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Researchers following this method illustrated the content of given document using a dependency tree.
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Their method proceeds in two steps: (i) For each trial matching, the total correlation in the MSA is estimated using a dependency-tree based approximation.
Dependency relations of words in a sentence are obtained using a dependency parser Minipar (Lin, 1994).
Such a dependency tree can still be managed quite efficiently, for instance, using data structures like binary balanced trees.
For example, Erkan et al. (2007) used the shortest path between two genes according to edit distance in a dependency tree to define a kernel function for extracting gene interactions.
For the machine learning models, as features we used two sets of bigrams taken from a forward dependency chain which is a dependency path from the root of a dependency tree to the first protein and from a backward chain which is a dependency path from the root to the second protein.
For the protein pair IL-8 and CXCR1 in Figure 6, a dependency parser outputs a dependency tree; partly shown in Figure 1.
The second row represents the result produced with an additional feature of dependency length which is the length of a dependency path from the root of a dependency tree to a protein.
By using a tree threaded at all levels, tree traversals for finding nearest neighbors are avoided.
The tree is constructed using a decision tree algorithm.
Long-term dependencies will be modeled with a hidden Markov model which, in each internal state, will deal with the local dynamics in the wavelet domain, using a hidden Markov tree.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com