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Lossy compression of matrices by black box optimisation of mixed integer nonlinear programming.

ABSTRACT: In edge computing, suppressing data size is a challenge for machine learning models that perform complex tasks such as autonomous driving, in which computational resources (speed, memory size and power) are limited. Efficient lossy compression of matrix data has been introduced by decomposing it into the product of an integer and real matrices. However, its optimisation is difficult as it requires simultaneous optimisation of an integer and real variables. In this paper, we improve this optimisation by utilising recently developed black-box optimisation (BBO) algorithms with an Ising solver for binary variables. In addition, the algorithm can be used to solve mixed-integer programming problems that are linear and non-linear in terms of real and integer variables, respectively. The differences between the choice of Ising solvers (simulated annealing, quantum annealing and simulated quenching) and the strategies of the BBO algorithms (BOCS, FMQA and their variations) are discussed for further development of the BBO techniques.

SUBMITTER: Kadowaki T

PROVIDER: S-EPMC9477857 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Lossy compression of matrices by black box optimisation of mixed integer nonlinear programming.

Kadowaki Tadashi T Ambai Mitsuru M

Scientific reports 20220915 1

In edge computing, suppressing data size is a challenge for machine learning models that perform complex tasks such as autonomous driving, in which computational resources (speed, memory size and power) are limited. Efficient lossy compression of matrix data has been introduced by decomposing it into the product of an integer and real matrices. However, its optimisation is difficult as it requires simultaneous optimisation of an integer and real variables. In this paper, we improve this optimisa ...[more]

PMID: 36109622

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Project description:The use of computational models in metabolic engineering has been increasing as more genome-scale metabolic models and computational approaches become available. Various computational approaches have been developed to predict how genetic perturbations affect metabolic behavior at a systems level, and have been successfully used to engineer microbial strains with improved primary or secondary metabolite production. However, identification of metabolic engineering strategies involving a large number of perturbations is currently limited by computational resources due to the size of genome-scale models and the combinatorial nature of the problem. In this study, we present (i) two new bi-level strain design approaches using mixed-integer programming (MIP), and (ii) general solution techniques that improve the performance of MIP-based bi-level approaches. The first approach (SimOptStrain) simultaneously considers gene deletion and non-native reaction addition, while the second approach (BiMOMA) uses minimization of metabolic adjustment to predict knockout behavior in a MIP-based bi-level problem for the first time. Our general MIP solution techniques significantly reduced the CPU times needed to find optimal strategies when applied to an existing strain design approach (OptORF) (e.g., from ?10 days to ?5 minutes for metabolic engineering strategies with 4 gene deletions), and identified strategies for producing compounds where previous studies could not (e.g., malate and serine). Additionally, we found novel strategies using SimOptStrain with higher predicted production levels (for succinate and glycerol) than could have been found using an existing approach that considers network additions and deletions in sequential steps rather than simultaneously. Finally, using BiMOMA we found novel strategies involving large numbers of modifications (for pyruvate and glutamate), which sequential search and genetic algorithms were unable to find. The approaches and solution techniques developed here will facilitate the strain design process and extend the scope of its application to metabolic engineering.

Dataset Information

Lossy compression of matrices by black box optimisation of mixed integer nonlinear programming.

Publications

Lossy compression of matrices by black box optimisation of mixed integer nonlinear programming.

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