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However, since network completion is more complex than network inference, the method in [ 27] cannot be directly applied.
Our results suggest that while hundreds of loci are not always essential for accurate topological inference, the method used for tree estimation may affect the resulting phylogeny and that for smaller datasets (<50 loci), full-coalescent models of tree inference are likely more accurate than summary statistics methods.
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In this paper, we introduce a new method, mediation analysis, which is somewhere between the overlap analysis (the first method) and causal inference (the second method).
This can reduce the recall of the inference method to miss the inferring genes in the interaction networks.
On the accepted species tree, the inference method affected the number of duplications inferred for 154 clusters but had no effect on the other 323 clusters.
As a result, we have found that the inference method of the proposed system is similar to the human expert.
The overall accuracy of the inference method and correctness of the modeling approach is evaluated by four widely accepted performance measures given below.
CP and AC dealt with the program coding the mathematical expressions and the data structures of the inference method to allow its execution on computer.
The core of the Inference method was built as a combination of string matching rules that mapped the text annotated strings to the controlled vocabulary terms.
Notice that the focus here is not on reducing the computational cost of the inference method, and thus, we allow ourselves to use resource-consuming algorithms.
In this section, we analyze the performance of the inference methods on the experimental data described in Methods.
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