Temporal relation discovery between events and temporal expressions identified in clinical narrative

AbstractThe automatic detection of temporal relations between events in electronic medical records has the potential to greatly augment the value of such records for understanding disease progression and patients’ responses to treatments. We present a three-step methodology for labeling temporal relations using machine learning and deterministic rules over an annotated corpus provided by the 2012 i2b2 Shared Challenge. We first create an expanded training network of relations by computing the transitive closure over the annotated data; we then apply hand-written rules and machine learning with a feature set that casts a wide net across potentially relevant lexical and syntactic information; finally, we employ a voting mechanism to resolve global contradictions between the local predictions made by the learned classifier. Results over the testing data illustrate the contributions of initial prediction and conflict resolution

Extracting Temporal and Causal Relations between Events

Structured information resulting from temporal information processing is crucial for a variety of natural language processing tasks, for instance to generate timeline summarization of events from news documents, or to answer temporal/causal-related questions about some events. In this thesis we present a framework for an integrated temporal and causal relation extraction system. We first develop a robust extraction component for each type of relations, i.e. temporal order and causality. We then combine the two extraction components into an integrated relation extraction system, CATENA---CAusal and Temporal relation Extraction from NAtural language texts---, by utilizing the presumption about event precedence in causality, that causing events must happened BEFORE resulting events. Several resources and techniques to improve our relation extraction systems are also discussed, including word embeddings and training data expansion. Finally, we report our adaptation efforts of temporal information processing for languages other than English, namely Italian and Indonesian.Comment: PhD Thesi

Eesti keele üldvaldkonna tekstide laia kattuvusega automaatne sündmusanalüüs

Seoses tekstide suuremahulise digitaliseerimisega ning digitaalse tekstiloome järjest laiema levikuga on tohutul hulgal loomuliku keele tekste muutunud ja muutumas masinloetavaks. Masinloetavus omab potentsiaali muuta tekstimassiivid inimeste jaoks lihtsamini hallatavaks, nt lubada rakendusi nagu automaatne sisukokkuvõtete tegemine ja tekstide põhjal küsimustele vastamine, ent paraku ei ulatu praegused automaatanalüüsi võimalused tekstide sisu tegeliku mõistmiseni. Oletatakse, tekstide sisu mõistvale automaatanalüüsile viib meid lähemale sündmusanalüüs – kuna paljud tekstid on narratiivse ülesehitusega, tõlgendatavad kui „sündmuste kirjeldused”, peaks tekstidest sündmuste eraldamine ja formaalsel kujul esitamine pakkuma alust mitmete „teksti mõistmist” nõudvate keeletehnoloogia rakenduste loomisel. Käesolevas väitekirjas uuritakse, kuivõrd saab eestikeelsete tekstide sündmusanalüüsi käsitleda kui avatud sündmuste hulka ja üldvaldkonna tekste hõlmavat automaatse lingvistilise analüüsi ülesannet. Probleemile lähenetakse eesti keele automaatanalüüsi kontekstis uudsest, sündmuste ajasemantikale keskenduvast perspektiivist. Töös kohandatakse eesti keelele TimeML märgendusraamistik ja luuakse raamistikule toetuv automaatne ajaväljendite tuvastaja ning ajasemantilise märgendusega (sündmusviidete, ajaväljendite ning ajaseoste märgendusega) tekstikorpus; analüüsitakse korpuse põhjal inimmärgendajate kooskõla sündmusviidete ja ajaseoste määramisel ning lõpuks uuritakse võimalusi ajasemantika-keskse sündmusanalüüsi laiendamiseks geneeriliseks sündmusanalüüsiks sündmust väljendavate keelendite samaviitelisuse lahendamise näitel. Töö pakub suuniseid tekstide ajasemantika ja sündmusstruktuuri märgenduse edasiarendamiseks tulevikus ning töös loodud keeleressurssid võimaldavad nii konkreetsete lõpp-rakenduste (nt automaatne ajaküsimustele vastamine) katsetamist kui ka automaatsete märgendustööriistade edasiarendamist.  Due to massive scale digitalisation processes and a switch from traditional means of written communication to digital written communication, vast amounts of human language texts are becoming machine-readable. Machine-readability holds a potential for easing human effort on searching and organising large text collections, allowing applications such as automatic text summarisation and question answering. However, current tools for automatic text analysis do not reach for text understanding required for making these applications generic. It is hypothesised that automatic analysis of events in texts leads us closer to the goal, as many texts can be interpreted as stories/narratives that are decomposable into events. This thesis explores event analysis as broad-coverage and general domain automatic language analysis problem in Estonian, and provides an investigation starting from time-oriented event analysis and tending towards generic event analysis. We adapt TimeML framework to Estonian, and create an automatic temporal expression tagger and a news corpus manually annotated for temporal semantics (event mentions, temporal expressions, and temporal relations) for the language; we analyse consistency of human annotation of event mentions and temporal relations, and, finally, provide a preliminary study on event coreference resolution in Estonian news. The current work also makes suggestions on how future research can improve Estonian event and temporal semantic annotation, and the language resources developed in this work will allow future experimentation with end-user applications (such as automatic answering of temporal questions) as well as provide a basis for developing automatic semantic analysis tools

Processing temporal information in unstructured documents

Tese de doutoramento, Informática (Ciência da Computação), Universidade de Lisboa, Faculdade de Ciências, 2013Temporal information processing has received substantial attention in the last few years, due to the appearance of evaluation challenges focused on the extraction of temporal information from texts written in natural language. This research area belongs to the broader field of information extraction, which aims to automatically find specific pieces of information in texts, producing structured representations of that information, which can then be easily used by other computer applications. It has the potential to be useful in several applications that deal with natural language, given that many languages, among which we find Portuguese, extensively refer to time. Despite that, temporal processing is still incipient for many language, Portuguese being one of them. The present dissertation has various goals. On one hand, it addresses this current gap, by developing and making available resources that support the development of tools for this task, employing this language, and also by developing precisely this kind of tools. On the other hand, its purpose is also to report on important results of the research on this area of temporal processing. This work shows how temporal processing requires and benefits from modeling different kinds of knowledge: grammatical knowledge, logical knowledge, knowledge about the world, etc. Additionally, both machine learning methods and rule-based approaches are explored and used in the development of hybrid systems that are capable of taking advantage of the strengths of each of these two types of approach.O processamento de informação temporal tem recebido bastante atenção nos últimos anos, devido ao surgimento de desafios de avaliação focados na extração de informação temporal de textos escritos em linguagem natural. Esta área de investigação enquadra-se no campo mais lato da extração de informação, que visa encontrar automaticamente informação específica presente em textos, produzindo representações estruturadas da mesma, que podem depois ser facilmente utilizadas por outras aplicações computacionais. Tem o potencial de ser útil em diversas aplicações que lidam com linguagem natural, dado o caráter quase ubíquo da referência ao tempo cronólogico em muitas línguas, entre as quais o Português. Apesar de tudo, o processamento temporal encontra-se ainda incipiente para bastantes línguas, sendo o Português uma delas. A presente dissertação tem vários objetivos. Por um lado vem colmatar esta lacuna existente, desenvolvendo e disponibilizando recursos que suportam o desenvolvimento de ferramentas para esta tarefa, utilizando esta língua, e desenvolvendo também precisamente este tipo de ferramentas. Por outro serve também para relatar resultados importantes da pesquisa nesta área do processamento temporal. Neste trabalho, mostra- -se como o processamento temporal requer e beneficia da modelação de conhecimento de diversos níveis: gramatical, lógico, acerca do mundo, etc. Adicionalmente, são explorados tanto métodos de aprendizagem automática como abordagens baseadas em regras, desenvolvendo-se sistemas híbridos capazes de tirar partido das vantagens de cada um destes dois tipos de abordagem.Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/40140/2007

Novel Event Detection and Classification for Historical Texts

Event processing is an active area of research in the Natural Language Processing community but resources and automatic systems developed so far have mainly addressed contemporary texts. However, the recognition and elaboration of events is a crucial step when dealing with historical texts particularly in the current era of massive digitization of historical sources: research in this domain can lead to the development of methodologies and tools that can assist historians in enhancing their work, while having an impact also on the field of Natural Language Processing. Our work aims at shedding light on the complex concept of events when dealing with historical texts. More specifically, we introduce new annotation guidelines for event mentions and types, categorised into 22 classes. Then, we annotate a historical corpus accordingly, and compare two approaches for automatic event detection and classification following this novel scheme. We believe that this work can foster research in a field of inquiry so far underestimated in the area of Temporal Information Processing. To this end, we release new annotation guidelines, a corpus and new models for automatic annotation

Improving Syntactic Parsing of Clinical Text Using Domain Knowledge

Syntactic parsing is one of the fundamental tasks of Natural Language Processing (NLP). However, few studies have explored syntactic parsing in the medical domain. This dissertation systematically investigated different methods to improve the performance of syntactic parsing of clinical text, including (1) Constructing two clinical treebanks of discharge summaries and progress notes by developing annotation guidelines that handle missing elements in clinical sentences; (2) Retraining four state-of-the-art parsers, including the Stanford parser, Berkeley parser, Charniak parser, and Bikel parser, using clinical treebanks, and comparing their performance to identify better parsing approaches; and (3) Developing new methods to reduce syntactic ambiguity caused by Prepositional Phrase (PP) attachment and coordination using semantic information. Our evaluation showed that clinical treebanks greatly improved the performance of existing parsers. The Berkeley parser achieved the best F-1 score of 86.39% on the MiPACQ treebank. For PP attachment, our proposed methods improved the accuracies of PP attachment by 2.35% on the MiPACQ corpus and 1.77% on the I2b2 corpus. For coordination, our method achieved a precision of 94.9% and a precision of 90.3% for the MiPACQ and i2b2 corpus, respectively. To further demonstrate the effectiveness of the improved parsing approaches, we applied outputs of our parsers to two external NLP tasks: semantic role labeling and temporal relation extraction. The experimental results showed that performance of both tasks’ was improved by using the parse tree information from our optimized parsers, with an improvement of 3.26% in F-measure for semantic role labelling and an improvement of 1.5% in F-measure for temporal relation extraction

Content Selection for Timeline Generation from Single History Articles

This thesis investigates the problem of content selection for timeline generation from single history articles. While the task of timeline generation has been addressed before, most previous approaches assume the existence of a large corpus of history articles from the same era. They exploit the fact that salient information is likely to be mentioned multiple times in such corpora. However, large resources of this kind are only available for historical events that happened in the most recent decades. In this thesis, I present approaches which can be used to create history timelines for any historical period, even for eras such as the Middle Ages, for which no large corpora of supplementary text exist. The thesis first presents a system that selects relevant historical figures in a given article, a task which is substantially easier than full timeline generation. I show that a supervised approach which uses linguistic, structural and semantic features outperforms a competitive baseline on this task. Based on the observations made in this initial study, I then develop approaches for timeline generation. I find that an unsupervised approach that takes into account the article's subject area outperforms several supervised and unsupervised baselines. A main focus of this thesis is the development of evaluation methodologies and resources, as no suitable corpora existed when work began. For the initial experiment on important historical figures, I construct a corpus of existing timelines and textual articles, and devise a method for evaluating algorithms based on this resource. For timeline generation, I present a comprehensive evaluation methodology which is based on the interpretation of the task as a special form of single-document summarisation. This methodology scores algorithms based on meaning units rather than surface similarity. Unlike previous semantic-units-based evaluation methods for summarisation, my evaluation method does not require any manual annotation of system timelines. Once an evaluation resource has been created, which involves only annotation of the input texts, new timeline generation algorithms can be tested at no cost. This crucial advantage should make my new evaluation methodology attractive for the evaluation of general single-document summaries beyond timelines. I also present an evaluation resource which is based on this methodology. It was constructed using gold-standard timelines elicited from 30 human timeline writers, and has been made publicly available. This thesis concentrates on the content selection stage of timeline generation, and leaves the surface realisation step for future work. However, my evaluation methodology is designed in such a way that it can in principle also quantify the degree to which surface realisation is successful