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Next, the significance of motif representations was evaluated by analyzing gene expression correlations in representative cancer datasets.
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In calculating representational priority, representations are evaluated with two indicators: ambiguity, which estimates the risk of recognition failure for the target in a region of interest (ROI), and stationarity, which indicates a steadiness of the ambiguity over time.
Two previous exergy representations are evaluated and compared with the proposed one.
Contrasting stochastic and deterministic trend representations are evaluated.
Completeness of gene-space representation was evaluated with the BUSCO pipeline23 (Extended Data Fig. 2b).
Moreover, the optimized representation was evaluated in noise conditions.
The completeness/contiguity of the gene representation was evaluated using the CEGMA (Core Eukaryotic Genes Mapping Approach) pipeline35,36 and found ranging across species between 61.29% to 77.02% and 90.32% to 96.77% for complete and partial genes, respectively.
The effectiveness of content representation was evaluated using these different properties and their combinations in 10 sets of replica retrieval experiments with 5% random sample fractions of ground-truth identified Australian Pine image objects as query templates.
The approximate reliability of over- or under- representation was evaluated by graphical presentation of standard errors based on 100 bootstraps of the input set.
The newly developed physics-based potential energy function (described in Methods) for a coarse grained protein representation, was evaluated on structure fit to sequence (the fold recognition problem) and sequence fit to structure (the inverse folding problem).
Each representation was evaluated by comparing the final size of the epidemics, the impact of the seed role class, and the final attack rates in each role class against simulations based on the much richer network-based representations (HET and DYN), which retain several heterogeneities and correlations of the empirical dataset.
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CEO of Professional Science Editing for Scientists @ prosciediting.com