Cold-start universal information extraction

Who? What? When? Where? Why? are fundamental questions asked when gathering knowledge about and understanding a concept, topic, or event. The answers to these questions underpin the key information conveyed in the overwhelming majority, if not all, of language-based communication. At the core of my research in Information Extraction (IE) is the desire to endow machines with the ability to automatically extract, assess, and understand text in order to answer these fundamental questions. IE has been serving as one of the most important components for many downstream natural language processing (NLP) tasks, such as knowledge base completion, machine reading comprehension, machine translation and so on. The proliferation of the Web also intensifies the need of dealing with enormous amount of unstructured data from various sources, such as languages, genres and domains. When building an IE system, the conventional pipeline is to (1) ask expert linguists to rigorously define a target set of knowledge types we wish to extract by examining a large data set, (2) collect resources and human annotations for each type, and (3) design features and train machine learning models to extract knowledge elements. In practice, this process is very expensive as each step involves extensive human effort which is not always available, for example, to specify the knowledge types for a particular scenario, both consumers and expert linguists need to examine a lot of data from that domain and write detailed annotation guidelines for each type. Hand-crafted schemas, which define the types and complex templates of the expected knowledge elements, often provide low coverage and fail to generalize to new domains. For example, none of the traditional event extraction programs, such as ACE (Automatic Content Extraction) and TAC-KBP, include "donation'' and "evacuation'' in their schemas in spite of their potential relevance to natural disaster management users. Additionally, these approaches are highly dependent on linguistic resources and human labeled data tuned to pre-defined types, so they suffer from poor scalability and portability when moving to a new language, domain, or genre. The focus of this thesis is to develop effective theories and algorithms for IE which not only yield satisfactory quality by incorporating prior linguistic and semantic knowledge, but also greater portability and scalability by moving away from the high cost and narrow focus of large-scale manual annotation. This thesis opens up a new research direction called Cold-Start Universal Information Extraction, where the full extraction and analysis starts from scratch and requires little or no prior manual annotation or pre-defined type schema. In addition to this new research paradigm, we also contribute effective algorithms and models towards resolving the following three challenges: How can machines extract knowledge without any pre-defined types or any human annotated data? We develop an effective bottom-up and unsupervised Liberal Information Extraction framework based on the hypothesis that the meaning and underlying knowledge conveyed by linguistic expressions is usually embodied by their usages in language, which makes it possible to automatically induces a type schema based on rich contextual representations of all knowledge elements by combining their symbolic and distributional semantics using unsupervised hierarchical clustering. How can machines benefit from available resources, e.g., large-scale ontologies or existing human annotations? My research has shown that pre-defined types can also be encoded by rich contextual or structured representations, through which knowledge elements can be mapped to their appropriate types. Therefore, we design a weakly supervised Zero-shot Learning and a Semi-Supervised Vector Quantized Variational Auto-Encoder approach that frames IE as a grounding problem instead of classification, where knowledge elements are grounded into any types from an extensible and large-scale target ontology or induced from the corpora, with available annotations for a few types. How can IE approaches be extent to low-resource languages without any extra human effort? There are more than 6000 living languages in the real world while public gold-standard annotations are only available for a few dominant languages. To facilitate the adaptation of these IE frameworks to other languages, especially low resource languages, a Multilingual Common Semantic Space is further proposed to serve as a bridge for transferring existing resources and annotated data from dominant languages to more than 300 low resource languages. Moreover, a Multi-Level Adversarial Transfer framework is also designed to learn language-agnostic features across various languages

Agile in-litero experiments:how can semi-automated information extraction from neuroscientific literature help neuroscience model building?

In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles in peer-reviewed journals. One challenge for modern neuroinformatics is to design methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and its integration into computational models. In this thesis, we introduce novel natural language processing (NLP) models and systems to mine the neuroscientific literature. In addition to in vivo, in vitro or in silico experiments, we coin the NLP methods developed in this thesis as in litero experiments, aiming at analyzing and making accessible the extended body of neuroscientific literature. In particular, we focus on two important neuroscientific entities: brain regions and neural cells. An integrated NLP model is designed to automatically extract brain region connectivity statements from very large corpora. This system is applied to a large corpus of 25M PubMed abstracts and 600K full-text articles. Central to this system is the creation of a searchable database of brain region connectivity statements, allowing neuroscientists to gain an overview of all brain regions connected to a given region of interest. More importantly, the database enables researcher to provide feedback on connectivity results and links back to the original article sentence to provide the relevant context. The database is evaluated by neuroanatomists on real connectomics tasks (targets of Nucleus Accumbens) and results in significant effort reduction in comparison to previous manual methods (from 1 week to 2h). Subsequently, we introduce neuroNER to identify, normalize and compare instances of identify neuronsneurons in the scientific literature. Our method relies on identifying and analyzing each of the domain features used to annotate a specific neuron mention, like the morphological term 'basket' or brain region 'hippocampus'. We apply our method to the same corpus of 25M PubMed abstracts and 600K full-text articles and find over 500K unique neuron type mentions. To demonstrate the utility of our approach, we also apply our method towards cross-comparing the NeuroLex and Human Brain Project (HBP) cell type ontologies. By decoupling a neuron mention's identity into its specific compositional features, our method can successfully identify specific neuron types even if they are not explicitly listed within a predefined neuron type lexicon, thus greatly facilitating cross-laboratory studies. In order to build such large databases, several tools and infrastructureslarge-scale NLP were developed: a robust pipeline to preprocess full-text PDF articles, as well as bluima, an NLP processing pipeline specialized on neuroscience to perform text-mining at PubMed scale. During the development of those two NLP systems, we acknowledged the need for novel NLP approaches to rapidly develop custom text mining solutions. This led to the formalization of the agile text miningagile text-mining methodology to improve the communication and collaboration between subject matter experts and text miners. Agile text mining is characterized by short development cycles, frequent tasks redefinition and continuous performance monitoring through integration tests. To support our approach, we developed Sherlok, an NLP framework designed for the development of agile text mining applications

Natural Language Processing: Integration of Automatic and Manual Analysis

There is a current trend to combine natural language analysis with research questions from the humanities. This requires an integration of automatic analysis with manual analysis, e.g. to develop a theory behind the analysis, to test the theory against a corpus, to generate training data for automatic analysis based on machine learning algorithms, and to evaluate the quality of the results from automatic analysis. Manual analysis is traditionally the domain of linguists, philosophers, and researchers from other humanities disciplines, who are often not expert programmers. Automatic analysis, on the other hand, is traditionally done by expert programmers, such as computer scientists and more recently computational linguists. It is important to bring these communities, their tools, and data closer together, to produce analysis of a higher quality with less effort. However, promising cooperations involving manual and automatic analysis, e.g. for the purpose of analyzing a large corpus, are hindered by many problems: - No comprehensive set of interoperable automatic analysis components is available. - Assembling automatic analysis components into workflows is too complex. - Automatic analysis tools, exploration tools, and annotation editors are not interoperable. - Workflows are not portable between computers. - Workflows are not easily deployable to a compute cluster. - There are no adequate tools for the selective annotation of large corpora. - In automatic analysis, annotation type systems are predefined, but manual annotation requires customizability. - Implementing new interoperable automatic analysis components is too complex. - Workflows and components are not sufficiently debuggable and refactorable. - Workflows that change dynamically via parametrization are not readily supported. - The user has no control over workflows that rely on expert skills from a different domain, undocumented knowledge, or third-party infrastructures, e.g. web services. In cooperation with researchers from the humanities, we develop innovative technical solutions and designs to facilitate the use of automatic analysis and to promote the integration of manual and automatic analysis. To address these issues, we set foundations in four areas: - Usability is improved by reducing the complexity of the APIs for building workflows and creating custom components, improving the handling of resources required by such components, and setting up auto-configuration mechanisms. - Reproducibility is improved through a concept for self-contained, portable analysis components and workflows combined with a declarative modeling approach for dynamic parametrized workflows, that facilitates avoiding unnecessary auxiliary manual steps in automatic workflows. - Flexibility is achieved by providing an extensive collection of interoperable automatic analysis components. We also compare annotation type systems used by different automatic analysis components to locate design patterns that allow for customization when used in manual analysis tasks. - Interactivity is achieved through a novel "annotation-by-query" process combining corpus search with annotation in a multi-user scenario. The process is supported by a web-based tool. We demonstrate the adequacy of our concepts through examples which represent whole classes of research problems. Additionally, we integrated all our concepts into existing open-source projects, or we implemented and published them within new open-source projects

Reflektierte algorithmische Textanalyse. Interdisziplinäre(s) Arbeiten in der CRETA-Werkstatt

The Center for Reflected Text Analytics (CRETA) develops interdisciplinary mixed methods for text analytics in the research fields of the digital humanities. This volume is a collection of text analyses from specialty fields including literary studies, linguistics, the social sciences, and philosophy. It thus offers an overview of the methodology of the reflected algorithmic analysis of literary and non-literary texts

Doing Research - Wissenschaftspraktiken zwischen Positionierung und Suchanfrage

Forschung wird zunehmend aus Sicht ihrer Ergebnisse gedacht - nicht zuletzt aufgrund der Umwälzungen im System Wissenschaft. Der Band lenkt den Fokus jedoch auf diejenigen Prozesse, die Forschungsergebnisse erst ermöglichen und Wissenschaft konturieren. Dabei ist der Titel Doing Research als Verweis darauf zu verstehen, dass forschendes Handeln von spezifischen Positionierungen, partiellen Perspektiven und Suchbewegungen geformt ist. So knüpfen alle Beitragenden auf reflexive Weise an ihre jeweiligen Forschungspraktiken an. Ausgangspunkt sind Abkürzungen - die vermeintlich kleinsten Einheiten wissenschaftlicher Aushandlung und Verständigung. Der in den Erziehungs-, Sozial-, Medien- und Kunstwissenschaften verankerte Band zeichnet ein vieldimensionales Bild gegenwärtigen Forschens mit transdisziplinären Anknüpfungspunkten zwischen Digitalität und Bildung