These possibilities must be searched to find a tree that best fits the data according to the optimality criterion.
2.
This problem is certainly not unique to MP; any method that uses an optimality criterion faces the same problem, and none offer easy solutions.
3.
The most common optimality criterion used to select this parameter is the expected " L " 2 risk function, also termed the mean integrated squared error:
4.
The "'Mumford Shah functional "'is a functional that is used to establish an optimality criterion for segmenting an image into sub-regions.
5.
The " system " consists of both the car and the road, and the " optimality criterion " is the minimization of the total traveling time.
6.
High-quality statistical software provide a combination of libraries of optimal designs or iterative methods for constructing approximately optimal designs, depending on the model specified and the optimality criterion.
7.
However, it lacks any sort of tree search and optimality criterion, and so there is no guarantee that the recovered tree is the one that best fits the data.
8.
A more appropriate analytical procedure would be to use NJ to produce a starting tree, then employ a tree search using an optimality criterion, to ensure that the best tree is recovered.
9.
To counter potential complications noted above, and to find the best tree for the data, distance analysis can also incorporate a tree-search protocol that seeks to satisfy an explicit optimality criterion.
10.
For example, in order to determine the best topology between two phylogenetic trees using the maximum likelihood optimality criterion, one would calculate the maximum likelihood score of each tree and choose the one that had the better score.
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