Distributional Semantic Models for Clinical Text Applied to Health Record Summarization

As information systems in the health sector are becoming increasingly computerized, large amounts of care-related information are being stored electronically. In hospitals clinicians continuously document treatment and care given to patients in electronic health record (EHR) systems. Much of the information being documented is in the form of clinical notes, or narratives, containing primarily unstructured free-text information. For each care episode, clinical notes are written on a regular basis, ending with a discharge summary that basically summarizes the care episode. Although EHR systems are helpful for storing and managing such information, there is an unrealized potential in utilizing this information for smarter care assistance, as well as for secondary purposes such as research and education. Advances in clinical language processing are enabling computers to assist clinicians in their interaction with the free-text information documented in EHR systems. This includes assisting in tasks like query-based search, terminology development, knowledge extraction, translation, and summarization. This thesis explores various computerized approaches and methods aimed at enabling automated semantic textual similarity assessment and information extraction based on the free-text information in EHR systems. The focus is placed on the task of (semi-)automated summarization of the clinical notes written during individual care episodes. The overall theme of the presented work is to utilize resource-light approaches and methods, circumventing the need to manually develop knowledge resources or training data. Thus, to enable computational semantic textual similarity assessment, word distribution statistics are derived from large training corpora of clinical free text and stored as vector-based representations referred to as distributional semantic models. Also resource-light methods are explored in the task of performing automatic summarization of clinical freetext information, relying on semantic textual similarity assessment. Novel and experimental methods are presented and evaluated that focus on: a) distributional semantic models trained in an unsupervised manner from statistical information derived from large unannotated clinical free-text corpora; b) representing and computing semantic similarities between linguistic items of different granularity, primarily words, sentences and clinical notes; and c) summarizing clinical free-text information from individual care episodes. Results are evaluated against gold standards that reflect human judgements. The results indicate that the use of distributional semantics is promising as a resource-light approach to automated capturing of semantic textual similarity relations from unannotated clinical text corpora. Here it is important that the semantics correlate with the clinical terminology, and with various semantic similarity assessment tasks. Improvements over classical approaches are achieved when the underlying vector-based representations allow for a broader range of semantic features to be captured and represented. These are either distributed over multiple semantic models trained with different features and training corpora, or use models that store multiple sense-vectors per word. Further, the use of structured meta-level information accompanying care episodes is explored as training features for distributional semantic models, with the aim of capturing semantic relations suitable for care episode-level information retrieval. Results indicate that such models performs well in clinical information retrieval. It is shown that a method called Random Indexing can be modified to construct distributional semantic models that capture multiple sense-vectors for each word in the training corpus. This is done in a way that retains the original training properties of the Random Indexing method, by being incremental, scalable and distributional. Distributional semantic models trained with a framework called Word2vec, which relies on the use of neural networks, outperform those trained using the classic Random Indexing method in several semantic similarity assessment tasks, when training is done using comparable parameters and the same training corpora. Finally, several statistical features in clinical text are explored in terms of their ability to indicate sentence significance in a text summary generated from the clinical notes. This includes the use of distributional semantics to enable case-based similarity assessment, where cases are other care episodes and their “solutions”, i.e., discharge summaries. A type of manual evaluation is performed, where human experts rates the different aspects of the summaries using a evaluation scheme/tool. In addition, the original clinician-written discharge summaries are explored as gold standard for the purpose of automated evaluation. Evaluation shows a high correlation between manual and automated evaluation, suggesting that such a gold standard can function as a proxy for human evaluations. --- This thesis has been published jointly with Norwegian University of Science and Technology, Norway and University of Turku, Finland.This thesis has beenpublished jointly with Norwegian University of Science and Technology, Norway.Siirretty Doriast

The Word-Space Model: using distributional analysis to represent syntagmatic and paradigmatic relations between words in high-dimensional vector spaces

The word-space model is a computational model of word meaning that utilizes the distributional patterns of words collected over large text data to represent semantic similarity between words in terms of spatial proximity. The model has been used for over a decade, and has demonstrated its mettle in numerous experiments and applications. It is now on the verge of moving from research environments to practical deployment in commercial systems. Although extensively used and intensively investigated, our theoretical understanding of the word-space model remains unclear. The question this dissertation attempts to answer is: what kind of semantic information does the word-space model acquire and represent? The answer is derived through an identification and discussion of the three main theoretical cornerstones of the word-space model: the geometric metaphor of meaning, the distributional methodology, and the structuralist meaning theory. It is argued that the word-space model acquires and represents two different types of relations between words – syntagmatic and paradigmatic relations – depending on how the distributional patterns of words are used to accumulate word spaces. The difference between syntagmatic and paradigmatic word spaces is empirically demonstrated in a number of experiments, including comparisons with thesaurus entries, association norms, a synonym test, a list of antonym pairs, and a record of part-of-speech assignments.För att köpa boken skicka en beställning till [email protected]/ To order the book send an e-mail to [email protected]

Constructing a biodiversity terminological inventory.

The increasing growth of literature in biodiversity presents challenges to users who need to discover pertinent information in an efficient and timely manner. In response, text mining techniques offer solutions by facilitating the automated discovery of knowledge from large textual data. An important step in text mining is the recognition of concepts via their linguistic realisation, i.e., terms. However, a given concept may be referred to in text using various synonyms or term variants, making search systems likely to overlook documents mentioning less known variants, which are albeit relevant to a query term. Domain-specific terminological resources, which include term variants, synonyms and related terms, are thus important in supporting semantic search over large textual archives. This article describes the use of text mining methods for the automatic construction of a large-scale biodiversity term inventory. The inventory consists of names of species, amongst which naming variations are prevalent. We apply a number of distributional semantic techniques on all of the titles in the Biodiversity Heritage Library, to compute semantic similarity between species names and support the automated construction of the resource. With the construction of our biodiversity term inventory, we demonstrate that distributional semantic models are able to identify semantically similar names that are not yet recorded in existing taxonomies. Such methods can thus be used to update existing taxonomies semi-automatically by deriving semantically related taxonomic names from a text corpus and allowing expert curators to validate them. We also evaluate our inventory as a means to improve search by facilitating automatic query expansion. Specifically, we developed a visual search interface that suggests semantically related species names, which are available in our inventory but not always in other repositories, to incorporate into the search query. An assessment of the interface by domain experts reveals that our query expansion based on related names is useful for increasing the number of relevant documents retrieved. Its exploitation can benefit both users and developers of search engines and text mining applications

A Survey of Paraphrasing and Textual Entailment Methods

Paraphrasing methods recognize, generate, or extract phrases, sentences, or longer natural language expressions that convey almost the same information. Textual entailment methods, on the other hand, recognize, generate, or extract pairs of natural language expressions, such that a human who reads (and trusts) the first element of a pair would most likely infer that the other element is also true. Paraphrasing can be seen as bidirectional textual entailment and methods from the two areas are often similar. Both kinds of methods are useful, at least in principle, in a wide range of natural language processing applications, including question answering, summarization, text generation, and machine translation. We summarize key ideas from the two areas by considering in turn recognition, generation, and extraction methods, also pointing to prominent articles and resources.Comment: Technical Report, Natural Language Processing Group, Department of Informatics, Athens University of Economics and Business, Greece, 201

Cross-language Ontology Learning: Incorporating and Exploiting Cross-language Data in the Ontology Learning Process

Hans Hjelm. Cross-language Ontology Learning: Incorporating and Exploiting Cross-language Data in the Ontology Learning Process. NEALT Monograph Series, Vol. 1 (2009), 159 pages. © 2009 Hans Hjelm. Published by Northern European Association for Language Technology (NEALT) http://omilia.uio.no/nealt . Electronically published at Tartu University Library (Estonia) http://hdl.handle.net/10062/10126

Applying Wikipedia to Interactive Information Retrieval

There are many opportunities to improve the interactivity of information retrieval systems beyond the ubiquitous search box. One idea is to use knowledge bases—e.g. controlled vocabularies, classification schemes, thesauri and ontologies—to organize, describe and navigate the information space. These resources are popular in libraries and specialist collections, but have proven too expensive and narrow to be applied to everyday webscale search. Wikipedia has the potential to bring structured knowledge into more widespread use. This online, collaboratively generated encyclopaedia is one of the largest and most consulted reference works in existence. It is broader, deeper and more agile than the knowledge bases put forward to assist retrieval in the past. Rendering this resource machine-readable is a challenging task that has captured the interest of many researchers. Many see it as a key step required to break the knowledge acquisition bottleneck that crippled previous efforts. This thesis claims that the roadblock can be sidestepped: Wikipedia can be applied effectively to open-domain information retrieval with minimal natural language processing or information extraction. The key is to focus on gathering and applying human-readable rather than machine-readable knowledge. To demonstrate this claim, the thesis tackles three separate problems: extracting knowledge from Wikipedia; connecting it to textual documents; and applying it to the retrieval process. First, we demonstrate that a large thesaurus-like structure can be obtained directly from Wikipedia, and that accurate measures of semantic relatedness can be efficiently mined from it. Second, we show that Wikipedia provides the necessary features and training data for existing data mining techniques to accurately detect and disambiguate topics when they are mentioned in plain text. Third, we provide two systems and user studies that demonstrate the utility of the Wikipedia-derived knowledge base for interactive information retrieval

Graph-based methods for large-scale multilingual knowledge integration

Given that much of our knowledge is expressed in textual form, information systems are increasingly dependent on knowledge about words and the entities they represent. This thesis investigates novel methods for automatically building large repositories of knowledge that capture semantic relationships between words, names, and entities, in many different languages. Three major contributions are made, each involving graph algorithms and statistical techniques that combine evidence from multiple sources of information. The lexical integration method involves learning models that disambiguate word meanings based on contextual information in a graph, thereby providing a means to connect words to the entities that they denote. The entity integration method combines semantic items from different sources into a single unified registry of entities by reconciling equivalence and distinctness information and solving a combinatorial optimization problem. Finally, the taxonomic integration method adds a comprehensive and coherent taxonomic hierarchy on top of this registry, capturing how different entities relate to each other. Together, these methods can be used to produce a large-scale multilingual knowledge base semantically describing over 5 million entities and over 16 million natural language words and names in more than 200 different languages.Da ein großer Teil unseres Wissens in textueller Form vorliegt, sind Informationssysteme in zunehmendem Maße auf Wissen über Wörter und den von ihnen repräsentierten Entitäten angewiesen. Gegenstand dieser Arbeit sind neue Methoden zur automatischen Erstellung großer multilingualer Wissensbanken, welche semantische Beziehungen zwischen Wörtern bzw. Namen und Konzepten bzw. Entitäten formal erfassen. In drei Hauptbeiträgen werden jeweils graphtheoretische bzw. statistische Verfahren zur Verknüpfung von Indizien aus mehreren Wissensquellen vorgestellt. Bei der lexikalischen Integration werden statistische Modelle zur Disambiguierung gebildet. Die Entitäten-Integration fasst semantische Einheiten unter Auflösung von Konflikten zwischen Äquivalenz- und Verschiedenheitsinformationen zusammen. Diese werden schließlich bei der taxonomischen Integration durch eine umfassende taxonomische Hierarchie ergänzt. Zusammen können diese Methoden zur Induzierung einer großen multilingualen Wissensbank eingesetzt werden, welche über 5 Millionen Entitäten und über 16 Millionen Wörter und Namen in mehr als 200 Sprachen semantisch beschreibt