Detecting Biomedical Relations using Distant Supervision

This work concerns the detection of relationships between key information in biomedical publications, such as treatments for diseases or side-effects of drugs. Given a sentence containing some medical concepts the goal is to determine their relationship to each other. Supervised machine learning methods are a very popular way to address this problem and often provide reliable results. Those methods require manually labelled examples to extract characteristics of particular relationships in order to detect similar information in unlabelled data. However, manually labelled data is not always available and its generation is time consuming and expensive. The main objective of this thesis is the exploration of distant supervision, a method which generates those labelled examples automatically using prior knowledge to detect relationships between key facts. First, relation extraction using a limited amount of training data is explored to detect adverse-drug effects in natural language. Then, work focuses on automatically labelling data using a large biomedical knowledge base, the Unified Medical Language System (UMLS). The effectiveness of a popular evaluation method that does not require manually labelled data is examined in more detail. The main goal is the investigation of whether UMLS is suitable to be used to label data automatically so as to detect similar information in natural language. Finally, a method to reduce falsely labelled instances in the automatically generated data is presented and found to improve the detection of relationships

Commonsense knowledge acquisition and applications

Computers are increasingly expected to make smart decisions based on what humans consider commonsense. This would require computers to understand their environment, including properties of objects in the environment (e.g., a wheel is round), relations between objects (e.g., two wheels are part of a bike, or a bike is slower than a car) and interactions of objects (e.g., a driver drives a car on the road). The goal of this dissertation is to investigate automated methods for acquisition of large-scale, semantically organized commonsense knowledge. Prior state-of-the-art methods to acquire commonsense are either not automated or based on shallow representations. Thus, they cannot produce large-scale, semantically organized commonsense knowledge. To achieve the goal, we divide the problem space into three research directions, constituting our core contributions: 1. Properties of objects: acquisition of properties like hasSize, hasShape, etc. We develop WebChild, a semi-supervised method to compile semantically organized properties. 2. Relationships between objects: acquisition of relations like largerThan, partOf, memberOf, etc. We develop CMPKB, a linear-programming based method to compile comparative relations, and, we develop PWKB, a method based on statistical and logical inference to compile part-whole relations. 3. Interactions between objects: acquisition of activities like drive a car, park a car, etc., with attributes such as temporal or spatial attributes. We develop Knowlywood, a method based on semantic parsing and probabilistic graphical models to compile activity knowledge. Together, these methods result in the construction of a large, clean and semantically organized Commonsense Knowledge Base that we call WebChild KB.Von Computern wird immer mehr erwartet, dass sie kluge Entscheidungen treffen können, basierend auf Allgemeinwissen. Dies setzt voraus, dass Computer ihre Umgebung, einschließlich der Eigenschaften von Objekten (z. B. das Rad ist rund), Beziehungen zwischen Objekten (z. B. ein Fahrrad hat zwei Räder, ein Fahrrad ist langsamer als ein Auto) und Interaktionen von Objekten (z. B. ein Fahrer fährt ein Auto auf der Straße), verstehen können. Das Ziel dieser Dissertation ist es, automatische Methoden für die Erfassung von großmaßstäblichem, semantisch organisiertem Allgemeinwissen zu schaffen. Dies ist schwierig aufgrund folgender Eigenschaften des Allgemeinwissens. Es ist: (i) implizit und spärlich, da Menschen nicht explizit das Offensichtliche ausdrücken, (ii) multimodal, da es über textuelle und visuelle Inhalte verteilt ist, (iii) beeinträchtigt vom Einfluss des Berichtenden, da ungewöhnliche Fakten disproportional häufig berichtet werden, (iv) Kontextabhängig, und hat aus diesem Grund eine eingeschränkte statistische Konfidenz. Vorherige Methoden, auf diesem Gebiet sind entweder nicht automatisiert oder basieren auf flachen Repräsentationen. Daher können sie kein großmaßstäbliches, semantisch organisiertes Allgemeinwissen erzeugen. Um unser Ziel zu erreichen, teilen wir den Problemraum in drei Forschungsrichtungen, welche den Hauptbeitrag dieser Dissertation formen: 1. Eigenschaften von Objekten: Erfassung von Eigenschaften wie hasSize, hasShape, usw. Wir entwickeln WebChild, eine halbüberwachte Methode zum Erfassen semantisch organisierter Eigenschaften. 2. Beziehungen zwischen Objekten: Erfassung von Beziehungen wie largerThan, partOf, memberOf, usw. Wir entwickeln CMPKB, eine Methode basierend auf linearer Programmierung um vergleichbare Beziehungen zu erfassen. Weiterhin entwickeln wir PWKB, eine Methode basierend auf statistischer und logischer Inferenz welche zugehörigkeits Beziehungen erfasst. 3. Interaktionen zwischen Objekten: Erfassung von Aktivitäten, wie drive a car, park a car, usw. mit temporalen und räumlichen Attributen. Wir entwickeln Knowlywood, eine Methode basierend auf semantischem Parsen und probabilistischen grafischen Modellen um Aktivitätswissen zu erfassen. Als Resultat dieser Methoden erstellen wir eine große, saubere und semantisch organisierte Allgemeinwissensbasis, welche wir WebChild KB nennen

From Texts to Prerequisites. Identifying and Annotating Propaedeutic Relations in Educational Textual Resources

openPrerequisite Relations (PRs) are dependency relations established between two distinct concepts expressing which piece(s) of information a student has to learn first in order to understand a certain target concept. Such relations are one of the most fundamental in Education, playing a crucial role not only for what concerns new knowledge acquisition, but also in the novel applications of Artificial Intelligence to distant and e-learning. Indeed, resources annotated with such information could be used to develop automatic systems able to acquire and organize the knowledge embodied in educational resources, possibly fostering educational applications personalized, e.g., on students' needs and prior knowledge. The present thesis discusses the issues and challenges of identifying PRs in educational textual materials with the purpose of building a shared understanding of the relation among the research community. To this aim, we present a methodology for dealing with prerequisite relations as established in educational textual resources which aims at providing a systematic approach for uncovering PRs in textual materials, both when manually annotating and automatically extracting the PRs. The fundamental principles of our methodology guided the development of a novel framework for PR identification which comprises three components, each tackling a different task: (i) an annotation protocol (PREAP), reporting the set of guidelines and recommendations for building PR-annotated resources; (ii) an annotation tool (PRET), supporting the creation of manually annotated datasets reflecting the principles of PREAP; (iii) an automatic PR learning method based on machine learning (PREL). The main novelty of our methodology and framework lies in the fact that we propose to uncover PRs from textual resources relying solely on the content of the instructional material: differently from other works, rather than creating de-contextualised PRs, we acknowledge the presence of a PR between two concepts only if emerging from the way they are presented in the text. By doing so, we anchor relations to the text while modelling the knowledge structure entailed in the resource. As an original contribution of this work, we explore whether linguistic complexity of the text influences the task of manual identification of PRs. To this aim, we investigate the interplay between text and content in educational texts through a crowd-sourcing experiment on concept sequencing. Our methodology values the content of educational materials as it incorporates the evidence acquired from such investigation which suggests that PR recognition is highly influenced by the way in which concepts are introduced in the resource and by the complexity of the texts. The thesis reports a case study dealing with every component of the PR framework which produced a novel manually-labelled PR-annotated dataset.openXXXIII CICLO - DIGITAL HUMANITIES. TECNOLOGIE DIGITALI, ARTI, LINGUE, CULTURE E COMUNICAZIONE - Lingue, culture e tecnologie digitaliAlzetta, Chiar

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

Commonsense knowledge acquisition and applications

Computers are increasingly expected to make smart decisions based on what humans consider commonsense. This would require computers to understand their environment, including properties of objects in the environment (e.g., a wheel is round), relations between objects (e.g., two wheels are part of a bike, or a bike is slower than a car) and interactions of objects (e.g., a driver drives a car on the road). The goal of this dissertation is to investigate automated methods for acquisition of large-scale, semantically organized commonsense knowledge. Prior state-of-the-art methods to acquire commonsense are either not automated or based on shallow representations. Thus, they cannot produce large-scale, semantically organized commonsense knowledge. To achieve the goal, we divide the problem space into three research directions, constituting our core contributions: 1. Properties of objects: acquisition of properties like hasSize, hasShape, etc. We develop WebChild, a semi-supervised method to compile semantically organized properties. 2. Relationships between objects: acquisition of relations like largerThan, partOf, memberOf, etc. We develop CMPKB, a linear-programming based method to compile comparative relations, and, we develop PWKB, a method based on statistical and logical inference to compile part-whole relations. 3. Interactions between objects: acquisition of activities like drive a car, park a car, etc., with attributes such as temporal or spatial attributes. We develop Knowlywood, a method based on semantic parsing and probabilistic graphical models to compile activity knowledge. Together, these methods result in the construction of a large, clean and semantically organized Commonsense Knowledge Base that we call WebChild KB.Von Computern wird immer mehr erwartet, dass sie kluge Entscheidungen treffen können, basierend auf Allgemeinwissen. Dies setzt voraus, dass Computer ihre Umgebung, einschließlich der Eigenschaften von Objekten (z. B. das Rad ist rund), Beziehungen zwischen Objekten (z. B. ein Fahrrad hat zwei Räder, ein Fahrrad ist langsamer als ein Auto) und Interaktionen von Objekten (z. B. ein Fahrer fährt ein Auto auf der Straße), verstehen können. Das Ziel dieser Dissertation ist es, automatische Methoden für die Erfassung von großmaßstäblichem, semantisch organisiertem Allgemeinwissen zu schaffen. Dies ist schwierig aufgrund folgender Eigenschaften des Allgemeinwissens. Es ist: (i) implizit und spärlich, da Menschen nicht explizit das Offensichtliche ausdrücken, (ii) multimodal, da es über textuelle und visuelle Inhalte verteilt ist, (iii) beeinträchtigt vom Einfluss des Berichtenden, da ungewöhnliche Fakten disproportional häufig berichtet werden, (iv) Kontextabhängig, und hat aus diesem Grund eine eingeschränkte statistische Konfidenz. Vorherige Methoden, auf diesem Gebiet sind entweder nicht automatisiert oder basieren auf flachen Repräsentationen. Daher können sie kein großmaßstäbliches, semantisch organisiertes Allgemeinwissen erzeugen. Um unser Ziel zu erreichen, teilen wir den Problemraum in drei Forschungsrichtungen, welche den Hauptbeitrag dieser Dissertation formen: 1. Eigenschaften von Objekten: Erfassung von Eigenschaften wie hasSize, hasShape, usw. Wir entwickeln WebChild, eine halbüberwachte Methode zum Erfassen semantisch organisierter Eigenschaften. 2. Beziehungen zwischen Objekten: Erfassung von Beziehungen wie largerThan, partOf, memberOf, usw. Wir entwickeln CMPKB, eine Methode basierend auf linearer Programmierung um vergleichbare Beziehungen zu erfassen. Weiterhin entwickeln wir PWKB, eine Methode basierend auf statistischer und logischer Inferenz welche zugehörigkeits Beziehungen erfasst. 3. Interaktionen zwischen Objekten: Erfassung von Aktivitäten, wie drive a car, park a car, usw. mit temporalen und räumlichen Attributen. Wir entwickeln Knowlywood, eine Methode basierend auf semantischem Parsen und probabilistischen grafischen Modellen um Aktivitätswissen zu erfassen. Als Resultat dieser Methoden erstellen wir eine große, saubere und semantisch organisierte Allgemeinwissensbasis, welche wir WebChild KB nennen

Semantically-guided evolutionary knowledge discovery from texts

This thesis proposes a new approach for structured knowledge discovery from texts which considers both the mining process itself, the evaluation of this knowledge by the model, and the human assessment of the quality of the outcome.This is achieved by integrating Natural-Language technology and Genetic Algorithms to produce explanatory novel hypotheses. Natural-Language techniques are specifically used to extract genre-based information from text documents. Additional semantic and rhetorical information for generating training data and for feeding a semistructured Latent Semantic Analysis process is also captured.The discovery process is modeled by a semantically-guided Genetic Algorithm which uses training data to guide the search and optimization process. A number of novel criteria to evaluate the quality of the new knowledge are proposed. Consequently, new genetic operations suitable for text mining are designed, and techniques for Evolutionary Multi-Objective Optimization are adapted for the model to trade off between different criteria in the hypotheses.Domain experts were used in an experiment to assess the quality of the hypotheses produced by the model so as to establish their effectiveness in terms of novel and interesting knowledge. The assessment showed encouraging results for the discovered knowledge and for the correlation between the model and the human opinions

Automatically Acquiring A Semantic Network Of Related Concepts

We describe the automatic acquisition of a semantic network in which over 7,500 of the most frequently occurring nouns in the English language are linked to their semantically related concepts in the WordNet noun ontology. Relatedness between nouns is discovered automatically from lexical co-occurrence in Wikipedia texts using a novel adaptation of an information theoretic inspired measure. Our algorithm then capitalizes on salient sense clustering among these semantic associates to automatically disambiguate them to their corresponding WordNet noun senses (i.e., concepts). The resultant concept-to-concept associations, stemming from 7,593 target nouns, with 17,104 distinct senses among them, constitute a large-scale semantic network with 208,832 undirected edges between related concepts. Our work can thus be conceived of as augmenting the WordNet noun ontology with RelatedTo links. The network, which we refer to as the Szumlanski-Gomez Network (SGN), has been subjected to a variety of evaluative measures, including manual inspection by human judges and quantitative comparison to gold standard data for semantic relatedness measurements. We have also evaluated the network’s performance in an applied setting on a word sense disambiguation (WSD) task in which the network served as a knowledge source for established graph-based spreading activation algorithms, and have shown: a) the network is competitive with WordNet when used as a stand-alone knowledge source for WSD, b) combining our network with WordNet achieves disambiguation results that exceed the performance of either resource individually, and c) our network outperforms a similar resource, WordNet++ (Ponzetto & Navigli, 2010), that has been automatically derived from annotations in the Wikipedia corpus. iii Finally, we present a study on human perceptions of relatedness. In our study, we elicited quantitative evaluations of semantic relatedness from human subjects using a variation of the classical methodology that Rubenstein and Goodenough (1965) employed to investigate human perceptions of semantic similarity. Judgments from individual subjects in our study exhibit high average correlation to the elicited relatedness means using leave-one-out sampling (r = 0.77, σ = 0.09, N = 73), although not as high as average human correlation in previous studies of similarity judgments, for which Resnik (1995) established an upper bound of r = 0.90 (σ = 0.07, N = 10). These results suggest that human perceptions of relatedness are less strictly constrained than evaluations of similarity, and establish a clearer expectation for what constitutes human-like performance by a computational measure of semantic relatedness. We also contrast the performance of a variety of similarity and relatedness measures on our dataset to their performance on similarity norms and introduce our own dataset as a supplementary evaluative standard for relatedness measures

Acquiring and Harnessing Verb Knowledge for Multilingual Natural Language Processing

Advances in representation learning have enabled natural language processing models to derive non-negligible linguistic information directly from text corpora in an unsupervised fashion. However, this signal is underused in downstream tasks, where they tend to fall back on superficial cues and heuristics to solve the problem at hand. Further progress relies on identifying and filling the gaps in linguistic knowledge captured in their parameters. The objective of this thesis is to address these challenges focusing on the issues of resource scarcity, interpretability, and lexical knowledge injection, with an emphasis on the category of verbs. To this end, I propose a novel paradigm for efficient acquisition of lexical knowledge leveraging native speakers’ intuitions about verb meaning to support development and downstream performance of NLP models across languages. First, I investigate the potential of acquiring semantic verb classes from non-experts through manual clustering. This subsequently informs the development of a two-phase semantic dataset creation methodology, which combines semantic clustering with fine-grained semantic similarity judgments collected through spatial arrangements of lexical stimuli. The method is tested on English and then applied to a typologically diverse sample of languages to produce the first large-scale multilingual verb dataset of this kind. I demonstrate its utility as a diagnostic tool by carrying out a comprehensive evaluation of state-of-the-art NLP models, probing representation quality across languages and domains of verb meaning, and shedding light on their deficiencies. Subsequently, I directly address these shortcomings by injecting lexical knowledge into large pretrained language models. I demonstrate that external manually curated information about verbs’ lexical properties can support data-driven models in tasks where accurate verb processing is key. Moreover, I examine the potential of extending these benefits from resource-rich to resource-poor languages through translation-based transfer. The results emphasise the usefulness of human-generated lexical knowledge in supporting NLP models and suggest that time-efficient construction of lexicons similar to those developed in this work, especially in under-resourced languages, can play an important role in boosting their linguistic capacity.ESRC Doctoral Fellowship [ES/J500033/1], ERC Consolidator Grant LEXICAL [648909