In Positional-Slotted Object-Applicative (PSOA) RuleML, a predicate application (atom) can have an Object IDentifier (OID) and descriptors that may be positional arguments (tuples) or attribute-value pairs (slots). PSOA RuleML 1.0 specifies for each descriptor whether it is to be interpreted under the perspective of the predicate in whose scope it occurs. This perspectivity dimension refines the space between oidless, positional atoms (relationships) and oidful, slotted atoms (frames): While relationships use only a predicate-scope-sensitive (predicate-dependent) tuple and frames use only predicate-scope-insensitive (predicate-independent) slots, PSOA RuleML 1.0 uses a systematics of orthogonal constructs also permitting atoms with (predicate-)independent tuples and atoms with (predicate-)dependent slots. This supports data and knowledge representation where a slot attribute can have different values depending on the predicate. PSOA thus extends object-oriented multi-membership and multiple inheritance. Based on objectification, PSOA laws are given: Besides unscoping and centralization, the semantic restriction and transformation of describution permits rescoping of one atom's independent descriptors to another atom with the same OID but a different predicate. For inheritance, default descriptors are realized by rules. On top of a metamodel and a Grailog visualization, PSOA's atom systematics for facts, queries, and rules is explained. The presentation and (XML-)serialization syntaxes of PSOA RuleML 1.0 are introduced. Its model-theoretic semantics is formalized by extending the interpretation functions for dependent descriptors. The open PSOATransRun system since Version 1.3 realizes PSOA RuleML 1.0 by a translator to runtime predicates, including for dependent tuples (prdtupterm) and slots (prdsloterm). Our tests show efficiency advantages of dependent and tupled modeling.

Journal of Parallel and Distributed Computing 104, 19-35.

In this work we address the problem of fast and scalable learning of neuro-symbolic representations for general biological knowledge. Based on a recently published comprehensive biological knowledge graph (Alshahrani, 2017) that was used for demonstrating neuro-symbolic representation learning, we show how to train fast (under 1 minute) log-linear neural embeddings of the entities. We utilize these representations as inputs for machine learning classifiers to enable important tasks such as biological link prediction. Classifiers are trained by concatenating learned entity embeddings to represent entity relations, and training classifiers on the concatenated embeddings to discern true relations from automatically generated negative examples. Our simple embedding methodology greatly improves on classification error compared to previously published state-of-the-art results, yielding a maximum increase of $+0.28$ F-measure and $+0.22$ ROC AUC scores for the most difficult biological link prediction problem. Finally, our embedding approach is orders of magnitude faster to train ($\leq$ 1 minute vs. hours), much more economical in terms of embedding dimensions ($d=50$ vs. $d=512$), and naturally encodes the directionality of the asymmetric biological relations, that can be controlled by the order with which we concatenate the embeddings.

Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information that characterize ontology classes. Annotations commonly used in ontologies include class labels, descriptions, or synonyms. Despite being a rich source of semantic information, the ontology meta-data are generally unexploited by ontology-based analysis methods such as semantic similarity measures. Results: We propose a novel method, OPA2Vec, to generate vector representations of biological entities in ontologies by combining formal ontology axioms and annotation axioms from the ontology meta-data. We apply a Word2Vec model that has been pre-trained on PubMed abstracts to produce feature vectors from our collected data. We validate our method in two different ways: first, we use the obtained vector representations of proteins as a similarity measure to predict protein-protein interaction (PPI) on two different datasets. Second, we evaluate our method on predicting gene-disease associations based on phenotype similarity by generating vector representations of genes and diseases using a phenotype ontology, and applying the obtained vectors to predict gene-disease associations. These two experiments are just an illustration of the possible applications of our method. OPA2Vec can be used to produce vector representations of any biomedical entity given any type of biomedical ontology. Availability: https://github.com/bio-ontology-research-group/opa2vec Contact: robert.hoehndorf@kaust.edu.sa and xin.gao@kaust.edu.sa.

In this paper we discuss some of the issues concerning the Memory and Content aspects in the recent debate on the identification of a Standard Model of the Mind (Laird, Lebiere, and Rosenbloom in press). In particular, we focus on the representational models concerning the Declarative Memories of current Cognitive Architectures (CAs). In doing so we outline some of the main problems affecting the current CAs and suggest that the Conceptual Spaces, a representational framework developed by Gardenfors, is worth-considering to address such problems. Finally, we briefly analyze the alternative representational assumptions employed in the three CAs constituting the current baseline for the Standard Model (i.e. SOAR, ACT-R and Sigma). In doing so, we point out the respective differences and discuss their implications in the light of the analyzed problems.

The question whether an ontology can safely be replaced by another, possibly simpler, one is fundamental for many ontology engineering and maintenance tasks. It underpins, for example, ontology versioning, ontology modularization, forgetting, and knowledge exchange. What safe replacement means depends on the intended application of the ontology. If, for example, it is used to query data, then the answers to any relevant ontology-mediated query should be the same over any relevant data set; if, in contrast, the ontology is used for conceptual reasoning, then the entailed subsumptions between concept expressions should coincide. This gives rise to different notions of ontology inseparability such as query inseparability and concept inseparability, which generalize corresponding notions of conservative extensions. We survey results on various notions of inseparability in the context of description logic ontologies, discussing their applications, useful model-theoretic characterizations, algorithms for determining whether two ontologies are inseparable (and, sometimes, for computing the difference between them if they are not), and the computational complexity of this problem.

Ontology alignment is widely-used to find the correspondences between different ontologies in diverse fields.After discovering the alignments,several performance scores are available to evaluate them.The scores typically require the identified alignment and a reference containing the underlying actual correspondences of the given ontologies.The current trend in the alignment evaluation is to put forward a new score(e.g., precision, weighted precision, etc.)and to compare various alignments by juxtaposing the obtained scores. However,it is substantially provocative to select one measure among others for comparison.On top of that, claiming if one system has a better performance than one another cannot be substantiated solely by comparing two scalars.In this paper,we propose the statistical procedures which enable us to theoretically favor one system over one another.The McNemar's test is the statistical means by which the comparison of two ontology alignment systems over one matching task is drawn.The test applies to a 2x2 contingency table which can be constructed in two different ways based on the alignments,each of which has their own merits/pitfalls.The ways of the contingency table construction and various apposite statistics from the McNemar's test are elaborated in minute detail.In the case of having more than two alignment systems for comparison, the family-wise error rate is expected to happen. Thus, the ways of preventing such an error are also discussed.A directed graph visualizes the outcome of the McNemar's test in the presence of multiple alignment systems.From this graph, it is readily understood if one system is better than one another or if their differences are imperceptible.The proposed statistical methodologies are applied to the systems participated in the OAEI 2016 anatomy track, and also compares several well-known similarity metrics for the same matching problem.

Conjunctive query answering over expressive Horn Description Logic ontologies is a relevant and challenging problem which, in some cases, can be addressed by application of the chase algorithm. In this paper, we define a novel acyclicity notion which provides a sufficient condition for termination of the restricted chase over Horn-SRIQ TBoxes. We show that this notion generalizes most of the existing acyclicity conditions (both theoretically and empirically). Furthermore, this new acyclicity notion gives rise to a very efficient reasoning procedure. We provide evidence for this by providing a materialization based reasoner for acyclic ontologies which outperforms other state-of-the-art systems.

In ontology-based data access (OBDA), the classical database is enhanced with an ontology in the form of logical assertions generating new intensional knowledge. A powerful form of such logical assertions is the tuple-generating dependencies (TGDs), also called existential rules, where Horn rules are extended by allowing existential quantifiers to appear in the rule heads. In this paper we introduce a new language called loop restricted (LR) TGDs (existential rules), which are TGDs with certain restrictions on the loops embedded in the underlying rule set. We study the complexity of this new language. We show that the conjunctive query answering (CQA) under the LR TGDs is decid- able. In particular, we prove that this language satisfies the so-called bounded derivation-depth prop- erty (BDDP), which implies that the CQA is first-order rewritable, and its data complexity is in AC0 . We also prove that the combined complexity of the CQA is EXPTIME complete, while the language membership is PSPACE complete. Then we extend the LR TGDs language to the generalised loop restricted (GLR) TGDs language, and prove that this class of TGDs still remains to be first-order rewritable and properly contains most of other first-order rewritable TGDs classes discovered in the literature so far.

In this paper we introduce a new class of tuple-generating dependencies (TGDs) called triangularly-guarded TGDs, which are TGDs with certain restrictions on the atomic derivation track embedded in the underlying rule set. We show that conjunctive query answering under this new class of TGDs is decidable. We further show that this new class strictly contains some other decidable classes such as weak-acyclic, guarded, sticky and shy, which, to the best of our knowledge, provides a unified representation of all these aforementioned classes.