13,192 research outputs found
Optimal network topologies: Expanders, Cages, Ramanujan graphs, Entangled networks and all that
We report on some recent developments in the search for optimal network
topologies. First we review some basic concepts on spectral graph theory,
including adjacency and Laplacian matrices, and paying special attention to the
topological implications of having large spectral gaps. We also introduce
related concepts as ``expanders'', Ramanujan, and Cage graphs. Afterwards, we
discuss two different dynamical feautures of networks: synchronizability and
flow of random walkers and so that they are optimized if the corresponding
Laplacian matrix have a large spectral gap. From this, we show, by developing a
numerical optimization algorithm that maximum synchronizability and fast random
walk spreading are obtained for a particular type of extremely homogeneous
regular networks, with long loops and poor modular structure, that we call
entangled networks. These turn out to be related to Ramanujan and Cage graphs.
We argue also that these graphs are very good finite-size approximations to
Bethe lattices, and provide almost or almost optimal solutions to many other
problems as, for instance, searchability in the presence of congestion or
performance of neural networks. Finally, we study how these results are
modified when studying dynamical processes controlled by a normalized (weighted
and directed) dynamics; much more heterogeneous graphs are optimal in this
case. Finally, a critical discussion of the limitations and possible extensions
of this work is presented.Comment: 17 pages. 11 figures. Small corrections and a new reference. Accepted
for pub. in JSTA
Topological modes bound to dislocations in mechanical metamaterials
Mechanical metamaterials are artificial structures with unusual properties,
such as negative Poisson ratio, bistability or tunable vibrational properties,
that originate in the geometry of their unit cell. At the heart of such unusual
behaviour is often a soft mode: a motion that does not significantly stretch or
compress the links between constituent elements. When activated by motors or
external fields, soft modes become the building blocks of robots and smart
materials. Here, we demonstrate the existence of topological soft modes that
can be positioned at desired locations in a metamaterial while being robust
against a wide range of structural deformations or changes in material
parameters. These protected modes, localized at dislocations, are the
mechanical analogue of topological states bound to defects in electronic
systems. We create physical realizations of the topological modes in prototypes
of kagome lattices built out of rigid triangular plates. We show mathematically
that they originate from the interplay between two Berry phases: the Burgers
vector of the dislocation and the topological polarization of the lattice. Our
work paves the way towards engineering topologically protected nano-mechanical
structures for molecular robotics or information storage and read-out.Comment: 13 pages, 6 figures; changes to text and figures and added analysis
on mode localization; see
http://www.lorentz.leidenuniv.nl/~paulose/dislocation-modes/ for accompanying
video
Network Topology Mapping from Partial Virtual Coordinates and Graph Geodesics
For many important network types (e.g., sensor networks in complex harsh
environments and social networks) physical coordinate systems (e.g.,
Cartesian), and physical distances (e.g., Euclidean), are either difficult to
discern or inapplicable. Accordingly, coordinate systems and characterizations
based on hop-distance measurements, such as Topology Preserving Maps (TPMs) and
Virtual-Coordinate (VC) systems are attractive alternatives to Cartesian
coordinates for many network algorithms. Herein, we present an approach to
recover geometric and topological properties of a network with a small set of
distance measurements. In particular, our approach is a combination of shortest
path (often called geodesic) recovery concepts and low-rank matrix completion,
generalized to the case of hop-distances in graphs. Results for sensor networks
embedded in 2-D and 3-D spaces, as well as a social networks, indicates that
the method can accurately capture the network connectivity with a small set of
measurements. TPM generation can now also be based on various context
appropriate measurements or VC systems, as long as they characterize different
nodes by distances to small sets of random nodes (instead of a set of global
anchors). The proposed method is a significant generalization that allows the
topology to be extracted from a random set of graph shortest paths, making it
applicable in contexts such as social networks where VC generation may not be
possible.Comment: 17 pages, 9 figures. arXiv admin note: substantial text overlap with
arXiv:1712.1006
Entangled networks, synchronization, and optimal network topology
A new family of graphs, {\it entangled networks}, with optimal properties in
many respects, is introduced. By definition, their topology is such that
optimizes synchronizability for many dynamical processes. These networks are
shown to have an extremely homogeneous structure: degree, node-distance,
betweenness, and loop distributions are all very narrow. Also, they are
characterized by a very interwoven (entangled) structure with short average
distances, large loops, and no well-defined community-structure. This family of
nets exhibits an excellent performance with respect to other flow properties
such as robustness against errors and attacks, minimal first-passage time of
random walks, efficient communication, etc. These remarkable features convert
entangled networks in a useful concept, optimal or almost-optimal in many
senses, and with plenty of potential applications computer science or
neuroscience.Comment: Slightly modified version, as accepted in Phys. Rev. Let
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Complex biological systems have been successfully modeled by biochemical and
genetic interaction networks, typically gathered from high-throughput (HTP)
data. These networks can be used to infer functional relationships between
genes or proteins. Using the intuition that the topological role of a gene in a
network relates to its biological function, local or diffusion based
"guilt-by-association" and graph-theoretic methods have had success in
inferring gene functions. Here we seek to improve function prediction by
integrating diffusion-based methods with a novel dimensionality reduction
technique to overcome the incomplete and noisy nature of network data. In this
paper, we introduce diffusion component analysis (DCA), a framework that plugs
in a diffusion model and learns a low-dimensional vector representation of each
node to encode the topological properties of a network. As a proof of concept,
we demonstrate DCA's substantial improvement over state-of-the-art
diffusion-based approaches in predicting protein function from molecular
interaction networks. Moreover, our DCA framework can integrate multiple
networks from heterogeneous sources, consisting of genomic information,
biochemical experiments and other resources, to even further improve function
prediction. Yet another layer of performance gain is achieved by integrating
the DCA framework with support vector machines that take our node vector
representations as features. Overall, our DCA framework provides a novel
representation of nodes in a network that can be used as a plug-in architecture
to other machine learning algorithms to decipher topological properties of and
obtain novel insights into interactomes.Comment: RECOMB 201
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