79 research outputs found
Searching for network modules
When analyzing complex networks a key target is to uncover their modular
structure, which means searching for a family of modules, namely node subsets
spanning each a subnetwork more densely connected than the average. This work
proposes a novel type of objective function for graph clustering, in the form
of a multilinear polynomial whose coefficients are determined by network
topology. It may be thought of as a potential function, to be maximized, taking
its values on fuzzy clusterings or families of fuzzy subsets of nodes over
which every node distributes a unit membership. When suitably parametrized,
this potential is shown to attain its maximum when every node concentrates its
all unit membership on some module. The output thus is a partition, while the
original discrete optimization problem is turned into a continuous version
allowing to conceive alternative search strategies. The instance of the problem
being a pseudo-Boolean function assigning real-valued cluster scores to node
subsets, modularity maximization is employed to exemplify a so-called quadratic
form, in that the scores of singletons and pairs also fully determine the
scores of larger clusters, while the resulting multilinear polynomial potential
function has degree 2. After considering further quadratic instances, different
from modularity and obtained by interpreting network topology in alternative
manners, a greedy local-search strategy for the continuous framework is
analytically compared with an existing greedy agglomerative procedure for the
discrete case. Overlapping is finally discussed in terms of multiple runs, i.e.
several local searches with different initializations.Comment: 10 page
A Special Structural Based Weighted Network Approach for the Analysis of Protein Complexes
The detection and analysis of protein complexes is essential for understanding the functional mechanism and cellular integrity. Recently, several techniques for detecting and analysing protein complexes from ProteinâProtein Interaction (PPI) dataset have been developed. Most of those techniques are inefficient in terms of detecting, overlapping complexes, exclusion of attachment protein in complex core, inability to detect inherent structures of underlying complexes, have high false-positive rates and an enrichment analysis. To address these limitations, we introduce a special structural-based weighted network approach for the analysis of protein complexes based on a Weighted Edge, Core-Attachment and Local Modularity structures (WECALM). Experimental results indicate that WECALM performs relatively better than existing algorithms in terms of accuracy, computational time, and p-value. A functional enrichment analysis also shows that WECALM is able to identify a large number of biologically significant protein complexes. Overall, WECALM outperforms other approaches by striking a better balance of accuracy and efficiency in the detection of protein complexes
Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics
Background: Network communities help the functional organization and
evolution of complex networks. However, the development of a method, which is
both fast and accurate, provides modular overlaps and partitions of a
heterogeneous network, has proven to be rather difficult. Methodology/Principal
Findings: Here we introduce the novel concept of ModuLand, an integrative
method family determining overlapping network modules as hills of an influence
function-based, centrality-type community landscape, and including several
widely used modularization methods as special cases. As various adaptations of
the method family, we developed several algorithms, which provide an efficient
analysis of weighted and directed networks, and (1) determine pervasively
overlapping modules with high resolution; (2) uncover a detailed hierarchical
network structure allowing an efficient, zoom-in analysis of large networks;
(3) allow the determination of key network nodes and (4) help to predict
network dynamics. Conclusions/Significance: The concept opens a wide range of
possibilities to develop new approaches and applications including network
routing, classification, comparison and prediction.Comment: 25 pages with 6 figures and a Glossary + Supporting Information
containing pseudo-codes of all algorithms used, 14 Figures, 5 Tables (with 18
module definitions, 129 different modularization methods, 13 module
comparision methods) and 396 references. All algorithms can be downloaded
from this web-site: http://www.linkgroup.hu/modules.ph
Geometric, Feature-based and Graph-based Approaches for the Structural Analysis of Protein Binding Sites : Novel Methods and Computational Analysis
In this thesis, protein binding sites are considered. To enable the extraction of information from the space of protein binding sites, these binding sites must be mapped onto a mathematical space. This can be done by mapping binding sites onto vectors, graphs or point clouds. To finally enable a structure on the mathematical space, a distance measure is required, which is introduced in this thesis. This distance measure eventually can be used to extract information by means of data mining techniques
A survey of statistical network models
Networks are ubiquitous in science and have become a focal point for
discussion in everyday life. Formal statistical models for the analysis of
network data have emerged as a major topic of interest in diverse areas of
study, and most of these involve a form of graphical representation.
Probability models on graphs date back to 1959. Along with empirical studies in
social psychology and sociology from the 1960s, these early works generated an
active network community and a substantial literature in the 1970s. This effort
moved into the statistical literature in the late 1970s and 1980s, and the past
decade has seen a burgeoning network literature in statistical physics and
computer science. The growth of the World Wide Web and the emergence of online
networking communities such as Facebook, MySpace, and LinkedIn, and a host of
more specialized professional network communities has intensified interest in
the study of networks and network data. Our goal in this review is to provide
the reader with an entry point to this burgeoning literature. We begin with an
overview of the historical development of statistical network modeling and then
we introduce a number of examples that have been studied in the network
literature. Our subsequent discussion focuses on a number of prominent static
and dynamic network models and their interconnections. We emphasize formal
model descriptions, and pay special attention to the interpretation of
parameters and their estimation. We end with a description of some open
problems and challenges for machine learning and statistics.Comment: 96 pages, 14 figures, 333 reference
Community detection in graphs
The modern science of networks has brought significant advances to our
understanding of complex systems. One of the most relevant features of graphs
representing real systems is community structure, or clustering, i. e. the
organization of vertices in clusters, with many edges joining vertices of the
same cluster and comparatively few edges joining vertices of different
clusters. Such clusters, or communities, can be considered as fairly
independent compartments of a graph, playing a similar role like, e. g., the
tissues or the organs in the human body. Detecting communities is of great
importance in sociology, biology and computer science, disciplines where
systems are often represented as graphs. This problem is very hard and not yet
satisfactorily solved, despite the huge effort of a large interdisciplinary
community of scientists working on it over the past few years. We will attempt
a thorough exposition of the topic, from the definition of the main elements of
the problem, to the presentation of most methods developed, with a special
focus on techniques designed by statistical physicists, from the discussion of
crucial issues like the significance of clustering and how methods should be
tested and compared against each other, to the description of applications to
real networks.Comment: Review article. 103 pages, 42 figures, 2 tables. Two sections
expanded + minor modifications. Three figures + one table + references added.
Final version published in Physics Report
Methods for the Efficient Comparison of Protein Binding Sites and for the Assessment of Protein-Ligand Complexes
In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented.
Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases.
Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. These programs are utilized to screen entire libraries of molecules for a possible ligand of a binding site and to furthermore estimate in which conformation the ligand will most likely bind. By employing this information, molecule libraries can be filtered for subsequent affinity assays and molecular structures can be refined with regard to affinity and selectivity
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A Survey of Statistical Network Models
Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active ânetwork communityâ and a substantial liter- ature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning net- work literature in statistical physics and computer science. The growthof the World Wide Web and the emergence of online ânetworking com- munitiesâ such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry point to this burgeoning literature. We begin with an overview of the historical development of statistical network modeling and then we introduce a number of examples that have been studied in the network literature. Our subsequent discussion focuses on a number of prominent static and dynamic network models and their interconnections. We emphasize for- mal model descriptions, and pay special attention to the interpretation of parameters and their estimation. We end with a description of some open problems and challenges for machine learning and statistics.Statistic
Algorithms For Community Identification In Complex Networks
First and foremost, I would like to extend my deepest gratitude to my advisor, Professor Narsingh Deo, for his excellent guidance and encouragement, and also for introducing me to this wonderful science of complex networks. Without his support this dissertation would not have been possible. I would also like to thank the members of my research committee, professors Charles Hughes, Ratan Guha, Mainak Chatterjee and Yue Zhao for their advice and guidance during the entire process. I am indebted to the faculty and the staff of the Department of Electrical Engineering and Computer Science for providing me the resources and environment to perform this research. I am grateful to my colleagues in the Parallel and Quantum computing lab for the stimulating discussions and support. I would also like to thank Dr. Hemant Balakrishnan and Dr. Sanjeeb Nanda for their valuable suggestions and guidance. My heartfelt thanks to my parents, Vasudevan and Raji, who have always been supportive of my decisions and encouraged me with their best wishes. I would also like to thank my sister Gomathy, for her words of care and affection during tough times. Special thanks to my friends in Orlando for being there when I needed the
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