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An extensive body of literature has shown that combining forecasts can improve forecast accuracy, and that a simple average of the forecasts (the mean) often does better than more complex combining schemes.
"Simplicity is often underrated; simple static strategies (balanced portfolios) have been shown to perform well, and often better, than more complex strategies in a wide variety of settings.
We found that cRBH almost always outperformed all other algorithms, suggesting that simpler algorithms may often perform better than more complex ones in identifying orthologs across species, but that the false discovery rate of all algorithms was dramatically increased when groups of paralogs stemming from the WGD event were examined.
Surprisingly, KStar, a relatively simple instance-based model performed significantly better than more complex algorithms, e.g. neural networks.
None of these six tools consistently performed better than the others, and simple tools often did as well as or better than more complex tools including FRAX.
Ben-Dor et al (2000) also compared several methods on several public data sets and found that nearest neighbour classification generally performed as well or better than more complex methods.
Similar(52)
These results suggest that simple algorithms, like cRBH, may be better ortholog predictors than more complex ones (e.g., OrthoMCL and MultiParanoid) for evolutionary and functional genomics studies where the objective is the accurate inference of single-copy orthologs (e.g., molecular phylogenetics), but that all algorithms fail to accurately predict orthologs when paralogy is rampant.
In addition to being very simple and providing a better fit to data than more complex models, the linear model is also conceptually justified by the residue packing argument that we put forward.
SVMs have been shown to perform considerably well in microarray data [ 21] and SVMs with a linear kernel has been suggested to perform better in gene expression data than more complex SVM versions (Manual BRB Array Tools, [ 22]), and additionally, no parameter tuning is necessary for linear SVMs.
Our results suggest that simpler algorithms, like cRBH and cRSD, might be better choices for many downstream evolutionary analyses than more complex ones in cases where the objective is to identify orthogroups and that the trend of several studies toward using more complex ortholog prediction strategies is not always justified.
Of the similarity metrics tested here, the fast RDKit fingerprint method performed as well as or better than the more complex alternatives.
More suggestions(16)
better than more conservative
better than more soggy
better than more generic
better than more advantaged
better than more moderate
better than more expensive
better than more fragile
better than more conventional
better than more fit
better than more primitive
better than more mature
better than more frequent
better than more concentrated
better than more complicated
better than more recent
better than more homogenous
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com