KnowLife: A Versatile Approach for Constructing a Large Knowledge Graph for Biomedical Sciences

BACKGROUND: Biomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS: We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION: KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users

ATOMIC: An Atlas of Machine Commonsense for If-Then Reasoning

We present ATOMIC, an atlas of everyday commonsense reasoning, organized through 877k textual descriptions of inferential knowledge. Compared to existing resources that center around taxonomic knowledge, ATOMIC focuses on inferential knowledge organized as typed if-then relations with variables (e.g., "if X pays Y a compliment, then Y will likely return the compliment"). We propose nine if-then relation types to distinguish causes vs. effects, agents vs. themes, voluntary vs. involuntary events, and actions vs. mental states. By generatively training on the rich inferential knowledge described in ATOMIC, we show that neural models can acquire simple commonsense capabilities and reason about previously unseen events. Experimental results demonstrate that multitask models that incorporate the hierarchical structure of if-then relation types lead to more accurate inference compared to models trained in isolation, as measured by both automatic and human evaluation.Comment: AAAI 2019 C

Predicting reading difficulty for readers with autism spectrum disorder

People with autism experience various reading comprehension difficulties, which is one explanation for the early school dropout, reduced academic achievement and lower levels of employment in this population. To overcome this issue, content developers who want to make their textbooks, websites or social media accessible to people with autism (and thus for every other user) but who are not necessarily experts in autism, can benefit from tools which are easy to use, which can assess the accessibility of their content, and which are sensitive to the difficulties that autistic people might have when processing texts/websites. In this paper we present a preliminary machine learning readability model for English developed specifically for the needs of adults with autism. We evaluate the model on the ASD corpus, which has been developed specifically for this task and is, so far, the only corpus for which readability for people with autism has been evaluated. The results show that out model outperforms the baseline, which is the widely-used Flesch-Kincaid Grade Level formula.paper presented at LREC 2016 Workshop ”Improving Social Inclusion Using NLP: Tools and Resources” held on 23 May 2016 – Portorož, Slovenia

Automatic domain-specific learning: towards a methodology for ontology enrichment

[EN] At the current rate of technological development, in a world where enormous amount of data are constantly created and in which the Internet is used as the primary means for information exchange, there exists a need for tools that help processing, analyzing and using that information. However, while the growth of information poses many opportunities for social and scientific advance, it has also highlighted the difficulties of extracting meaningful patterns from massive data. Ontologies have been claimed to play a major role in the processing of large-scale data, as they serve as universal models of knowledge representation, and are being studied as possible solutions to this. This paper presents a method for the automatic expansion of ontologies based on corpus and terminological data exploitation. The proposed ¿ontology enrichment method¿ (OEM) consists of a sequence of tasks aimed at classifying an input keyword automatically under its corresponding node within a target ontology. Results prove that the method can be successfully applied for the automatic classification of specialized units into a reference ontology.Financial support for this research has been provided by the DGI, Spanish Ministry of Education and Science, grant FFI2011-29798-C0201.Ureña Gómez-Moreno, P.; Mestre-Mestre, EM. (2017). Automatic domain-specific learning: towards a methodology for ontology enrichment. LFE. Revista de Lenguas para Fines Específicos. 23(2):63-85. http://hdl.handle.net/10251/148357S638523

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

Medical WordNet: A new methodology for the construction and validation of information resources for consumer health

A consumer health information system must be able to comprehend both expert and non-expert medical vocabulary and to map between the two. We describe an ongoing project to create a new lexical database called Medical WordNet (MWN), consisting of medically relevant terms used by and intelligible to non-expert subjects and supplemented by a corpus of natural-language sentences that is designed to provide medically validated contexts for MWN terms. The corpus derives primarily from online health information sources targeted to consumers, and involves two sub-corpora, called Medical FactNet (MFN) and Medical BeliefNet (MBN), respectively. The former consists of statements accredited as true on the basis of a rigorous process of validation, the latter of statements which non-experts believe to be true. We summarize the MWN / MFN / MBN project, and describe some of its applications

ELECTRONIC CORPORA IN TRANSLATION BOOTCAT-BOOTSTRAPPING CORPORA AND TERMS FROM THE WEB

In the new world of technology, the translation profession, like other disciplines, cannot be deprived of modern tools such as electronic corpora. Recently, large monolingual, comparable and parallel corpora have played a crucial role in solving various problems of linguistics, including translation. During recent years, a large number of studies within the discipline of translation studies have focused on corpora and their applications in translation classes. Such studies mainly look into the kind of information trainee translators can elicit from corpora and the effect of using corpus data on the quality of translations produced. Corpora, however, have a lot more to offer to both translation teachers and translation students. Corpus-based translation classrooms, by their very nature, can offer considerable advantages far beyond what traditional translation classes have to offer. This article, in fact, aims to elaborate on advantages of using corpora in translation classrooms for teachers and students of translation. Furthermore, we present types of corpora and a new method of compiling specialized corpora- BootCaT.BOOTCAT, BOOTSTRAPPING

Lexical Co-occurrence: The Missing Link

Aside from syntax, linguistic knowledge can be separated into two distinct parts, encyclopedic knowledge and dictionary knowledge. Encyclopedic knowledge describes the world whereas the dictionary describes individual word features, thus capturing lexical knowledge. Among the various types of lexical knowledge, one has generally been overlooked and should bring new results in computational linguistics: co-occurrence knowledge. Co-occurrence knowledge stands for the extent to which an item is specified by its environment independently of syntactic or semantic reasons. The basic concept is that of a lexical relation due to Saussure [49]. A lexical relation between two units of language stands for a correlation of common appearance of the two units in the utterances of the language