Improving Relation Extraction From Unstructured Genealogical Texts Using Fine-Tuned Transformers

Though exploring one’s family lineage through genealogical family trees can be insightful to developing one’s identity, this knowledge is typically held behind closed doors by private companies or require expensive technologies, such as DNA testing, to uncover. With the ever-booming explosion of data on the world wide web, many unstructured text documents, both old and new, are being discovered, written, and processed which contain rich genealogical information. With access to this immense amount of data, however, entails a costly process whereby people, typically volunteers, have to read large amounts of text to find relationships between people. This delays having genealogical information be open and accessible to all. This thesis explores state-of-the-art methods for relation extraction across the genealogical and biomedical domains and bridges new and old research by proposing an updated three-tier system for parsing unstructured documents. This system makes use of recently developed and massively pretrained transformers and fine-tuning techniques to take advantage of these deep neural models’ inherent understanding of English syntax and semantics for classification. With only a fraction of labeled data typically needed to train large models, fine-tuning a LUKE relation classification model with minimal added features can identify genealogical relationships with macro precision, recall, and F1 scores of 0.880, 0.867, and 0.871, respectively, in data sets with scarce (∼10%) positive relations. Further- more, with the advent of a modern coreference resolution system utilizing SpanBERT embeddings and a modern named entity parser, our end-to-end pipeline can extract and correctly classify relationships within unstructured documents with macro precision, recall, and F1 scores of 0.794, 0.616, and 0.676, respectively. This thesis also evaluates individual components of the system and discusses future improvements to be made

A Survey on Semantic Processing Techniques

Semantic processing is a fundamental research domain in computational linguistics. In the era of powerful pre-trained language models and large language models, the advancement of research in this domain appears to be decelerating. However, the study of semantics is multi-dimensional in linguistics. The research depth and breadth of computational semantic processing can be largely improved with new technologies. In this survey, we analyzed five semantic processing tasks, e.g., word sense disambiguation, anaphora resolution, named entity recognition, concept extraction, and subjectivity detection. We study relevant theoretical research in these fields, advanced methods, and downstream applications. We connect the surveyed tasks with downstream applications because this may inspire future scholars to fuse these low-level semantic processing tasks with high-level natural language processing tasks. The review of theoretical research may also inspire new tasks and technologies in the semantic processing domain. Finally, we compare the different semantic processing techniques and summarize their technical trends, application trends, and future directions.Comment: Published at Information Fusion, Volume 101, 2024, 101988, ISSN 1566-2535. The equal contribution mark is missed in the published version due to the publication policies. Please contact Prof. Erik Cambria for detail

Cross-Domain information extraction from scientific articles for research knowledge graphs

Today’s scholarly communication is a document-centred process and as such, rather inefficient. Fundamental contents of research papers are not accessible by computers since they are only present in unstructured PDF files. Therefore, current research infrastructures are not able to assist scientists appropriately in their core research tasks. This thesis addresses this issue and proposes methods to automatically extract relevant information from scientific articles for Research Knowledge Graphs (RKGs) that represent scholarly knowledge structured and interlinked. First, this thesis conducts a requirements analysis for an Open Research Knowledge Graph (ORKG). We present literature-related use cases of researchers that should be supported by an ORKG-based system and their specific requirements for the underlying ontology and instance data. Based on this analysis, the identified use cases are categorised into two groups: The first group of use cases needs manual or semi-automatic approaches for knowledge graph (KG) construction since they require high correctness of the instance data. The second group requires high completeness and can tolerate noisy instance data. Thus, this group needs automatic approaches for KG population. This thesis focuses on the second group of use cases and provides contributions for machine learning tasks that aim to support them. To assess the relevance of a research paper, scientists usually skim through titles, abstracts, introductions, and conclusions. An organised presentation of the articles' essential information would make this process more time-efficient. The task of sequential sentence classification addresses this issue by classifying sentences in an article in categories like research problem, used methods, or obtained results. To address this problem, we propose a novel unified cross-domain multi-task deep learning approach that makes use of datasets from different scientific domains (e.g. biomedicine and computer graphics) and varying structures (e.g. datasets covering either only abstracts or full papers). Our approach outperforms the state of the art on full paper datasets significantly while being competitive for datasets consisting of abstracts. Moreover, our approach enables the categorisation of sentences in a domain-independent manner. Furthermore, we present the novel task of domain-independent information extraction to extract scientific concepts from research papers in a domain-independent manner. This task aims to support the use cases find related work and get recommended articles. For this purpose, we introduce a set of generic scientific concepts that are relevant over ten domains in Science, Technology, and Medicine (STM) and release an annotated dataset of 110 abstracts from these domains. Since the annotation of scientific text is costly, we suggest an active learning strategy based on a state-of-the-art deep learning approach. The proposed method enables us to nearly halve the amount of required training data. Then, we extend this domain-independent information extraction approach with the task of \textit{coreference resolution}. Coreference resolution aims to identify mentions that refer to the same concept or entity. Baseline results on our corpus with current state-of-the-art approaches for coreference resolution showed that current approaches perform poorly on scientific text. Therefore, we propose a sequential transfer learning approach that exploits annotated datasets from non-academic domains. Our experimental results demonstrate that our approach noticeably outperforms the state-of-the-art baselines. Additionally, we investigate the impact of coreference resolution on KG population. We demonstrate that coreference resolution has a small impact on the number of resulting concepts in the KG, but improved its quality significantly. Consequently, using our domain-independent information extraction approach, we populate an RKG from 55,485 abstracts of the ten investigated STM domains. We show that every domain mainly uses its own terminology and that the populated RKG contains useful concepts. Moreover, we propose a novel approach for the task of \textit{citation recommendation}. This task can help researchers improve the quality of their work by finding or recommending relevant related work. Our approach exploits RKGs that interlink research papers based on mentioned scientific concepts. Using our automatically populated RKG, we demonstrate that the combination of information from RKGs with existing state-of-the-art approaches is beneficial. Finally, we conclude the thesis and sketch possible directions of future work.Die Kommunikation von Forschungsergebnissen erfolgt heutzutage in Form von Dokumenten und ist aus verschiedenen Gründen ineffizient. Wesentliche Inhalte von Forschungsarbeiten sind für Computer nicht zugänglich, da sie in unstrukturierten PDF-Dateien verborgen sind. Daher können derzeitige Forschungsinfrastrukturen Forschende bei ihren Kernaufgaben nicht angemessen unterstützen. Diese Arbeit befasst sich mit dieser Problemstellung und untersucht Methoden zur automatischen Extraktion von relevanten Informationen aus Forschungspapieren für Forschungswissensgraphen (Research Knowledge Graphs). Solche Graphen sollen wissenschaftliches Wissen maschinenlesbar strukturieren und verknüpfen. Zunächst wird eine Anforderungsanalyse für einen Open Research Knowledge Graph (ORKG) durchgeführt. Wir stellen literaturbezogene Anwendungsfälle von Forschenden vor, die durch ein ORKG-basiertes System unterstützt werden sollten, und deren spezifische Anforderungen an die zugrundeliegende Ontologie und die Instanzdaten. Darauf aufbauend werden die identifizierten Anwendungsfälle in zwei Gruppen eingeteilt: Die erste Gruppe von Anwendungsfällen benötigt manuelle oder halbautomatische Ansätze für die Konstruktion eines ORKG, da sie eine hohe Korrektheit der Instanzdaten erfordern. Die zweite Gruppe benötigt eine hohe Vollständigkeit der Instanzdaten und kann fehlerhafte Daten tolerieren. Daher erfordert diese Gruppe automatische Ansätze für die Konstruktion des ORKG. Diese Arbeit fokussiert sich auf die zweite Gruppe von Anwendungsfällen und schlägt Methoden für maschinelle Aufgabenstellungen vor, die diese Anwendungsfälle unterstützen können. Um die Relevanz eines Forschungsartikels effizient beurteilen zu können, schauen sich Forschende in der Regel die Titel, Zusammenfassungen, Einleitungen und Schlussfolgerungen an. Durch eine strukturierte Darstellung von wesentlichen Informationen des Artikels könnte dieser Prozess zeitsparender gestaltet werden. Die Aufgabenstellung der sequenziellen Satzklassifikation befasst sich mit diesem Problem, indem Sätze eines Artikels in Kategorien wie Forschungsproblem, verwendete Methoden oder erzielte Ergebnisse automatisch klassifiziert werden. In dieser Arbeit wird für diese Aufgabenstellung ein neuer vereinheitlichter Multi-Task Deep-Learning-Ansatz vorgeschlagen, der Datensätze aus verschiedenen wissenschaftlichen Bereichen (z. B. Biomedizin und Computergrafik) mit unterschiedlichen Strukturen (z. B. Datensätze bestehend aus Zusammenfassungen oder vollständigen Artikeln) nutzt. Unser Ansatz übertrifft State-of-the-Art-Verfahren der Literatur auf Benchmark-Datensätzen bestehend aus vollständigen Forschungsartikeln. Außerdem ermöglicht unser Ansatz die Klassifizierung von Sätzen auf eine domänenunabhängige Weise. Darüber hinaus stellen wir die neue Aufgabenstellung domänenübergreifende Informationsextraktion vor. Hierbei werden, unabhängig vom behandelten wissenschaftlichen Fachgebiet, inhaltliche Konzepte aus Forschungspapieren extrahiert. Damit sollen die Anwendungsfälle Finden von verwandten Arbeiten und Empfehlung von Artikeln unterstützt werden. Zu diesem Zweck führen wir eine Reihe von generischen wissenschaftlichen Konzepten ein, die in zehn Bereichen der Wissenschaft, Technologie und Medizin (STM) relevant sind, und veröffentlichen einen annotierten Datensatz von 110 Zusammenfassungen aus diesen Bereichen. Da die Annotation wissenschaftlicher Texte aufwändig ist, kombinieren wir ein Active-Learning-Verfahren mit einem aktuellen Deep-Learning-Ansatz, um die notwendigen Trainingsdaten zu reduzieren. Die vorgeschlagene Methode ermöglicht es uns, die Menge der erforderlichen Trainingsdaten nahezu zu halbieren. Anschließend erweitern wir unseren domänenunabhängigen Ansatz zur Informationsextraktion um die Aufgabe der Koreferenzauflösung. Die Auflösung von Koreferenzen zielt darauf ab, Erwähnungen zu identifizieren, die sich auf dasselbe Konzept oder dieselbe Entität beziehen. Experimentelle Ergebnisse auf unserem Korpus mit aktuellen Ansätzen zur Koreferenzauflösung haben gezeigt, dass diese bei wissenschaftlichen Texten unzureichend abschneiden. Daher schlagen wir eine Transfer-Learning-Methode vor, die annotierte Datensätze aus nicht-akademischen Bereichen nutzt. Die experimentellen Ergebnisse zeigen, dass unser Ansatz deutlich besser abschneidet als die bisherigen Ansätze. Darüber hinaus untersuchen wir den Einfluss der Koreferenzauflösung auf die Erstellung von Wissensgraphen. Wir zeigen, dass diese einen geringen Einfluss auf die Anzahl der resultierenden Konzepte in dem Wissensgraphen hat, aber die Qualität des Wissensgraphen deutlich verbessert. Mithilfe unseres domänenunabhängigen Ansatzes zur Informationsextraktion haben wir aus 55.485 Zusammenfassungen der zehn untersuchten STM-Domänen einen Forschungswissensgraphen erstellt. Unsere Analyse zeigt, dass jede Domäne hauptsächlich ihre eigene Terminologie verwendet und dass der erstellte Wissensgraph nützliche Konzepte enthält. Schließlich schlagen wir einen Ansatz für die Empfehlung von passenden Referenzen vor. Damit können Forschende einfacher relevante verwandte Arbeiten finden oder passende Empfehlungen erhalten. Unser Ansatz nutzt Forschungswissensgraphen, die Forschungsarbeiten mit in ihnen erwähnten wissenschaftlichen Konzepten verknüpfen. Wir zeigen, dass aktuelle Verfahren zur Empfehlung von Referenzen von zusätzlichen Informationen aus einem automatisch erstellten Wissensgraphen profitieren. Zum Schluss wird ein Fazit gezogen und ein Ausblick für mögliche zukünftige Arbeiten gegeben

Thinking outside the graph: scholarly knowledge graph construction leveraging natural language processing

Despite improved digital access to scholarly knowledge in recent decades, scholarly communication remains exclusively document-based. The document-oriented workflows in science publication have reached the limits of adequacy as highlighted by recent discussions on the increasing proliferation of scientific literature, the deficiency of peer-review and the reproducibility crisis. In this form, scientific knowledge remains locked in representations that are inadequate for machine processing. As long as scholarly communication remains in this form, we cannot take advantage of all the advancements taking place in machine learning and natural language processing techniques. Such techniques would facilitate the transformation from pure text based into (semi-)structured semantic descriptions that are interlinked in a collection of big federated graphs. We are in dire need for a new age of semantically enabled infrastructure adept at storing, manipulating, and querying scholarly knowledge. Equally important is a suite of machine assistance tools designed to populate, curate, and explore the resulting scholarly knowledge graph. In this thesis, we address the issue of constructing a scholarly knowledge graph using natural language processing techniques. First, we tackle the issue of developing a scholarly knowledge graph for structured scholarly communication, that can be populated and constructed automatically. We co-design and co-implement the Open Research Knowledge Graph (ORKG), an infrastructure capable of modeling, storing, and automatically curating scholarly communications. Then, we propose a method to automatically extract information into knowledge graphs. With Plumber, we create a framework to dynamically compose open information extraction pipelines based on the input text. Such pipelines are composed from community-created information extraction components in an effort to consolidate individual research contributions under one umbrella. We further present MORTY as a more targeted approach that leverages automatic text summarization to create from the scholarly article's text structured summaries containing all required information. In contrast to the pipeline approach, MORTY only extracts the information it is instructed to, making it a more valuable tool for various curation and contribution use cases. Moreover, we study the problem of knowledge graph completion. exBERT is able to perform knowledge graph completion tasks such as relation and entity prediction tasks on scholarly knowledge graphs by means of textual triple classification. Lastly, we use the structured descriptions collected from manual and automated sources alike with a question answering approach that builds on the machine-actionable descriptions in the ORKG. We propose JarvisQA, a question answering interface operating on tabular views of scholarly knowledge graphs i.e., ORKG comparisons. JarvisQA is able to answer a variety of natural language questions, and retrieve complex answers on pre-selected sub-graphs. These contributions are key in the broader agenda of studying the feasibility of natural language processing methods on scholarly knowledge graphs, and lays the foundation of which methods can be used on which cases. Our work indicates what are the challenges and issues with automatically constructing scholarly knowledge graphs, and opens up future research directions

Towards the extraction of cross-sentence relations through event extraction and entity coreference

Cross-sentence relation extraction deals with the extraction of relations beyond the sentence boundary. This thesis focuses on two of the NLP tasks which are of importance to the successful extraction of cross-sentence relation mentions: event extraction and coreference resolution. The first part of the thesis focuses on addressing data sparsity issues in event extraction. We propose a self-training approach for obtaining additional labeled examples for the task. The process starts off with a Bi-LSTM event tagger trained on a small labeled data set which is used to discover new event instances in a large collection of unstructured text. The high confidence model predictions are selected to construct a data set of automatically-labeled training examples. We present several ways in which the resulting data set can be used for re-training the event tagger in conjunction with the initial labeled data. The best configuration achieves statistically significant improvement over the baseline on the ACE 2005 test set (macro-F1), as well as in a 10-fold cross validation (micro- and macro-F1) evaluation. Our error analysis reveals that the augmentation approach is especially beneficial for the classification of the most under-represented event types in the original data set. The second part of the thesis focuses on the problem of coreference resolution. While a certain level of precision can be reached by modeling surface information about entity mentions, their successful resolution often depends on semantic or world knowledge. This thesis investigates an unsupervised source of such knowledge, namely distributed word representations. We present several ways in which word embeddings can be utilized to extract features for a supervised coreference resolver. Our evaluation results and error analysis show that each of these features helps improve over the baseline coreference system’s performance, with a statistically significant improvement (CoNLL F1) achieved when the proposed features are used jointly. Moreover, all features lead to a reduction in the amount of precision errors in resolving references between common nouns, demonstrating that they successfully incorporate semantic information into the process