basic introduction to both fields, and aims to show that good linguistic annotations are the essential foundation for good text analytics. After briefly reviewing the basics of XML, with practical exercises illustrating in-line and stand-off annotations, a chapter is devoted to explaining the different levels of linguistic annotations. The reader is encouraged to create example annotations using the WordFreak linguistic annotation tool. The next chapter shows how annotations can be created automatically using statistical NLP tools, and compares two sets of tools, the OpenNLP and Stanford NLP tools. The second half of the book describes different annotation formats and gives practical examples of how to interchange annotations between different formats using XSLT transformations. The two main text analytics architectures, GATE and UIMA, are then described and compared, with practical exercises showing how to configure and customize them. The final chapter is an introduction to text analytics, describing the main applications and functions including named entity recognition, coreference resolution and information extraction, with practical examples using both open source and commercial tools. Copies of the example files, scripts, and stylesheets used in the book are available from the companion website, located at http://sites.morganclaypool.com/wilcock. Table of Contents: Working with XML / Linguistic Annotation / Using Statistical NLP Tools / Annotation Interchange / Annotation Architectures / Text Analytics

Ubiquitous annotation systems: technologies and challenges

Abstract: Ubiquitous annotation systems allow users to annotate physical places, objects, and persons with digital information. Especially in the field of location based information systems much work has been done to implement adaptive and context-aware systems, but few efforts have focused on the general requirements for linking information to objects in both physical and digital space. This paper surveys annotation techniques from open hypermedia systems, Web based annotation systems, and mobile and augmented reality systems to illustrate different approaches to four central challenges ubiquitous annotation systems have to deal with: anchoring, structuring, presentation, and authoring. Through a number of examples each challenge is discussed and HyCon, a context-aware hypermedia framework developed at the University of Aarhus, Denmark, is used to illustrate an integrated approach to ubiquitous annotations. Finally, a taxonomy of annotation systems is presented. The taxonomy can be used both to categorize system based on the way they present annotations and to choose the right technology for interfacing with annotations when implementing new systems.