Optimised Storage for Datalog Reasoning

Materialisation facilitates Datalog reasoning by precomputing all consequences of the facts and the rules so that queries can be directly answered over the materialised facts. However, storing all materialised facts may be infeasible in practice, especially when the rules are complex and the given set of facts is large. We observe that for certain combinations of rules, there exist data structures that compactly represent the reasoning result and can be efficiently queried when necessary. In this paper, we present a general framework that allows for the integration of such optimised storage schemes with standard materialisation algorithms. Moreover, we devise optimised storage schemes targeting at transitive rules and union rules, two types of (combination of) rules that commonly occur in practice. Our experimental evaluation shows that our approach significantly improves memory consumption, sometimes by orders of magnitude, while remaining competitive in terms of query answering time.

Enhancing Datalog Reasoning with Hypertree Decompositions

Datalog reasoning based on the semina\"ive evaluation strategy evaluates rules using traditional join plans, which often leads to redundancy and inefficiency in practice, especially when the rules are complex. Hypertree decompositions help identify efficient query plans and reduce similar redundancy in query answering. However, it is unclear how this can be applied to materialisation and incremental reasoning with recursive Datalog programs. Moreover, hypertree decompositions require additional data structures and thus introduce nonnegligible overhead in both runtime and memory consumption. In this paper, we provide algorithms that exploit hypertree decompositions for the materialisation and incremental evaluation of Datalog programs. Furthermore, we combine this approach with standard Datalog reasoning algorithms in a modular fashion so that the overhead caused by the decompositions is reduced. Our empirical evaluation shows that, when the program contains complex rules, the combined approach is usually significantly faster than the baseline approach, sometimes by orders of magnitude.

MeTeoR: Practical Reasoning in Datalog with Metric Temporal Operators

DatalogMTL is an extension of Datalog with operators from metric temporal logic which has received significant attention in recent years. It is a highly expressive knowledge representation language that is well-suited for applications in temporal ontology-based query answering and stream processing. Reasoning in DatalogMTL is, however, of high computational complexity, making implementation challenging and hindering its adoption in applications. In this paper, we present a novel approach for practical reasoning in DatalogMTL which combines materialisation (a.k.a. forward chaining) with automata-based techniques. We have implemented this approach in a reasoner called MeTeoR and evaluated its performance using a temporal extension of the Lehigh University Benchmark and a benchmark based on real-world meteorological data. Our experiments show that MeTeoR is a scalable system which enables reasoning over complex temporal rules and datasets involving tens of millions of temporal facts.

OWL2Vec*: Embedding of OWL Ontologies

Semantic embedding of knowledge graphs has been widely studied and used for prediction and statistical analysis tasks across various domains such as Natural Language Processing and the Semantic Web. However, less attention has been paid to developing robust methods for embedding OWL (Web Ontology Language) ontologies. In this paper, we propose a language model based ontology embedding method named OWL2Vec*, which encodes the semantics of an ontology by taking into account its graph structure, lexical information and logic constructors. Our empirical evaluation with three real world datasets suggests that OWL2Vec* benefits from these three different aspects of an ontology in class membership prediction and class subsumption prediction tasks. Furthermore, OWL2Vec* often significantly outperforms the state-of-the-art methods in our experiments.

Interpretable Machine Learning Model for Early Prediction of Mortality in Elderly Patients with Multiple Organ Dysfunction Syndrome (MODS): a Multicenter Retrospective Study and Cross Validation

Background: Elderly patients with MODS have high risk of death and poor prognosis. The performance of current scoring systems assessing the severity of MODS and its mortality remains unsatisfactory. This study aims to develop an interpretable and generalizable model for early mortality prediction in elderly patients with MODS. Methods: The MIMIC-III, eICU-CRD and PLAGH-S databases were employed for model generation and evaluation. We used the eXtreme Gradient Boosting model with the SHapley Additive exPlanations method to conduct early and interpretable predictions of patients' hospital outcome. Three types of data source combinations and five typical evaluation indexes were adopted to develop a generalizable model. Findings: The interpretable model, with optimal performance developed by using MIMIC-III and eICU-CRD datasets, was separately validated in MIMIC-III, eICU-CRD and PLAGH-S datasets (no overlapping with training set). The performances of the model in predicting hospital mortality as validated by the three datasets were: AUC of 0.858, sensitivity of 0.834 and specificity of 0.705; AUC of 0.849, sensitivity of 0.763 and specificity of 0.784; and AUC of 0.838, sensitivity of 0.882 and specificity of 0.691, respectively. Comparisons of AUC between this model and baseline models with MIMIC-III dataset validation showed superior performances of this model; In addition, comparisons in AUC between this model and commonly used clinical scores showed significantly better performance of this model. Interpretation: The interpretable machine learning model developed in this study using fused datasets with large sample sizes was robust and generalizable. This model outperformed the baseline models and several clinical scores for early prediction of mortality in elderly ICU patients. The interpretative nature of this model provided clinicians with the ranking of mortality risk features.

Datalog Reasoning over Compressed RDF Knowledge Bases

Materialisation is often used in RDF systems as a preprocessing step to derive all facts implied by given RDF triples and rules. Although widely used, materialisation considers all possible rule applications and can use a lot of memory for storing the derived facts, which can hinder performance. We present a novel materialisation technique that compresses the RDF triples so that the rules can sometimes be applied to multiple facts at once, and the derived facts can be represented using structure sharing. Our technique can thus require less space, as well as skip certain rule applications. Our experiments show that our technique can be very effective: when the rules are relatively simple, our system is both faster and requires less memory than prominent state-of-the-art RDF systems.

Modular Materialisation of Datalog Programs

The semina\"ive algorithm can materialise all consequences of arbitrary datalog rules, and it also forms the basis for incremental algorithms that update a materialisation as the input facts change. Certain (combinations of) rules, however, can be handled much more efficiently using custom algorithms. To integrate such algorithms into a general reasoning approach that can handle arbitrary rules, we propose a modular framework for materialisation computation and its maintenance. We split a datalog program into modules that can be handled using specialised algorithms, and handle the remaining rules using the semina\"ive algorithm. We also present two algorithms for computing the transitive and the symmetric-transitive closure of a relation that can be used within our framework. Finally, we show empirically that our framework can handle arbitrary datalog programs while outperforming existing approaches, often by orders of magnitude.

Optimised Maintenance of Datalog Materialisations

To efficiently answer queries, datalog systems often materialise all consequences of a datalog program, so the materialisation must be updated whenever the input facts change. Several solutions to the materialisation update problem have been proposed. The Delete/Rederive (DRed) and the Backward/Forward (B/F) algorithms solve this problem for general datalog, but both contain steps that evaluate rules 'backwards' by matching their heads to a fact and evaluating the partially instantiated rule bodies as queries. We show that this can be a considerable source of overhead even on very small updates. In contrast, the Counting algorithm does not evaluate the rules 'backwards', but it can handle only nonrecursive rules. We present two hybrid approaches that combine DRed and B/F with Counting so as to reduce or even eliminate 'backward' rule evaluation while still handling arbitrary datalog programs. We show empirically that our hybrid algorithms are usually significantly faster than existing approaches, sometimes by orders of magnitude.