In this work we propose the problem of computing the DCJ distance of two given genomes without prior gene family assignment, directly using the pairwise similarities between genes.
For example, the interactions between members of the flagellar machinery are detected by this method with sensitivity and specificity higher than those obtained using the pairwise similarities alone (Juan et al, 2008).
For the affinity propagation clustering, we first use the pairwise similarity s i, j) to describe the fitness of the RP j to be selected as the cluster center with respect to the RP i.
The current study used collaborative filtering to generate recommendation scores as classification features, and therefore help the transparent interpretation of drug-specific or ADR-specific information, while Gottlieb et al. used the pairwise similarity-based inference scheme to generate classification features, which are not easily interpretable.
Regions matching the HMM with E-values better than 10 were extracted and analyzed using the pairwise sequence similarity visualization and analysis program CLANS [56], [57].
At this point it is possible to introduce the necessary dependence measures that will be used as the pairwise similarity measure d in Equation (16): Rényi generalized divergence between two distributions f(x) and g(x) of order α, where α ≥ 0, is defined [36] as d α ( f ( x ) | | g ( x ) ) = 1 α - 1 log ∫ f α ( x ) g 1 - α ( x ) d x. (21).
Figure 2 summarizes the entire process of the proposed framework, which includes three main steps: (1) create the affinity matrix using the pairwise distances and class similarity, (2) create discretization schemes, and (3) discretize the datasets by applying the discretization schemes.
Similarity (1 – distance) was calculated by using the pairwise distance method generated by MEGA3 (8 ).
The Jiang and Conrath method was used to calculate the pairwise similarity between terms, using a scaled (0 1) cutoff of 0.7 to define a clustering of "highly similar terms".
The BLASTP algorithm as implemented in WU BLAST 2.0 [28] was used to compute the pairwise similarity scores of each protein against all other members of the training set.
