From Text to Knowledge

The global information space provided by the World Wide Web has changed dramatically the way knowledge is shared all over the world. To make this unbelievable huge information space accessible, search engines index the uploaded contents and provide efficient algorithmic machinery for ranking the importance of documents with respect to an input query. All major search engines such as Google, Yahoo or Bing are keyword-based, which is indisputable a very powerful tool for accessing information needs centered around documents. However, this unstructured, document-oriented paradigm of the World Wide Web has serious drawbacks, when searching for specific knowledge about real-world entities. When asking for advanced facts about entities, today's search engines are not very good in providing accurate answers. Hand-built knowledge bases such as Wikipedia or its structured counterpart DBpedia are excellent sources that provide common facts. However, these knowledge bases are far from being complete and most of the knowledge lies still buried in unstructured documents. Statistical machine learning methods have the great potential to help to bridge the gap between text and knowledge by (semi-)automatically transforming the unstructured representation of the today's World Wide Web to a more structured representation. This thesis is devoted to reduce this gap with Probabilistic Graphical Models. Probabilistic Graphical Models play a crucial role in modern pattern recognition as they merge two important fields of applied mathematics: Graph Theory and Probability Theory. The first part of the thesis will present a novel system called Text2SemRel that is able to (semi-)automatically construct knowledge bases from textual document collections. The resulting knowledge base consists of facts centered around entities and their relations. Essential part of the system is a novel algorithm for extracting relations between entity mentions that is based on Conditional Random Fields, which are Undirected Probabilistic Graphical Models. In the second part of the thesis, we will use the power of Directed Probabilistic Graphical Models to solve important knowledge discovery tasks in semantically annotated large document collections. In particular, we present extensions of the Latent Dirichlet Allocation framework that are able to learn in an unsupervised way the statistical semantic dependencies between unstructured representations such as documents and their semantic annotations. Semantic annotations of documents might refer to concepts originating from a thesaurus or ontology but also to user-generated informal tags in social tagging systems. These forms of annotations represent a first step towards the conversion to a more structured form of the World Wide Web. In the last part of the thesis, we prove the large-scale applicability of the proposed fact extraction system Text2SemRel. In particular, we extract semantic relations between genes and diseases from a large biomedical textual repository. The resulting knowledge base contains far more potential disease genes exceeding the number of disease genes that are currently stored in curated databases. Thus, the proposed system is able to unlock knowledge currently buried in the literature. The literature-derived human gene-disease network is subject of further analysis with respect to existing curated state of the art databases. We analyze the derived knowledge base quantitatively by comparing it with several curated databases with regard to size of the databases and properties of known disease genes among other things. Our experimental analysis shows that the facts extracted from the literature are of high quality

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Understanding and controlling leakage in machine learning

Machine learning models are being increasingly adopted in a variety of real-world scenarios. However, the privacy and confidentiality implications introduced in these scenarios are not well understood. Towards better understanding such implications, we focus on scenarios involving interactions between numerous parties prior to, during, and after training relevant models. Central to these interactions is sharing information for a purpose e.g., contributing data samples towards a dataset, returning predictions via an API. This thesis takes a step toward understanding and controlling leakage of private information during such interactions. In the first part of the thesis we investigate leakage of private information in visual data and specifically, photos representative of content shared on social networks. There is a long line of work to tackle leakage of personally identifiable information in social photos, especially using face- and body-level visual cues. However, we argue this presents only a narrow perspective as images reveal a wide spectrum of multimodal private information (e.g., disabilities, name-tags). Consequently, we work towards a Visual Privacy Advisor that aims to holistically identify and mitigate private risks when sharing social photos. In the second part, we address leakage during training of ML models. We observe learning algorithms are being increasingly used to train models on rich decentralized datasets e.g., personal data on numerous mobile devices. In such cases, information in the form of high-dimensional model parameter updates are anonymously aggregated from participating individuals. However, we find that the updates encode sufficient identifiable information and allows them to be linked back to participating individuals. We additionally propose methods to mitigate this leakage while maintaining high utility of the updates. In the third part, we discuss leakage of confidential information during inference time of black-box models. In particular, we find models lend themselves to model functionality stealing attacks: an adversary can interact with the black-box model towards creating a replica `knock-off' model that exhibits similar test-set performances. As such attacks pose a severe threat to the intellectual property of the model owner, we also work towards effective defenses. Our defense strategy by introducing bounded and controlled perturbations to predictions can significantly amplify model stealing attackers' error rates. In summary, this thesis advances understanding of privacy leakage when information is shared in raw visual forms, during training of models, and at inference time when deployed as black-boxes. In each of the cases, we further propose techniques to mitigate leakage of information to enable wide-spread adoption of techniques in real-world scenarios.Modelle für maschinelles Lernen werden zunehmend in einer Vielzahl realer Szenarien eingesetzt. Die in diesen Szenarien vorgestellten Auswirkungen auf Datenschutz und Vertraulichkeit wurden jedoch nicht vollständig untersucht. Um solche Implikationen besser zu verstehen, konzentrieren wir uns auf Szenarien, die Interaktionen zwischen mehreren Parteien vor, während und nach dem Training relevanter Modelle beinhalten. Das Teilen von Informationen für einen Zweck, z. B. das Einbringen von Datenproben in einen Datensatz oder die Rückgabe von Vorhersagen über eine API, ist zentral für diese Interaktionen. Diese Arbeit verhilft zu einem besseren Verständnis und zur Kontrolle des Verlusts privater Informationen während solcher Interaktionen. Im ersten Teil dieser Arbeit untersuchen wir den Verlust privater Informationen bei visuellen Daten und insbesondere bei Fotos, die für Inhalte repräsentativ sind, die in sozialen Netzwerken geteilt werden. Es gibt eine lange Reihe von Arbeiten, die das Problem des Verlustes persönlich identifizierbarer Informationen in sozialen Fotos angehen, insbesondere mithilfe visueller Hinweise auf Gesichts- und Körperebene. Wir argumentieren jedoch, dass dies nur eine enge Perspektive darstellt, da Bilder ein breites Spektrum multimodaler privater Informationen (z. B. Behinderungen, Namensschilder) offenbaren. Aus diesem Grund arbeiten wir auf einen Visual Privacy Advisor hin, der darauf abzielt, private Risiken beim Teilen sozialer Fotos ganzheitlich zu identifizieren und zu minimieren. Im zweiten Teil befassen wir uns mit Datenverlusten während des Trainings von ML-Modellen. Wir beobachten, dass zunehmend Lernalgorithmen verwendet werden, um Modelle auf umfangreichen dezentralen Datensätzen zu trainieren, z. B. persönlichen Daten auf zahlreichen Mobilgeräten. In solchen Fällen werden Informationen von teilnehmenden Personen in Form von hochdimensionalen Modellparameteraktualisierungen anonym verbunden. Wir stellen jedoch fest, dass die Aktualisierungen ausreichend identifizierbare Informationen codieren und es ermöglichen, sie mit teilnehmenden Personen zu verknüpfen. Wir schlagen zudem Methoden vor, um diesen Datenverlust zu verringern und gleichzeitig die hohe Nützlichkeit der Aktualisierungen zu erhalten. Im dritten Teil diskutieren wir den Verlust vertraulicher Informationen während der Inferenzzeit von Black-Box-Modellen. Insbesondere finden wir, dass sich Modelle für die Entwicklung von Angriffen, die auf Funktionalitätsdiebstahl abzielen, eignen: Ein Gegner kann mit dem Black-Box-Modell interagieren, um ein Replikat-Knock-Off-Modell zu erstellen, das ähnliche Test-Set-Leistungen aufweist. Da solche Angriffe eine ernsthafte Bedrohung für das geistige Eigentum des Modellbesitzers darstellen, arbeiten wir auch an einer wirksamen Verteidigung. Unsere Verteidigungsstrategie durch die Einführung begrenzter und kontrollierter Störungen in Vorhersagen kann die Fehlerraten von Modelldiebstahlangriffen erheblich verbessern. Zusammenfassend lässt sich sagen, dass diese Arbeit das Verständnis von Datenschutzverlusten beim Informationsaustausch verbessert, sei es bei rohen visuellen Formen, während des Trainings von Modellen oder während der Inferenzzeit von Black-Box-Modellen. In jedem Fall schlagen wir ferner Techniken zur Verringerung des Informationsverlusts vor, um eine weit verbreitete Anwendung von Techniken in realen Szenarien zu ermöglichen.Max Planck Institute for Informatic

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This thesis explores the potential of using textual patterns for Information Extraction from the World Wide Web

Social Measurement and Causal Inference with Text

The digital age has dramatically increased access to large-scale collections of digitized text documents. These corpora include, for example, digital traces from social media, decades of archived news reports, and transcripts of spoken interactions in political, legal, and economic spheres. For social scientists, this new widespread data availability has potential for improved quantitative analysis of relationships between language use and human thought, actions, and societal structure. However, the large-scale nature of these collections means that traditional manual approaches to analyzing content are extremely costly and do not scale. Furthermore, incorporating unstructured text data into quantitative analysis is difficult due to texts’ high-dimensional nature and linguistic complexity. This thesis blends (a) the computational strengths of natural language processing (NLP) and machine learning to automate and scale-up quantitative text analysis with (b) two themes central to social scientific studies but often under-addressed in NLP: measurement—creating quantifiable summaries of empirical phenomena—and causal inference—estimating the effects of interventions. First, we address measuring class prevalence in document collections; we contribute a generative probabilistic modeling approach to prevalence estimation and show empirically that our model is more robust to shifts in class priors between training and inference. Second, we examine cross- document entity-event measurement; we contribute an empirical pipeline and a novel latent disjunction model to identify the names of civilians killed by police from our corpus of web-scraped news reports. Third, we gather and categorize applications that use text to reduce confounding from causal estimates and contribute a list of open problems as well as guidance about data processing and evaluation decisions in this area. Finally, we contribute a new causal research design to estimate the natural indirect and direct effects of social group signals (e.g. race or gender) on conversational outcomes with separate aspects of language as causal mediators; this chapter is motivated by a theoretical case study of U.S. Supreme Court oral arguments and the effect of an advocate’s gender on interruptions from justices. We conclude by discussing the relationship between measurement and causal inference with text and future work at this intersection

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This work explores the potential of using textual patterns for Information Extraction from the World Wide Web

Application of information extraction techniques to pharmacological domain : extracting drug-drug interactions

Una interacción farmacológica ocurre cuando los efectos de un fármaco se modifican por la presencia de otro. Las consecuencias pueden ser perjudiciales si la interacción causa un aumento de la toxicidad del fármaco o la disminución de su efecto, pudiendo provocar incluso la muerte del paciente en los peores casos. Las interacciones farmacológicas no sólo suponen un grave problema para la seguridad del paciente, sino que además también conllevan un importante incremento en el gasto médico. En la actualidad, el personal sanitario tiene a su disposición diversas bases de datos sobre interacciones que permiten evitar posibles interacciones a la hora de prescribir un determinado tratamiento, sin embargo, estas bases de datos no están completas. Por este motivo, médicos y farmacéuticos se ven obligados a revisar una gran cantidad de artículos científicos e informes sobre seguridad de medicamentos para estar al día de todo lo publicado en relación al tema. Desgraciadamente, el gran volumen de información al respecto hace que estos profesionales estén desbordados ante tal avalancha. El desarrollo de métodos automáticos que permitan recopilar, mantener e interpretar toda esta información es crucial a la hora de conseguir una mejora real en la detección temprana de las interacciones entre fármacos. Por tanto, la extracción de información podría reducir el tiempo empleado por el personal médico en la revisión de la literatura médica. Sin embargo, la extracción de interacciones farmacológicas a partir textos biomédicos no ha sido dirigida hasta el momento. Motivados por estos aspectos, en esta tesis hemos realizado un estudio detallado sobre diversas técnicas de extracción de información aplicadas al dominio farmacológico. Basándonos en este estudio, hemos propuesto dos aproximaciones distintas para la extracción de interacciones farmacológicas de los textos. Nuestra primera aproximación propone un enfoque híbrido, que combina análisis sintáctico superficial y la aplicación de patrones léxicos definidos por un farmacéutico. La segunda aproximación se aborda mediante aprendizaje supervisado, concretamente, el uso de métodos kernels. Además, se han desarrollado las siguientes tareas auxiliares: (1) el análisis de los textos utilizando la herramienta UMLS MetaMap Transfer (MMTx), que proporciona información sintáctica y semántica, (2) un proceso para identificar y clasificar los nombres de fármacos que ocurren en los textos, y (3) un proceso para reconoger las expresiones anafóricas que se refieren a fármacos. Un prototipo ha sido desarrollado para integrar y combinar las distintas técnicas propuestas en esta tesis. Para la evaluación de las dos propuestas, con la ayuda de un farmacéutico desarrollamos y anotamos un corpus con interacciones farmacológicas. El corpus DrugDDI es una de las principales aportaciones de la tesis, ya que es el primer corpus en el dominio biomédico anotado con este tipo de información y porque creemos que puede alentar la investigación sobre extracción de información en el dominio farmacológico. Los experimentos realizados demuestran que el enfoque basado en kernels consigue mejores resultados que los reportados por el enfoque que utiliza información sintáctica y patrones léxicos. Además, los kernels consiguen resultados comparables a los obtenidos en dominios similares como son las interacciones entre proteínas. Esta tesis se ha llevado a cabo en el marco del consorcio de investigación MAVIRCM (Mejorando el acceso y visibilidad de la información multilingüe en red para la Comunidad de Madrid, www.mavir.net) dentro del Programa de Actividades de I+D en Tecnologías 2005-2008 de la Comunidad de Madrid (S-0505/TIC-0267) así como en el proyecto de investigación BRAVO: ”Búsqueda de Respuestas Avanzada Multimodal y Multilingüe” (TIN2007-67407-C03-01).----------------------------------------------------------------------------------------A drug-drug interaction occurs when one drug influences the level or activity of another drug. The detection of drug interactions is an important research area in patient safety since these interactions can become very dangerous and increase health care costs. Although there are different databases supporting health care professionals in the detection of drug interactions, this kind of resource is rarely complete. Drug interactions are frequently reported in journals of clinical pharmacology, making medical literature the most effective source for the detection of drug interactions. However, the increasing volume of the literature overwhelms health care professionals trying to keep an up-to-date collection of all reported drug-drug interactions. The development of automatic methods for collecting, maintaining and interpreting this information is crucial for achieving a real improvement in their early detection. Information Extraction (IE) techniques can provide an interesting way of reducing the time spent by health care professionals on reviewing the literature. Nevertheless, no approach has been carried out to extract drug-drug interactions from biomedical texts. In this thesis, we have conducted a detailed study on various IE techniques applied to biomedical domain. Based on this study, we have proposed two different approximations for the extraction of drug-drug interactions from texts. The first approximation proposes a hybrid approach, which combines shallow parsing and pattern matching to extract relations between drugs from biomedical texts. The second approximation is based on a supervised machine learning approach, in particular, kernel methods. In addition, we have created and annotated the first corpus, DrugDDI, annotated with drug-drug interactions, which allow us to evaluate and compare both approximations. To the best of our knowledge, the DrugDDI corpus is the only available corpus annotated for drug-drug interactions and this thesis is the first work which addresses the problem of extracting drug-drug interactions from biomedical texts. We believe the DrugDDI corpus is an important contribution because it could encourage other research groups to research into this problem. We have also defined three auxiliary processes to provide crucial information, which will be used by the aforementioned approximations. These auxiliary tasks are as follows: (1) a process for text analysis based on the UMLS MetaMap Transfer tool (MMTx) to provide shallow syntactic and semantic information from texts, (2) a process for drug name recognition and classification, and (3) a process for drug anaphora resolution. Finally, we have developed a pipeline prototype which integrates the different auxiliary processes. The pipeline architecture allows us to easily integrate these modules with each of the approaches proposed in this thesis: pattern-matching or kernels. Several experiments were performed on the DrugDDI corpus. They show that while the first approximation based on pattern matching achieves low performance, the approach based on kernel-methods achieves a performance comparable to those obtained by approaches which carry out a similar task such as the extraction of protein-protein interactions. This work has been partially supported by the Spanish research projects: MAVIR consortium (S-0505/TIC-0267, www.mavir.net), a network of excellence funded by the Madrid Regional Government and TIN2007-67407-C03-01 (BRAVO: Advanced Multimodal and Multilingual Question Answering)