1,518 research outputs found
Inferring Coupling of Distributed Dynamical Systems via Transfer Entropy
In this work, we are interested in structure learning for a set of spatially distributed dynamical systems, where individual subsystems are coupled via latent variables and observed through a filter. We represent this model as a directed acyclic graph (DAG) that characterises the unidirectional coupling between subsystems. Standard approaches to structure learning are not applicable in this framework due to the hidden variables, however we can exploit the properties of certain dynamical systems to formulate exact methods based on state space reconstruction. We approach the problem by using reconstruction theorems to analytically derive a tractable expression for the KL-divergence of a candidate DAG from the observed dataset. We show this measure can be decomposed as a function of two information-theoretic measures, transfer entropy and stochastic interaction. We then present two mathematically robust scoring functions based on transfer entropy and statistical independence tests. These results support the previously held conjecture that transfer entropy can be used to infer effective connectivity in complex networks
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks
Gene and protein networks are very important to model complex large-scale
systems in molecular biology. Inferring or reverseengineering such networks can
be defined as the process of identifying gene/protein interactions from
experimental data through computational analysis. However, this task is
typically complicated by the enormously large scale of the unknowns in a rather
small sample size. Furthermore, when the goal is to study causal relationships
within the network, tools capable of overcoming the limitations of correlation
networks are required. In this work, we make use of Bayesian Graphical Models
to attach this problem and, specifically, we perform a comparative study of
different state-of-the-art heuristics, analyzing their performance in inferring
the structure of the Bayesian Network from breast cancer data
Control of asymmetric Hopfield networks and application to cancer attractors
The asymmetric Hopfield model is used to simulate signaling dynamics in
gene/transcription factor networks. The model allows for a direct mapping of a
gene expression pattern into attractor states. We analyze different control
strategies aiming at disrupting attractor patterns using selective local fields
representing therapeutic interventions. The control strategies are based on the
identification of signaling , which are single nodes or strongly
connected clusters of nodes that have a large impact on the signaling. We
provide a theorem with bounds on the minimum number of nodes that guarantee
controllability of bottlenecks consisting of strongly connected components. The
control strategies are applied to the identification of sets of proteins that,
when inhibited, selectively disrupt the signaling of cancer cells while
preserving the signaling of normal cells. We use an experimentally validated
non-specific network and a specific B cell interactome reconstructed from gene
expression data to model cancer signaling in lung and B cells, respectively.
This model could help in the rational design of novel robust therapeutic
interventions based on our increasing knowledge of complex gene signaling
networks
Organising metabolic networks: cycles in flux distributions
Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes in trophic networks. Subsequently, we apply this methodology to the analysis of three metabolic systems, including the central metabolism of wild type and a deletion mutant of Escherichia coli, erythrocyte metabolism and the central metabolism of the bacterium Methylobacterium extorquens. The role of cycles in driving and maintaining the performance of metabolic functions upon perturbations is unveiled through these examples. This methodology may be used to further investigate the role of cycles in living organisms, their pro-activity and organisational invariance, leading to a better understanding of biological entailment and information processing
Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles
Reconstructing transcriptional regulatory networks is an important task in
functional genomics. Data obtained from experiments that perturb genes by
knockouts or RNA interference contain useful information for addressing this
reconstruction problem. However, such data can be limited in size and/or are
expensive to acquire. On the other hand, observational data of the organism in
steady state (e.g. wild-type) are more readily available, but their
informational content is inadequate for the task at hand. We develop a
computational approach to appropriately utilize both data sources for
estimating a regulatory network. The proposed approach is based on a three-step
algorithm to estimate the underlying directed but cyclic network, that uses as
input both perturbation screens and steady state gene expression data. In the
first step, the algorithm determines causal orderings of the genes that are
consistent with the perturbation data, by combining an exhaustive search method
with a fast heuristic that in turn couples a Monte Carlo technique with a fast
search algorithm. In the second step, for each obtained causal ordering, a
regulatory network is estimated using a penalized likelihood based method,
while in the third step a consensus network is constructed from the highest
scored ones. Extensive computational experiments show that the algorithm
performs well in reconstructing the underlying network and clearly outperforms
competing approaches that rely only on a single data source. Further, it is
established that the algorithm produces a consistent estimate of the regulatory
network.Comment: 24 pages, 4 figures, 6 table
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