We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological properties observed in the images can be represented as Linked Open Data. The metadata are used to develop a large-scale imaging viewer that provides a straightforward graphical user interface to visualise a large microstructural tiling image at the gigabyte level. We applied the database to accumulate comprehensive microstructural imaging data produced by automated scanning electron microscopy. As a result, we have successfully managed vast numbers of images and their metadata, including the interpretation of morphological phenotypes occurring in sub-cellular components and biosamples captured in the images. We also discuss advanced utilisation of morphological imaging data that can be promoted by this database.

Embedding-based entity alignment (EEA) has recently received great attention. Despite significant performance improvement, few efforts have been paid to facilitate understanding of EEA methods. Most existing studies rest on the assumption that a small number of pre-aligned entities can serve as anchors connecting the embedding spaces of two KGs. Nevertheless, no one investigates the rationality of such an assumption. To fill the research gap, we define a typical paradigm abstracted from existing EEA methods and analyze how the embedding discrepancy between two potentially aligned entities is implicitly bounded by a predefined margin in the scoring function. Further, we find that such a bound cannot guarantee to be tight enough for alignment learning. We mitigate this problem by proposing a new approach, named NeoEA, to explicitly learn KG-invariant and principled entity embeddings. In this sense, an EEA model not only pursues the closeness of aligned entities based on geometric distance, but also aligns the neural ontologies of two KGs by eliminating the discrepancy in embedding distribution and underlying ontology knowledge. Our experiments demonstrate consistent and significant improvement in performance against the best-performing EEA methods.

Knowledge Graph (KG) embeddings provide a low-dimensional representation of entities and relations of a Knowledge Graph and are used successfully for various applications such as question answering and search, reasoning, inference, and missing link prediction. However, most of the existing KG embeddings only consider the network structure of the graph and ignore the semantics and the characteristics of the underlying ontology that provides crucial information about relationships between entities in the KG. Recent efforts in this direction involve learning embeddings for a Description Logic (logical underpinning for ontologies) named EL++. However, such methods consider all the relations defined in the ontology to be one-to-one which severely limits their performance and applications. We provide a simple and effective solution to overcome this shortcoming that allows such methods to consider many-to-many relationships while learning embedding representations. Experiments conducted using three different EL++ ontologies show substantial performance improvement over five baselines. Our proposed solution also paves the way for learning embedding representations for even more expressive description logics such as SROIQ.

Statistical modeling of outcomes based on a patient's presenting symptoms (symptomatology) can help deliver high quality care and allocate essential resources, which is especially important during the COVID-19 pandemic. Patient symptoms are typically found in unstructured notes, and thus not readily available for clinical decision making. In an attempt to fill this gap, this study compared two methods for symptom extraction from Emergency Department (ED) admission notes. Both methods utilized a lexicon derived by expanding The Center for Disease Control and Prevention's (CDC) Symptoms of Coronavirus list. The first method utilized a word2vec model to expand the lexicon using a dictionary mapping to the Uni ed Medical Language System (UMLS). The second method utilized the expanded lexicon as a rule-based gazetteer and the UMLS. These methods were evaluated against a manually annotated reference (f1-score of 0.87 for UMLS-based ensemble; and 0.85 for rule-based gazetteer with UMLS). Through analyses of associations of extracted symptoms used as features against various outcomes, salient risks among the population of COVID-19 patients, including increased risk of in-hospital mortality (OR 1.85, p-value < 0.001), were identified for patients presenting with dyspnea. Disparities between English and non-English speaking patients were also identified, the most salient being a concerning finding of opposing risk signals between fatigue and in-hospital mortality (non-English: OR 1.95, p-value = 0.02; English: OR 0.63, p-value = 0.01). While use of symptomatology for modeling of outcomes is not unique, unlike previous studies this study showed that models built using symptoms with the outcome of in-hospital mortality were not significantly different from models using data collected during an in-patient encounter (AUC of 0.9 with 95% CI of [0.88, 0.91] using only vital signs; AUC of 0.87 with 95% CI of [0.85, 0.88] using only symptoms). These findings indicate that prognostic models based on symptomatology could aid in extending COVID-19 patient care through telemedicine, replacing the need for in-person options. The methods presented in this study have potential for use in development of symptomatology-based models for other diseases, including for the study of Post-Acute Sequelae of COVID-19 (PASC).

One of the main issues of every business process is to be compliant with legal rules. This work presents a methodology to check in a semi-automated way the regulatory compliance of a business process. We analyse an e-Health hospital service in particular: the Hospital at Home (HaH) service. The paper shows, at first, the analysis of the hospital business using the Business Process Management and Notation (BPMN) standard language, then, the formalization in Defeasible Deontic Logic (DDL) of some rules of the European General Data Protection Regulation (GDPR). The aim is to show how to combine a set of tasks of a business with a set of rules to be compliant with, using a tool.

Reified Input/Output (I/O) logic[21] has been recently proposed to model real-world norms in terms of the logic in [11]. This is massively grounded on the notion of reification, and it has specifically designed to model meaning of natural language sentences, such as the ones occurring in existing legislation. This paper presents a methodology to carry out compliance checking on reified I/O logic formulae. These are translated in SHACL (Shapes Constraint Language) shapes, a recent W3C recommendation to validate and reason with RDF triplestores. Compliance checking is then enforced by validating RDF graphs describing states of affairs with respect to these SHACL shapes.

Semantic parsing in KBQA aims to parse natural language questions into logical forms, whose execution against a knowledge base produces answers. Learning semantic parsers from question-answer pairs requires searching over a huge space of logical forms for ones consistent with answers. Current methods utilize various prior knowlege or entity-level KB constraints to reduce the search space. In this paper, we investigate for the first time prior knowledge from external logical form annotations and ontology-level constraints. We design a hierarchical architecture for program transfer, and propose an ontology-guided pruning algorithm to reduce the search space. The experiments on ComplexWebQuestions show that our method improves the state-of-the-art F1 score from 44.0% to 58.7%, with an absolute gain of 14.7%, which demonstrates the effectiveness of program transfer and ontology awareness.

Many legal professionals think that the explosion of information about local, regional, national, and international legislation makes their practice more costly, time-consuming, and even error-prone. The two main reasons for this are that most legislation is usually unstructured, and the tremendous amount and pace with which laws are released causes information overload in their daily tasks. In the case of the legal domain, the research community agrees that a system allowing to generate automatic responses to legal questions could substantially impact many practical implications in daily activities. The degree of usefulness is such that even a semi-automatic solution could significantly help to reduce the workload to be faced. This is mainly because a Question Answering system could be able to automatically process a massive amount of legal resources to answer a question or doubt in seconds, which means that it could save resources in the form of effort, money, and time to many professionals in the legal sector. In this work, we quantitatively and qualitatively survey the solutions that currently exist to meet this challenge.

CaLiGraph is a large-scale cross-domain knowledge graph generated from Wikipedia by exploiting the category system, list pages, and other list structures in Wikipedia, containing more than 15 million typed entities and around 10 million relation assertions. Other than knowledge graphs such as DBpedia and YAGO, whose ontologies are comparably simplistic, CaLiGraph also has a rich ontology, comprising more than 200,000 class restrictions. Those two properties - a large A-box and a rich ontology - make it an interesting challenge for benchmarking reasoners. In this paper, we show that a reasoning task which is particularly relevant for CaLiGraph, i.e., the materialization of owl:hasValue constraints into assertions between individuals and between individuals and literals, is insufficiently supported by available reasoning systems. We provide differently sized benchmark subsets of CaLiGraph, which can be used for performance analysis of reasoning systems.

Research in artificial intelligence (AI) is addressing a growing number of tasks through a rapidly growing number of models and methodologies. This makes it difficult to keep track of where novel AI methods are successfully -- or still unsuccessfully -- applied, how progress is measured, how different advances might synergize with each other, and how future research should be prioritized. To help address these issues, we created the Intelligence Task Ontology and Knowledge Graph (ITO), a comprehensive, richly structured and manually curated resource on artificial intelligence tasks, benchmark results and performance metrics. The current version of ITO contain 685,560 edges, 1,100 classes representing AI processes and 1,995 properties representing performance metrics. The goal of ITO is to enable precise and network-based analyses of the global landscape of AI tasks and capabilities. ITO is based on technologies that allow for easy integration and enrichment with external data, automated inference and continuous, collaborative expert curation of underlying ontological models. We make the ITO dataset and a collection of Jupyter notebooks utilising ITO openly available.