Implicit Incremental Model Analyses and Transformations

When models of a system change, analyses based on them have to be reevaluated in order for the results to stay meaningful. In many cases, the time to get updated analysis results is critical. This thesis proposes multiple, combinable approaches and a new formalism based on category theory for implicitly incremental model analyses and transformations. The advantages of the implementation are validated using seven case studies, partially drawn from the Transformation Tool Contest (TTC)

Implicit Incremental Model Analyses and Transformations

In vielen Ingenieursdisziplinen werden Modelle verwendet, um Systeme verschiedenster Art auf einem hohen Abstraktionsgrad zu beschreiben. Auf diesem Abstraktionsgrad ist es häufig einfacher, Aussagen über den Zustand des Systems zu treffen. Wenn sich Modelle eines Systems ändern – beispielsweise, weil sich das System selbst geändert hat – müssen Analysen auf Grundlage dieses Modells jedoch neu berechnet werden, um weiterhin gültig zu sein. In vielen Fällen ist diese Neuberechnung der Analyseergebnisse zeitkritisch. Da sich oft nur kleine Teile des Modells ändern, könnten zwar große Teile des letzten Analysedurchlaufs durch eine inkrementelle Ausführung der Analyse wiederverwendet werden, in der Praxis ist eine solche Inkrementalisierung aber nicht trivial und oft fehleranfällig. Eine Lösungsmöglichkeit für dieses Problem bietet der Ansatz der impliziten Inkrementalisierung, bei der ein inkrementeller Algorithmus für eine gegebene Analyse aus der Batch-Spezifikation abgeleitet wird. Aus der Spezifikation wird ein dynamischer Abhängigkeitsgraph konstruiert, der es erlaubt, nur die Teile einer Analyse neu auszuwerten, die von einer Änderung tatsächlich betroffen sind. Damit lassen sich Vorteile einer Inkrementalisierung nutzen, ohne dass der Code angepasst werden muss und die Lesbarkeit des Analysecodes leidet. Leider unterstützen derzeitige Verfahren für implizite Inkrementalisierung nur eine bestimmte Klasse von Analysen, sind auf eine Inkrementalisierung auf Ebene von einzelnen Instruktionen beschränkt oder benötigen eine explizite Zustandsverwaltung. Auch mit diesen Verbesserungen ist unklar, in welchen Fällen eine Inkrementalisierung Vorteile bringt, da in einigen Szenarien Änderungen Schmetterlingseffekte verursachen können und eine Wiederverwertung des letzten Analysedurchlaufs keinerlei Beschleunigungspotential hat. Diese Dissertation behandelt diese Probleme bei impliziter Inkrementalisierung von Modellanalysen mittels mehrerer Verfahren, die größtenteils kombinierbar sind. Desweiteren wird ein neuer Formalismus vorgestellt, mit dessen Hilfe Inkrementalisierungssysteme auch für uni- oder bidirektionale Modelltransformationen einsetzbar sind. Um die Korrektheit der entstehenden inkrementellen Modellanalysen zu definieren und zu zeigen, wird Inkrementalisierung in Kategorientheorie als Funktor beschrieben. Ein erstes Verfahren ermöglicht als direkte Konsequenz der formalen Darstellung die Inkrementalisierung auf Ebene von Methodenaufrufen, sodass für häufig verwendete Operatoren eine optimierte Inkrementalisierung zur Verfügung gestellt werden kann. Durch Erweiterung des Funktors auf Verteilung lassen sich auf ähnliche Weise auch etwaige Speicherprobleme lösen. Ein zweites Verfahren vereinfacht die entstehenden dynamischen Abhängigkeitsgraphen, indem Teile der Analyse durch eine generalisierte Betrachtung von Modelländerungen mit mehreren Strategien zusammengefasst werden können. Die Auswahl der Strategien ermöglicht dem Entwickler eine Anpassung der Inkrementalisierung auf einen konkreten Anwendungsfall. Alternativ kann für ein gegebenes Szenario auch durch automatische Entwurfsraumexploration eine (Pareto-) optimale Konfiguration hinsichtlich Speicherverbrauch und Antwortzeit der Aktualisierung eines Analyseergebnisses nach einer Modelländerung gefunden werden. Die Kombination dieser Verfahren ermöglicht es, die Performanz von Inkrementalisierungen so zu verbessern, dass diese bis auf einmalige Initialisierung nie schlechter ist als die batchmäßige Wiederholung der Analyse, in vielen Fällen aber teils deutlich schneller sein kann. Generische Operatoren, die in vielen Modellanalysen wiederverwendet werden, können für die Inkrementalisierung durch geeignete Algorithmen spezifisch optimiert werden, während komplexe Domänenlogik durch das System optimiert werden kann. Durch den impliziten Ansatz geschehen diese Verbesserungen vollautomatisch und transparent für den Entwickler der Modellanalyse. Obwohl der so geschaffene Ansatz Turing-mächtig und somit universell einsetzbar ist, gibt es doch gerade in der modellgetriebenen Entwicklung eine Klasse von Artefakten, die eine besondere Betrachtung erfordern, da sie sich im Allgemeinen nur schwer mit gewöhnlichen objekt-orientierten Sprachen beschreiben lassen: Modelltransformationen. Daher wird in dieser Dissertation ein neuer Formalismus und eine darauf aufbauende Sprache vorgestellt, die Modelltransformationen so beschreiben, dass diese leicht mit Hilfe eines Inkrementalisierungssystems inkrementell ausgeführt werden können. Die Synchronisierung einer Modelländerung ist hierbei bewiesen korrekt und hippokratisch. Alle Verfahren wurden implementiert und in das .NET Modeling Framework integriert, welches Entwickler auf der .NET Plattform bei der modellgetriebenen Entwicklung unterstützen soll. Die entstandenen Vorteile aller Verfahren hinsichtlich Performanz werden anhand von sieben Fallstudien in verschiedenen Domänen validiert. Insbesondere werden hierzu fünf Fallstudien des Transformation Tool Contests (TTC) der Jahre 2015 bis 2017 herangezogen, für die auch mit anderen Ansätzen verfasste Lösungen zur Verfügung stehen. Die Ausdrucksmächtigkeit der Modelltransformationssprache wird durch eine Transformation der in der modellgetriebenen Entwicklung weit verbreiteten Transformationssprache ATL in die neu geschaffene Transformationssprache validiert. Mithilfe dieser Transformation wird weiterhin die Ausführungsgeschwindigkeit von Modelltransformationen mit der von ATL in einigen Modelltransformationen verglichen. Die Ergebnisse aus den Fallstudien zeigen gerade bei der Anwendung des Inkrementalisierungssystems auf Modelltransformationen deutliche Performance-Steigerungen im Vergleich zu herkömmlichen Modelltransformationen, aber auch gegenüber anderen inkrementellen Modelltransformationssprachen zeigt der vorgestellte Ansatz deutliche Beschleunigungen, teils um mehrere Größenordnungen. Insbesondere weisen die Fallstudien darauf hin, dass die benötigte Zeit für die Propagation von Änderungen des Eingabemodells in vielen Fällen unabhängig von der Größe des Eingabemodells ist. Gerade bei großen Eingabemodellen kommen so sehr hohe Beschleunigungen zustande. Die Inkrementalisierung einer Analyse ist dabei immer an das Metamodell gebunden. In der Praxis verwenden aber die meisten eingesetzten Metamodelle nur den eingeschränkten Modellierungsstandard EMOF, der teilweise zu einer unnötigen Komplexität des Metamodells führt und viele Analysen überhaupt erst notwendig macht. Eine Erweiterung des Modellierungsstandards kann hier einige Klassen von Modellanalysen komplett überflüssig machen und andere Analysen deutlich vereinfachen, sowie auch die Performance der entsprechenden Analyse beschleunigen

Neural information extraction from natural language text

Natural language processing (NLP) deals with building computational techniques that allow computers to automatically analyze and meaningfully represent human language. With an exponential growth of data in this digital era, the advent of NLP-based systems has enabled us to easily access relevant information via a wide range of applications, such as web search engines, voice assistants, etc. To achieve it, a long-standing research for decades has been focusing on techniques at the intersection of NLP and machine learning. In recent years, deep learning techniques have exploited the expressive power of Artificial Neural Networks (ANNs) and achieved state-of-the-art performance in a wide range of NLP tasks. Being one of the vital properties, Deep Neural Networks (DNNs) can automatically extract complex features from the input data and thus, provide an alternative to the manual process of handcrafted feature engineering. Besides ANNs, Probabilistic Graphical Models (PGMs), a coupling of graph theory and probabilistic methods have the ability to describe causal structure between random variables of the system and capture a principled notion of uncertainty. Given the characteristics of DNNs and PGMs, they are advantageously combined to build powerful neural models in order to understand the underlying complexity of data. Traditional machine learning based NLP systems employed shallow computational methods (e.g., SVM or logistic regression) and relied on handcrafting features which is time-consuming, complex and often incomplete. However, deep learning and neural network based methods have recently shown superior results on various NLP tasks, such as machine translation, text classification, namedentity recognition, relation extraction, textual similarity, etc. These neural models can automatically extract an effective feature representation from training data. This dissertation focuses on two NLP tasks: relation extraction and topic modeling. The former aims at identifying semantic relationships between entities or nominals within a sentence or document. Successfully extracting the semantic relationships greatly contributes in building structured knowledge bases, useful in downstream NLP application areas of web search, question-answering, recommendation engines, etc. On other hand, the task of topic modeling aims at understanding the thematic structures underlying in a collection of documents. Topic modeling is a popular text-mining tool to automatically analyze a large collection of documents and understand topical semantics without actually reading them. In doing so, it generates word clusters (i.e., topics) and document representations useful in document understanding and information retrieval, respectively. Essentially, the tasks of relation extraction and topic modeling are built upon the quality of representations learned from text. In this dissertation, we have developed task-specific neural models for learning representations, coupled with relation extraction and topic modeling tasks in the realms of supervised and unsupervised machine learning paradigms, respectively. More specifically, we make the following contributions in developing neural models for NLP tasks: 1. Neural Relation Extraction: Firstly, we have proposed a novel recurrent neural network based architecture for table-filling in order to jointly perform entity and relation extraction within sentences. Then, we have further extended our scope of extracting relationships between entities across sentence boundaries, and presented a novel dependency-based neural network architecture. The two contributions lie in the supervised paradigm of machine learning. Moreover, we have contributed in building a robust relation extractor constrained by the lack of labeled data, where we have proposed a novel weakly-supervised bootstrapping technique. Given the contributions, we have further explored interpretability of the recurrent neural networks to explain their predictions for the relation extraction task. 2. Neural Topic Modeling: Besides the supervised neural architectures, we have also developed unsupervised neural models to learn meaningful document representations within topic modeling frameworks. Firstly, we have proposed a novel dynamic topic model that captures topics over time. Next, we have contributed in building static topic models without considering temporal dependencies, where we have presented neural topic modeling architectures that also exploit external knowledge, i.e., word embeddings to address data sparsity. Moreover, we have developed neural topic models that incorporate knowledge transfers using both the word embeddings and latent topics from many sources. Finally, we have shown improving neural topic modeling by introducing language structures (e.g., word ordering, local syntactic and semantic information, etc.) that deals with bag-of-words issues in traditional topic models. The class of proposed neural NLP models in this section are based on techniques at the intersection of PGMs, deep learning and ANNs. Here, the task of neural relation extraction employs neural networks to learn representations typically at the sentence level, without access to the broader document context. However, topic models have access to statistical information across documents. Therefore, we advantageously combine the two complementary learning paradigms in a neural composite model, consisting of a neural topic and a neural language model that enables us to jointly learn thematic structures in a document collection via the topic model, and word relations within a sentence via the language model. Overall, our research contributions in this dissertation extend NLP-based systems for relation extraction and topic modeling tasks with state-of-the-art performances

The role of common genetic variants for predicting the modulation of cardiovascular outcomes

Attrition is a major issue in the drug development process with 79% of clinical failures due to safety and efficacy concerns. Genetic research can provide supporting evidence of a clear causal relationship between the drug target and disease or reveal unintended effects through associations with non-relevant phenotypes informing on potential drug safety. However, due to the underlying genetic architecture, it is often unclear which gene or variant in the loci identified through genetic analyses is driving the association. Due to recent advancements in CRISPR-Cas9 gene-editing, it is now possible to relatively easily perform whole gene knock-out studies and single base-edits to validate genetic findings of the most likely causal variant and gene. Utilising a combination of genetic approaches and functional studies can provide supporting evidence of the therapeutic profile and potential effects of drug therapies and improve our overall understanding of biological pathways and disease mechanisms. The primary aim of this thesis is to provide genetic data to support the ongoing clinical development of hypoxia-inducible factor (HIF)-prolyl hydroxylase inhibitors (PHIs) for treating anaemia of chronic kidney disease (CKD). Genome-wide association studies (GWAS) were used to identify genetic variants lying within or nearby genes encoding the drug target (prolyl hydroxylase [PHD] enzymes). These identified variants were used in Mendelian Randomisation analysis and phenome-wide association studies to genetically mirror the pharmaceutical effects of PHIs and investigate cardiovascular safety. Functional validation studies were employed to functionally validate a genetic variant for use as a proxy and to obtain a better understanding of the downstream causal pathways and biological mechanisms of the drug target. In summary, this thesis demonstrates how a combination of genetic analyses and functional validation studies is a powerful approach to validate GWAS results and further characterise therapeutic effects. This PhD project identified relevant genetic markers to genetically proxy therapeutic modulation of biomarker levels through PHD inhibition and could potentially inform further research using patient-level clinical data from Phase III trials

Attention-based machine perception for intelligent cyber-physical systems

Cyber-physical systems (CPS) fundamentally change the way of how information systems interact with the physical world. They integrate the sensing, computing, and communication capabilities on heterogeneous platforms and infrastructures. Efficient and effective perception of the environment lays the foundation of proper operations in other CPS components (e.g., planning and control). Recent advances in artificial intelligence (AI) have unprecedentedly changed the way of how cyber systems extract knowledge from the collected sensing data, and understand the physical surroundings. This novel data-to-knowledge transformation capability pushes a wide spectrum of recognition tasks (e.g., visual object detection, speech recognition, and sensor-based human activity recognition) to a higher level, and opens an new era of intelligent cyber-physical systems. However, the state-of-the-art neural perception models are typically computation-intensive and sensitive to data noises, which induce significant challenges when they are deployed on resources-limited embedded platforms. This dissertation works on optimizing both the efficiency and efficacy of deep-neural- network (DNN)-based machine perception in intelligent cyber-physical systems. We extensively exploit and apply the design philosophy of attention, originated from cognitive psychology field, from multiple perspectives of machine perception. It generally means al- locating different degrees of concentration to different perceived stimuli. Specifically, we address the following five research questions: First, can we run the computation-intensive neural perception models in real-time by only looking at (i.e., scheduling) the important parts of the perceived scenes, with the cueing from an external sensor? Second, can we eliminate the dependency on the external cueing and make the scheduling framework a self- cueing system? Third, how to distribute the workloads among cameras in a distributed (visual) perception system, where multiple cameras can observe the same parts of the environment? Fourth, how to optimize the achieved perception quality when sensing data from heterogeneous locations and sensor types are collected and utilized? Fifth, how to handle sensor failures in a distributed sensing system, when the deployed neural perception models are sensitive to missing data? We formulate the above problems, and introduce corresponding attention-based solutions for each, to construct the fundamental building blocks for envisioning an attention-based machine perception system in intelligent CPS with both efficiency and efficacy guarantees

Neural information extraction from natural language text

Natural language processing (NLP) deals with building computational techniques that allow computers to automatically analyze and meaningfully represent human language. With an exponential growth of data in this digital era, the advent of NLP-based systems has enabled us to easily access relevant information via a wide range of applications, such as web search engines, voice assistants, etc. To achieve it, a long-standing research for decades has been focusing on techniques at the intersection of NLP and machine learning. In recent years, deep learning techniques have exploited the expressive power of Artificial Neural Networks (ANNs) and achieved state-of-the-art performance in a wide range of NLP tasks. Being one of the vital properties, Deep Neural Networks (DNNs) can automatically extract complex features from the input data and thus, provide an alternative to the manual process of handcrafted feature engineering. Besides ANNs, Probabilistic Graphical Models (PGMs), a coupling of graph theory and probabilistic methods have the ability to describe causal structure between random variables of the system and capture a principled notion of uncertainty. Given the characteristics of DNNs and PGMs, they are advantageously combined to build powerful neural models in order to understand the underlying complexity of data. Traditional machine learning based NLP systems employed shallow computational methods (e.g., SVM or logistic regression) and relied on handcrafting features which is time-consuming, complex and often incomplete. However, deep learning and neural network based methods have recently shown superior results on various NLP tasks, such as machine translation, text classification, namedentity recognition, relation extraction, textual similarity, etc. These neural models can automatically extract an effective feature representation from training data. This dissertation focuses on two NLP tasks: relation extraction and topic modeling. The former aims at identifying semantic relationships between entities or nominals within a sentence or document. Successfully extracting the semantic relationships greatly contributes in building structured knowledge bases, useful in downstream NLP application areas of web search, question-answering, recommendation engines, etc. On other hand, the task of topic modeling aims at understanding the thematic structures underlying in a collection of documents. Topic modeling is a popular text-mining tool to automatically analyze a large collection of documents and understand topical semantics without actually reading them. In doing so, it generates word clusters (i.e., topics) and document representations useful in document understanding and information retrieval, respectively. Essentially, the tasks of relation extraction and topic modeling are built upon the quality of representations learned from text. In this dissertation, we have developed task-specific neural models for learning representations, coupled with relation extraction and topic modeling tasks in the realms of supervised and unsupervised machine learning paradigms, respectively. More specifically, we make the following contributions in developing neural models for NLP tasks: 1. Neural Relation Extraction: Firstly, we have proposed a novel recurrent neural network based architecture for table-filling in order to jointly perform entity and relation extraction within sentences. Then, we have further extended our scope of extracting relationships between entities across sentence boundaries, and presented a novel dependency-based neural network architecture. The two contributions lie in the supervised paradigm of machine learning. Moreover, we have contributed in building a robust relation extractor constrained by the lack of labeled data, where we have proposed a novel weakly-supervised bootstrapping technique. Given the contributions, we have further explored interpretability of the recurrent neural networks to explain their predictions for the relation extraction task. 2. Neural Topic Modeling: Besides the supervised neural architectures, we have also developed unsupervised neural models to learn meaningful document representations within topic modeling frameworks. Firstly, we have proposed a novel dynamic topic model that captures topics over time. Next, we have contributed in building static topic models without considering temporal dependencies, where we have presented neural topic modeling architectures that also exploit external knowledge, i.e., word embeddings to address data sparsity. Moreover, we have developed neural topic models that incorporate knowledge transfers using both the word embeddings and latent topics from many sources. Finally, we have shown improving neural topic modeling by introducing language structures (e.g., word ordering, local syntactic and semantic information, etc.) that deals with bag-of-words issues in traditional topic models. The class of proposed neural NLP models in this section are based on techniques at the intersection of PGMs, deep learning and ANNs. Here, the task of neural relation extraction employs neural networks to learn representations typically at the sentence level, without access to the broader document context. However, topic models have access to statistical information across documents. Therefore, we advantageously combine the two complementary learning paradigms in a neural composite model, consisting of a neural topic and a neural language model that enables us to jointly learn thematic structures in a document collection via the topic model, and word relations within a sentence via the language model. Overall, our research contributions in this dissertation extend NLP-based systems for relation extraction and topic modeling tasks with state-of-the-art performances

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum