2,823 research outputs found
RASCAL: calculation of graph similarity using maximum common edge subgraphs
A new graph similarity calculation procedure is introduced for comparing labeled graphs. Given a minimum similarity threshold, the procedure consists of an initial screening process to determine whether it is possible for the measure of similarity between the two graphs to exceed the minimum threshold, followed by a rigorous maximum common edge subgraph (MCES) detection algorithm to compute the exact degree and composition of similarity. The proposed MCES algorithm is based on a maximum clique formulation of the problem and is a significant improvement over other published algorithms. It presents new approaches to both lower and upper bounding as well as vertex selection
Inductive queries for a drug designing robot scientist
It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments
Probing the Space of Toric Quiver Theories
We demonstrate a practical and efficient method for generating toric Calabi-Yau quiver theories, applicable to both D3 and M2 brane world-volume physics. A new analytic method is presented at low order parametres and an algorithm for the general case is developed which has polynomial complexity in the number of edges in the quiver. Using this algorithm, carefully implemented, we classify the quiver diagram and assign possible superpotentials for various small values of the number of edges and nodes. We examine some preliminary statistics on this space of toric quiver theories
A simple yet effective baseline for non-attributed graph classification
Graphs are complex objects that do not lend themselves easily to typical
learning tasks. Recently, a range of approaches based on graph kernels or graph
neural networks have been developed for graph classification and for
representation learning on graphs in general. As the developed methodologies
become more sophisticated, it is important to understand which components of
the increasingly complex methods are necessary or most effective.
As a first step, we develop a simple yet meaningful graph representation, and
explore its effectiveness in graph classification. We test our baseline
representation for the graph classification task on a range of graph datasets.
Interestingly, this simple representation achieves similar performance as the
state-of-the-art graph kernels and graph neural networks for non-attributed
graph classification. Its performance on classifying attributed graphs is
slightly weaker as it does not incorporate attributes. However, given its
simplicity and efficiency, we believe that it still serves as an effective
baseline for attributed graph classification. Our graph representation is
efficient (linear-time) to compute. We also provide a simple connection with
the graph neural networks.
Note that these observations are only for the task of graph classification
while existing methods are often designed for a broader scope including node
embedding and link prediction. The results are also likely biased due to the
limited amount of benchmark datasets available. Nevertheless, the good
performance of our simple baseline calls for the development of new, more
comprehensive benchmark datasets so as to better evaluate and analyze different
graph learning methods. Furthermore, given the computational efficiency of our
graph summary, we believe that it is a good candidate as a baseline method for
future graph classification (or even other graph learning) studies.Comment: 13 pages. Shorter version appears at 2019 ICLR Workshop:
Representation Learning on Graphs and Manifolds. arXiv admin note: text
overlap with arXiv:1810.00826 by other author
A Survey on Graph Kernels
Graph kernels have become an established and widely-used technique for
solving classification tasks on graphs. This survey gives a comprehensive
overview of techniques for kernel-based graph classification developed in the
past 15 years. We describe and categorize graph kernels based on properties
inherent to their design, such as the nature of their extracted graph features,
their method of computation and their applicability to problems in practice. In
an extensive experimental evaluation, we study the classification accuracy of a
large suite of graph kernels on established benchmarks as well as new datasets.
We compare the performance of popular kernels with several baseline methods and
study the effect of applying a Gaussian RBF kernel to the metric induced by a
graph kernel. In doing so, we find that simple baselines become competitive
after this transformation on some datasets. Moreover, we study the extent to
which existing graph kernels agree in their predictions (and prediction errors)
and obtain a data-driven categorization of kernels as result. Finally, based on
our experimental results, we derive a practitioner's guide to kernel-based
graph classification
Efficient Generation of Stable Planar Cages for Chemistry
In this paper we describe an algorithm which generates all colored planar
maps with a good minimum sparsity from simple motifs and rules to connect them.
An implementation of this algorithm is available and is used by chemists who
want to quickly generate all sound molecules they can obtain by mixing some
basic components.Comment: 17 pages, 7 figures. Accepted at the 14th International Symposium on
Experimental Algorithms (SEA 2015
Shared Memory Parallel Subgraph Enumeration
The subgraph enumeration problem asks us to find all subgraphs of a target
graph that are isomorphic to a given pattern graph. Determining whether even
one such isomorphic subgraph exists is NP-complete---and therefore finding all
such subgraphs (if they exist) is a time-consuming task. Subgraph enumeration
has applications in many fields, including biochemistry and social networks,
and interestingly the fastest algorithms for solving the problem for
biochemical inputs are sequential. Since they depend on depth-first tree
traversal, an efficient parallelization is far from trivial. Nevertheless,
since important applications produce data sets with increasing difficulty,
parallelism seems beneficial.
We thus present here a shared-memory parallelization of the state-of-the-art
subgraph enumeration algorithms RI and RI-DS (a variant of RI for dense graphs)
by Bonnici et al. [BMC Bioinformatics, 2013]. Our strategy uses work stealing
and our implementation demonstrates a significant speedup on real-world
biochemical data---despite a highly irregular data access pattern. We also
improve RI-DS by pruning the search space better; this further improves the
empirical running times compared to the already highly tuned RI-DS.Comment: 18 pages, 12 figures, To appear at the 7th IEEE Workshop on Parallel
/ Distributed Computing and Optimization (PDCO 2017
- …