Ontology Pre-training for Poison Prediction

Integrating human knowledge into neural networks has the potential to improve their robustness and interpretability. We have developed a novel approach to integrate knowledge from ontologies into the structure of a Transformer network which we call ontology pre-training: we train the network to predict membership in ontology classes as a way to embed the structure of the ontology into the network, and subsequently fine-tune the network for the particular prediction task. We apply this approach to a case study in predicting the potential toxicity of a small molecule based on its molecular structure, a challenging task for machine learning in life sciences chemistry. Our approach improves on the state of the art, and moreover has several additional benefits. First, we are able to show that the model learns to focus attention on more meaningful chemical groups when making predictions with ontology pre-training than without, paving a path towards greater robustness and interpretability. Second, the training time is reduced after ontology pre-training, indicating that the model is better placed to learn what matters for toxicity prediction with the ontology pre-training than without. This strategy has general applicability as a neuro-symbolic approach to embed meaningful semantics into neural networks.

When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies

In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous 'FOWL' ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level ontology BFO via our approach enables us to detect several inconsistencies. Furthermore, existing OWL ontologies can benefit from FOL annotations. We illustrate this with FOWL ontologies containing mereotopological axioms that enable new meaningful inferences. Finally, we show that even for large domain ontologies such as ChEBI, automatic reasoning with FOL annotations can be used to detect previously unnoticed errors in the classification.

Automated and Explainable Ontology Extension Based on Deep Learning: A Case Study in the Chemical Domain

Reference ontologies provide a shared vocabulary and knowledge resource for their domain. Manual construction enables them to maintain a high quality, allowing them to be widely accepted across their community. However, the manual development process does not scale for large domains. We present a new methodology for automatic ontology extension and apply it to the ChEBI ontology, a prominent reference ontology for life sciences chemistry. We trained a Transformer-based deep learning model on the leaf node structures from the ChEBI ontology and the classes to which they belong. The model is then capable of automatically classifying previously unseen chemical structures. The proposed model achieved an overall F1 score of 0.80, an improvement of 6 percentage points over our previous results on the same dataset. Additionally, we demonstrate how visualizing the model's attention weights can help to explain the results by providing insight into how the model made its decisions.

Generic Ontology Design Patterns at Work

Generic Ontology Design Patterns, GODPs, are defined in Generic DOL, an extension of DOL, the Distributed Ontology, Model and Specification Language, and implemented using Heterogeneous Tool Set. Parameters such as classes, properties, individuals, or whole ontologies may be instantiated with arguments in a host ontology. The potential of Generic DOL is illustrated with GODPs for an example from the literature, namely the Role design pattern. We also discuss how larger GODPs may be composed by instantiating smaller GODPs.

What is an Ontology?

In the knowledge engineering community "ontology" is usually defined in the tradition of Gruber as an "explicit specification of a conceptualization". Several variations of this definition exist. In the paper we argue that (with one notable exception) these definitions are of no explanatory value, because they violate one of the basic rules for good definitions: The defining statement (the definiens) should be clearer than the term that is defined (the definiendum). In the paper we propose a different definition of "ontology" and discuss how it helps to explain various phenomena: the ability of ontologies to change, the role of the choice of vocabulary, the significance of annotations, the possibility of collaborative ontology development, and the relationship between ontological conceptualism and ontological realism.

Modular Semantics and Characteristics for Bipolar Weighted Argumentation Graphs

This paper addresses the semantics of weighted argumentation graphs that are bipolar, i.e. contain both attacks and supports for arguments. It builds on previous work by Amgoud, Ben-Naim et. al. We study the various characteristics of acceptability semantics that have been introduced in these works, and introduce the notion of a modular acceptability semantics. A semantics is modular if it cleanly separates aggregation of attacking and supporting arguments (for a given argument $a$) from the computation of their influence on $a$'s initial weight. We show that the various semantics for bipolar argumentation graphs from the literature may be analysed as a composition of an aggregation function with an influence function. Based on this modular framework, we prove general convergence and divergence theorems. We demonstrate that all well-behaved modular acceptability semantics converge for all acyclic graphs and that no sum-based semantics can converge for all graphs. In particular, we show divergence of Euler-based semantics (Amgoud et al.) for certain cyclic graphs. Further, we provide the first semantics for bipolar weighted graphs that converges for all graphs.

Bipolar Weighted Argumentation Graphs

This paper discusses the semantics of weighted argumentation graphs that are biplor, i.e. contain both attacks and support graphs. The work builds on previous work by Amgoud, Ben-Naim et. al., which presents and compares several semantics for argumentation graphs that contain only supports or only attacks relationships, respectively.

Ontohub: A semantic repository for heterogeneous ontologies

Ontohub is a repository engine for managing distributed heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate ontologies written in various ontology languages. Ontohub supports a wide range of formal logical and ontology languages, as well as various structuring and modularity constructs and inter-theory (concept) mappings, building on the OMG-standardized DOL language. Ontohub repositories are organised as Git repositories, thus inheriting all features of this popular version control system. Moreover, Ontohub is the first repository engine meeting a substantial amount of the requirements formulated in the context of the Open Ontology Repository (OOR) initiative, including an API for federation as well as support for logical inference and axiom selection.

What's in an `is about' link? Chemical diagrams and the Information Artifact Ontology

The Information Artifact Ontology is an ontology in the domain of information entities. Core to the definition of what it is to be an information entity is the claim that an information entity must be `about' something, which is encoded in an axiom expressing that all information entities are about some entity. This axiom comes into conflict with ontological realism, since many information entities seem to be about non-existing entities, such as hypothetical molecules. We discuss this problem in the context of diagrams of molecules, a kind of information entity pervasively used throughout computational chemistry. We then propose a solution that recognizes that information entities such as diagrams are expressions of diagrammatic languages. In so doing, we not only address the problem of classifying diagrams that seem to be about non-existing entities but also allow a more sophisticated categorisation of information entities.