We describe a datalog query evaluation approach based on efficient and composable boolean matrix manipulation modules. We first define an overarching problem, Boolean Matrix Logic Programming (BMLP), which uses boolean matrices as an alternative computation to evaluate datalog programs. We develop two novel BMLP modules for bottom-up inferences on linear dyadic recursive datalog programs, and show how additional modules can extend this capability to compute both linear and non-linear recursive datalog programs of arity two. Our empirical results demonstrate that these modules outperform general-purpose and specialised systems by factors of 30x and 9x, respectively, when evaluating large programs with millions of facts. This boolean matrix approach significantly enhances the efficiency of datalog querying to support logic programming techniques.

Techniques to autonomously drive research have been prominent in Computational Scientific Discovery, while Synthetic Biology is a field of science that focuses on designing and constructing new biological systems for useful purposes. Here we seek to apply logic-based machine learning techniques to facilitate cellular engineering and drive biological discovery. Comprehensive databases of metabolic processes called genome-scale metabolic network models (GEMs) are often used to evaluate cellular engineering strategies to optimise target compound production. However, predicted host behaviours are not always correctly described by GEMs, often due to errors in the models. The task of learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To address these, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging boolean matrices to evaluate large logic programs. We introduce a new system, $BMLP_{active}$, which efficiently explores the genomic hypothesis space by guiding informative experimentation through active learning. In contrast to sub-symbolic methods, $BMLP_{active}$ encodes a state-of-the-art GEM of a widely accepted bacterial host in an interpretable and logical representation using datalog logic programs. Notably, $BMLP_{active}$ can successfully learn the interaction between a gene pair with fewer training examples than random experimentation, overcoming the increase in experimental design space. $BMLP_{active}$ enables rapid optimisation of metabolic models to reliably engineer biological systems for producing useful compounds. It offers a realistic approach to creating a self-driving lab for microbial engineering.

Recent attention to relational knowledge bases has sparked a demand for understanding how relations change between entities. Petri nets can represent knowledge structure and dynamically simulate interactions between entities, and thus they are well suited for achieving this goal. However, logic programs struggle to deal with extensive Petri nets due to the limitations of high-level symbol manipulations. To address this challenge, we introduce a novel approach called Boolean Matrix Logic Programming (BMLP), utilising boolean matrices as an alternative computation mechanism for Prolog to evaluate logic programs. Within this framework, we propose two novel BMLP algorithms for simulating a class of Petri nets known as elementary nets. This is done by transforming elementary nets into logically equivalent datalog programs. We demonstrate empirically that BMLP algorithms can evaluate these programs 40 times faster than tabled B-Prolog, SWI-Prolog, XSB-Prolog and Clingo. Our work enables the efficient simulation of elementary nets using Prolog, expanding the scope of analysis, learning and verification of complex systems with logic programming techniques.

In this paper we establish an abstraction of on-the-fly determinization of finite-state automata using transition monoids and demonstrate how it can be applied to bound the asymptotics. We present algebraic and combinatorial properties that are sufficient for a polynomial state complexity of the deterministic automaton constructed on-the-fly. A special case of our findings is that automata with many non-deterministic transitions almost always admit a determinization of polynomial complexity. Furthermore, we extend our ideas to weighted finite-state automata.

During the past few years Boolean matrix factorization (BMF) has become an important direction in data analysis. The minimum description length principle (MDL) was successfully adapted in BMF for the model order selection. Nevertheless, a BMF algorithm performing good results from the standpoint of standard measures in BMF is missing. In this paper, we propose a novel from-below Boolean matrix factorization algorithm based on formal concept analysis. The algorithm utilizes the MDL principle as a criterion for the factor selection. On various experiments we show that the proposed algorithm outperforms---from different standpoints---existing state-of-the-art BMF algorithms.

Covering is an important type of data structure while covering-based rough sets provide an efficient and systematic theory to deal with covering data. In this paper, we use boolean matrices to represent and axiomatize three types of covering approximation operators. First, we define two types of characteristic matrices of a covering which are essentially square boolean ones, and their properties are studied. Through the characteristic matrices, three important types of covering approximation operators are concisely equivalently represented. Second, matrix representations of covering approximation operators are used in boolean matrix decomposition. We provide a sufficient and necessary condition for a square boolean matrix to decompose into the boolean product of another one and its transpose. And we develop an algorithm for this boolean matrix decomposition. Finally, based on the above results, these three types of covering approximation operators are axiomatized using boolean matrices. In a word, this work borrows extensively from boolean matrices and present a new view to study covering-based rough sets.