Efficient path-based computations on pedigree graphs with compact encodings

A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increasingly important. In large pedigree graphs, path-based methods for efficiently computing genealogical measurements, such as inbreeding and kinship coefficients of individuals, depend on efficient identification and processing of paths. In this paper, we propose a new compact path encoding scheme on large pedigrees, accompanied by an efficient algorithm for identifying paths. We demonstrate the utilization of our proposed method by applying it to the inbreeding coefficient computation. We present time and space complexity analysis, and also manifest the efficiency of our method for evaluating inbreeding coefficients as compared to previous methods by experimental results using pedigree graphs with real and synthetic data. Both theoretical and experimental results demonstrate that our method is more scalable and efficient than previous methods in terms of time and space requirements

Knowledge extraction from fictional texts

Knowledge extraction from text is a key task in natural language processing, which involves many sub-tasks, such as taxonomy induction, named entity recognition and typing, relation extraction, knowledge canonicalization and so on. By constructing structured knowledge from natural language text, knowledge extraction becomes a key asset for search engines, question answering and other downstream applications. However, current knowledge extraction methods mostly focus on prominent real-world entities with Wikipedia and mainstream news articles as sources. The constructed knowledge bases, therefore, lack information about long-tail domains, with fiction and fantasy as archetypes. Fiction and fantasy are core parts of our human culture, spanning from literature to movies, TV series, comics and video games. With thousands of fictional universes which have been created, knowledge from fictional domains are subject of search-engine queries - by fans as well as cultural analysts. Unlike the real-world domain, knowledge extraction on such specific domains like fiction and fantasy has to tackle several key challenges: - Training data: Sources for fictional domains mostly come from books and fan-built content, which is sparse and noisy, and contains difficult structures of texts, such as dialogues and quotes. Training data for key tasks such as taxonomy induction, named entity typing or relation extraction are also not available. - Domain characteristics and diversity: Fictional universes can be highly sophisticated, containing entities, social structures and sometimes languages that are completely different from the real world. State-of-the-art methods for knowledge extraction make assumptions on entity-class, subclass and entity-entity relations that are often invalid for fictional domains. With different genres of fictional domains, another requirement is to transfer models across domains. - Long fictional texts: While state-of-the-art models have limitations on the input sequence length, it is essential to develop methods that are able to deal with very long texts (e.g. entire books), to capture multiple contexts and leverage widely spread cues. This dissertation addresses the above challenges, by developing new methodologies that advance the state of the art on knowledge extraction in fictional domains. - The first contribution is a method, called TiFi, for constructing type systems (taxonomy induction) for fictional domains. By tapping noisy fan-built content from online communities such as Wikia, TiFi induces taxonomies through three main steps: category cleaning, edge cleaning and top-level construction. Exploiting a variety of features from the original input, TiFi is able to construct taxonomies for a diverse range of fictional domains with high precision. - The second contribution is a comprehensive approach, called ENTYFI, for named entity recognition and typing in long fictional texts. Built on 205 automatically induced high-quality type systems for popular fictional domains, ENTYFI exploits the overlap and reuse of these fictional domains on unseen texts. By combining different typing modules with a consolidation stage, ENTYFI is able to do fine-grained entity typing in long fictional texts with high precision and recall. - The third contribution is an end-to-end system, called KnowFi, for extracting relations between entities in very long texts such as entire books. KnowFi leverages background knowledge from 142 popular fictional domains to identify interesting relations and to collect distant training samples. KnowFi devises a similarity-based ranking technique to reduce false positives in training samples and to select potential text passages that contain seed pairs of entities. By training a hierarchical neural network for all relations, KnowFi is able to infer relations between entity pairs across long fictional texts, and achieves gains over the best prior methods for relation extraction.Wissensextraktion ist ein Schlüsselaufgabe bei der Verarbeitung natürlicher Sprache, und umfasst viele Unteraufgaben, wie Taxonomiekonstruktion, Entitätserkennung und Typisierung, Relationsextraktion, Wissenskanonikalisierung, etc. Durch den Aufbau von strukturiertem Wissen (z.B. Wissensdatenbanken) aus Texten wird die Wissensextraktion zu einem Schlüsselfaktor für Suchmaschinen, Question Answering und andere Anwendungen. Aktuelle Methoden zur Wissensextraktion konzentrieren sich jedoch hauptsächlich auf den Bereich der realen Welt, wobei Wikipedia und Mainstream- Nachrichtenartikel die Hauptquellen sind. Fiktion und Fantasy sind Kernbestandteile unserer menschlichen Kultur, die sich von Literatur bis zu Filmen, Fernsehserien, Comics und Videospielen erstreckt. Für Tausende von fiktiven Universen wird Wissen aus Suchmaschinen abgefragt – von Fans ebenso wie von Kulturwissenschaftler. Im Gegensatz zur realen Welt muss die Wissensextraktion in solchen spezifischen Domänen wie Belletristik und Fantasy mehrere zentrale Herausforderungen bewältigen: • Trainingsdaten. Quellen für fiktive Domänen stammen hauptsächlich aus Büchern und von Fans erstellten Inhalten, die spärlich und fehlerbehaftet sind und schwierige Textstrukturen wie Dialoge und Zitate enthalten. Trainingsdaten für Schlüsselaufgaben wie Taxonomie-Induktion, Named Entity Typing oder Relation Extraction sind ebenfalls nicht verfügbar. • Domain-Eigenschaften und Diversität. Fiktive Universen können sehr anspruchsvoll sein und Entitäten, soziale Strukturen und manchmal auch Sprachen enthalten, die sich von der realen Welt völlig unterscheiden. Moderne Methoden zur Wissensextraktion machen Annahmen über Entity-Class-, Entity-Subclass- und Entity- Entity-Relationen, die für fiktive Domänen oft ungültig sind. Bei verschiedenen Genres fiktiver Domänen müssen Modelle auch über fiktive Domänen hinweg transferierbar sein. • Lange fiktive Texte. Während moderne Modelle Einschränkungen hinsichtlich der Länge der Eingabesequenz haben, ist es wichtig, Methoden zu entwickeln, die in der Lage sind, mit sehr langen Texten (z.B. ganzen Büchern) umzugehen, und mehrere Kontexte und verteilte Hinweise zu erfassen. Diese Dissertation befasst sich mit den oben genannten Herausforderungen, und entwickelt Methoden, die den Stand der Kunst zur Wissensextraktion in fiktionalen Domänen voranbringen. • Der erste Beitrag ist eine Methode, genannt TiFi, zur Konstruktion von Typsystemen (Taxonomie induktion) für fiktive Domänen. Aus von Fans erstellten Inhalten in Online-Communities wie Wikia induziert TiFi Taxonomien in drei wesentlichen Schritten: Kategoriereinigung, Kantenreinigung und Top-Level- Konstruktion. TiFi nutzt eine Vielzahl von Informationen aus den ursprünglichen Quellen und ist in der Lage, Taxonomien für eine Vielzahl von fiktiven Domänen mit hoher Präzision zu erstellen. • Der zweite Beitrag ist ein umfassender Ansatz, genannt ENTYFI, zur Erkennung von Entitäten, und deren Typen, in langen fiktiven Texten. Aufbauend auf 205 automatisch induzierten hochwertigen Typsystemen für populäre fiktive Domänen nutzt ENTYFI die Überlappung und Wiederverwendung dieser fiktiven Domänen zur Bearbeitung neuer Texte. Durch die Zusammenstellung verschiedener Typisierungsmodule mit einer Konsolidierungsphase ist ENTYFI in der Lage, in langen fiktionalen Texten eine feinkörnige Entitätstypisierung mit hoher Präzision und Abdeckung durchzuführen. • Der dritte Beitrag ist ein End-to-End-System, genannt KnowFi, um Relationen zwischen Entitäten aus sehr langen Texten wie ganzen Büchern zu extrahieren. KnowFi nutzt Hintergrundwissen aus 142 beliebten fiktiven Domänen, um interessante Beziehungen zu identifizieren und Trainingsdaten zu sammeln. KnowFi umfasst eine ähnlichkeitsbasierte Ranking-Technik, um falsch positive Einträge in Trainingsdaten zu reduzieren und potenzielle Textpassagen auszuwählen, die Paare von Kandidats-Entitäten enthalten. Durch das Trainieren eines hierarchischen neuronalen Netzwerkes für alle Relationen ist KnowFi in der Lage, Relationen zwischen Entitätspaaren aus langen fiktiven Texten abzuleiten, und übertrifft die besten früheren Methoden zur Relationsextraktion

Sharing Semantic Resources

The Semantic Web is an extension of the current Web in which information, so far created for human consumption, becomes machine readable, “enabling computers and people to work in cooperation”. To turn into reality this vision several challenges are still open among which the most important is to share meaning formally represented with ontologies or more generally with semantic resources. This Semantic Web long-term goal has many convergences with the activities in the field of Human Language Technology and in particular in the development of Natural Language Processing applications where there is a great need of multilingual lexical resources. For instance, one of the most important lexical resources, WordNet, is also commonly regarded and used as an ontology. Nowadays, another important phenomenon is represented by the explosion of social collaboration, and Wikipedia, the largest encyclopedia in the world, is object of research as an up to date omni comprehensive semantic resource. The main topic of this thesis is the management and exploitation of semantic resources in a collaborative way, trying to use the already available resources as Wikipedia and Wordnet. This work presents a general environment able to turn into reality the vision of shared and distributed semantic resources and describes a distributed three-layer architecture to enable a rapid prototyping of cooperative applications for developing semantic resources

Ontology-based infrastructure for intelligent applications

Ontologies currently are a hot topic in the areas of knowledge management and enterprise application integration. In this thesis, we investigate how ontologies can also be used as an infrastructure for developing applications that intelligently support a user with various tasks. Based on recent developments in the area of the Semantic Web, we provide three major contributions. We introduce inference engines, which allow the execution of business logic that is specified in a declarative way, while putting strong emphasis on scalability and ease of use. Secondly, we suggest various solutions for interfacing applications that are developed under this new paradigm with existing IT infrastructure. This includes the first running solution, to our knowledge, for combining the emerging areas of the Semantic Web Services. Finally, we introduce a set of intelligent applications, which is built on top of onologies and Semantic Web standards, providing a proof of concept that the engineering effort can largely be based on standard components.Ontologien sind derzeit ein viel diskutiertes Thema in Bereichen wie Wissensmanagement oder Enterprise Application Integration. Diese Arbeit stellt dar, wie Ontologien als Infrastruktur zur Entwicklung neuartiger Applikationen verwendet werden können, die den User bei verschiedenen Arbeiten unterstützen. Aufbauend auf den im Rahmen des Semantischen Webs entstandenen Spezifikationen, werden drei wesentliche Beiträge geleistet. Zum einen stellen wir Inferenzmaschinen vor, die das Ausführen von deklarativ spezifizierter Applikationslogik erlauben, wobei besonderes Augenmerk auf die Skalierbarkeit gelegt wird. Zum anderen schlagen wir mehrere Lösungen zum Anschluss solcher Systeme an bestehende IT Infrastruktur vor. Dies beinhaltet den, unseres Wissens nach, ersten lauffähigen Prototyp der die beiden aufstrebenden Felder des Semantischen Webs und Web Services verbindet. Schließlich stellen wir einige intelligente Applikationen vor, die auf Ontologien basieren und somit großteils von Werkzeugen automatisch generiert werden können

Semantic multimedia modelling & interpretation for annotation

The emergence of multimedia enabled devices, particularly the incorporation of cameras in mobile phones, and the accelerated revolutions in the low cost storage devices, boosts the multimedia data production rate drastically. Witnessing such an iniquitousness of digital images and videos, the research community has been projecting the issue of its significant utilization and management. Stored in monumental multimedia corpora, digital data need to be retrieved and organized in an intelligent way, leaning on the rich semantics involved. The utilization of these image and video collections demands proficient image and video annotation and retrieval techniques. Recently, the multimedia research community is progressively veering its emphasis to the personalization of these media. The main impediment in the image and video analysis is the semantic gap, which is the discrepancy among a user’s high-level interpretation of an image and the video and the low level computational interpretation of it. Content-based image and video annotation systems are remarkably susceptible to the semantic gap due to their reliance on low-level visual features for delineating semantically rich image and video contents. However, the fact is that the visual similarity is not semantic similarity, so there is a demand to break through this dilemma through an alternative way. The semantic gap can be narrowed by counting high-level and user-generated information in the annotation. High-level descriptions of images and or videos are more proficient of capturing the semantic meaning of multimedia content, but it is not always applicable to collect this information. It is commonly agreed that the problem of high level semantic annotation of multimedia is still far from being answered. This dissertation puts forward approaches for intelligent multimedia semantic extraction for high level annotation. This dissertation intends to bridge the gap between the visual features and semantics. It proposes a framework for annotation enhancement and refinement for the object/concept annotated images and videos datasets. The entire theme is to first purify the datasets from noisy keyword and then expand the concepts lexically and commonsensical to fill the vocabulary and lexical gap to achieve high level semantics for the corpus. This dissertation also explored a novel approach for high level semantic (HLS) propagation through the images corpora. The HLS propagation takes the advantages of the semantic intensity (SI), which is the concept dominancy factor in the image and annotation based semantic similarity of the images. As we are aware of the fact that the image is the combination of various concepts and among the list of concepts some of them are more dominant then the other, while semantic similarity of the images are based on the SI and concept semantic similarity among the pair of images. Moreover, the HLS exploits the clustering techniques to group similar images, where a single effort of the human experts to assign high level semantic to a randomly selected image and propagate to other images through clustering. The investigation has been made on the LabelMe image and LabelMe video dataset. Experiments exhibit that the proposed approaches perform a noticeable improvement towards bridging the semantic gap and reveal that our proposed system outperforms the traditional systems

Term-driven E-Commerce

Die Arbeit nimmt sich der textuellen Dimension des E-Commerce an. Grundlegende Hypothese ist die textuelle Gebundenheit von Information und Transaktion im Bereich des elektronischen Handels. Überall dort, wo Produkte und Dienstleistungen angeboten, nachgefragt, wahrgenommen und bewertet werden, kommen natürlichsprachige Ausdrücke zum Einsatz. Daraus resultiert ist zum einen, wie bedeutsam es ist, die Varianz textueller Beschreibungen im E-Commerce zu erfassen, zum anderen können die umfangreichen textuellen Ressourcen, die bei E-Commerce-Interaktionen anfallen, im Hinblick auf ein besseres Verständnis natürlicher Sprache herangezogen werden

Interactive Visual Analysis of Translations

This thesis is the result of a collaboration with the College of Arts and Humanities at Swansea University. The goal of this collaboration is to design novel visualization techniques to enable digital humanities scholars to explore and analyze parallel translations. To this end, chapter 2 introduces the first survey of surveys on text visualization which reviews all of the surveys and state-of-the-art reports on text visualization techniques, classifies them, provides recommendations, and discusses reported challenges.Following this, we present three visual interactive designs that support the typical digital humanities scholars workflow. In Chapter 4, we present VNLP, a visual, interactive design that enables users to explicitly observe the NLP pipeline processes and update the parameters at each processing stage. Chapter 5 presents AlignVis, a visual tool that provides a semi-automatic alignment framework to build a correspondence between multiple translations. It presents the results of using text similarity measurements and enables the user to create, verify, and edit alignments using a novel visual interface. Chapter 6 introduce TransVis, a novel visual design that supports comparison of multiple parallel translations. It incorporates customized mechanisms for rapid and interactive filtering and selection of a large number of German translations of Shakespeare’s Othello. All of the visual designs are evaluated using examples, detailed observations, case studies, and/or domain expert feedback from a specialist in modern and contemporary German literature and culture.Chapter 7 reports our collaborative experience and proposes a methodological workflow to guide such interdisciplinary research projects. This chapter also includes a summary of outcomes and lessons learned from our collaboration with the domain expert. Finally, Chapter 8 presents a summary of the thesis and future work directions

Semantic Domains in Akkadian Text

The article examines the possibilities offered by language technology for analyzing semantic fields in Akkadian. The corpus of data for our research group is the existing electronic corpora, Open richly annotated cuneiform corpus (ORACC). In addition to more traditional Assyriological methods, the article explores two language technological methods: Pointwise mutual information (PMI) and Word2vec.Peer reviewe