18,929 research outputs found
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
Construction and analysis of causally dynamic hybrid bond graphs
Engineering systems are frequently abstracted to models with discontinuous behaviour (such as a switch or contact),
and a hybrid model is one which contains continuous and discontinuous behaviours. Bond graphs are an established
physical modelling method, but there are several methods for constructing switched or ‘hybrid’ bond graphs, developed
for either qualitative ‘structural’ analysis or efficient numerical simulation of engineering systems. This article proposes a
general hybrid bond graph suitable for both. The controlled junction is adopted as an intuitive way of modelling a discontinuity in the model structure. This element gives rise to ‘dynamic causality’ that is facilitated by a new bond graph notation. From this model, the junction structure and state equations are derived and compared to those obtained by
existing methods. The proposed model includes all possible modes of operation and can be represented by a single set
of equations. The controlled junctions manifest as Boolean variables in the matrices of coefficients. The method is more
compact and intuitive than existing methods and dispenses with the need to derive various modes of operation from a
given reference representation. Hence, a method has been developed, which can reach common usage and form a platform for further study
Exploring Causal Influences
Recent data mining techniques exploit patterns of statistical independence in multivariate data to make conjectures about cause/effect relationships. These relationships can be used to construct causal graphs, which are sometimes represented by weighted node-link diagrams, with nodes representing variables and combinations of weighted links and/or nodes showing the strength of causal relationships. We present an interactive visualization for causal graphs (ICGs), inspired in part by the Influence Explorer. The key principles of this visualization are as follows: Variables are represented with vertical bars attached to nodes in a graph. Direct manipulation of variables is achieved by sliding a variable value up and down, which reveals causality by producing instantaneous change in causally and/or probabilistically linked variables. This direct manipulation technique gives users the impression they are causally influencing the variables linked to the one they are manipulating. In this context, we demonstrate the subtle distinction between seeing and setting of variable values, and in an extended example, show how this visualization can help a user understand the relationships in a large variable set, and with some intuitions about the domain and a few basic concepts, quickly detect bugs in causal models constructed from these data mining techniques
Learning Hybrid Process Models From Events: Process Discovery Without Faking Confidence
Process discovery techniques return process models that are either formal
(precisely describing the possible behaviors) or informal (merely a "picture"
not allowing for any form of formal reasoning). Formal models are able to
classify traces (i.e., sequences of events) as fitting or non-fitting. Most
process mining approaches described in the literature produce such models. This
is in stark contrast with the over 25 available commercial process mining tools
that only discover informal process models that remain deliberately vague on
the precise set of possible traces. There are two main reasons why vendors
resort to such models: scalability and simplicity. In this paper, we propose to
combine the best of both worlds: discovering hybrid process models that have
formal and informal elements. As a proof of concept we present a discovery
technique based on hybrid Petri nets. These models allow for formal reasoning,
but also reveal information that cannot be captured in mainstream formal
models. A novel discovery algorithm returning hybrid Petri nets has been
implemented in ProM and has been applied to several real-life event logs. The
results clearly demonstrate the advantages of remaining "vague" when there is
not enough "evidence" in the data or standard modeling constructs do not "fit".
Moreover, the approach is scalable enough to be incorporated in
industrial-strength process mining tools.Comment: 25 pages, 12 figure
Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches
In the past two decades, functional Magnetic Resonance Imaging has been used
to relate neuronal network activity to cognitive processing and behaviour.
Recently this approach has been augmented by algorithms that allow us to infer
causal links between component populations of neuronal networks. Multiple
inference procedures have been proposed to approach this research question but
so far, each method has limitations when it comes to establishing whole-brain
connectivity patterns. In this work, we discuss eight ways to infer causality
in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality,
Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and
Transfer Entropy. We finish with formulating some recommendations for the
future directions in this area
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