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A Proximity Weighted Evidential k Nearest Neighbor Classifier for Imbalanced Data

ABSTRACT: In k Nearest Neighbor (kNN) classifier, a query instance is classified based on the most frequent class of its nearest neighbors among the training instances. In imbalanced datasets, kNN becomes biased towards the majority instances of the training space. To solve this problem, we propose a method called Proximity weighted Evidential kNN classifier. In this method, each neighbor of a query instance is considered as a piece of evidence from which we calculate the probability of class label given feature values to provide more preference to the minority instances. This is then discounted by the proximity of the neighbor to prioritize the closer instances in the local neighborhood. These evidences are then combined using Dempster-Shafer theory of evidence. A rigorous experiment over 30 benchmark imbalanced datasets shows that our method performs better compared to 12 popular methods. In pairwise comparison of these 12 methods with our method, in the best case, our method wins in 29 datasets, and in the worst case it wins in least 19 datasets. More importantly, according to Friedman test the proposed method ranks higher than all other methods in terms of AUC at 5% level of significance.

SUBMITTER: Lauw H

PROVIDER: S-EPMC7206335 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. However, quantitation of the antisense contributions of motifs is problematic, since individual motifs are not isolated from the effects of neighboring nucleotides, and motifs may be overlapping. These problems are circumvented by a next-nearest-neighbor (NNN) analysis of antisense DNA effects in which the overlapping nature of nearest-neighbors is taken into account.ResultsNext-nearest-neighbor triplet combinations of nucleotides are the simplest that include overlapping sequence effects and therefore can encompass interactions beyond those of nearest neighbors. We used singular value decomposition (SVD) to fit experimental data from our laboratory in which phosphorothioate-modified antisense DNAs (S-DNAs) 20 nucleotides long were used to inhibit cellular protein expression in 112 experiments involving four gene targets and two cell lines. Data were fitted using a NNN model, neglecting end effects, to derive NNN inhibition parameters that could be combined to give parameters for a set of 49 sequences that represents the inhibitory effects of all possible overlapping triplet interactions in the cellular targets of these antisense S-DNAs. We also show that parameters to describe subsets of the data, such as the mRNAs being targeted and the cell lines used, can be included in such a derivation. While NNN triplet parameters provided an adequate model to fit our data, NN doublet parameters did not.ConclusionsThe methodology presented illustrates how NNN antisense inhibitory information can be derived from in vivo cellular experiments. Subsequent calculations of the antisense inhibitory parameters for any mRNA target sequence automatically take into account the effects of all possible overlapping combinations of nearest-neighbors in the sequence. This procedure is more robust than the tallying of tetrameric motifs that have positive or negative antisense effects. The specific parameters derived in this work are limited in their applicability by the relatively small database of experiments that was used in their derivation.

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A Proximity Weighted Evidential k Nearest Neighbor Classifier for Imbalanced Data

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