brat: a Web-based Tool for NLP-Assisted Text Annotation

We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss several case studies of real-world annotation projects using pre-release versions of BRAT and present an evaluation of annotation assisted by semantic class disambiguation on a multicategory entity mention annotation task, showing a 15 % decrease in total annotation time. BRAT is available under an opensource license from

Annotation graphs as a framework for multidimensional linguistic data analysis

In recent work we have presented a formal framework for linguistic annotation based on labeled acyclic digraphs. These `annotation graphs' offer a simple yet powerful method for representing complex annotation structures incorporating hierarchy and overlap. Here, we motivate and illustrate our approach using discourse-level annotations of text and speech data drawn from the CALLHOME, COCONUT, MUC-7, DAMSL and TRAINS annotation schemes. With the help of domain specialists, we have constructed a hybrid multi-level annotation for a fragment of the Boston University Radio Speech Corpus which includes the following levels: segment, word, breath, ToBI, Tilt, Treebank, coreference and named entity. We show how annotation graphs can represent hybrid multi-level structures which derive from a diverse set of file formats. We also show how the approach facilitates substantive comparison of multiple annotations of a single signal based on different theoretical models. The discussion shows how annotation graphs open the door to wide-ranging integration of tools, formats and corpora.Comment: 10 pages, 10 figures, Towards Standards and Tools for Discourse Tagging, Proceedings of the Workshop. pp. 1-10. Association for Computational Linguistic

A Practical Incremental Learning Framework For Sparse Entity Extraction

This work addresses challenges arising from extracting entities from textual data, including the high cost of data annotation, model accuracy, selecting appropriate evaluation criteria, and the overall quality of annotation. We present a framework that integrates Entity Set Expansion (ESE) and Active Learning (AL) to reduce the annotation cost of sparse data and provide an online evaluation method as feedback. This incremental and interactive learning framework allows for rapid annotation and subsequent extraction of sparse data while maintaining high accuracy. We evaluate our framework on three publicly available datasets and show that it drastically reduces the cost of sparse entity annotation by an average of 85% and 45% to reach 0.9 and 1.0 F-Scores respectively. Moreover, the method exhibited robust performance across all datasets.Comment: https://www.aclweb.org/anthology/C18-1059

Information structure

The guidelines for Information Structure include instructions for the annotation of Information Status (or ‘givenness’), Topic, and Focus, building upon a basic syntactic annotation of nominal phrases and sentences. A procedure for the annotation of these features is proposed

Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation

Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this paper, we aim to address the following question: With limited effort (e.g., time) for annotation, what instances should be annotated in order to attain the best performance? We present a deep active learning framework that combines fully convolutional network (FCN) and active learning to significantly reduce annotation effort by making judicious suggestions on the most effective annotation areas. We utilize uncertainty and similarity information provided by FCN and formulate a generalized version of the maximum set cover problem to determine the most representative and uncertain areas for annotation. Extensive experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node ultrasound image segmentation dataset show that, using annotation suggestions by our method, state-of-the-art segmentation performance can be achieved by using only 50% of training data.Comment: Accepted at MICCAI 201