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Spatial cluster detection using dynamic programming.

Sverchkov Y, Jiang X, Cooper GF - BMC Med Inform Decis Mak (2012)

Bottom Line: In a probabilistic setting this task can be expressed as finding a region where some event is significantly more likely than usual.Spatial cluster detection is of interest in fields such as biosurveillance, mining of astronomical data, military surveillance, and analysis of fMRI images.When compared to baseline methods, tests indicate that the new algorithm can improve MAP estimates under certain conditions: the greedy algorithm we compared our method to was found to be more sensitive to smaller outbreaks, while as the size of the outbreaks increases, in terms of area affected and proportion of individuals affected, our method overtakes the greedy algorithm in spatial precision and recall.

View Article: PubMed Central - HTML - PubMed

Affiliation: Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA. yus24@pitt.edu

ABSTRACT

Background: The task of spatial cluster detection involves finding spatial regions where some property deviates from the norm or the expected value. In a probabilistic setting this task can be expressed as finding a region where some event is significantly more likely than usual. Spatial cluster detection is of interest in fields such as biosurveillance, mining of astronomical data, military surveillance, and analysis of fMRI images. In almost all such applications we are interested both in the question of whether a cluster exists in the data, and if it exists, we are interested in finding the most accurate characterization of the cluster.

Methods: We present a general dynamic programming algorithm for grid-based spatial cluster detection. The algorithm can be used for both Bayesian maximum a-posteriori (MAP) estimation of the most likely spatial distribution of clusters and Bayesian model averaging over a large space of spatial cluster distributions to compute the posterior probability of an unusual spatial clustering. The algorithm is explained and evaluated in the context of a biosurveillance application, specifically the detection and identification of Influenza outbreaks based on emergency department visits. A relatively simple underlying model is constructed for the purpose of evaluating the algorithm, and the algorithm is evaluated using the model and semi-synthetic test data.

Results: When compared to baseline methods, tests indicate that the new algorithm can improve MAP estimates under certain conditions: the greedy algorithm we compared our method to was found to be more sensitive to smaller outbreaks, while as the size of the outbreaks increases, in terms of area affected and proportion of individuals affected, our method overtakes the greedy algorithm in spatial precision and recall. The new algorithm performs on-par with baseline methods in the task of Bayesian model averaging.

Conclusions: We conclude that the dynamic programming algorithm performs on-par with other available methods for spatial cluster detection and point to its low computational cost and extendability as advantages in favor of further research and use of the algorithm.

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Simple disease model. A plate representation of the simplified entity-based model used.
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Figure 1: Simple disease model. A plate representation of the simplified entity-based model used.

Mentions: We define the disease model as a Bayesian Network (BN) model, which is a type of graphical model for representing joint probability distributions; it is particularly suited for modeling conditional independence between variables. In the graphical representation each node represents a random variable and the distribution of each variable is defined as a conditional distribution that is conditioned on the variables from which it receives incoming edges, or as a prior probability distribution if the node has no incoming edges [22]. An extension to the BN representation employs plates when subgraphs of the network are replicated many times. In the graphical plate representation, plates are shown as boxes, the nodes and edges that are on each plate are replicated the number of times shown on the plate, replicated nodes are indexed, and edges that cross plate boundaries are also replicated [23]. In particular, in Figure 1 we have m copies of nodes Li, Di, and Ii. We further extend the notation by allowing the number of replications to depend on random variables, as represented by the dotted arrow from SUB to the plate indexed by j. Here, the values that SUB takes are ordered sets and the number of replications n is defined to equal the size of the set /SUB/. The model is explained in further detail below, where we first describe the model and the meanings of the variables in general terms, and then provide the particular parameterization that we used to instantiate the variables in our tests.


Spatial cluster detection using dynamic programming.

Sverchkov Y, Jiang X, Cooper GF - BMC Med Inform Decis Mak (2012)

Simple disease model. A plate representation of the simplified entity-based model used.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3403878&req=5

Figure 1: Simple disease model. A plate representation of the simplified entity-based model used.
Mentions: We define the disease model as a Bayesian Network (BN) model, which is a type of graphical model for representing joint probability distributions; it is particularly suited for modeling conditional independence between variables. In the graphical representation each node represents a random variable and the distribution of each variable is defined as a conditional distribution that is conditioned on the variables from which it receives incoming edges, or as a prior probability distribution if the node has no incoming edges [22]. An extension to the BN representation employs plates when subgraphs of the network are replicated many times. In the graphical plate representation, plates are shown as boxes, the nodes and edges that are on each plate are replicated the number of times shown on the plate, replicated nodes are indexed, and edges that cross plate boundaries are also replicated [23]. In particular, in Figure 1 we have m copies of nodes Li, Di, and Ii. We further extend the notation by allowing the number of replications to depend on random variables, as represented by the dotted arrow from SUB to the plate indexed by j. Here, the values that SUB takes are ordered sets and the number of replications n is defined to equal the size of the set /SUB/. The model is explained in further detail below, where we first describe the model and the meanings of the variables in general terms, and then provide the particular parameterization that we used to instantiate the variables in our tests.

Bottom Line: In a probabilistic setting this task can be expressed as finding a region where some event is significantly more likely than usual.Spatial cluster detection is of interest in fields such as biosurveillance, mining of astronomical data, military surveillance, and analysis of fMRI images.When compared to baseline methods, tests indicate that the new algorithm can improve MAP estimates under certain conditions: the greedy algorithm we compared our method to was found to be more sensitive to smaller outbreaks, while as the size of the outbreaks increases, in terms of area affected and proportion of individuals affected, our method overtakes the greedy algorithm in spatial precision and recall.

View Article: PubMed Central - HTML - PubMed

Affiliation: Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA. yus24@pitt.edu

ABSTRACT

Background: The task of spatial cluster detection involves finding spatial regions where some property deviates from the norm or the expected value. In a probabilistic setting this task can be expressed as finding a region where some event is significantly more likely than usual. Spatial cluster detection is of interest in fields such as biosurveillance, mining of astronomical data, military surveillance, and analysis of fMRI images. In almost all such applications we are interested both in the question of whether a cluster exists in the data, and if it exists, we are interested in finding the most accurate characterization of the cluster.

Methods: We present a general dynamic programming algorithm for grid-based spatial cluster detection. The algorithm can be used for both Bayesian maximum a-posteriori (MAP) estimation of the most likely spatial distribution of clusters and Bayesian model averaging over a large space of spatial cluster distributions to compute the posterior probability of an unusual spatial clustering. The algorithm is explained and evaluated in the context of a biosurveillance application, specifically the detection and identification of Influenza outbreaks based on emergency department visits. A relatively simple underlying model is constructed for the purpose of evaluating the algorithm, and the algorithm is evaluated using the model and semi-synthetic test data.

Results: When compared to baseline methods, tests indicate that the new algorithm can improve MAP estimates under certain conditions: the greedy algorithm we compared our method to was found to be more sensitive to smaller outbreaks, while as the size of the outbreaks increases, in terms of area affected and proportion of individuals affected, our method overtakes the greedy algorithm in spatial precision and recall. The new algorithm performs on-par with baseline methods in the task of Bayesian model averaging.

Conclusions: We conclude that the dynamic programming algorithm performs on-par with other available methods for spatial cluster detection and point to its low computational cost and extendability as advantages in favor of further research and use of the algorithm.

Show MeSH
Related in: MedlinePlus