Knowledge Infused Learning (K-IL): Towards Deep Incorporation of Knowledge in Deep Learning

Learning the underlying patterns in data goes beyond instance-based generalization to external knowledge represented in structured graphs or networks. Deep learning that primarily constitutes neural computing stream in AI has shown significant advances in probabilistically learning latent patterns using a multi-layered network of computational nodes (i.e., neurons/hidden units). Structured knowledge that underlies symbolic computing approaches and often supports reasoning, has also seen significant growth in recent years, in the form of broad-based (e.g., DBPedia, Yago) and domain, industry or application specific knowledge graphs. A common substrate with careful integration of the two will raise opportunities to develop neuro-symbolic learning approaches for AI, where conceptual and probabilistic representations are combined. As the incorporation of external knowledge will aid in supervising the learning of features for the model, deep infusion of representational knowledge from knowledge graphs within hidden layers will further enhance the learning process. Although much work remains, we believe that knowledge graphs will play an increasing role in developing hybrid neuro-symbolic intelligent systems (bottom-up deep learning with top-down symbolic computing) as well as in building explainable AI systems for which knowledge graphs will provide scaffolding for punctuating neural computing. In this position paper, we describe our motivation for such a neuro-symbolic approach and framework that combines knowledge graph and neural networks

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies

Ontologies are formal representations of concepts and complex relationships among them. They have been widely used to capture comprehensive domain knowledge in areas such as biology and medicine, where large and complex ontologies can contain hundreds of thousands of concepts. Especially due to the large size of ontologies, visualisation is useful for authoring, exploring and understanding their underlying data. Existing ontology visualisation tools generally focus on the hierarchical structure, giving much less emphasis to non-hierarchical associations. In this paper we present OntoPlot, a novel visualisation specifically designed to facilitate the exploration of all concept associations whilst still showing an ontology's large hierarchical structure. This hybrid visualisation combines icicle plots, visual compression techniques and interactivity, improving space-efficiency and reducing visual structural complexity. We conducted a user study with domain experts to evaluate the usability of OntoPlot, comparing it with the de facto ontology editor Prot{\'e}g{\'e}. The results confirm that OntoPlot attains our design goals for association-related tasks and is strongly favoured by domain experts.Comment: Accepted at IEEE InfoVis 201

The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Methodologically Grounded SemanticAnalysis of Large Volume of Chilean Medical Literature Data Applied to the Analysis of Medical Research Funding Efficiency in Chile

Background Medical knowledge is accumulated in scientific research papers along time. In order to exploit this knowledge by automated systems, there is a growing interest in developing text mining methodologies to extract, structure, and analyze in the shortest time possible the knowledge encoded in the large volume of medical literature. In this paper, we use the Latent Dirichlet Allocation approach to analyze the correlation between funding efforts and actually published research results in order to provide the policy makers with a systematic and rigorous tool to assess the efficiency of funding programs in the medical area. Results We have tested our methodology in the Revista Medica de Chile, years 2012-2015. 50 relevant semantic topics were identified within 643 medical scientific research papers. Relationships between the identified semantic topics were uncovered using visualization methods. We have also been able to analyze the funding patterns of scientific research underlying these publications. We found that only 29% of the publications declare funding sources, and we identified five topic clusters that concentrate 86% of the declared funds. Conclusions Our methodology allows analyzing and interpreting the current state of medical research at a national level. The funding source analysis may be useful at the policy making level in order to assess the impact of actual funding policies, and to design new policies.This research was partially funded by CONICYT, Programa de Formacion de Capital Humano avanzado (CONICYT-PCHA/Doctorado Nacional/2015-21150115). MG work in this paper has been partially supported by FEDER funds for the MINECO project TIN2017-85827-P, and projects KK-2018/00071 and KK2018/00082 of the Elkartek 2018 funding program. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 777720. No role has been played by funding bodies in the design of the study and collection, analysis, or interpretation of data or in writing the manuscript

KNIT: Ontology reusability through knowledge graph exploration

Ontologies have become a standard for knowledge representation across several domains. In Life Sciences, numerous ontologies have been introduced to represent human knowledge, often providing overlapping or conflicting perspectives. These ontologies are usually published as OWL or OBO, and are often registered in open repositories, e.g., BioPortal. However, the task of finding the concepts (classes and their properties) defined in the existing ontologies and the relationships between these concepts across different ontologies – for example, for developing a new ontology aligned with the existing ones – requires a great deal of manual effort in searching through the public repositories for candidate ontologies and their entities. In this work, we develop a new tool, KNIT, to automatically explore open repositories to help users fetch the previously designed concepts using keywords. User-specified keywords are then used to retrieve matching names of classes or properties. KNIT then creates a draft knowledge graph populated with the concepts and relationships retrieved from the existing ontologies. Furthermore, following the process of ontology learning, our tool refines this first draft of an ontology. We present three BioPortal-specific use cases for our tool. These use cases outline the development of new knowledge graphs and ontologies in the sub-domains of biology: genes and diseases, virome and drugs.This work has been funded by grant PID2020-112540RB-C4121, AETHER-UMA (A smart data holistic approach for context-aware data analytics: semantics and context exploitation). Funding for open access charge: Universidad de Málaga / CBUA

Predicting the Outcomes of Important Events based on Social Media and Social Network Analysis

Twitter is a famous social network website that lets users post their opinions about current affairs, share their social events, and interact with others. It has now become one of the largest sources of news, with over 200 million active users monthly. It is possible to predict the outcomes of events based on social networks using machine learning and big data analytics. Massive data available from social networks can be utilized to improve prediction efficacy and accuracy. It is a challenging problem to achieve high accuracy in predicting the outcomes of political events using Twitter data. The focus of this thesis is to investigate novel approaches to predicting the outcomes of political events from social media and social networks. The first proposed method is to predict election results based on Twitter data analysis. The method extracts and analyses sentimental information from microblogs to predict the popularity of candidates. Experimental results have shown its advantages over the existing method for predicting outcomes of politic events. The second proposed method is to predict election results based on Twitter data analysis that analyses sentimental information using term weighting and selection to predict the popularity of candidates. Scaling factors are used for different types of terms, which help to select informative terms more effectively and achieve better prediction results than the previous method. The third method proposed in this thesis represents the social network by using network connectivity constructed based on retweet data and social media contents as well, leading to a new approach to predicting the outcome of political events. Two approaches, whole-network and sub-network, have been developed and compared. Experimental results show that the sub-network approach, which constructs sub-networks based on different topics, outperformed the whole-network approach

Knowledge Infused Learning (K-IL): Towards Deep Incorporation of Knowledge in Deep Learning

Learning the underlying patterns in data goes beyondinstance-based generalization to external knowledge repre-sented in structured graphs or networks. Deep learning thatprimarily constitutes neural computing stream in AI hasshown significant advances in probabilistically learning la-tent patterns using a multi-layered network of computationalnodes (i.e., neurons/hidden units). Structured knowledge thatunderlies symbolic computing approaches and often supportsreasoning, has also seen significant growth in recent years,in the form of broad-based (e.g., DBPedia, Yago) and do-main, industry or application specific knowledge graphs. Acommon substrate with careful integration of the two willraise opportunities to develop neuro-symbolic learning ap-proaches for AI, where conceptual and probabilistic repre-sentations are combined. As the incorporation of externalknowledge will aid in supervising the learning of features forthe model, deep infusion of representational knowledge fromknowledge graphs within hidden layers will further enhancethe learning process. Although much work remains, we be-lieve that knowledge graphs will play an increasing role in de-veloping hybrid neuro-symbolic intelligent systems (bottom-up deep learning with top-down symbolic computing) as wellas in building explainable AI systems for which knowledgegraphs will provide scaffolding for punctuating neural com-puting. In this position paper, we describe our motivation forsuch a neuro-symbolic approach and framework that com-bines knowledge graph and neural networks