title: A framework for optimal kernel-based manifold embedding of medical image data.
abstract: Kernel-based dimensionality reduction is a widely used technique in medical image analysis. To fully unravel the underlying nonlinear manifold the selection of an adequate kernel function and of its free parameters is critical. In practice, however, the kernel function is generally chosen as Gaussian or polynomial and such standard kernels might not always be optimal for a given image dataset or application. In this paper, we present a study on the effect of the kernel functions in nonlinear manifold embedding of medical image data. To this end, we first carry out a literature review on existing advanced kernels developed in the statistics, machine learning, and signal processing communities. In addition, we implement kernel-based formulations of well-known nonlinear dimensional reduction techniques such as Isomap and Locally Linear Embedding, thus obtaining a unified framework for manifold embedding using kernels. Subsequently, we present a method to automatically choose a kernel function and its associated parameters from a pool of kernel candidates, with the aim to generate the most optimal manifold embeddings. Furthermore, we show how the calculated selection measures can be extended to take into account the spatial relationships in images, or used to combine several kernels to further improve the embedding results. Experiments are then carried out on various synthetic and phantom datasets for numerical assessment of the methods. Furthermore, the workflow is applied to real data that include brain manifolds and multispectral images to demonstrate the importance of the kernel selection in the analysis of high-dimensional medical images.
authors.affiliation: Information and Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain. Electronic address: veronika.zimmer@upf.edu.
authors.forename: Veronika A
authors.initials: VA
authors.lastname: Zimmer
authors.affiliation: Information and Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Karim
authors.initials: K
authors.lastname: Lekadir
authors.affiliation: Information and Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Corné
authors.initials: C
authors.lastname: Hoogendoorn
authors.affiliation: Information and Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain; Department of Mechanical Engineering, The University of Sheffield, United Kingdom.
authors.forename: Alejandro F
authors.initials: AF
authors.lastname: Frangi
authors.affiliation: Information and Communication Technologies Department, Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Gemma
authors.initials: G
authors.lastname: Piella
mesh_terms: D000465:Algorithms; D001921:Brain / Q000033:anatomy & histology*; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D000069550:Machine Learning; D008279:Magnetic Resonance Imaging / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
keywords: Kernel principal component analysis; Manifold embedding quality; Multilevel kernel combinations; Nonlinear dimensionality reduction