Is attention all you need in medical image analysis? A review

Medical imaging is a key component in clinical diagnosis, treatment planning and clinical trial design, accounting for almost 90% of all healthcare data. CNNs achieved performance gains in medical image analysis (MIA) over the last years. CNNs can efficiently model local pixel interactions and be trained on small-scale MI data. The main disadvantage of typical CNN models is that they ignore global pixel relationships within images, which limits their generalisation ability to understand out-of-distribution data with different 'global' information. The recent progress of Artificial Intelligence gave rise to Transformers, which can learn global relationships from data. However, full Transformer models need to be trained on large-scale data and involve tremendous computational complexity. Attention and Transformer compartments (Transf/Attention) which can well maintain properties for modelling global relationships, have been proposed as lighter alternatives of full Transformers. Recently, there is an increasing trend to co-pollinate complementary local-global properties from CNN and Transf/Attention architectures, which led to a new era of hybrid models. The past years have witnessed substantial growth in hybrid CNN-Transf/Attention models across diverse MIA problems. In this systematic review, we survey existing hybrid CNN-Transf/Attention models, review and unravel key architectural designs, analyse breakthroughs, and evaluate current and future opportunities as well as challenges. We also introduced a comprehensive analysis framework on generalisation opportunities of scientific and clinical impact, based on which new data-driven domain generalisation and adaptation methods can be stimulated

A Survey on Knowledge Graphs: Representation, Acquisition and Applications

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions

Semantic Representation and Inference for NLP

Semantic representation and inference is essential for Natural Language Processing (NLP). The state of the art for semantic representation and inference is deep learning, and particularly Recurrent Neural Networks (RNNs), Convolutional Neural Networks (CNNs), and transformer Self-Attention models. This thesis investigates the use of deep learning for novel semantic representation and inference, and makes contributions in the following three areas: creating training data, improving semantic representations and extending inference learning. In terms of creating training data, we contribute the largest publicly available dataset of real-life factual claims for the purpose of automatic claim verification (MultiFC), and we present a novel inference model composed of multi-scale CNNs with different kernel sizes that learn from external sources to infer fact checking labels. In terms of improving semantic representations, we contribute a novel model that captures non-compositional semantic indicators. By definition, the meaning of a non-compositional phrase cannot be inferred from the individual meanings of its composing words (e.g., hot dog). Motivated by this, we operationalize the compositionality of a phrase contextually by enriching the phrase representation with external word embeddings and knowledge graphs. Finally, in terms of inference learning, we propose a series of novel deep learning architectures that improve inference by using syntactic dependencies, by ensembling role guided attention heads, incorporating gating layers, and concatenating multiple heads in novel and effective ways. This thesis consists of seven publications (five published and two under review).Comment: PhD thesis, the University of Copenhage

Transformers in Machine Learning: Literature Review

In this study, the researcher presents an approach regarding methods in Transformer Machine Learning. Initially, transformers are neural network architectures that are considered as inputs. Transformers are widely used in various studies with various objects. The transformer is one of the deep learning architectures that can be modified. Transformers are also mechanisms that study contextual relationships between words. Transformers are used for text compression in readings. Transformers are used to recognize chemical images with an accuracy rate of 96%. Transformers are used to detect a person's emotions. Transformer to detect emotions in social media conversations, for example, on Facebook with happy, sad, and angry categories. Figure 1 illustrates the encoder and decoder process through the input process and produces output. the purpose of this study is to only review literature from various journals that discuss transformers. This explanation is also done by presenting the subject or dataset, data analysis method, year, and accuracy achieved. By using the methods presented, researchers can conclude results in search of the highest accuracy and opportunities for further research

Data-efficient methods for information extraction

Strukturierte Wissensrepräsentationssysteme wie Wissensdatenbanken oder Wissensgraphen bieten Einblicke in Entitäten und Beziehungen zwischen diesen Entitäten in der realen Welt. Solche Wissensrepräsentationssysteme können in verschiedenen Anwendungen der natürlichen Sprachverarbeitung eingesetzt werden, z. B. bei der semantischen Suche, der Beantwortung von Fragen und der Textzusammenfassung. Es ist nicht praktikabel und ineffizient, diese Wissensrepräsentationssysteme manuell zu befüllen. In dieser Arbeit entwickeln wir Methoden, um automatisch benannte Entitäten und Beziehungen zwischen den Entitäten aus Klartext zu extrahieren. Unsere Methoden können daher verwendet werden, um entweder die bestehenden unvollständigen Wissensrepräsentationssysteme zu vervollständigen oder ein neues strukturiertes Wissensrepräsentationssystem von Grund auf zu erstellen. Im Gegensatz zu den gängigen überwachten Methoden zur Informationsextraktion konzentrieren sich unsere Methoden auf das Szenario mit wenigen Daten und erfordern keine große Menge an kommentierten Daten. Im ersten Teil der Arbeit haben wir uns auf das Problem der Erkennung von benannten Entitäten konzentriert. Wir haben an der gemeinsamen Aufgabe von Bacteria Biotope 2019 teilgenommen. Die gemeinsame Aufgabe besteht darin, biomedizinische Entitätserwähnungen zu erkennen und zu normalisieren. Unser linguistically informed Named-Entity-Recognition-System besteht aus einem Deep-Learning-basierten Modell, das sowohl verschachtelte als auch flache Entitäten extrahieren kann; unser Modell verwendet mehrere linguistische Merkmale und zusätzliche Trainingsziele, um effizientes Lernen in datenarmen Szenarien zu ermöglichen. Unser System zur Entitätsnormalisierung verwendet String-Match, Fuzzy-Suche und semantische Suche, um die extrahierten benannten Entitäten mit den biomedizinischen Datenbanken zu verknüpfen. Unser System zur Erkennung von benannten Entitäten und zur Entitätsnormalisierung erreichte die niedrigste Slot-Fehlerrate von 0,715 und belegte den ersten Platz in der gemeinsamen Aufgabe. Wir haben auch an zwei gemeinsamen Aufgaben teilgenommen: Adverse Drug Effect Span Detection (Englisch) und Profession Span Detection (Spanisch); beide Aufgaben sammeln Daten von der Social Media Plattform Twitter. Wir haben ein Named-Entity-Recognition-Modell entwickelt, das die Eingabedarstellung des Modells durch das Stapeln heterogener Einbettungen aus verschiedenen Domänen verbessern kann; unsere empirischen Ergebnisse zeigen komplementäres Lernen aus diesen heterogenen Einbettungen. Unser Beitrag belegte den 3. Platz in den beiden gemeinsamen Aufgaben. Im zweiten Teil der Arbeit untersuchten wir Strategien zur Erweiterung synthetischer Daten, um ressourcenarme Informationsextraktion in spezialisierten Domänen zu ermöglichen. Insbesondere haben wir backtranslation an die Aufgabe der Erkennung von benannten Entitäten auf Token-Ebene und der Extraktion von Beziehungen auf Satzebene angepasst. Wir zeigen, dass die Rückübersetzung sprachlich vielfältige und grammatikalisch kohärente synthetische Sätze erzeugen kann und als wettbewerbsfähige Erweiterungsstrategie für die Aufgaben der Erkennung von benannten Entitäten und der Extraktion von Beziehungen dient. Bei den meisten realen Aufgaben zur Extraktion von Beziehungen stehen keine kommentierten Daten zur Verfügung, jedoch ist häufig ein großer unkommentierter Textkorpus vorhanden. Bootstrapping-Methoden zur Beziehungsextraktion können mit diesem großen Korpus arbeiten, da sie nur eine Handvoll Startinstanzen benötigen. Bootstrapping-Methoden neigen jedoch dazu, im Laufe der Zeit Rauschen zu akkumulieren (bekannt als semantische Drift), und dieses Phänomen hat einen drastischen negativen Einfluss auf die endgültige Genauigkeit der Extraktionen. Wir entwickeln zwei Methoden zur Einschränkung des Bootstrapping-Prozesses, um die semantische Drift bei der Extraktion von Beziehungen zu minimieren. Unsere Methoden nutzen die Graphentheorie und vortrainierte Sprachmodelle, um verrauschte Extraktionsmuster explizit zu identifizieren und zu entfernen. Wir berichten über die experimentellen Ergebnisse auf dem TACRED-Datensatz für vier Relationen. Im letzten Teil der Arbeit demonstrieren wir die Anwendung der Domänenanpassung auf die anspruchsvolle Aufgabe der mehrsprachigen Akronymextraktion. Unsere Experimente zeigen, dass die Domänenanpassung die Akronymextraktion in wissenschaftlichen und juristischen Bereichen in sechs Sprachen verbessern kann, darunter auch Sprachen mit geringen Ressourcen wie Persisch und Vietnamesisch.The structured knowledge representation systems such as knowledge base or knowledge graph can provide insights regarding entities and relationship(s) among these entities in the real-world, such knowledge representation systems can be employed in various natural language processing applications such as semantic search, question answering and text summarization. It is infeasible and inefficient to manually populate these knowledge representation systems. In this work, we develop methods to automatically extract named entities and relationships among the entities from plain text and hence our methods can be used to either complete the existing incomplete knowledge representation systems to create a new structured knowledge representation system from scratch. Unlike mainstream supervised methods for information extraction, our methods focus on the low-data scenario and do not require a large amount of annotated data. In the first part of the thesis, we focused on the problem of named entity recognition. We participated in the shared task of Bacteria Biotope 2019, the shared task consists of recognizing and normalizing the biomedical entity mentions. Our linguistically informed named entity recognition system consists of a deep learning based model which can extract both nested and flat entities; our model employed several linguistic features and auxiliary training objectives to enable efficient learning in data-scarce scenarios. Our entity normalization system employed string match, fuzzy search and semantic search to link the extracted named entities to the biomedical databases. Our named entity recognition and entity normalization system achieved the lowest slot error rate of 0.715 and ranked first in the shared task. We also participated in two shared tasks of Adverse Drug Effect Span detection (English) and Profession Span Detection (Spanish); both of these tasks collect data from the social media platform Twitter. We developed a named entity recognition model which can improve the input representation of the model by stacking heterogeneous embeddings from a diverse domain(s); our empirical results demonstrate complementary learning from these heterogeneous embeddings. Our submission ranked 3rd in both of the shared tasks. In the second part of the thesis, we explored synthetic data augmentation strategies to address low-resource information extraction in specialized domains. Specifically, we adapted backtranslation to the token-level task of named entity recognition and sentence-level task of relation extraction. We demonstrate that backtranslation can generate linguistically diverse and grammatically coherent synthetic sentences and serve as a competitive augmentation strategy for the task of named entity recognition and relation extraction. In most of the real-world relation extraction tasks, the annotated data is not available, however, quite often a large unannotated text corpus is available. Bootstrapping methods for relation extraction can operate on this large corpus as they only require a handful of seed instances. However, bootstrapping methods tend to accumulate noise over time (known as semantic drift) and this phenomenon has a drastic negative impact on the final precision of the extractions. We develop two methods to constrain the bootstrapping process to minimise semantic drift for relation extraction; our methods leverage graph theory and pre-trained language models to explicitly identify and remove noisy extraction patterns. We report the experimental results on the TACRED dataset for four relations. In the last part of the thesis, we demonstrate the application of domain adaptation to the challenging task of multi-lingual acronym extraction. Our experiments demonstrate that domain adaptation can improve acronym extraction within scientific and legal domains in 6 languages including low-resource languages such as Persian and Vietnamese