Resource-Bound Quantification for Graph Transformation

Graph transformation has been used to model concurrent systems in software engineering, as well as in biochemistry and life sciences. The application of a transformation rule can be characterised algebraically as construction of a double-pushout (DPO) diagram in the category of graphs. We show how intuitionistic linear logic can be extended with resource-bound quantification, allowing for an implicit handling of the DPO conditions, and how resource logic can be used to reason about graph transformation systems

Relaxed Dissimilarity-based Symbolic Histogram Variants for Granular Graph Embedding

Graph embedding is an established and popular approach when designing graph-based pattern recognition systems. Amongst the several strategies, in the last ten years, Granular Computing emerged as a promising framework for structural pattern recognition. In the late 2000\u2019s, symbolic histograms have been proposed as the driving force in order to perform the graph embedding procedure by counting the number of times each granule of information appears in the graph to be embedded. Similarly to a bag-of-words representation of a text corpora, symbolic histograms have been originally conceived as integer-valued vectorial representation of the graphs. In this paper, we propose six \u2018relaxed\u2019 versions of symbolic histograms, where the proper dissimilarity values between the information granules and the constituent parts of the graph to be embedded are taken into account, information which is discarded in the original symbolic histogram formulation due to the hard-limited nature of the counting procedure. Experimental results on six open-access datasets of fully-labelled graphs show comparable performance in terms of classification accuracy with respect to the original symbolic histograms (average accuracy shift ranging from -7% to +2%), counterbalanced by a great improvement in terms of number of resulting information granules, hence number of features in the embedding space (up to 75% less features, on average)

On the Hardness of Category Tree Construction

Category trees, or taxonomies, are rooted trees where each node, called a category, corresponds to a set of related items. The construction of taxonomies has been studied in various domains, including e-commerce, document management, and question answering. Multiple algorithms for automating construction have been proposed, employing a variety of clustering approaches and crowdsourcing. However, no formal model to capture such categorization problems has been devised, and their complexity has not been studied. To address this, we propose in this work a combinatorial model that captures many practical settings and show that the aforementioned empirical approach has been warranted, as we prove strong inapproximability bounds for various problem variants and special cases when the goal is to produce a categorization of the maximum utility. In our model, the input is a set of n weighted item sets that the tree would ideally contain as categories. Each category, rather than perfectly match the corresponding input set, is allowed to exceed a given threshold for a given similarity function. The goal is to produce a tree that maximizes the total weight of the sets for which it contains a matching category. A key parameter is an upper bound on the number of categories an item may belong to, which produces the hardness of the problem, as initially each item may be contained in an arbitrary number of input sets. For this model, we prove inapproximability bounds, of order ??(?n) or ??(n), for various problem variants and special cases, loosely justifying the aforementioned heuristic approach. Our work includes reductions based on parameterized randomized constructions that highlight how various problem parameters and properties of the input may affect the hardness. Moreover, for the special case where the category must be identical to the corresponding input set, we devise an algorithm whose approximation guarantee depends solely on a more granular parameter, allowing improved worst-case guarantees. Finally, we also generalize our results to DAG-based and non-hierarchical categorization

Simplicial complexes and complex systems

© 2018 European Physical Society. We provide a short introduction to the field of topological data analysis (TDA) and discuss its possible relevance for the study of complex systems. TDA provides a set of tools to characterise the shape of data, in terms of the presence of holes or cavities between the points. The methods, based on the notion of simplicial complexes, generalise standard network tools by naturally allowing for many-body interactions and providing results robust under continuous deformations of the data. We present strengths and weaknesses of current methods, as well as a range of empirical studies relevant to the field of complex systems, before identifying future methodological challenges to help understand the emergence of collective phenomena

Scalable neural network models and terascale datasets for particle-flow reconstruction

We study scalable machine learning models for full event reconstruction in high-energy electron-positron collisions based on a highly granular detector simulation. Particle-flow (PF) reconstruction can be formulated as a supervised learning task using tracks and calorimeter clusters or hits. We compare a graph neural network and kernel-based transformer and demonstrate that both avoid quadratic memory allocation and computational cost while achieving realistic PF reconstruction. We show that hyperparameter tuning on a supercomputer significantly improves the physics performance of the models. We also demonstrate that the resulting model is highly portable across hardware processors, supporting Nvidia, AMD, and Intel Habana cards. Finally, we demonstrate that the model can be trained on highly granular inputs consisting of tracks and calorimeter hits, resulting in a competitive physics performance with the baseline. Datasets and software to reproduce the studies are published following the findable, accessible, interoperable, and reusable (FAIR) principles.Comment: 19 pages, 7 figure

Decapodes: A Diagrammatic Tool for Representing, Composing, and Computing Spatialized Partial Differential Equations

We present Decapodes, a diagrammatic tool for representing, composing, and solving partial differential equations. Decapodes provides an intuitive diagrammatic representation of the relationships between variables in a system of equations, a method for composing systems of partial differential equations using an operad of wiring diagrams, and an algorithm for deriving solvers using hypergraphs and string diagrams. The string diagrams are in turn compiled into executable programs using the techniques of categorical data migration, graph traversal, and the discrete exterior calculus. The generated solvers produce numerical solutions consistent with state-of-the-art open source tools as demonstrated by benchmark comparisons with SU2. These numerical experiments demonstrate the feasibility of this approach to multiphysics simulation and identify areas requiring further development

Hypergraph-Transformer (HGT) for Interactive Event Prediction in Laparoscopic and Robotic Surgery

Understanding and anticipating intraoperative events and actions is critical for intraoperative assistance and decision-making during minimally invasive surgery. Automated prediction of events, actions, and the following consequences is addressed through various computational approaches with the objective of augmenting surgeons' perception and decision-making capabilities. We propose a predictive neural network that is capable of understanding and predicting critical interactive aspects of surgical workflow from intra-abdominal video, while flexibly leveraging surgical knowledge graphs. The approach incorporates a hypergraph-transformer (HGT) structure that encodes expert knowledge into the network design and predicts the hidden embedding of the graph. We verify our approach on established surgical datasets and applications, including the detection and prediction of action triplets, and the achievement of the Critical View of Safety (CVS). Moreover, we address specific, safety-related tasks, such as predicting the clipping of cystic duct or artery without prior achievement of the CVS. Our results demonstrate the superiority of our approach compared to unstructured alternatives