Semi-automated Ontology Generation for Biocuration and Semantic Search

Background: In the life sciences, the amount of literature and experimental data grows at a tremendous rate. In order to effectively access and integrate these data, biomedical ontologies – controlled, hierarchical vocabularies – are being developed. Creating and maintaining such ontologies is a difficult, labour-intensive, manual process. Many computational methods which can support ontology construction have been proposed in the past. However, good, validated systems are largely missing. Motivation: The biocuration community plays a central role in the development of ontologies. Any method that can support their efforts has the potential to have a huge impact in the life sciences. Recently, a number of semantic search engines were created that make use of biomedical ontologies for document retrieval. To transfer the technology to other knowledge domains, suitable ontologies need to be created. One area where ontologies may prove particularly useful is the search for alternative methods to animal testing, an area where comprehensive search is of special interest to determine the availability or unavailability of alternative methods. Results: The Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG) developed in this thesis is a system which supports the creation and extension of ontologies by semi-automatically generating terms, definitions, and parent-child relations from text in PubMed, the web, and PDF repositories. The system is seamlessly integrated into OBO-Edit and Protégé, two widely used ontology editors in the life sciences. DOG4DAG generates terms by identifying statistically significant noun-phrases in text. For definitions and parent-child relations it employs pattern-based web searches. Each generation step has been systematically evaluated using manually validated benchmarks. The term generation leads to high quality terms also found in manually created ontologies. Definitions can be retrieved for up to 78% of terms, child ancestor relations for up to 54%. No other validated system exists that achieves comparable results. To improve the search for information on alternative methods to animal testing an ontology has been developed that contains 17,151 terms of which 10% were newly created and 90% were re-used from existing resources. This ontology is the core of Go3R, the first semantic search engine in this field. When a user performs a search query with Go3R, the search engine expands this request using the structure and terminology of the ontology. The machine classification employed in Go3R is capable of distinguishing documents related to alternative methods from those which are not with an F-measure of 90% on a manual benchmark. Approximately 200,000 of the 19 million documents listed in PubMed were identified as relevant, either because a specific term was contained or due to the automatic classification. The Go3R search engine is available on-line under www.Go3R.org

Innovations for Requirements Analysis, From Stakeholders' Needs to Formal Designs

14th MontereyWorkshop 2007 Monterey, CA, USA, September 10-13, 2007 Revised Selected PapersWe are pleased to present the proceedings of the 14thMontereyWorkshop, which took place September 10–13, 2007 in Monterey, CA, USA. In this preface, we give the reader an overview of what took place at the workshop and introduce the contributions in this Lecture Notes in Computer Science volume. A complete introduction to the theme of the workshop, as well as to the history of the Monterey Workshop series, can be found in Luqi and Kordon’s “Advances in Requirements Engineering: Bridging the Gap between Stakeholders’ Needs and Formal Designs” in this volume. This paper also contains the case study that many participants used as a problem to frame their analyses, and a summary of the workshop’s results

Embedding Predications

Written communication is rarely a sequence of simple assertions. More often, in addition to simple assertions, authors express subjectivity, such as beliefs, speculations, opinions, intentions, and desires. Furthermore, they link statements of various kinds to form a coherent discourse that reflects their pragmatic intent. In computational semantics, extraction of simple assertions (propositional meaning) has attracted the greatest attention, while research that focuses on extra-propositional aspects of meaning has remained sparse overall and has been largely limited to narrowly defined categories, such as hedging or sentiment analysis, treated in isolation. In this thesis, we contribute to the understanding of extra-propositional meaning in natural language understanding, by providing a comprehensive account of the semantic phenomena that occur beyond simple assertions and examining how a coherent discourse is formed from lower level semantic elements. Our approach is linguistically based, and we propose a general, unified treatment of the semantic phenomena involved, within a computationally viable framework. We identify semantic embedding as the core notion involved in expressing extra-propositional meaning. The embedding framework is based on the structural distinction between embedding and atomic predications, the former corresponding to extra-propositional aspects of meaning. It incorporates the notions of predication source, modality scale, and scope. We develop an embedding categorization scheme and a dictionary based on it, which provide the necessary means to interpret extra-propositional meaning with a compositional semantic interpretation methodology. Our syntax-driven methodology exploits syntactic dependencies to construct a semantic embedding graph of a document. Traversing the graph in a bottom-up manner guided by compositional operations, we construct predications corresponding to extra-propositional semantic content, which form the basis for addressing practical tasks. We focus on text from two distinct domains: news articles from the Wall Street Journal, and scientific articles focusing on molecular biology. Adopting a task-based evaluation strategy, we consider the easy adaptability of the core framework to practical tasks that involve some extra-propositional aspect as a measure of its success. The computational tasks we consider include hedge/uncertainty detection, scope resolution, negation detection, biological event extraction, and attribution resolution. Our competitive results in these tasks demonstrate the viability of our proposal

Proceedings

Proceedings of the Ninth International Workshop on Treebanks and Linguistic Theories. Editors: Markus Dickinson, Kaili Müürisep and Marco Passarotti. NEALT Proceedings Series, Vol. 9 (2010), 268 pages. © 2010 The editors and contributors. 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/10062/15891

A Study on Learning Representations for Relations Between Words

Reasoning about relations between words or entities plays an important role in human cognition. It is thus essential for a computational system which processes human languages to be able to understand the semantics of relations to simulate human intelligence. Automatic relation learning provides valuable information for many natural language processing tasks including ontology creation, question answering and machine translation, to name a few. This need brings us to the topic of this thesis where the main goal is to explore multiple resources and methodologies to effectively represent relations between words. How to effectively represent semantic relations between words remains a problem that is underexplored. A line of research makes use of relational patterns, which are the linguistic contexts in which two words co-occur in a corpus to infer a relation between them (e.g., X leads to Y). This approach suffers from data sparseness because not every related word-pair co-occurs even in a large corpus. In contrast, prior work on learning word embeddings have found that certain relations between words could be captured by applying linear arithmetic operators on the corresponding pre-trained word embeddings. Specifically, it has been shown that the vector offset (expressed as PairDiff) from one word to the other in a pair encodes the relation that holds between them, if any. Such a compositional method addresses the data sparseness by inferring a relation from constituent words in a word-pair and obviates the need of relational patterns. This thesis investigates the best way to compose word embeddings to represent relational instances. A systematic comparison is carried out for unsupervised operators, which in general reveals the superiority of the PairDiff operator on multiple word embedding models and benchmark datasets. Despite the empirical success, no theoretical analysis has been conducted so far explaining why and under what conditions PairDiff is optimal. To this end, a theoretical analysis is conducted for the generalised bilinear operators that can be used to measure the relational distance between two word-pairs. The main conclusion is that, under certain assumptions, the bilinear operator can be simplified to a linear form, where the widely used PairDiff operator is a special case. Multiple recent works raised concerns about existing unsupervised operators for inferring relations from pre-trained word embeddings. Thus, the question of whether it is possible to learn better parametrised relational compositional operators is addressed in this thesis. A supervised relation representation operator is proposed using a non-linear neural network that performs relation prediction. The evaluation on two benchmark datasets reveals that the penultimate layer of the trained neural network-based relational predictor acts as a good representation for the relations between words. Because we believe that both relational patterns and word embeddings provide complementary information to learn relations, a self-supervised context-guided relation embedding method that is trained on the two sources of information has been proposed. Experimentally, incorporating relational contexts shows improvement in the performance of a compositional operator for representing unseen word-pairs. Besides unstructured text corpora, knowledge graphs provide another source for relational facts in the form of nodes (i.e., entities) connected by edges (i.e., relations). Knowledge graphs are employed widely in natural language processing applications such as question answering and dialogue systems. Embedding entities and relations in a graph have shown impressive results for inferring previously unseen relations between entities. This thesis contributes to developing a theoretical model to infer a relationship between the connections in the graph and the embeddings of entities and relations. Learning graph embeddings that satisfy the proven theorem demonstrates efficient performance compared to existing heuristically derived graph embedding methods. As graph embedding methods generate representations for only existing relation types, a relation composition task is proposed in the thesis to tackle this limitation