Annotation Protocol for Textbook Enrichment with Prerequisite Knowledge Graph

Extracting and formally representing the knowledge embedded in textbooks, such as the concepts explained and the relations between them, can support the provision of advanced knowledge-based services for learning environments and digital libraries. In this paper, we consider a specific type of relation in textbooks referred to as prerequisite relations (PR). PRs represent precedence relations between concepts aimed to provide the reader with the knowledge needed to understand a further concept(s). Their annotation in educational texts produces datasets that can be represented as a graph of concepts connected by PRs. However, building good-quality and reliable datasets of PRs from a textbook is still an open issue, not just for automated annotation methods but even for manual annotation. In turn, the lack of good-quality datasets and well-defined criteria to identify PRs affect the development and validation of automated methods for prerequisite identification. As a contribution to this issue, in this paper, we propose PREAP, a protocol for the annotation of prerequisite relations in textbooks aimed at obtaining reliable annotated data that can be shared, compared, and reused in the research community. PREAP defines a novel textbook-driven annotation method aimed to capture the structure of prerequisites underlying the text. The protocol has been evaluated against baseline methods for manual and automatic annotation. The findings show that PREAP enables the creation of prerequisite knowledge graphs that have higher inter-annotator agreement, accuracy, and alignment with text than the baseline methods. This suggests that the protocol is able to accurately capture the PRs expressed in the text. Furthermore, the findings show that the time required to complete the annotation using PREAP are significantly shorter than with the other manual baseline methods. The paper includes also guidelines for using PREAP in three annotation scenarios, experimentally tested. We also provide example datasets and a user interface that we developed to support prerequisite annotation

Bringing Structure into Summaries: Crowdsourcing a Benchmark Corpus of Concept Maps

Concept maps can be used to concisely represent important information and bring structure into large document collections. Therefore, we study a variant of multi-document summarization that produces summaries in the form of concept maps. However, suitable evaluation datasets for this task are currently missing. To close this gap, we present a newly created corpus of concept maps that summarize heterogeneous collections of web documents on educational topics. It was created using a novel crowdsourcing approach that allows us to efficiently determine important elements in large document collections. We release the corpus along with a baseline system and proposed evaluation protocol to enable further research on this variant of summarization.Comment: Published at EMNLP 201

Annotating patient clinical records with syntactic chunks and named entities: the Harvey corpus

The free text notes typed by physicians during patient consultations contain valuable information for the study of disease and treatment. These notes are difficult to process by existing natural language analysis tools since they are highly telegraphic (omitting many words), and contain many spelling mistakes, inconsistencies in punctuation, and non-standard word order. To support information extraction and classification tasks over such text, we describe a de-identified corpus of free text notes, a shallow syntactic and named entity annotation scheme for this kind of text, and an approach to training domain specialists with no linguistic background to annotate the text. Finally, we present a statistical chunking system for such clinical text with a stable learning rate and good accuracy, indicating that the manual annotation is consistent and that the annotation scheme is tractable for machine learning

From Texts to Prerequisites. Identifying and Annotating Propaedeutic Relations in Educational Textual Resources

openPrerequisite Relations (PRs) are dependency relations established between two distinct concepts expressing which piece(s) of information a student has to learn first in order to understand a certain target concept. Such relations are one of the most fundamental in Education, playing a crucial role not only for what concerns new knowledge acquisition, but also in the novel applications of Artificial Intelligence to distant and e-learning. Indeed, resources annotated with such information could be used to develop automatic systems able to acquire and organize the knowledge embodied in educational resources, possibly fostering educational applications personalized, e.g., on students' needs and prior knowledge. The present thesis discusses the issues and challenges of identifying PRs in educational textual materials with the purpose of building a shared understanding of the relation among the research community. To this aim, we present a methodology for dealing with prerequisite relations as established in educational textual resources which aims at providing a systematic approach for uncovering PRs in textual materials, both when manually annotating and automatically extracting the PRs. The fundamental principles of our methodology guided the development of a novel framework for PR identification which comprises three components, each tackling a different task: (i) an annotation protocol (PREAP), reporting the set of guidelines and recommendations for building PR-annotated resources; (ii) an annotation tool (PRET), supporting the creation of manually annotated datasets reflecting the principles of PREAP; (iii) an automatic PR learning method based on machine learning (PREL). The main novelty of our methodology and framework lies in the fact that we propose to uncover PRs from textual resources relying solely on the content of the instructional material: differently from other works, rather than creating de-contextualised PRs, we acknowledge the presence of a PR between two concepts only if emerging from the way they are presented in the text. By doing so, we anchor relations to the text while modelling the knowledge structure entailed in the resource. As an original contribution of this work, we explore whether linguistic complexity of the text influences the task of manual identification of PRs. To this aim, we investigate the interplay between text and content in educational texts through a crowd-sourcing experiment on concept sequencing. Our methodology values the content of educational materials as it incorporates the evidence acquired from such investigation which suggests that PR recognition is highly influenced by the way in which concepts are introduced in the resource and by the complexity of the texts. The thesis reports a case study dealing with every component of the PR framework which produced a novel manually-labelled PR-annotated dataset.openXXXIII CICLO - DIGITAL HUMANITIES. TECNOLOGIE DIGITALI, ARTI, LINGUE, CULTURE E COMUNICAZIONE - Lingue, culture e tecnologie digitaliAlzetta, Chiar

A framework for structuring prerequisite relations between concepts in educational textbooks

In our age we are experiencing an increasing availability of digital educational resources and self-regulated learning. In this scenario, the development of automatic strategies for organizing the knowledge embodied in educational resources has a tremendous potential for building personalized learning paths and applications such as intelligent textbooks and recommender systems of learning materials. To this aim, a straightforward approach consists in enriching the educational materials with a concept graph, i.a. a knowledge structure where key concepts of the subject matter are represented as nodes and prerequisite dependencies among such concepts are also explicitly represented. This thesis focuses therefore on prerequisite relations in textbooks and it has two main research goals. The first goal is to define a methodology for systematically annotating prerequisite relations in textbooks, which is functional for analysing the prerequisite phenomenon and for evaluating and training automatic methods of extraction. The second goal concerns the automatic extraction of prerequisite relations from textbooks. These two research goals will guide towards the design of PRET, i.e. a comprehensive framework for supporting researchers involved in this research issue. The framework described in the present thesis allows indeed researchers to conduct the following tasks: 1) manual annotation of educational texts, in order to create datasets to be used for machine learning algorithms or for evaluation as gold standards; 2) annotation analysis, for investigating inter-annotator agreement, graph metrics and in-context linguistic features; 3) data visualization, for visually exploring datasets and gaining insights of the problem that may lead to improve algorithms; 4) automatic extraction of prerequisite relations. As for the automatic extraction, we developed a method that is based on burst analysis of concepts in the textbook and we used the gold dataset with PR annotation for its evaluation, comparing the method with other metrics for PR extraction

The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge

Biomedical text mining methods and technologies have improved significantly in the last decade. Considerable efforts have been invested in understanding the main challenges of biomedical literature retrieval and extraction and proposing solutions to problems of practical interest. Most notably, community-oriented initiatives such as the BioCreative challenge have enabled controlled environments for the comparison of automatic systems while pursuing practical biomedical tasks. Under this scenario, the present work describes the Markyt Web-based document curation platform, which has been implemented to support the visualisation, prediction and benchmark of chemical and gene mention annotations at BioCreative/CHEMDNER challenge. Creating this platform is an important step for the systematic and public evaluation of automatic prediction systems and the reusability of the knowledge compiled for the challenge. Markyt was not only critical to support the manual annotation and annotation revision process but also facilitated the comparative visualisation of automated results against the manually generated Gold Standard annotations and comparative assessment of generated results. We expect that future biomedical text mining challenges and the text mining community may benefit from the Markyt platform to better explore and interpret annotations and improve automatic system predictions. Database URL: http://www.markyt.org, https://github.com/sing-group/MarkytThis work was partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273) as well as by the Foundation for Applied Medical Research, University of Navarra (Pamplona, Spain). The research leading to these results has received funding from the European Union's Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement no 316265, BIOCAPS

Collaborative relation annotation and quality analysis in Markyt environment

Text mining is showing potential to help in biomedical knowledge integration and discovery at various levels. However, results depend largely on the specifics of the knowledge problem and, in particular, on the ability to produce high-quality benchmarking corpora that may support the training and evaluation of automatic prediction systems. Annotation tools enabling the flexible and customizable production of such corpora are thus pivotal. The open-source Markyt annotation environment brings together the latest web technologies to offer a wide range of annotation capabilities in a domain-agnostic way. It enables the management of multi-user and multi-round annotation projects, including inter-annotator agreement and consensus assessments. Also, Markyt supports the description of entity and relation annotation guidelines on a project basis, being flexible to partial word tagging and the occurrence of annotation overlaps. This paper describes the current release of Markyt, namely new annotation perspectives, which enable the annotation of relations among entities, and enhanced analysis capabilities. Several demos, inspired by public biomedical corpora, are presented as means to better illustrate such functionalities. Markyt aims to bring together annotation capabilities of broad interest to those producing annotated corpora. Markyt demonstration projects describe 20 different annotation tasks of varied document sources (e.g. abstracts, twitters or drug labels) and languages (e.g. English, Spanish or Chinese). Continuous development is based on feedback from practical applications as well as community reports on short- and medium-term mining challenges. Markyt is freely available for non-commercial use at http://markyt.org.This work was partially supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). The authors also acknowledge the PhD grants of M.P.-P. and G.P.-R., funded by the Xunta de Galicia.info:eu-repo/semantics/publishedVersio

Working out a common task: design and evaluation of user-intelligent system collaboration

This paper describes the design and user evaluation of an intelligent user interface intended to mediate between users and an Adaptive Information Extraction (AIE) system. The design goal was to support a synergistic and cooperative work. Laboratory tests showed the approach was efficient and effective; focus groups were run to assess its ease of use. Logs, user satisfaction questionnaires, and interviews were exploited to investigate the interaction experience. We found that user’ attitude is mainly hierarchical with the user wishing to control and check the system’s initiatives. However when confidence in the system capabilities rises, a more cooperative interaction is adopted