Freely annotating C#

Reflective programming is becoming popular due to the increasing set of dynamic services provided by execution environments like JVM and CLR. With custom attributes Microsoft introduced an extensible model of reflection for CLR: they can be used as additional decorations on element declarations. The same notion has been introduced in Java 1.5. The annotation model, both in Java and in C#, limits annotations to classes and class members. In this paper we describe [a]C#a, an extension of the C# programming language, that allows programmers to annotate statements and code blocks and retrieve these annotations at run-time. We show how this extension can be reduced to the existing model. A set of operations on annotated code blocks to retrieve annotations and manipulate bytecode is introduced. We also discuss how to use [a]C# to annotate programs giving hints on how to parallelize a sequential method and how it can be implemented by means of the abstractions provided by the run-time of the language. Finally, we show how our model for custom attributes has been realized

Automating image analysis by annotating landmarks with deep neural networks

Image and video analysis is often a crucial step in the study of animal behavior and kinematics. Often these analyses require that the position of one or more animal landmarks are annotated (marked) in numerous images. The process of annotating landmarks can require a significant amount of time and tedious labor, which motivates the need for algorithms that can automatically annotate landmarks. In the community of scientists that use image and video analysis to study the 3D flight of animals, there has been a trend of developing more automated approaches for annotating landmarks, yet they fall short of being generally applicable. Inspired by the success of Deep Neural Networks (DNNs) on many problems in the field of computer vision, we investigate how suitable DNNs are for accurate and automatic annotation of landmarks in video datasets representative of those collected by scientists studying animals. Our work shows, through extensive experimentation on videos of hawkmoths, that DNNs are suitable for automatic and accurate landmark localization. In particular, we show that one of our proposed DNNs is more accurate than the current best algorithm for automatic localization of landmarks on hawkmoth videos. Moreover, we demonstrate how these annotations can be used to quantitatively analyze the 3D flight of a hawkmoth. To facilitate the use of DNNs by scientists from many different fields, we provide a self contained explanation of what DNNs are, how they work, and how to apply them to other datasets using the freely available library Caffe and supplemental code that we provide.https://arxiv.org/abs/1702.00583Published versio

Temporal expression normalisation in natural language texts

Automatic annotation of temporal expressions is a research challenge of great interest in the field of information extraction. In this report, I describe a novel rule-based architecture, built on top of a pre-existing system, which is able to normalise temporal expressions detected in English texts. Gold standard temporally-annotated resources are limited in size and this makes research difficult. The proposed system outperforms the state-of-the-art systems with respect to TempEval-2 Shared Task (value attribute) and achieves substantially better results with respect to the pre-existing system on top of which it has been developed. I will also introduce a new free corpus consisting of 2822 unique annotated temporal expressions. Both the corpus and the system are freely available on-line.Comment: 7 pages, 1 figure, 5 table

E-book readers in higher education

Ebook readers have received a mixed press, with some hailing them as the future of reading and others believing that they will never be popular. The study outlined here aims to understand the attitudes of, and issues of importance to, lecturers in UK academia, with a view to improving the design of ebook readers for education in the future. An evaluation of five portable devices is presented, in which lecturers were given the opportunity to read an ebook and provide feedback via a questionnaire. Results are compared with concerns arising from other experiments in the same field, and recommendations are made for successful ebook design

Word Affect Intensities

Words often convey affect -- emotions, feelings, and attitudes. Lexicons of word-affect association have applications in automatic emotion analysis and natural language generation. However, existing lexicons indicate only coarse categories of affect association. Here, for the first time, we create an affect intensity lexicon with real-valued scores of association. We use a technique called best-worst scaling that improves annotation consistency and obtains reliable fine-grained scores. The lexicon includes terms common from both general English and terms specific to social media communications. It has close to 6,000 entries for four basic emotions. We will be adding entries for other affect dimensions shortly

Multiple hierarchies : new aspects of an old solution

In this paper, we present the Multiple Annotation approach, which solves two problems: the problem of annotating overlapping structures, and the problem that occurs when documents should be annotated according to different, possibly heterogeneous tag sets. This approach has many advantages: it is based on XML, the modeling of alternative annotations is possible, each level can be viewed separately, and new levels can be added at any time. The files can be regarded as an interrelated unit, with the text serving as the implicit link. Two representations of the information contained in the multiple files (one in Prolog and one in XML) are described. These representations serve as a base for several applications

A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License