9,822 research outputs found

    DeepOnto: A Python Package for Ontology Engineering with Deep Learning

    Full text link
    Applying deep learning techniques, particularly language models (LMs), in ontology engineering has raised widespread attention. However, deep learning frameworks like PyTorch and Tensorflow are predominantly developed for Python programming, while widely-used ontology APIs, such as the OWL API and Jena, are primarily Java-based. To facilitate seamless integration of these frameworks and APIs, we present Deeponto, a Python package designed for ontology engineering. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to include other essential components including reasoning, verbalisation, normalisation, projection, and more. Building on this module, Deeponto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methodologies, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of Deeponto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).Comment: under review at Semantic Web Journa

    Modular lifelong machine learning

    Get PDF
    Deep learning has drastically improved the state-of-the-art in many important fields, including computer vision and natural language processing (LeCun et al., 2015). However, it is expensive to train a deep neural network on a machine learning problem. The overall training cost further increases when one wants to solve additional problems. Lifelong machine learning (LML) develops algorithms that aim to efficiently learn to solve a sequence of problems, which become available one at a time. New problems are solved with less resources by transferring previously learned knowledge. At the same time, an LML algorithm needs to retain good performance on all encountered problems, thus avoiding catastrophic forgetting. Current approaches do not possess all the desired properties of an LML algorithm. First, they primarily focus on preventing catastrophic forgetting (Diaz-Rodriguez et al., 2018; Delange et al., 2021). As a result, they neglect some knowledge transfer properties. Furthermore, they assume that all problems in a sequence share the same input space. Finally, scaling these methods to a large sequence of problems remains a challenge. Modular approaches to deep learning decompose a deep neural network into sub-networks, referred to as modules. Each module can then be trained to perform an atomic transformation, specialised in processing a distinct subset of inputs. This modular approach to storing knowledge makes it easy to only reuse the subset of modules which are useful for the task at hand. This thesis introduces a line of research which demonstrates the merits of a modular approach to lifelong machine learning, and its ability to address the aforementioned shortcomings of other methods. Compared to previous work, we show that a modular approach can be used to achieve more LML properties than previously demonstrated. Furthermore, we develop tools which allow modular LML algorithms to scale in order to retain said properties on longer sequences of problems. First, we introduce HOUDINI, a neurosymbolic framework for modular LML. HOUDINI represents modular deep neural networks as functional programs and accumulates a library of pre-trained modules over a sequence of problems. Given a new problem, we use program synthesis to select a suitable neural architecture, as well as a high-performing combination of pre-trained and new modules. We show that our approach has most of the properties desired from an LML algorithm. Notably, it can perform forward transfer, avoid negative transfer and prevent catastrophic forgetting, even across problems with disparate input domains and problems which require different neural architectures. Second, we produce a modular LML algorithm which retains the properties of HOUDINI but can also scale to longer sequences of problems. To this end, we fix the choice of a neural architecture and introduce a probabilistic search framework, PICLE, for searching through different module combinations. To apply PICLE, we introduce two probabilistic models over neural modules which allows us to efficiently identify promising module combinations. Third, we phrase the search over module combinations in modular LML as black-box optimisation, which allows one to make use of methods from the setting of hyperparameter optimisation (HPO). We then develop a new HPO method which marries a multi-fidelity approach with model-based optimisation. We demonstrate that this leads to improvement in anytime performance in the HPO setting and discuss how this can in turn be used to augment modular LML methods. Overall, this thesis identifies a number of important LML properties, which have not all been attained in past methods, and presents an LML algorithm which can achieve all of them, apart from backward transfer

    Using machine learning to predict pathogenicity of genomic variants throughout the human genome

    Get PDF
    Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität. Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores. Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt. Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity. Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants. The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency. In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org

    An empirical investigation of the relationship between integration, dynamic capabilities and performance in supply chains

    Get PDF
    This research aimed to develop an empirical understanding of the relationships between integration, dynamic capabilities and performance in the supply chain domain, based on which, two conceptual frameworks were constructed to advance the field. The core motivation for the research was that, at the stage of writing the thesis, the combined relationship between the three concepts had not yet been examined, although their interrelationships have been studied individually. To achieve this aim, deductive and inductive reasoning logics were utilised to guide the qualitative study, which was undertaken via multiple case studies to investigate lines of enquiry that would address the research questions formulated. This is consistent with the author’s philosophical adoption of the ontology of relativism and the epistemology of constructionism, which was considered appropriate to address the research questions. Empirical data and evidence were collected, and various triangulation techniques were employed to ensure their credibility. Some key features of grounded theory coding techniques were drawn upon for data coding and analysis, generating two levels of findings. These revealed that whilst integration and dynamic capabilities were crucial in improving performance, the performance also informed the former. This reflects a cyclical and iterative approach rather than one purely based on linearity. Adopting a holistic approach towards the relationship was key in producing complementary strategies that can deliver sustainable supply chain performance. The research makes theoretical, methodological and practical contributions to the field of supply chain management. The theoretical contribution includes the development of two emerging conceptual frameworks at the micro and macro levels. The former provides greater specificity, as it allows meta-analytic evaluation of the three concepts and their dimensions, providing a detailed insight into their correlations. The latter gives a holistic view of their relationships and how they are connected, reflecting a middle-range theory that bridges theory and practice. The methodological contribution lies in presenting models that address gaps associated with the inconsistent use of terminologies in philosophical assumptions, and lack of rigor in deploying case study research methods. In terms of its practical contribution, this research offers insights that practitioners could adopt to enhance their performance. They can do so without necessarily having to forgo certain desired outcomes using targeted integrative strategies and drawing on their dynamic capabilities

    Knowledge Graph Building Blocks: An easy-to-use Framework for developing FAIREr Knowledge Graphs

    Full text link
    Knowledge graphs and ontologies provide promising technical solutions for implementing the FAIR Principles for Findable, Accessible, Interoperable, and Reusable data and metadata. However, they also come with their own challenges. Nine such challenges are discussed and associated with the criterion of cognitive interoperability and specific FAIREr principles (FAIR + Explorability raised) that they fail to meet. We introduce an easy-to-use, open source knowledge graph framework that is based on knowledge graph building blocks (KGBBs). KGBBs are small information modules for knowledge-processing, each based on a specific type of semantic unit. By interrelating several KGBBs, one can specify a KGBB-driven FAIREr knowledge graph. Besides implementing semantic units, the KGBB Framework clearly distinguishes and decouples an internal in-memory data model from data storage, data display, and data access/export models. We argue that this decoupling is essential for solving many problems of knowledge management systems. We discuss the architecture of the KGBB Framework as we envision it, comprising (i) an openly accessible KGBB-Repository for different types of KGBBs, (ii) a KGBB-Engine for managing and operating FAIREr knowledge graphs (including automatic provenance tracking, editing changelog, and versioning of semantic units); (iii) a repository for KGBB-Functions; (iv) a low-code KGBB-Editor with which domain experts can create new KGBBs and specify their own FAIREr knowledge graph without having to think about semantic modelling. We conclude with discussing the nine challenges and how the KGBB Framework provides solutions for the issues they raise. While most of what we discuss here is entirely conceptual, we can point to two prototypes that demonstrate the principle feasibility of using semantic units and KGBBs to manage and structure knowledge graphs

    Endogenous measures for contextualising large-scale social phenomena: a corpus-based method for mediated public discourse

    Get PDF
    This work presents an interdisciplinary methodology for developing endogenous measures of group membership through analysis of pervasive linguistic patterns in public discourse. Focusing on political discourse, this work critiques the conventional approach to the study of political participation, which is premised on decontextualised, exogenous measures to characterise groups. Considering the theoretical and empirical weaknesses of decontextualised approaches to large-scale social phenomena, this work suggests that contextualisation using endogenous measures might provide a complementary perspective to mitigate such weaknesses. This work develops a sociomaterial perspective on political participation in mediated discourse as affiliatory action performed through language. While the affiliatory function of language is often performed consciously (such as statements of identity), this work is concerned with unconscious features (such as patterns in lexis and grammar). This work argues that pervasive patterns in such features that emerge through socialisation are resistant to change and manipulation, and thus might serve as endogenous measures of sociopolitical contexts, and thus of groups. In terms of method, the work takes a corpus-based approach to the analysis of data from the Twitter messaging service whereby patterns in users’ speech are examined statistically in order to trace potential community membership. The method is applied in the US state of Michigan during the second half of 2018—6 November having been the date of midterm (i.e. non-Presidential) elections in the United States. The corpus is assembled from the original posts of 5,889 users, who are nominally geolocalised to 417 municipalities. These users are clustered according to pervasive language features. Comparing the linguistic clusters according to the municipalities they represent finds that there are regular sociodemographic differentials across clusters. This is understood as an indication of social structure, suggesting that endogenous measures derived from pervasive patterns in language may indeed offer a complementary, contextualised perspective on large-scale social phenomena

    Knowledge-based Modelling of Additive Manufacturing for Sustainability Performance Analysis and Decision Making

    Get PDF
    Additiivista valmistusta on pidetty käyttökelpoisena monimutkaisissa geometrioissa, topologisesti optimoiduissa kappaleissa ja kappaleissa joita on muuten vaikea valmistaa perinteisillä valmistusprosesseilla. Eduista huolimatta, yksi additiivisen valmistuksen vallitsevista haasteista on ollut heikko kyky tuottaa toimivia osia kilpailukykyisillä tuotantomäärillä perinteisen valmistuksen kanssa. Mallintaminen ja simulointi ovat tehokkaita työkaluja, jotka voivat auttaa lyhentämään suunnittelun, rakentamisen ja testauksen sykliä mahdollistamalla erilaisten tuotesuunnitelmien ja prosessiskenaarioiden nopean analyysin. Perinteisten ja edistyneiden valmistusteknologioiden mahdollisuudet ja rajoitukset määrittelevät kuitenkin rajat uusille tuotekehityksille. Siksi on tärkeää, että suunnittelijoilla on käytettävissään menetelmät ja työkalut, joiden avulla he voivat mallintaa ja simuloida tuotteen suorituskykyä ja siihen liittyvän valmistusprosessin suorituskykyä, toimivien korkea arvoisten tuotteiden toteuttamiseksi. Motivaation tämän väitöstutkimuksen tekemiselle on, meneillään oleva kehitystyö uudenlaisen korkean lämpötilan suprajohtavan (high temperature superconducting (HTS)) magneettikokoonpanon kehittämisessä, joka toimii kryogeenisissä lämpötiloissa. Sen monimutkaisuus edellyttää monitieteisen asiantuntemuksen lähentymistä suunnittelun ja prototyyppien valmistuksen aikana. Tutkimus hyödyntää tietopohjaista mallinnusta valmistusprosessin analysoinnin ja päätöksenteon apuna HTS-magneettien mekaanisten komponenttien suunnittelussa. Tämän lisäksi, tutkimus etsii mahdollisuuksia additiivisen valmistuksen toteutettavuuteen HTS-magneettikokoonpanon tuotannossa. Kehitetty lähestymistapa käyttää fysikaalisiin kokeisiin perustuvaa tuote-prosessi-integroitua mallinnusta tuottamaan kvantitatiivista ja laadullista tietoa, joka määrittelee prosessi-rakenne-ominaisuus-suorituskyky-vuorovaikutuksia tietyille materiaali-prosessi-yhdistelmille. Tuloksina saadut vuorovaikutukset integroidaan kaaviopohjaiseen malliin, joka voi auttaa suunnittelutilan tutkimisessa ja täten auttaa varhaisessa suunnittelu- ja valmistuspäätöksenteossa. Tätä varten testikomponentit valmistetaan käyttämällä kahta metallin additiivista valmistus prosessia: lankakaarihitsaus additiivista valmistusta (wire arc additive manufacturing) ja selektiivistä lasersulatusta (selective laser melting). Rakenteellisissa sovelluksissa yleisesti käytetyistä metalliseoksista (ruostumaton teräs, pehmeä teräs, luja niukkaseosteinen teräs, alumiini ja kupariseokset) testataan niiden mekaaniset, lämpö- ja sähköiset ominaisuudet. Lisäksi tehdään metalliseosten mikrorakenteen karakterisointi, jotta voidaan ymmärtää paremmin valmistusprosessin parametrien vaikutusta materiaalin ominaisuuksiin. Integroitu mallinnustapa yhdistää kerätyn kokeellisen tiedon, olemassa olevat analyyttiset ja empiiriset vuorovaikutus suhteet, sekä muut tietopohjaiset mallit (esim. elementtimallit, koneoppimismallit) päätöksenteon tukijärjestelmän muodossa, joka mahdollistaa optimaalisen materiaalin, valmistustekniikan, prosessiparametrien ja muitten ohjausmuuttujien valinnan, lopullisen 3d-tulosteun komponentin halutun rakenteen, ominaisuuksien ja suorituskyvyn saavuttamiseksi. Valmistuspäätöksenteko tapahtuu todennäköisyysmallin, eli Bayesin verkkomallin toteuttamisen kautta, joka on vankka, modulaarinen ja sovellettavissa muihin valmistusjärjestelmiin ja tuotesuunnitelmiin. Väitöstyössä esitetyn mallin kyky parantaa additiivisien valmistusprosessien suorituskykyä ja laatua, täten edistää kestävän tuotannon tavoitteita.Additive manufacturing (AM) has been considered viable for complex geometries, topology optimized parts, and parts that are otherwise difficult to produce using conventional manufacturing processes. Despite the advantages, one of the prevalent challenges in AM has been the poor capability of producing functional parts at production volumes that are competitive with traditional manufacturing. Modelling and simulation are powerful tools that can help shorten the design-build-test cycle by enabling rapid analysis of various product designs and process scenarios. Nevertheless, the capabilities and limitations of traditional and advanced manufacturing technologies do define the bounds for new product development. Thus, it is important that the designers have access to methods and tools that enable them to model and simulate product performance and associated manufacturing process performance to realize functional high value products. The motivation for this dissertation research stems from ongoing development of a novel high temperature superconducting (HTS) magnet assembly, which operates in cryogenic environment. Its complexity requires the convergence of multidisciplinary expertise during design and prototyping. The research applies knowledge-based modelling to aid manufacturing process analysis and decision making in the design of mechanical components of the HTS magnet. Further, it explores the feasibility of using AM in the production of the HTS magnet assembly. The developed approach uses product-process integrated modelling based on physical experiments to generate quantitative and qualitative information that define process-structure-property-performance interactions for given material-process combinations. The resulting interactions are then integrated into a graph-based model that can aid in design space exploration to assist early design and manufacturing decision-making. To do so, test components are fabricated using two metal AM processes: wire and arc additive manufacturing and selective laser melting. Metal alloys (stainless steel, mild steel, high-strength low-alloyed steel, aluminium, and copper alloys) commonly used in structural applications are tested for their mechanical-, thermal-, and electrical properties. In addition, microstructural characterization of the alloys is performed to further understand the impact of manufacturing process parameters on material properties. The integrated modelling approach combines the collected experimental data, existing analytical and empirical relationships, and other data-driven models (e.g., finite element models, machine learning models) in the form of a decision support system that enables optimal selection of material, manufacturing technology, process parameters, and other control variables for attaining desired structure, property, and performance characteristics of the final printed component. The manufacturing decision making is performed through implementation of a probabilistic model i.e., a Bayesian network model, which is robust, modular, and can be adapted for other manufacturing systems and product designs. The ability of the model to improve throughput and quality of additive manufacturing processes will boost sustainable manufacturing goals

    Meta-ontology fault detection

    Get PDF
    Ontology engineering is the field, within knowledge representation, concerned with using logic-based formalisms to represent knowledge, typically moderately sized knowledge bases called ontologies. How to best develop, use and maintain these ontologies has produced relatively large bodies of both formal, theoretical and methodological research. One subfield of ontology engineering is ontology debugging, and is concerned with preventing, detecting and repairing errors (or more generally pitfalls, bad practices or faults) in ontologies. Due to the logical nature of ontologies and, in particular, entailment, these faults are often both hard to prevent and detect and have far reaching consequences. This makes ontology debugging one of the principal challenges to more widespread adoption of ontologies in applications. Moreover, another important subfield in ontology engineering is that of ontology alignment: combining multiple ontologies to produce more powerful results than the simple sum of the parts. Ontology alignment further increases the issues, difficulties and challenges of ontology debugging by introducing, propagating and exacerbating faults in ontologies. A relevant aspect of the field of ontology debugging is that, due to the challenges and difficulties, research within it is usually notably constrained in its scope, focusing on particular aspects of the problem or on the application to only certain subdomains or under specific methodologies. Similarly, the approaches are often ad hoc and only related to other approaches at a conceptual level. There are no well established and widely used formalisms, definitions or benchmarks that form a foundation of the field of ontology debugging. In this thesis, I tackle the problem of ontology debugging from a more abstract than usual point of view, looking at existing literature in the field and attempting to extract common ideas and specially focussing on formulating them in a common language and under a common approach. Meta-ontology fault detection is a framework for detecting faults in ontologies that utilizes semantic fault patterns to express schematic entailments that typically indicate faults in a systematic way. The formalism that I developed to represent these patterns is called existential second-order query logic (abbreviated as ESQ logic). I further reformulated a large proportion of the ideas present in some of the existing research pieces into this framework and as patterns in ESQ logic, providing a pattern catalogue. Most of the work during my PhD has been spent in designing and implementing an algorithm to effectively automatically detect arbitrary ESQ patterns in arbitrary ontologies. The result is what we call minimal commitment resolution for ESQ logic, an extension of first-order resolution, drawing on important ideas from higher-order unification and implementing a novel approach to unification problems using dependency graphs. I have proven important theoretical properties about this algorithm such as its soundness, its termination (in a certain sense and under certain conditions) and its fairness or completeness in the enumeration of infinite spaces of solutions. Moreover, I have produced an implementation of minimal commitment resolution for ESQ logic in Haskell that has passed all unit tests and produces non-trivial results on small examples. However, attempts to apply this algorithm to examples of a more realistic size have proven unsuccessful, with computation times that exceed our tolerance levels. In this thesis, I have provided both details of the challenges faced in this regard, as well as other successful forms of qualitative evaluation of the meta-ontology fault detection approach, and discussions about both what I believe are the main causes of the computational feasibility problems, ideas on how to overcome them, and also ideas on other directions of future work that could use the results in the thesis to contribute to the production of foundational formalisms, ideas and approaches to ontology debugging that can properly combine existing constrained research. It is unclear to me whether minimal commitment resolution for ESQ logic can, in its current shape, be implemented efficiently or not, but I believe that, at the very least, the theoretical and conceptual underpinnings that I have presented in this thesis will be useful to produce more foundational results in the field

    Modelling, Monitoring, Control and Optimization for Complex Industrial Processes

    Get PDF
    This reprint includes 22 research papers and an editorial, collected from the Special Issue "Modelling, Monitoring, Control and Optimization for Complex Industrial Processes", highlighting recent research advances and emerging research directions in complex industrial processes. This reprint aims to promote the research field and benefit the readers from both academic communities and industrial sectors

    Interval Logic Tensor Networks

    Full text link
    In this paper, we introduce Interval Real Logic (IRL), a two-sorted logic that interprets knowledge such as sequential properties (traces) and event properties using sequences of real-featured data. We interpret connectives using fuzzy logic, event durations using trapezoidal fuzzy intervals, and fuzzy temporal relations using relationships between the intervals' areas. We propose Interval Logic Tensor Networks (ILTN), a neuro-symbolic system that learns by propagating gradients through IRL. In order to support effective learning, ILTN defines smoothened versions of the fuzzy intervals and temporal relations of IRL using softplus activations. We show that ILTN can successfully leverage knowledge expressed in IRL in synthetic tasks that require reasoning about events to predict their fuzzy durations. Our results show that the system is capable of making events compliant with background temporal knowledge
    corecore