Building a semantically annotated corpus of clinical texts

In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains

Annotating, Understanding, and Predicting Long-term Video Memorability

International audienceMemorability can be regarded as a useful metric of video importance to help make a choice between competing videos. Research on computational understanding of video memorability is however in its early stages. There is no available dataset for modelling purposes, and the few previous attempts provided protocols to collect video memorability data that would be difficult to generalize. Furthermore, the computational features needed to build a robust memorability predictor remain largely undiscovered. In this article, we propose a new protocol to collect long-term video memorability annotations. We measure the memory performances of 104 participants from weeks to years after memorization to build a dataset of 660 videos for video memorability prediction. This dataset is made available for the research community. We then analyze the collected data in order to better understand video memorability, in particular the effects of response time, duration of memory retention and repetition of visualization on video memorability. We finally investigate the use of various types of audio and visual features and build a computational model for video memorability prediction. We conclude that high level visual semantics help better predict the memorability of videos

CASAM: Collaborative Human-machine Annotation of Multimedia.

The CASAM multimedia annotation system implements a model of cooperative annotation between a human annotator and automated components. The aim is that they work asynchronously but together. The system focuses upon the areas where automated recognition and reasoning are most effective and the user is able to work in the areas where their unique skills are required. The system’s reasoning is influenced by the annotations provided by the user and, similarly, the user can see the system’s work and modify and, implicitly, direct it. The CASAM system interacts with the user by providing a window onto the current state of annotation, and by generating requests for information which are important for the final annotation or to constrain its reasoning. The user can modify the annotation, respond to requests and also add their own annotations. The objective is that the human annotator’s time is used more effectively and that the result is an annotation that is both of higher quality and produced more quickly. This can be especially important in circumstances where the annotator has a very restricted amount of time in which to annotate the document. In this paper we describe our prototype system. We expand upon the techniques used for automatically analysing the multimedia document, for reasoning over the annotations generated and for the generation of an effective interaction with the end-user. We also present the results of evaluations undertaken with media professionals in order to validate the approach and gain feedback to drive further research

Are We There Yet?: The Development of a Corpus Annotated for Social Acts in Multilingual Online Discourse

We present the AAWD and AACD corpora, a collection of discussions drawn from Wikipedia talk pages and small group IRC discussions in English, Russian and Mandarin. Our datasets are annotated with labels capturing two kinds of social acts: alignment moves and authority claims. We describe these social acts, describe our annotation process, highlight challenges we encountered and strategies we employed during annotation, and present some analyses of resulting data set which illustrate the utility of our corpus and identify interactions among social acts and between participant status and social acts and in online discourse

Doctor of Philosophy

dissertationManual annotation of clinical texts is often used as a method of generating reference standards that provide data for training and evaluation of Natural Language Processing (NLP) systems. Manually annotating clinical texts is time consuming, expensive, and requires considerable cognitive effort on the part of human reviewers. Furthermore, reference standards must be generated in ways that produce consistent and reliable data but must also be valid in order to adequately evaluate the performance of those systems. The amount of labeled data necessary varies depending on the level of analysis, the complexity of the clinical use case, and the methods that will be used to develop automated machine systems for information extraction and classification. Evaluating methods that potentially reduce cost, manual human workload, introduce task efficiencies, and reduce the amount of labeled data necessary to train NLP tools for specific clinical use cases are active areas of research inquiry in the clinical NLP domain. This dissertation integrates a mixed methods approach using methodologies from cognitive science and artificial intelligence with manual annotation of clinical texts. Aim 1 of this dissertation identifies factors that affect manual annotation of clinical texts. These factors are further explored by evaluating approaches that may introduce efficiencies into manual review tasks applied to two different NLP development areas - semantic annotation of clinical concepts and identification of information representing Protected Health Information (PHI) as defined by HIPAA. Both experiments integrate iv different priming mechanisms using noninteractive and machine-assisted methods. The main hypothesis for this research is that integrating pre-annotation or other machineassisted methods within manual annotation workflows will improve efficiency of manual annotation tasks without diminishing the quality of generated reference standards

The (In-)Consistency of Literary Concepts. Operationalising, Annotating and Detecting Literary Comment

This paper explores how both annotation procedures and automatic detection (i.e. classifiers) can be used to assess the consistency of textual literary concepts. We developed an annotation tagset for the ‘literary comment’ – a frequently used but rarely defined concept – and its subtypes (interpretative comment, attitude comment and metanarrative/metafictional comment) and trained a multi-output and a binary classifier. The multi-output classifier shows F-scores of 28% for attitude comment, 36% for interpretative comment and 48% for meta comment, whereas the binary classifier achieves F-scores up to 59%. Crucially, both our annotation and the automatic classification struggle with the same subtypes of comment, although annotation and classification follow completely different procedures. Our findings suggest an inconsistency in the overall literary concept ‘comment’ and most prominently the subtypes ‘attitude comment’ and ‘interpretative comment’. As a best-practice-example, our approach illustrates that the contribution of Digital Humanities to Literary Studies may go beyond the automatic recognition of literary phenomena