11,499 research outputs found
Dysfunctions of highly parallel real-time machines as 'developmental disorders': Security concerns and a Caveat Emptor
A cognitive paradigm for gene expression in developmental biology that is based on rigorous application of the asymptotic limit theorems of information theory can be adapted to highly parallel real-time computing. The coming Brave New World of massively parallel 'autonomic' and 'Self-X' machines driven by the explosion of multiple core and molecular computing technologies will not be spared patterns of canonical and idiosyncratic failure analogous to the developmental disorders affecting organisms that have had the relentless benefit of a billion years of evolutionary pruning. This paper provides a warning both to potential users of these machines and, given that many such disorders can be induced by external agents, to those concerned with larger scale matters of homeland security
Towards Autopoietic Computing
A key challenge in modern computing is to develop systems that address
complex, dynamic problems in a scalable and efficient way, because the
increasing complexity of software makes designing and maintaining efficient and
flexible systems increasingly difficult. Biological systems are thought to
possess robust, scalable processing paradigms that can automatically manage
complex, dynamic problem spaces, possessing several properties that may be
useful in computer systems. The biological properties of self-organisation,
self-replication, self-management, and scalability are addressed in an
interesting way by autopoiesis, a descriptive theory of the cell founded on the
concept of a system's circular organisation to define its boundary with its
environment. In this paper, therefore, we review the main concepts of
autopoiesis and then discuss how they could be related to fundamental concepts
and theories of computation. The paper is conceptual in nature and the emphasis
is on the review of other people's work in this area as part of a longer-term
strategy to develop a formal theory of autopoietic computing.Comment: 10 Pages, 3 figure
Correlation of Automorphism Group Size and Topological Properties with Program-size Complexity Evaluations of Graphs and Complex Networks
We show that numerical approximations of Kolmogorov complexity (K) applied to
graph adjacency matrices capture some group-theoretic and topological
properties of graphs and empirical networks ranging from metabolic to social
networks. That K and the size of the group of automorphisms of a graph are
correlated opens up interesting connections to problems in computational
geometry, and thus connects several measures and concepts from complexity
science. We show that approximations of K characterise synthetic and natural
networks by their generating mechanisms, assigning lower algorithmic randomness
to complex network models (Watts-Strogatz and Barabasi-Albert networks) and
high Kolmogorov complexity to (random) Erdos-Renyi graphs. We derive these
results via two different Kolmogorov complexity approximation methods applied
to the adjacency matrices of the graphs and networks. The methods used are the
traditional lossless compression approach to Kolmogorov complexity, and a
normalised version of a Block Decomposition Method (BDM) measure, based on
algorithmic probability theory.Comment: 15 2-column pages, 20 figures. Forthcoming in Physica A: Statistical
Mechanics and its Application
Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
Supervised machine learning techniques have traditionally been very successful at reconstructing biological networks, such as protein-ligand interaction, protein-protein interaction and gene regulatory networks. Many supervised techniques for network prediction use linear models on a possibly nonlinear pairwise feature representation of edges. Recently, much emphasis has been placed on the correct evaluation of such supervised models. It is vital to distinguish between using a model to either predict new interactions in a given network or to predict interactions for a new vertex not present in the original network. This distinction matters because (i) the performance might dramatically differ between the prediction settings and (ii) tuning the model hyperparameters to obtain the best possible model depends on the setting of interest. Specific cross-validation schemes need to be used to assess the performance in such different prediction settings. In this work we discuss a state-of-the-art kernel-based network inference technique called two-step kernel ridge regression. We show that this regression model can be trained efficiently, with a time complexity scaling with the number of vertices rather than the number of edges. Furthermore, this framework leads to a series of cross-validation shortcuts that allow one to rapidly estimate the model performance for any relevant network prediction setting. This allows computational biologists to fully assess the capabilities of their models
Detecting Multiple Communities Using Quantum Annealing on the D-Wave System
A very important problem in combinatorial optimization is partitioning a
network into communities of densely connected nodes; where the connectivity
between nodes inside a particular community is large compared to the
connectivity between nodes belonging to different ones. This problem is known
as community detection, and has become very important in various fields of
science including chemistry, biology and social sciences. The problem of
community detection is a twofold problem that consists of determining the
number of communities and, at the same time, finding those communities. This
drastically increases the solution space for heuristics to work on, compared to
traditional graph partitioning problems. In many of the scientific domains in
which graphs are used, there is the need to have the ability to partition a
graph into communities with the ``highest quality'' possible since the presence
of even small isolated communities can become crucial to explain a particular
phenomenon. We have explored community detection using the power of quantum
annealers, and in particular the D-Wave 2X and 2000Q machines. It turns out
that the problem of detecting at most two communities naturally fits into the
architecture of a quantum annealer with almost no need of reformulation. This
paper addresses a systematic study of detecting two or more communities in a
network using a quantum annealer
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