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.

Effective automatic image annotation via a coherent language model and active learning

Abstract: Image annotations allow users to access a large image database with textual queries. There have been several studies on automatic image annotation utilizing machine learning techniques, which automatically learn statistical models from annotated images and apply them to generate annotations for unseen images. One common problem shared by most previous learning approaches for automatic image annotation is that each annotated word is predicated for an image independently from other annotated words. In this paper, we proposed a coherent language model for automatic image annotation that takes into account the word-to-word correlation by estimating a coherent language model for an image. This new approach has two important advantages: 1) it is able to automatically determine the annotation length to improve the accuracy of retrieval results, and 2) it can be used with active learning to significantly reduce the required number of annotated image examples. Empirical studies with Corel dataset are presented to show the effectiveness of the coherent language model for automatic image annotation.

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

Abstract: Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu

Clinical Text Data in Machine Learning: Systematic Review.

Abstract: Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation.

Towards effective browsing of large scale social annotations

Abstract: This paper is concerned with the problem of browsing social annotations. Today, a lot of services (e.g., Del.icio.us, Filckr) have been provided for helping users to manage and share their favorite URLs and photos based on social annotations. Due to the exponential increasing of the social annotations, more and more users, however, are facing the problem how to effectively find desired resources from large annotation data. Existing methods such as tag cloud and annotation matching work well only on small annotation sets. Thus, an effective approach for browsing large scale annotation sets and the associated resources is in great demand by both ordinary users and service providers. In this paper, we propose a novel algorithm, namely Effective Large Scale Annotation Browser (ELSABer), to browse large-scale social annotation data. ELSABer helps the users browse huge number of annotations in a semantic, hierarchical and efficient way. More specifically, ELSABer has the following features: 1) the semantic relations between annotations are explored for browsing of similar resources; 2) the hierarchical relations between annotations are constructed for browsing in a top-down fashion; 3) the distribution of social annotations is studied for efficient browsing. By incorporating the personal and time information, ELSABer can be further extended for personalized and time-related browsing. A prototype system is implemented and shows promising results.

B2G-FAR, a species-centered GO annotation repository

Abstract: Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data. Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips. Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms. Availability: The annotation resource is available at http://www.b2gfar.org. Contact:[email protected]; [email protected] Supplementary information:Supplementary data are available at Bioinformatics online.