187,052 research outputs found
Point process modeling for directed interaction networks
Network data often take the form of repeated interactions between senders and
receivers tabulated over time. A primary question to ask of such data is which
traits and behaviors are predictive of interaction. To answer this question, a
model is introduced for treating directed interactions as a multivariate point
process: a Cox multiplicative intensity model using covariates that depend on
the history of the process. Consistency and asymptotic normality are proved for
the resulting partial-likelihood-based estimators under suitable regularity
conditions, and an efficient fitting procedure is described. Multicast
interactions--those involving a single sender but multiple receivers--are
treated explicitly. The resulting inferential framework is then employed to
model message sending behavior in a corporate e-mail network. The analysis
gives a precise quantification of which static shared traits and dynamic
network effects are predictive of message recipient selection.Comment: 36 pages, 13 figures; includes supplementary materia
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
Dynamic Influence Networks for Rule-based Models
We introduce the Dynamic Influence Network (DIN), a novel visual analytics
technique for representing and analyzing rule-based models of protein-protein
interaction networks. Rule-based modeling has proved instrumental in developing
biological models that are concise, comprehensible, easily extensible, and that
mitigate the combinatorial complexity of multi-state and multi-component
biological molecules. Our technique visualizes the dynamics of these rules as
they evolve over time. Using the data produced by KaSim, an open source
stochastic simulator of rule-based models written in the Kappa language, DINs
provide a node-link diagram that represents the influence that each rule has on
the other rules. That is, rather than representing individual biological
components or types, we instead represent the rules about them (as nodes) and
the current influence of these rules (as links). Using our interactive DIN-Viz
software tool, researchers are able to query this dynamic network to find
meaningful patterns about biological processes, and to identify salient aspects
of complex rule-based models. To evaluate the effectiveness of our approach, we
investigate a simulation of a circadian clock model that illustrates the
oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres
The Strength of Arcs and Edges in Interaction Networks: Elements of a Model-Based Approach
When analyzing interaction networks, it is common to interpret the amount of
interaction between two nodes as the strength of their relationship. We argue
that this interpretation may not be appropriate, since the interaction between
a pair of nodes could potentially be explained only by characteristics of the
nodes that compose the pair and, however, not by pair-specific features. In
interaction networks, where edges or arcs are count-valued, the above scenario
corresponds to a model of independence for the expected interaction in the
network, and consequently we propose the notions of arc strength, and edge
strength to be understood as departures from this model of independence. We
discuss how our notion of arc/edge strength can be used as a guidance to study
network structure, and in particular we develop a latent arc strength
stochastic blockmodel for directed interaction networks. We illustrate our
approach studying the interaction between the Kolkata users of the myGamma
mobile network.Comment: 23 pages, 5 figures, 4 table
Network estimation in State Space Model with L1-regularization constraint
Biological networks have arisen as an attractive paradigm of genomic science
ever since the introduction of large scale genomic technologies which carried
the promise of elucidating the relationship in functional genomics. Microarray
technologies coupled with appropriate mathematical or statistical models have
made it possible to identify dynamic regulatory networks or to measure time
course of the expression level of many genes simultaneously. However one of the
few limitations fall on the high-dimensional nature of such data coupled with
the fact that these gene expression data are known to include some hidden
process. In that regards, we are concerned with deriving a method for inferring
a sparse dynamic network in a high dimensional data setting. We assume that the
observations are noisy measurements of gene expression in the form of mRNAs,
whose dynamics can be described by some unknown or hidden process. We build an
input-dependent linear state space model from these hidden states and
demonstrate how an incorporated regularization constraint in an
Expectation-Maximization (EM) algorithm can be used to reverse engineer
transcriptional networks from gene expression profiling data. This corresponds
to estimating the model interaction parameters. The proposed method is
illustrated on time-course microarray data obtained from a well established
T-cell data. At the optimum tuning parameters we found genes TRAF5, JUND, CDK4,
CASP4, CD69, and C3X1 to have higher number of inwards directed connections and
FYB, CCNA2, AKT1 and CASP8 to be genes with higher number of outwards directed
connections. We recommend these genes to be object for further investigation.
Caspase 4 is also found to activate the expression of JunD which in turn
represses the cell cycle regulator CDC2.Comment: arXiv admin note: substantial text overlap with arXiv:1308.359
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