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Similarity search is a fundamental task for exploiting information in various applications dealing with graph data, such as citation networks or knowledge graphs. While this task has been intensively approached from heuristics to graph embeddings and graph neural networks (GNNs), providing explanations for similarity has received less attention. In this work we are concerned with explainable similarity search over graphs, by investigating how GNN-based methods for computing node similarities can be augmented with explanations. Specifically, we evaluate the performance of two prominent approaches towards explanations in GNNs, based on the concepts of mutual information (MI), and gradient-based explanations (GB). We discuss their suitability and empirically validate the properties of their explanations over different popular graph benchmarks. We find that unlike MI explanations, gradient-based explanations have three desirable properties. First, they are actionable: selecting inputs depending on them results in predictable changes in similarity scores. Second, they are consistent: the effect of selecting certain inputs overlaps very little with the effect of discarding them. Third, they can be pruned significantly to obtain sparse explanations that retain the effect on similarity scores.

At the heart of smart manufacturing is real-time semi-automatic decision-making. Such decisions are vital for optimizing production lines, e.g., reducing resource consumption, improving the quality of discrete manufacturing operations, and optimizing the actual products, e.g., optimizing the sampling rate for measuring product dimensions during production. Such decision-making relies on massive industrial data thus posing a real-time processing bottleneck.

Angiogenesis is the process wherein endothelial cells (ECs) form sprouts that elongate from the pre-existing vasculature to create new vascular networks. In addition to its essential role in normal development, angiogenesis plays a vital role in pathologies such as cancer, diabetes and atherosclerosis. Mathematical and computational modelling has contributed to unravelling its complexity. Many existing theoretical models of angiogenic sprouting are based on the 'snail-trail' hypothesis. This framework assumes that leading ECs positioned at sprout tips migrate towards low-oxygen regions while other ECs in the sprout passively follow the leaders' trails and proliferate to maintain sprout integrity. However, experimental results indicate that, contrary to the snail-trail assumption, ECs exchange positions within developing vessels, and the elongation of sprouts is primarily driven by directed migration of ECs. The functional role of cell rearrangements remains unclear. This review of the theoretical modelling of angiogenesis is the first to focus on the phenomenon of cell mixing during early sprouting. We start by describing the biological processes that occur during early angiogenesis, such as phenotype specification, cell rearrangements and cell interactions with the microenvironment. Next, we provide an overview of various theoretical approaches that have been employed to model angiogenesis, with particular emphasis on recent in silico models that account for the phenomenon of cell mixing. Finally, we discuss when cell mixing should be incorporated into theoretical models and what essential modelling components such models should include in order to investigate its functional role., Comment: 27 pages, 9 figures, 1 table

We present a continuation to our previous work, in which we developed the MR-CKR framework to reason with knowledge overriding across contexts organized in multi-relational hierarchies. Reasoning is realized via ASP with algebraic measures, allowing for flexible definitions of preferences. In this paper, we show how to apply our theoretical work to real autonomous-vehicle scene data. Goal of this work is to apply MR-CKR to the problem of generating challenging scenes for autonomous vehicle learning. In practice, most of the scene data for AV learning models common situations, thus it might be difficult to capture cases where a particular situation occurs (e.g. partial occlusions of a crossing pedestrian). The MR-CKR model allows for data organization exploiting the multi-dimensionality of such data (e.g., temporal and spatial). Reasoning over multiple contexts enables the verification and configuration of scenes, using the combination of different scene ontologies. We describe a framework for semantically guided data generation, based on a combination of MR-CKR and Algebraic Measures. The framework is implemented in a proof-of-concept prototype exemplifying some cases of scene generation., Comment: Technical Report for Humane-AI micro-project "Multi-Relational Contextual Reasoning for Complex Scene Generation for Autonomous Vehicle Data". 23 pages, 6 figures

We deal with a challenging scheduling problem on parallel machines with sequence-dependent setup times and release dates from a real-world application of semiconductor work-shop production. There, jobs can only be processed by dedicated machines, thus few machines can determine the makespan almost regardless of how jobs are scheduled on the remaining ones. This causes problems when machines fail and jobs need to be rescheduled. Instead of optimising only the makespan, we put the individual machine spans in non-ascending order and lexicographically minimise the resulting tuples. This achieves that all machines complete as early as possible and increases the robustness of the schedule. We study the application of Answer-Set Programming (ASP) to solve this problem. While ASP eases modelling, the combination of timing constraints and the considered objective function challenges current solving technology. The former issue is addressed by using an extension of ASP by difference logic. For the latter, we devise different algorithms that use multi-shot solving. To tackle industrial-sized instances, we study different approximations and heuristics. Our experimental results show that ASP is indeed a promising KRR paradigm for this problem and is competitive with state-of-the-art CP and MIP solvers. Under consideration in Theory and Practice of Logic Programming (TPLP)., Comment: Under consideration in Theory and Practice of Logic Programming (TPLP)

Smart factories are equipped with machines that can sense their manufacturing environments, interact with each other, and control production processes. Smooth operation of such factories requires that the machines and engineering personnel that conduct their monitoring and diagnostics share a detailed common industrial knowledge about the factory, e.g., in the form of knowledge graphs. Creation and maintenance of such knowledge is expensive and requires automation. In this work we show how machine learning that is specifically tailored towards industrial applications can help in knowledge graph completion. In particular, we show how knowledge completion can benefit from event logs that are common in smart factories. We evaluate this on the knowledge graph from a real world-inspired smart factory with encouraging results.

Current methods for embedding-based query answering over incomplete Knowledge Graphs (KGs) only focus on inductive reasoning, i.e., predicting answers by learning patterns from the data, and lack the complementary ability to do deductive reasoning, which requires the application of domain knowledge to infer further information. To address this shortcoming, we investigate the problem of incorporating ontologies into embedding-based query answering models by defining the task of embedding-based ontology-mediated query answering. We propose various integration strategies into prominent representatives of embedding models that involve (1) different ontology-driven data augmentation techniques and (2) adaptation of the loss function to enforce the ontology axioms. We design novel benchmarks for the considered task based on the LUBM and the NELL KGs and evaluate our methods on them. The achieved improvements in the setting that requires both inductive and deductive reasoning are from 20% to 55% in HITS@3.

Hybrid multiscale modelling has emerged as a useful framework for modelling complex biological phenomena. However, when accounting for stochasticity in the internal dynamics of agents, these models frequently become computationally expensive. Traditional techniques to reduce the computational intensity of such models can lead to a reduction in the richness of the dynamics observed, compared to the original system. Here we use large deviation theory to decrease the computational cost of a spatially-extended multi-agent stochastic system with a region of multi-stability by coarse-graining it to a continuous time Markov chain on the state space of stable steady states of the original system. Our technique preserves the original description of the stable steady states of the system and accounts for noise-induced transitions between them. We apply the method to a bistable system modelling phenotype specification of cells driven by a lateral inhibition mechanism. For this system, we demonstrate how the method may be used to explore different pattern configurations and unveil robust patterns emerging on longer timescales. We then compare the full stochastic, coarse-grained and mean-field descriptions via pattern quantification metrics and in terms of the numerical cost of each method. Our results show that the coarse-grained system exhibits the lowest computational cost while preserving the rich dynamics of the stochastic system. The method has the potential to reduce the computational complexity of hybrid multiscale models, making them more tractable for analysis, simulation and hypothesis testing.

Detecting small sets of relevant patterns from a given dataset is a central challenge in data mining. The relevance of a pattern is based on user-provided criteria; typically, all patterns that satisfy certain criteria are considered relevant. Rule-based languages like Answer Set Programming (ASP) seem well-suited for specifying such criteria in a form of constraints. Although progress has been made, on the one hand, on solving individual mining problems and, on the other hand, developing generic mining systems, the existing methods either focus on scalability or on generality. In this paper we make steps towards combining local (frequency, size, cost) and global (various condensed representations like maximal, closed, skyline) constraints in a generic and efficient way. We present a hybrid approach for itemset, sequence and graph mining which exploits dedicated highly optimized mining systems to detect frequent patterns and then filters the results using declarative ASP. To further demonstrate the generic nature of our hybrid framework we apply it to a problem of approximately tiling a database. Experiments on real-world datasets show the effectiveness of the proposed method and computational gains for itemset, sequence and graph mining, as well as approximate tiling. Under consideration in Theory and Practice of Logic Programming (TPLP)., Comment: 29 pages, 7 figures, 5 tables