Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction

Reliable Confidence Predictions Using Conformal Prediction

Conformal classifiers output confidence prediction regions, i.e., multi-valued predictions that are guaranteed to contain the true output value of each test pattern with some predefined probability. In order to fully utilize the predictions provided by a conformal classifier, it is essential that those predictions are reliable, i.e., that a user is able to assess the quality of the predictions ...

Off - diagonal density profiles and conformal invariance

Off-diagonal profiles φ od (v) of local densities (e.g. order parameter or energy density) are calculated at the bulk critical point, by conformal methods, on a strip with transverse coordinate v, for different types of boundary conditions (free, fixed and mixed). Such profiles, which are defined by the non-vanishing matrix element 0|ˆφ(v)|φ of the appropriate operatorˆφ(v) between the ground s...

Predicting an Aptamer’s Target Binding Affinity Using its Nucleotide Sequence

Modern molecular and cellular biology depends on markers that can very selectively bind to a target molecule. Unfortunately, the process of finding such a marker is generally slow, through trial and error, and often in vivo. Aptamers (short nucleotide sequences) are a promising type of marker that can be generated and evaluated synthetically. Currently, the process of aptamer selection involves...

TALENoffer: genome-wide TALEN off-target prediction

SUMMARY Transcription activator-like effector nucleases (TALENs) have become an accepted tool for targeted mutagenesis, but undesired off-targets remain an important issue. We present TALENoffer, a novel tool for the genome-wide prediction of TALEN off-targets. We show that TALENoffer successfully predicts known off-targets of engineered TALENs and yields a competitive runtime, scanning complet...

Prediction of DNA-binding sites in proteins using evolutionary profiles