6,706 research outputs found
Structure Learning in Coupled Dynamical Systems and Dynamic Causal Modelling
Identifying a coupled dynamical system out of many plausible candidates, each
of which could serve as the underlying generator of some observed measurements,
is a profoundly ill posed problem that commonly arises when modelling real
world phenomena. In this review, we detail a set of statistical procedures for
inferring the structure of nonlinear coupled dynamical systems (structure
learning), which has proved useful in neuroscience research. A key focus here
is the comparison of competing models of (ie, hypotheses about) network
architectures and implicit coupling functions in terms of their Bayesian model
evidence. These methods are collectively referred to as dynamical casual
modelling (DCM). We focus on a relatively new approach that is proving
remarkably useful; namely, Bayesian model reduction (BMR), which enables rapid
evaluation and comparison of models that differ in their network architecture.
We illustrate the usefulness of these techniques through modelling
neurovascular coupling (cellular pathways linking neuronal and vascular
systems), whose function is an active focus of research in neurobiology and the
imaging of coupled neuronal systems
Graphical continuous Lyapunov models
The linear Lyapunov equation of a covariance matrix parametrizes the
equilibrium covariance matrix of a stochastic process. This parametrization can
be interpreted as a new graphical model class, and we show how the model class
behaves under marginalization and introduce a method for structure learning via
-penalized loss minimization. Our proposed method is demonstrated to
outperform alternative structure learning algorithms in a simulation study, and
we illustrate its application for protein phosphorylation network
reconstruction.Comment: 10 pages, 5 figure
Optimal treatment allocations in space and time for on-line control of an emerging infectious disease
A key component in controlling the spread of an epidemic is deciding where, whenand to whom to apply an intervention.We develop a framework for using data to informthese decisionsin realtime.We formalize a treatment allocation strategy as a sequence of functions, oneper treatment period, that map up-to-date information on the spread of an infectious diseaseto a subset of locations where treatment should be allocated. An optimal allocation strategyoptimizes some cumulative outcome, e.g. the number of uninfected locations, the geographicfootprint of the disease or the cost of the epidemic. Estimation of an optimal allocation strategyfor an emerging infectious disease is challenging because spatial proximity induces interferencebetween locations, the number of possible allocations is exponential in the number oflocations, and because disease dynamics and intervention effectiveness are unknown at outbreak.We derive a Bayesian on-line estimator of the optimal allocation strategy that combinessimulationâoptimization with Thompson sampling.The estimator proposed performs favourablyin simulation experiments. This work is motivated by and illustrated using data on the spread ofwhite nose syndrome, which is a highly fatal infectious disease devastating bat populations inNorth America
Prediction, Retrodiction, and The Amount of Information Stored in the Present
We introduce an ambidextrous view of stochastic dynamical systems, comparing
their forward-time and reverse-time representations and then integrating them
into a single time-symmetric representation. The perspective is useful
theoretically, computationally, and conceptually. Mathematically, we prove that
the excess entropy--a familiar measure of organization in complex systems--is
the mutual information not only between the past and future, but also between
the predictive and retrodictive causal states. Practically, we exploit the
connection between prediction and retrodiction to directly calculate the excess
entropy. Conceptually, these lead one to discover new system invariants for
stochastic dynamical systems: crypticity (information accessibility) and causal
irreversibility. Ultimately, we introduce a time-symmetric representation that
unifies all these quantities, compressing the two directional representations
into one. The resulting compression offers a new conception of the amount of
information stored in the present.Comment: 17 pages, 7 figures, 1 table;
http://users.cse.ucdavis.edu/~cmg/compmech/pubs/pratisp.ht
Learning stable and predictive structures in kinetic systems: Benefits of a causal approach
Learning kinetic systems from data is one of the core challenges in many
fields. Identifying stable models is essential for the generalization
capabilities of data-driven inference. We introduce a computationally efficient
framework, called CausalKinetiX, that identifies structure from discrete time,
noisy observations, generated from heterogeneous experiments. The algorithm
assumes the existence of an underlying, invariant kinetic model, a key
criterion for reproducible research. Results on both simulated and real-world
examples suggest that learning the structure of kinetic systems benefits from a
causal perspective. The identified variables and models allow for a concise
description of the dynamics across multiple experimental settings and can be
used for prediction in unseen experiments. We observe significant improvements
compared to well established approaches focusing solely on predictive
performance, especially for out-of-sample generalization
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