TY  - JOUR
AU  - Breimann, Stephan
AU  - Frishman, Dmitrij
TI  - AAclust: k-optimized clustering for selecting redundancy-reduced sets of amino acid scales.
JO  - Bioinformatics advances
VL  - 4
IS  - 1
SN  - 2635-0041
CY  - Oxford
PB  - Oxford University Press
M1  - DZNE-2024-01329
SP  - vbae165
PY  - 2024
AB  - Amino acid scales are crucial for sequence-based protein prediction tasks, yet no gold standard scale set or simple scale selection methods exist. We developed AAclust, a wrapper for clustering models that require a pre-defined number of clusters k, such as k-means. AAclust obtains redundancy-reduced scale sets by clustering and selecting one representative scale per cluster, where k can either be optimized by AAclust or defined by the user. The utility of AAclust scale selections was assessed by applying machine learning models to 24 protein benchmark datasets. We found that top-performing scale sets were different for each benchmark dataset and significantly outperformed scale sets used in previous studies. Noteworthy is the strong dependence of the model performance on the scale set size. AAclust enables a systematic optimization of scale-based feature engineering in machine learning applications.The AAclust algorithm is part of AAanalysis, a Python-based framework for interpretable sequence-based protein prediction, which is documented and accessible at https://aaanalysis.readthedocs.io/en/latest and https://github.com/breimanntools/aaanalysis.
LB  - PUB:(DE-HGF)16
C6  - pmid:39544628
C2  - pmc:PMC11562964
DO  - DOI:10.1093/bioadv/vbae165
UR  - https://pub.dzne.de/record/272949
ER  -