4 research outputs found
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
Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction
Despite the recognized importance of the multi-scale spatio-temporal
organization of proteins, most computational tools can only access a limited
spectrum of time and spatial scales, thereby ignoring the effects on protein
behavior of the intricate coupling between the different scales. Starting from
a physico-chemical atomistic network of interactions that encodes the structure
of the protein, we introduce a methodology based on multi-scale graph
partitioning that can uncover partitions and levels of organization of proteins
that span the whole range of scales, revealing biological features occurring at
different levels of organization and tracking their effect across scales.
Additionally, we introduce a measure of robustness to quantify the relevance of
the partitions through the generation of biochemically-motivated surrogate
random graph models. We apply the method to four distinct conformations of
myosin tail interacting protein, a protein from the molecular motor of the
malaria parasite, and study properties that have been experimentally addressed
such as the closing mechanism, the presence of conserved clusters, and the
identification through computational mutational analysis of key residues for
binding.Comment: 13 pages, 7 Postscript figure
Fast unfolding of communities in large networks
We propose a simple method to extract the community structure of large
networks. Our method is a heuristic method that is based on modularity
optimization. It is shown to outperform all other known community detection
method in terms of computation time. Moreover, the quality of the communities
detected is very good, as measured by the so-called modularity. This is shown
first by identifying language communities in a Belgian mobile phone network of
2.6 million customers and by analyzing a web graph of 118 million nodes and
more than one billion links. The accuracy of our algorithm is also verified on
ad-hoc modular networks. .Comment: 6 pages, 5 figures, 1 table; new version with new figures in order to
clarify our method, where we look more carefully at the role played by the
ordering of the nodes and where we compare our method with that of Wakita and
Tsurum
Markov dynamics as a zooming lens for multiscale community detection: non clique-like communities and the field-of-view limit
In recent years, there has been a surge of interest in community detection
algorithms for complex networks. A variety of computational heuristics, some
with a long history, have been proposed for the identification of communities
or, alternatively, of good graph partitions. In most cases, the algorithms
maximize a particular objective function, thereby finding the `right' split
into communities. Although a thorough comparison of algorithms is still
lacking, there has been an effort to design benchmarks, i.e., random graph
models with known community structure against which algorithms can be
evaluated. However, popular community detection methods and benchmarks normally
assume an implicit notion of community based on clique-like subgraphs, a form
of community structure that is not always characteristic of real networks.
Specifically, networks that emerge from geometric constraints can have natural
non clique-like substructures with large effective diameters, which can be
interpreted as long-range communities. In this work, we show that long-range
communities escape detection by popular methods, which are blinded by a
restricted `field-of-view' limit, an intrinsic upper scale on the communities
they can detect. The field-of-view limit means that long-range communities tend
to be overpartitioned. We show how by adopting a dynamical perspective towards
community detection (Delvenne et al. (2010) PNAS:107: 12755-12760; Lambiotte et
al. (2008) arXiv:0812.1770), in which the evolution of a Markov process on the
graph is used as a zooming lens over the structure of the network at all
scales, one can detect both clique- or non clique-like communities without
imposing an upper scale to the detection. Consequently, the performance of
algorithms on inherently low-diameter, clique-like benchmarks may not always be
indicative of equally good results in real networks with local, sparser
connectivity.Comment: 20 pages, 6 figure