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We observe similar results for the relationships between in vitro activities and structural alerts, regardless of the size and composition of the datasets.
In the present case, clade III is expanded and clade IV contracted relative to published analyses, due to differences in composition of the datasets.
Since breast cancer is known to be a heterogeneous disease, we hypothesize that differences in the subtype composition of the datasets cause the poorer performance of the BCC modules.
However, this is highly dependent upon the composition of the datasets and patient characteristics.
Unbalancing the composition of the datasets from a 1 1 ratio of basal to luminal tumours to a 2 1 or 5 1 ratio of tumours reduced correspondence between datasets and caused a distortion across datasets (Additional File 7).
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The composition of the dataset is reported in Table 1.
It has been anticipated in Section 3 that the composition of the dataset plays a crucial role when developing a prediction system based on ML methodologies.
It is important to keep in mind that all performance measures should be interpreted in the context of the composition of the benchmarking datasets [34, 35] and that the score selection thresholds that would be estimated during the benchmark should be adapted to the composition of the dataset that will be used for prospective screening.
The HMM is trained on a subset of read-half alignments to best reflect the quality and base composition of the dataset and genome.
This analysis (see also Text S3) together with guidelines describing how the selection of the best tool depends on the composition of the dataset is summarized in Table 1.
The SLiMChance algorithm estimates the probability of returned motifs arising by chance, correcting for the size and composition of the dataset, and assigns a significance value to each motif.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com