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The Receiver Operating Characteristic (ROC) curve displaying the fraction of ranked actives (true positive rate) at a given fraction of ranked decoys (false positive rate) was plotted for each VS run.
To quantify the DFC test improvement over t- and CAT- tests, we calculated the sensitivity ratios 〈 τ(DFC)| ν〉 / 〈 τ other)| ν〉 and partial area ratios 〈SPA DFC)| ν〉 / 〈SPA other)| ν〉 as a function of ν (top fraction of ranked features).
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The prediction accuracy of any ranking method is the fraction of correctly ranked trials this can be determined, since we have the ground truth out of the grand total of 1000 trials.
Ranking accuracy using the default and optimized box size is evaluated by the enrichment factor for the top (a) 1 % and (b) 10%% of the ranked library, (c) Boltzmann-Enhanced Discrimination of Receiver Operating Characteristics, (d) the area under the enrichment curve, and (e) the top fraction of the ranked library that contains 50%% of actives.
The fraction of the ranked library that contain 50%% actives.
Finally, we calculate ACT-50 %, which corresponds to the top fraction of the ranked library that contains half of the active compounds.
These include enrichment factors calculated for the top 1 and 10%% of the ranked library (EF1 % and EF10%%), the Boltzmann-Enhanced Discrimination of Receiver Operating Characteristics (BEDROC20) score, the area under the enrichment curve (AUC), and the top fraction of the ranked library that contains 50%% of the active compounds (ACT-50ACT-50%
We also divide this number by N to obtain the fraction of first ranked test protein complexes and call this fraction precision (PRE).
Precision was the fraction of genes ranked within top k in the test data that were true known cancer genes; recall was the fraction of known breast cancer genes ranking within top k.
The goal of a VS is to enrich molecules that are biologically active against a protein target in a preferably small top fraction of the ranked library.
5) Average precision: defined as: a v e r a g e p r e c i s i o n f = 1 p ∑ i = 1 p 1 Y i ∑ y ∈ Y i L i r a n k f x i, y, L i = y ′ | r a n k f x i, y ′ ≤ r a n k f x i, y, y ′ ∈ Y i, which is used to evaluate the average fraction of labels ranked above a particular label y∈ Y which actually are in Y.
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