Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells

TY - JOUR

T1 - Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells

AU - Ritter, Christian

AU - Wollmann, Thomas

AU - Bernhard, Patrick

AU - Gunkel, Manuel

AU - Braun, Delia M

AU - Lee, Ji-Young

AU - Meiners, Jan

AU - Simon, Ronald

AU - Sauter, Guido

AU - Erfle, Holger

AU - Rippe, Karsten

AU - Bartenschlager, Ralf

AU - Rohr, Karl

PY - 2019/11

Y1 - 2019/11

N2 - PURPOSE: Automated analysis of microscopy image data typically requires complex pipelines that involve multiple methods for different image analysis tasks. To achieve best results of the analysis pipelines, method-dependent hyperparameters need to be optimized. However, complex pipelines often suffer from the fact that calculation of the gradient of the loss function is analytically or computationally infeasible. Therefore, first- or higher-order optimization methods cannot be applied.METHODS: We developed a new framework for zero-order black-box hyperparameter optimization called HyperHyper, which has a modular architecture that separates hyperparameter sampling and optimization. We also developed a visualization of the loss function based on infimum projection to obtain further insights into the optimization problem.RESULTS: We applied HyperHyper in three different experiments with different imaging modalities, and evaluated in total more than 400.000 hyperparameter combinations. HyperHyper was used for optimizing two pipelines for cell nuclei segmentation in prostate tissue microscopy images and two pipelines for detection of hepatitis C virus proteins in live cell microscopy data. We evaluated the impact of separating the sampling and optimization strategy using different optimizers and employed an infimum projection for visualizing the hyperparameter space.CONCLUSIONS: The separation of sampling and optimization strategy of the proposed HyperHyper optimization framework improves the result of the investigated image analysis pipelines. Visualization of the loss function based on infimum projection enables gaining further insights on the optimization process.

AB - PURPOSE: Automated analysis of microscopy image data typically requires complex pipelines that involve multiple methods for different image analysis tasks. To achieve best results of the analysis pipelines, method-dependent hyperparameters need to be optimized. However, complex pipelines often suffer from the fact that calculation of the gradient of the loss function is analytically or computationally infeasible. Therefore, first- or higher-order optimization methods cannot be applied.METHODS: We developed a new framework for zero-order black-box hyperparameter optimization called HyperHyper, which has a modular architecture that separates hyperparameter sampling and optimization. We also developed a visualization of the loss function based on infimum projection to obtain further insights into the optimization problem.RESULTS: We applied HyperHyper in three different experiments with different imaging modalities, and evaluated in total more than 400.000 hyperparameter combinations. HyperHyper was used for optimizing two pipelines for cell nuclei segmentation in prostate tissue microscopy images and two pipelines for detection of hepatitis C virus proteins in live cell microscopy data. We evaluated the impact of separating the sampling and optimization strategy using different optimizers and employed an infimum projection for visualizing the hyperparameter space.CONCLUSIONS: The separation of sampling and optimization strategy of the proposed HyperHyper optimization framework improves the result of the investigated image analysis pipelines. Visualization of the loss function based on infimum projection enables gaining further insights on the optimization process.

U2 - 10.1007/s11548-019-02010-3

DO - 10.1007/s11548-019-02010-3

M3 - SCORING: Journal article

C2 - 31177423

VL - 14

SP - 1847

EP - 1857

JO - INT J COMPUT ASS RAD

JF - INT J COMPUT ASS RAD

SN - 1861-6410

IS - 11

ER -