A1 Refereed original research article in a scientific journal
Predicting pairwise interaction affinities with ℓ0-penalized least squares-a nonsmooth bi-objective optimization based approach∗
Authors: Paasivirta Pauliina, Numminen Riikka, Airola Antti, Karmitsa Napsu, Pahikkala Tapio
Publisher: TAYLOR & FRANCIS LTD
Publishing place: ABINGDON
Publication year: 2024
Journal: Optimization Methods and Software
Journal name in source: OPTIMIZATION METHODS & SOFTWARE
Journal acronym: OPTIM METHOD SOFTW
Number of pages: 28
ISSN: 1055-6788
eISSN: 1029-4937
DOI: https://doi.org/10.1080/10556788.2023.2280784
Web address : https://doi.org/10.1080/10556788.2023.2280784
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/387007495
In this paper, we introduce a novel nonsmooth optimization-based method LMBM-Kron & ell;(0) LS for solving large-scale pairwise interaction affinity prediction problems. The aim of LMBM-Kron & ell;0LS is to produce accurate predictions using as sparse a model as possible. We apply the least squares approach with Kronecker product kernels for a loss function and a continuous formulation of & ell;(0) pseudonorm for regularization. Thus, we end up solving a nonsmooth optimization problem. In addition, we apply a specific bi-objective criterion to strike a balance between the prediction accuracy of the learned model and the sparsity of the obtained solution. We compare LMBM-Kron & ell;0LS with some state-of-the-art methods using three benchmark and two simulated data sets under four distinct experimental settings, including zero-shot learning. Moreover, both binary and continuous interaction affinity labels are considered with LMBM-Kron & ell;0LS. The results show that LMBM-Kron & ell;0LS finds sparse solutions without sacrificing too much in the prediction performance.
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