Lun Ai

Lun Ai, Johannes Langer, Stephen H. Muggleton et al.

The topic of comprehensibility of machine-learned theories has recently drawn increasing attention. Inductive Logic Programming (ILP) uses logic programming to derive logic theories from small data based on abduction and induction techniques. Learned theories are represented in the form of rules as declarative descriptions of obtained knowledge. In earlier work, the authors provided the first evidence of a measurable increase in human comprehension based on machine-learned logic rules for simple classification tasks. In a later study, it was found that the presentation of machine-learned explanations to humans can produce both beneficial and harmful effects in the context of game learning. We continue our investigation of comprehensibility by examining the effects of the ordering of concept presentations on human comprehension. In this work, we examine the explanatory effects of curriculum order and the presence of machine-learned explanations for sequential problem-solving. We show that 1) there exist tasks A and B such that learning A before B has a better human comprehension with respect to learning B before A and 2) there exist tasks A and B such that the presence of explanations when learning A contributes to improved human comprehension when subsequently learning B. We propose a framework for the effects of sequential teaching on comprehension based on an existing definition of comprehensibility and provide evidence for support from data collected in human trials. Empirical results show that sequential teaching of concepts with increasing complexity a) has a beneficial effect on human comprehension and b) leads to human re-discovery of divide-and-conquer problem-solving strategies, and c) studying machine-learned explanations allows adaptations of human problem-solving strategy with better performance.

Lun Ai, Shi-Shun Liang, Wang-Zhou Dai et al.

An important application of Synthetic Biology is the engineering of the host cell system to yield useful products. However, an increase in the scale of the host system leads to huge design space and requires a large number of validation trials with high experimental costs. A comprehensible machine learning approach that efficiently explores the hypothesis space and guides experimental design is urgently needed for the Design-Build-Test-Learn (DBTL) cycle of the host cell system. We introduce a novel machine learning framework ILP-iML1515 based on Inductive Logic Programming (ILP) that performs abductive logical reasoning and actively learns from training examples. In contrast to numerical models, ILP-iML1515 is built on comprehensible logical representations of a genome-scale metabolic model and can update the model by learning new logical structures from auxotrophic mutant trials. The ILP-iML1515 framework 1) allows high-throughput simulations and 2) actively selects experiments that reduce the experimental cost of learning gene functions in comparison to randomly selected experiments.

Lun Ai

Traditional logic programming relies on symbolic computation on the CPU, which can limit performance for large-scale inference tasks. Recent advances in GPU hardware enable high-throughput matrix operations, motivating a shift toward parallel logic inference. Boolean Matrix Logic Programming (BMLP) introduces a novel approach to datalog query evaluation using Boolean matrix algebra, well-suited to GPU acceleration. Building on this paradigm, we present two GPU-accelerated BMLP algorithms for bottom-up inference over linear dyadic recursive datalog programs. We further extend the BMLP theoretical framework to support general linear recursion with binary predicates. Empirical evaluations on reachability queries in large directed graphs and the Freebase 15K dataset show that our methods achieve 1-4 orders of magnitude speed up over state-of-the-art systems. These results demonstrate that Boolean matrix-based reasoning can significantly advance the scalability and efficiency of logic programming on modern hardware. Source code is available on https://github.com/lun-ai/BMLP.git.

Lun Ai, Johannes Langer, Ute Schmid et al.

Ultra Strong Machine Learning (USML) refers to symbolic learning systems that not only improve their own performance but can also teach their acquired knowledge to quantifiably improve human performance. In this work, we present LENS (Logic Programming Explanation via Neural Summarisation), a neuro-symbolic method that combines symbolic program synthesis with large language models (LLMs) to automate the explanation of machine-learned logic programs in natural language. LENS addresses a key limitation of prior USML approaches by replacing hand-crafted explanation templates with scalable automated generation. Through systematic evaluation using multiple LLM judges and human validation, we demonstrate that LENS generates superior explanations compared to direct LLM prompting and hand-crafted templates. To investigate whether LENS can teach transferable active learning strategies, we carried out a human learning experiment across three related domains. Our results show no significant human performance improvements, suggesting that comprehensive LLM responses may overwhelm users for simpler problems rather than providing learning support. Our work provides a solid foundation for building effective USML systems to support human learning. The source code is available on: https://github.com/lun-ai/LENS.git.

Lun Ai, Stephen H. Muggleton, Shi-shun Liang et al.

We apply logic-based machine learning techniques to facilitate cellular engineering and drive biological discovery, based on comprehensive databases of metabolic processes called genome-scale metabolic network models (GEMs). Predicted host behaviours are not always correctly described by GEMs. 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 and offers a realistic approach to a self-driving lab for microbial engineering.

Lun Ai, Stephen H. Muggleton, Shi-Shun Liang et al.

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation. Genome-scale metabolic network models (GEMs) - comprehensive representations of metabolic genes and reactions - are widely used to evaluate genetic engineering of biological systems. However, GEMs often fail to accurately predict the behaviour of genetically engineered cells, primarily due to incomplete annotations of gene interactions. The task of learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To efficiently predict using GEM, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging Boolean matrices to evaluate large logic programs. We developed a new system, $BMLP_{active}$, which guides cost-effective experimentation and uses interpretable logic programs to encode a state-of-the-art GEM of a model bacterial organism. Notably, $BMLP_{active}$ successfully learned 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 biological discovery, which would then facilitate microbial engineering for practical applications.

Yuanfang Xiang, Lun Ai

The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.

Lun Ai, Stephen H. Muggleton, Shi-Shun Liang et al.

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.

Lun Ai, Stephen H. Muggleton, Céline Hocquette et al.

Given the recent successes of Deep Learning in AI there has been increased interest in the role and need for explanations in machine learned theories. A distinct notion in this context is that of Michie's definition of Ultra-Strong Machine Learning (USML). USML is demonstrated by a measurable increase in human performance of a task following provision to the human of a symbolic machine learned theory for task performance. A recent paper demonstrates the beneficial effect of a machine learned logic theory for a classification task, yet no existing work to our knowledge has examined the potential harmfulness of machine's involvement for human comprehension during learning. This paper investigates the explanatory effects of a machine learned theory in the context of simple two person games and proposes a framework for identifying the harmfulness of machine explanations based on the Cognitive Science literature. The approach involves a cognitive window consisting of two quantifiable bounds and it is supported by empirical evidence collected from human trials. Our quantitative and qualitative results indicate that human learning aided by a symbolic machine learned theory which satisfies a cognitive window has achieved significantly higher performance than human self learning. Results also demonstrate that human learning aided by a symbolic machine learned theory that fails to satisfy this window leads to significantly worse performance than unaided human learning.