Proceedings of Machine Learning Research XX:1-12, 2019 Machine Learning for Health (ML4H) at NeurIPS 2019 1 Training without training data: Improving the generalizability of automated medical abbreviation disambiguation* Marta Skreta 1,2 martaskreta@cs.toronto.edu Michael Brudno 1,2 brudno@cs.toronto.edu 1 University of Toronto, Department of Computer Science 2 The Hospital for Sick Children, Center for Computational Medicine 3 Vector Institute for Artifical Intelligence, Toronto, Canada Abstract Abbreviation disambiguation is important for automated clinical note processing due to the frequent use of abbreviations in clinical settings. Current models for automated abbreviation disambiguation are restricted by the scarcity and imbalance of labeled training data, decreasing their generalizability to orthogonal sources. In this work we propose a novel data augmentation technique that utilizes information from related medical concepts, which improves our model's ability to generalize. Furthermore, we show that incorporating the global context information within the whole medical note (in addition to the traditional local context window), can significantly improve the model's representation for abbreviations. We train our model on a public dataset (MIMIC III) and test its performance on datasets from different sources (CASI, i2b2). Together, these two techniques boost the accuracy of abbreviation disambiguation by almost 14% on the CASI dataset and 4% on i2b2. 1. Introduction Health care practitioners typically use abbreviations when preparing clinical records, saving time and space with the cost of increased ambiguity.

Summary: Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms.

RDF [21] and Graph databases [27] are two approaches for data management that are based on modeling, storing and querying graph-like data. The database systems based on these models are gaining relevance in the industry due to their use in various application domains where complex data analytics is required [2]. RDF triplestores and graph database systems are tightly connected as they are based on graph data models. RDF databases are based on the RDF data model [21], their standard query language is SPARQL [15], and RDF Schema [8] allows to describe classes of resources and properties (i.e. the data schema). On the other hand, most graph databases are based on the Property Graph (PG) data model, there is no standard query language, and there is no standard notion of property graph schema [25]. Therefore, RDF and PG database systems are dissimilar in data model, schema constraints and query language.

The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO), which is based on mereotopology following Varzi and semiotics following Peirce, is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of data and metadata at the VIMMP marketplace frontend.

In this chapter, we give an introduction to symbolic artificial intelligence (AI) and discuss its relation and application to multimedia. We begin by defining what symbolic AI is, what distinguishes it from non-symbolic approaches, such as machine learning, and how it can used in the construction of advanced multimedia applications. We then introduce description logic (DL) and use it to discuss symbolic representation and reasoning. DL is the logical underpinning of OWL, the most successful family of ontology languages. After discussing DL, we present OWL and related Semantic Web technologies, such as RDF and SPARQL.

Vienna, November 19th of 2019, Semantic Web Company (Austria) and PANTOPIX (Germany) have announced a comprehensive cooperation to provide the machinery industry with expertise in metadata management and structured information. Semantic Web Company (SWC), based in Vienna, is the leading provider of graph-based metadata management. The Germany Company PANTOPIX is a high-end specialist for improving information processes, developing data models as well as providing intelligent information for technical documentation. The key pillar of the partnership is to develop taxonomies, ontologies and large-scale Enterprise Knowledge Graphs to make target-oriented technical content available to internal and external customers. Knowledge Graphs enable companies to process large amounts of data from various silos and adding value to it so that it can be used in meaningful and more intelligent ways. It provides a structure and common interface for all data and enables the creation of smart multilateral relations throughout databases.

We present, FT-SWRL, a fuzzy temporal extension to the Semantic Web Rule Language (SWRL), which combines fuzzy theories based on the valid-time temporal model to provide a standard approach for modeling imprecise temporal domain knowledge in OWL ontologies. The proposal introduces a fuzzy temporal model for the semantic web, which is syntactically defined as a fuzzy temporal SWRL ontology (SWRL-FTO) with a new set of fuzzy temporal SWRL built-ins for defining their semantics. The SWRL-FTO hierarchically defines the necessary linguistic terminologies and variables for the fuzzy temporal model. An example model demonstrating the usefulness of the fuzzy temporal SWRL built-ins to model imprecise temporal information is also represented. Fuzzification process of interval-based temporal logic is further discussed as a reasoning paradigm for our FT-SWRL rules, with the aim of achieving a complete OWL-based fuzzy temporal reasoning. Literature review on fuzzy temporal representation approaches, both within and without the use of ontologies, led to the conclusion that the FT-SWRL model can authoritatively serve as a formal specification for handling imprecise temporal expressions on the semantic web.

An ontology language for ontology mediated query answering (OMQA-language) is universal for a family of OMQA-languages if it is the most expressive one among this family. In this paper, we focus on three families of tractable OMQA-languages, including first-order rewritable languages and languages whose data complexity of the query answering is in AC0 or PTIME. On the negative side, we prove that there is, in general, no universal language for each of these families of languages. On the positive side, we propose a novel property, the locality, to approximate the first-order rewritability, and show that there exists a language of disjunctive embedded dependencies that is universal for the family of OMQA-languages with locality. All of these results apply to OMQA with query languages such as conjunctive queries, unions of conjunctive queries and acyclic conjunctive queries.

--In this paper, we give an overview of the semantic gap problem in multimedia and discuss how machine learning and symbolic AI can be combined to narrow this gap. We describe the gap in terms of a classical architecture for multimedia processing and discuss a structured approach to bridge it. This approach combines machine learning (for mapping signals to objects) and symbolic AI (for linking objects to meanings). Our main goal is to raise awareness and discuss the challenges involved in this structured approach to multimedia understanding, especially in the view of the latest developments in machine learning and symbolic AI. A classic problem in multimedia representation and understanding is the semantic gap problem [1].

The chase is a sound and complete algorithm for conjunctive query answering over ontologies of existential rules with equality. To enable its effective use, we can apply acyclicity notions; that is, sufficient conditions that guarantee chase termination. Unfortunately, most of these notions have only been defined for existential rule sets without equality. A proposed solution to circumvent this issue is to treat equality as an ordinary predicate with an explicit axiomatisation. We empirically show that this solution is not efficient in practice and propose an alternative approach. More precisely, we show that, if the chase terminates for any equality axiomatisation of an ontology, then it terminates for the original ontology (which may contain equality). Therefore, one can apply existing acyclicity notions to check chase termination over an axiomatisation of an ontology and then use the original ontology for reasoning. We show that, in practice, doing so results in a more efficient reasoning procedure. Furthermore, we present equality model-faithful acyclicity, a general acyclicity notion that can be directly applied to ontologies with equality.