Filipe Gouveia

Pedro T. Monteiro, Filipe Gouveia

Biological regulatory networks can be represented by computational models, which allow the study and analysis of biological behaviours, therefore providing a better understanding of a given biological process. However, as new information is acquired, biological models may need to be revised in order to also account for this new information. Current model revision tools are scarce and often lack the flexibility to integrate with broader analysis workflows. Here, we present pyModRev, an enhanced iteration of the model revision tool ModRev, capable of verifying the consistency of Boolean regulatory models, and finding minimal repairs in case of inconsistency. pyModRev supports model validation against both steady state observations as well as time-series data, being able to consider different update schemes simultaneously. pyModRev supports different model formats, and is available as a Python package in PyPI, for easy integration with other model analysis tools, significantly improving accessibility and utility for the logical modelling community.

Andrew Cropper, Filipe Gouveia, David M. Cerna

Inductive logic programming (ILP) is a form of logical machine learning. The goal is to search a hypothesis space for a hypothesis that generalises training examples and background knowledge. We introduce an approach that 'shrinks' the hypothesis space before an ILP system searches it. Our approach uses background knowledge to find rules that cannot be in an optimal hypothesis regardless of the training examples. For instance, our approach discovers relationships such as "even numbers cannot be odd" and "prime numbers greater than 2 are odd". It then removes violating rules from the hypothesis space. We implement our approach using answer set programming and use it to shrink the hypothesis space of a constraint-based ILP system. Our experiments on multiple domains, including visual reasoning and game playing, show that our approach can substantially reduce learning times whilst maintaining predictive accuracies. For instance, given just 10 seconds of preprocessing time, our approach can reduce learning times from over 10 hours to only 2 seconds.

Minghao Liu, David M. Cerna, Filipe Gouveia et al.

Knowledge refactoring compresses a logic program by introducing new rules. Current approaches struggle to scale to large programs. To overcome this limitation, we introduce a constrained optimisation refactoring approach. Our first key idea is to encode the problem with decision variables based on literals rather than rules. Our second key idea is to focus on linear invented rules. Our empirical results on multiple domains show that our approach can refactor programs quicker and with more compression than the previous state-of-the-art approach, sometimes by 60%.