Coreference resolution in clinical discharge summaries, progress notes, surgical and pathology reports: a unified lexical approach

We developed a lexical rule-based system that uses a unified approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA) provided for the fifth i2b2/VA shared task. Taking the unweighted mean between 4 coreference metrics, validation of the system against the i2b2/VA corpus attained an overall F-score of 87.7% across all mention classes, with a maximum of 93.1% for coreference of persons, and a minimum of 77.2% for coreference of tests. For the ODIE corpus the overall F-score across all mention classes was 79.4%, with a maximum of 82.0% for coreference of persons and a minimum of 13.1% for coreference of diagnostic reagents. For the ODIE corpus our results are comparable to the mean reported inter-annotator agreement with the gold standard. We discuss the four categories of errors we identified, and how these might be addressed. The system uses a number of reusable modules and techniques that may be of benefit to the research community

Lexical patterns, features and knowledge resources for coreference resolution in clinical notes

Generation of entity coreference chains provides a means to extract linked narrative events from clinical notes, but despite being a well-researched topic in natural language processing, general- purpose coreference tools perform poorly on clinical texts. This paper presents a knowledge-centric and pattern-based approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA). In addition, a method for generating coreference chains using progressively pruned linked lists is demonstrated that reduces the search space and facilitates evaluation by a number of metrics. Independent evaluation results show an F-measure for each corpus of 79.2% and 87.5%, respectively, which offers performance at least as good as human annotators, greatly increased performance over general- purpose tools, and improvement on previously reported clinical coreference systems. The system uses a number of open-source components that are available to download

Comparing knowledge sources for nominal anaphora resolution

We compare two ways of obtaining lexical knowledge for antecedent selection in other-anaphora and definite noun phrase coreference. Specifically, we compare an algorithm that relies on links encoded in the manually created lexical hierarchy WordNet and an algorithm that mines corpora by means of shallow lexico-semantic patterns. As corpora we use the British National Corpus (BNC), as well as the Web, which has not been previously used for this task. Our results show that (a) the knowledge encoded in WordNet is often insufficient, especially for anaphor-antecedent relations that exploit subjective or context-dependent knowledge; (b) for other-anaphora, the Web-based method outperforms the WordNet-based method; (c) for definite NP coreference, the Web-based method yields results comparable to those obtained using WordNet over the whole dataset and outperforms the WordNet-based method on subsets of the dataset; (d) in both case studies, the BNC-based method is worse than the other methods because of data sparseness. Thus, in our studies, the Web-based method alleviated the lexical knowledge gap often encountered in anaphora resolution, and handled examples with context-dependent relations between anaphor and antecedent. Because it is inexpensive and needs no hand-modelling of lexical knowledge, it is a promising knowledge source to integrate in anaphora resolution systems

A unified representation for morphological, syntactic, semantic, and referential annotations

This paper reports on the SYN-RA (SYNtax-based Reference Annotation) project, an on-going project of annotating German newspaper texts with referential relations. The project has developed an inventory of anaphoric and coreference relations for German in the context of a unified, XML-based annotation scheme for combining morphological, syntactic, semantic, and anaphoric information. The paper discusses how this unified annotation scheme relates to other formats currently discussed in the literature, in particular the annotation graph model of Bird and Liberman (2001) and the pie-in-thesky scheme for semantic annotation

Inter-Coder Agreement for Computational Linguistics

This article is a survey of methods for measuring agreement among corpus annotators. It exposes the mathematics and underlying assumptions of agreement coefficients, covering Krippendorff's alpha as well as Scott's pi and Cohen's kappa; discusses the use of coefficients in several annotation tasks; and argues that weighted, alpha-like coefficients, traditionally less used than kappa-like measures in computational linguistics, may be more appropriate for many corpus annotation tasks—but that their use makes the interpretation of the value of the coefficient even harder. </jats:p

Automatic extraction of knowledge from web documents

A large amount of digital information available is written as text documents in the form of web pages, reports, papers, emails, etc. Extracting the knowledge of interest from such documents from multiple sources in a timely fashion is therefore crucial. This paper provides an update on the Artequakt system which uses natural language tools to automatically extract knowledge about artists from multiple documents based on a predefined ontology. The ontology represents the type and form of knowledge to extract. This knowledge is then used to generate tailored biographies. The information extraction process of Artequakt is detailed and evaluated in this paper

Introduction: Modeling, Learning and Processing of Text-Technological Data Structures

Researchers in many disciplines, sometimes working in close cooperation, have been concerned with modeling textual data in order to account for texts as the prime information unit of written communication. The list of disciplines includes computer science and linguistics as well as more specialized disciplines like computational linguistics and text technology. What many of these efforts have in common is the aim to model textual data by means of abstract data types or data structures that support at least the semi-automatic processing of texts in any area of written communication

Resolving pronominal anaphora using commonsense knowledge

Coreference resolution is the task of resolving all expressions in a text that refer to the same entity. Such expressions are often used in writing and speech as shortcuts to avoid repetition. The most frequent form of coreference is the anaphor. To resolve anaphora not only grammatical and syntactical strategies are required, but also semantic approaches should be taken into consideration. This dissertation presents a framework for automatically resolving pronominal anaphora by integrating recent findings from the field of linguistics with new semantic features. Commonsense knowledge is the routine knowledge people have of the everyday world. Because such knowledge is widely used it is frequently omitted from social communications such as texts. It is understandable that without this knowledge computers will have difficulty making sense of textual information. In this dissertation a new set of computational and linguistic features are used in a supervised learning approach to resolve the pronominal anaphora in document. Commonsense knowledge sources such as ConceptNet and WordNet are used and similarity measures are extracted to uncover the elaborative information embedded in the words that can help in the process of anaphora resolution. The anaphoric system is tested on 350 Wall Street Journal articles from the BBN corpus. When compared with other systems available such as BART (Versley et al. 2008) and Charniak and Elsner 2009, our system performed better and also resolved a much wider range of anaphora. We were able to achieve a 92% F-measure on the BBN corpus and an average of 85% F-measure when tested on other genres of documents such as children stories and short stories selected from the web

Event-based Access to Historical Italian War Memoirs

The progressive digitization of historical archives provides new, often domain specific, textual resources that report on facts and events which have happened in the past; among these, memoirs are a very common type of primary source. In this paper, we present an approach for extracting information from Italian historical war memoirs and turning it into structured knowledge. This is based on the semantic notions of events, participants and roles. We evaluate quantitatively each of the key-steps of our approach and provide a graph-based representation of the extracted knowledge, which allows to move between a Close and a Distant Reading of the collection.Comment: 23 pages, 6 figure