Logspace computations in graph products

We consider three important and well-studied algorithmic problems in group theory: the word, geodesic, and conjugacy problem. We show transfer results from individual groups to graph products. We concentrate on logspace complexity because the challenge is actually in small complexity classes, only. The most difficult transfer result is for the conjugacy problem. We have a general result for graph products, but even in the special case of a graph group the result is new. Graph groups are closely linked to the theory of Mazurkiewicz traces which form an algebraic model for concurrent processes. Our proofs are combinatorial and based on well-known concepts in trace theory. We also use rewriting techniques over traces. For the group-theoretical part we apply Bass-Serre theory. But as we need explicit formulae and as we design concrete algorithms all our group-theoretical calculations are completely explicit and accessible to non-specialists

Graphs, Matrices, and the GraphBLAS: Seven Good Reasons

The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istc- bigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.Comment: 10 pages; International Conference on Computational Science workshop on the Applications of Matrix Computational Methods in the Analysis of Modern Dat

Multi-task Neural Network for Non-discrete Attribute Prediction in Knowledge Graphs

Many popular knowledge graphs such as Freebase, YAGO or DBPedia maintain a list of non-discrete attributes for each entity. Intuitively, these attributes such as height, price or population count are able to richly characterize entities in knowledge graphs. This additional source of information may help to alleviate the inherent sparsity and incompleteness problem that are prevalent in knowledge graphs. Unfortunately, many state-of-the-art relational learning models ignore this information due to the challenging nature of dealing with non-discrete data types in the inherently binary-natured knowledge graphs. In this paper, we propose a novel multi-task neural network approach for both encoding and prediction of non-discrete attribute information in a relational setting. Specifically, we train a neural network for triplet prediction along with a separate network for attribute value regression. Via multi-task learning, we are able to learn representations of entities, relations and attributes that encode information about both tasks. Moreover, such attributes are not only central to many predictive tasks as an information source but also as a prediction target. Therefore, models that are able to encode, incorporate and predict such information in a relational learning context are highly attractive as well. We show that our approach outperforms many state-of-the-art methods for the tasks of relational triplet classification and attribute value prediction.Comment: Accepted at CIKM 201

Towards a fully automated computation of RG-functions for the 3-dd O(N) vector model: Parametrizing amplitudes

Within the framework of field-theoretical description of second-order phase transitions via the 3-dimensional O(N) vector model, accurate predictions for critical exponents can be obtained from (resummation of) the perturbative series of Renormalization-Group functions, which are in turn derived --following Parisi's approach-- from the expansions of appropriate field correlators evaluated at zero external momenta. Such a technique was fully exploited 30 years ago in two seminal works of Baker, Nickel, Green and Meiron, which lead to the knowledge of the $\beta$-function up to the 6-loop level; they succeeded in obtaining a precise numerical evaluation of all needed Feynman amplitudes in momentum space by lowering the dimensionalities of each integration with a cleverly arranged set of computational simplifications. In fact, extending this computation is not straightforward, due both to the factorial proliferation of relevant diagrams and the increasing dimensionality of their associated integrals; in any case, this task can be reasonably carried on only in the framework of an automated environment. On the road towards the creation of such an environment, we here show how a strategy closely inspired by that of Nickel and coworkers can be stated in algorithmic form, and successfully implemented on the computer. As an application, we plot the minimized distributions of residual integrations for the sets of diagrams needed to obtain RG-functions to the full 7-loop level; they represent a good evaluation of the computational effort which will be required to improve the currently available estimates of critical exponents.Comment: 54 pages, 17 figures and 4 table

Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference