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Without proper cross-validation, the result can be overly optimistic.
Without proper cross-validation, the R-factor curves in Figure 1supplement 1 cannot be trusted.
Without proper cross-validation, the R-factor curves in Figure 1 figure supplement 1 cannot be trusted.
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Furthermore, the previous studies have relied on proprietary data and sometimes have not used proper cross-validation methods to assess the results.
As we can see here, the proper cross-validation procedures can often be quite computationally expensive.
Overfitting can only be detected when using proper cross-validation techniques or independent test set analysis.
Complicated learning schemes can make proper cross-validation too computational expensive to run.
However, using a proper cross-validation approach such as stratified random cross-validation can help us to overcome these problems while being independent of any prior biological knowledge.
To ensure proper cross-validation, CONTRAlign was retrained from scratch using 𝒯1, and CONTRAfold was retrained using 𝒯2.
As a result, the LOO correlation estimate becomes 0.85 with manual selection instead of 0.60 using proper cross-validation.
To perform proper cross-validation, separate training runs were carried out for each of the 29 test proteins.
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