18,796 research outputs found
Different approaches to community detection
A precise definition of what constitutes a community in networks has remained
elusive. Consequently, network scientists have compared community detection
algorithms on benchmark networks with a particular form of community structure
and classified them based on the mathematical techniques they employ. However,
this comparison can be misleading because apparent similarities in their
mathematical machinery can disguise different reasons for why we would want to
employ community detection in the first place. Here we provide a focused review
of these different motivations that underpin community detection. This
problem-driven classification is useful in applied network science, where it is
important to select an appropriate algorithm for the given purpose. Moreover,
highlighting the different approaches to community detection also delineates
the many lines of research and points out open directions and avenues for
future research.Comment: 14 pages, 2 figures. Written as a chapter for forthcoming Advances in
network clustering and blockmodeling, and based on an extended version of The
many facets of community detection in complex networks, Appl. Netw. Sci. 2: 4
(2017) by the same author
Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data
Determining the functional structure of biological networks is a central goal
of systems biology. One approach is to analyze gene expression data to infer a
network of gene interactions on the basis of their correlated responses to
environmental and genetic perturbations. The inferred network can then be
analyzed to identify functional communities. However, commonly used algorithms
can yield unreliable results due to experimental noise, algorithmic
stochasticity, and the influence of arbitrarily chosen parameter values.
Furthermore, the results obtained typically provide only a simplistic view of
the network partitioned into disjoint communities and provide no information of
the relationship between communities. Here, we present methods to robustly
detect coregulated and functionally enriched gene communities and demonstrate
their application and validity for Escherichia coli gene expression data.
Applying a recently developed community detection algorithm to the network of
interactions identified with the context likelihood of relatedness (CLR)
method, we show that a hierarchy of network communities can be identified.
These communities significantly enrich for gene ontology (GO) terms, consistent
with them representing biologically meaningful groups. Further, analysis of the
most significantly enriched communities identified several candidate new
regulatory interactions. The robustness of our methods is demonstrated by
showing that a core set of functional communities is reliably found when
artificial noise, modeling experimental noise, is added to the data. We find
that noise mainly acts conservatively, increasing the relatedness required for
a network link to be reliably assigned and decreasing the size of the core
communities, rather than causing association of genes into new communities.Comment: Due to appear in PLoS Computational Biology. Supplementary Figure S1
was not uploaded but is available by contacting the author. 27 pages, 5
figures, 15 supplementary file
A Method Based on Total Variation for Network Modularity Optimization using the MBO Scheme
The study of network structure is pervasive in sociology, biology, computer
science, and many other disciplines. One of the most important areas of network
science is the algorithmic detection of cohesive groups of nodes called
"communities". One popular approach to find communities is to maximize a
quality function known as {\em modularity} to achieve some sort of optimal
clustering of nodes. In this paper, we interpret the modularity function from a
novel perspective: we reformulate modularity optimization as a minimization
problem of an energy functional that consists of a total variation term and an
balance term. By employing numerical techniques from image processing
and compressive sensing -- such as convex splitting and the
Merriman-Bence-Osher (MBO) scheme -- we develop a variational algorithm for the
minimization problem. We present our computational results using both synthetic
benchmark networks and real data.Comment: 23 page
Communities in Networks
We survey some of the concepts, methods, and applications of community
detection, which has become an increasingly important area of network science.
To help ease newcomers into the field, we provide a guide to available
methodology and open problems, and discuss why scientists from diverse
backgrounds are interested in these problems. As a running theme, we emphasize
the connections of community detection to problems in statistical physics and
computational optimization.Comment: survey/review article on community structure in networks; published
version is available at
http://people.maths.ox.ac.uk/~porterm/papers/comnotices.pd
Community Detection in Quantum Complex Networks
Determining community structure is a central topic in the study of complex
networks, be it technological, social, biological or chemical, in static or
interacting systems. In this paper, we extend the concept of community
detection from classical to quantum systems---a crucial missing component of a
theory of complex networks based on quantum mechanics. We demonstrate that
certain quantum mechanical effects cannot be captured using current classical
complex network tools and provide new methods that overcome these problems. Our
approaches are based on defining closeness measures between nodes, and then
maximizing modularity with hierarchical clustering. Our closeness functions are
based on quantum transport probability and state fidelity, two important
quantities in quantum information theory. To illustrate the effectiveness of
our approach in detecting community structure in quantum systems, we provide
several examples, including a naturally occurring light-harvesting complex,
LHCII. The prediction of our simplest algorithm, semiclassical in nature,
mostly agrees with a proposed partitioning for the LHCII found in quantum
chemistry literature, whereas our fully quantum treatment of the problem
uncovers a new, consistent, and appropriately quantum community structure.Comment: 16 pages, 4 figures, 1 tabl
Stability of graph communities across time scales
The complexity of biological, social and engineering networks makes it
desirable to find natural partitions into communities that can act as
simplified descriptions and provide insight into the structure and function of
the overall system. Although community detection methods abound, there is a
lack of consensus on how to quantify and rank the quality of partitions. We
show here that the quality of a partition can be measured in terms of its
stability, defined in terms of the clustered autocovariance of a Markov process
taking place on the graph. Because the stability has an intrinsic dependence on
time scales of the graph, it allows us to compare and rank partitions at each
time and also to establish the time spans over which partitions are optimal.
Hence the Markov time acts effectively as an intrinsic resolution parameter
that establishes a hierarchy of increasingly coarser clusterings. Within our
framework we can then provide a unifying view of several standard partitioning
measures: modularity and normalized cut size can be interpreted as one-step
time measures, whereas Fiedler's spectral clustering emerges at long times. We
apply our method to characterize the relevance and persistence of partitions
over time for constructive and real networks, including hierarchical graphs and
social networks. We also obtain reduced descriptions for atomic level protein
structures over different time scales.Comment: submitted; updated bibliography from v
Magic-State Functional Units: Mapping and Scheduling Multi-Level Distillation Circuits for Fault-Tolerant Quantum Architectures
Quantum computers have recently made great strides and are on a long-term
path towards useful fault-tolerant computation. A dominant overhead in
fault-tolerant quantum computation is the production of high-fidelity encoded
qubits, called magic states, which enable reliable error-corrected computation.
We present the first detailed designs of hardware functional units that
implement space-time optimized magic-state factories for surface code
error-corrected machines. Interactions among distant qubits require surface
code braids (physical pathways on chip) which must be routed. Magic-state
factories are circuits comprised of a complex set of braids that is more
difficult to route than quantum circuits considered in previous work [1]. This
paper explores the impact of scheduling techniques, such as gate reordering and
qubit renaming, and we propose two novel mapping techniques: braid repulsion
and dipole moment braid rotation. We combine these techniques with graph
partitioning and community detection algorithms, and further introduce a
stitching algorithm for mapping subgraphs onto a physical machine. Our results
show a factor of 5.64 reduction in space-time volume compared to the best-known
previous designs for magic-state factories.Comment: 13 pages, 10 figure
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