Andrew J. Parkes

Yong En Kok, Bowen Deng, Alexander Bentley et al.

Optical aberrations significantly degrade image quality in microscopy, particularly when imaging deeper into samples. These aberrations arise from distortions in the optical wavefront and can be mathematically represented using Zernike polynomials. Existing methods often address only mild aberrations on limited sample types and modalities, typically treating the problem as a black-box mapping without leveraging the underlying optical physics of wavefront distortions. We propose ZRNet, a physics-informed framework that jointly performs Zernike coefficient prediction and optical image Restoration. We contribute a Zernike Graph module that explicitly models physical relationships between Zernike polynomials based on their azimuthal degrees-ensuring that learned corrections align with fundamental optical principles. To further enforce physical consistency between image restoration and Zernike prediction, we introduce a Frequency-Aware Alignment (FAA) loss, which better aligns Zernike coefficient prediction and image features in the Fourier domain. Extensive experiments on CytoImageNet demonstrates that our approach achieves state-of-the-art performance in both image restoration and Zernike coefficient prediction across diverse microscopy modalities and biological samples with complex, large-amplitude aberrations. Code is available at https://github.com/janetkok/ZRNet.

Daniel Karapetyan, Andrew J. Parkes, Thomas Stützle

One way to speed up the algorithm configuration task is to use short runs instead of long runs as much as possible, but without discarding the configurations that eventually do well on the long runs. We consider the problem of selecting the top performing configurations of the Conditional Markov Chain Search (CMCS), a general algorithm schema that includes, for examples, VNS. We investigate how the structure of performance on short tests links with those on long tests, showing that significant differences arise between test domains. We propose a "performance envelope" method to exploit the links; that learns when runs should be terminated, but that automatically adapts to the domain.

Daniel Karapetyan, Abraham P. Punnen, Andrew J. Parkes

We study the Bipartite Boolean Quadratic Programming Problem (BBQP) which is an extension of the well known Boolean Quadratic Programming Problem (BQP). Applications of the BBQP include mining discrete patterns from binary data, approximating matrices by rank-one binary matrices, computing the cut-norm of a matrix, and solving optimisation problems such as maximum weight biclique, bipartite maximum weight cut, maximum weight induced sub-graph of a bipartite graph, etc. For the BBQP, we first present several algorithmic components, specifically, hill climbers and mutations, and then show how to combine them in a high-performance metaheuristic. Instead of hand-tuning a standard metaheuristic to test the efficiency of the hybrid of the components, we chose to use an automated generation of a multi-component metaheuristic to save human time, and also improve objectivity in the analysis and comparisons of components. For this we designed a new metaheuristic schema which we call Conditional Markov Chain Search (CMCS). We show that CMCS is flexible enough to model several standard metaheuristics; this flexibility is controlled by multiple numeric parameters, and so is convenient for automated generation. We study the configurations revealed by our approach and show that the best of them outperforms the previous state-of-the-art BBQP algorithm by several orders of magnitude. In our experiments we use benchmark instances introduced in the preliminary version of this paper and described here, which have already become the de facto standard in the BBQP literature.

Daniel Karapetyan, Andrew J. Parkes, Gregory Gutin et al.

The fixed parameter tractable (FPT) approach is a powerful tool in tackling computationally hard problems. In this paper, we link FPT results to classic artificial intelligence (AI) techniques to show how they complement each other. Specifically, we consider the workflow satisfiability problem (WSP) which asks whether there exists an assignment of authorised users to the steps in a workflow specification, subject to certain constraints on the assignment. It was shown by Cohen et al. (JAIR 2014) that WSP restricted to the class of user-independent constraints (UI), covering many practical cases, admits FPT algorithms, i.e. can be solved in time exponential only in the number of steps $k$ and polynomial in the number of users $n$. Since usually $k << n$ in WSP, such FPT algorithms are of great practical interest. We present a new interpretation of the FPT nature of the WSP with UI constraints giving a decomposition of the problem into two levels. Exploiting this two-level split, we develop a new FPT algorithm that is by many orders of magnitude faster than the previous state-of-the-art WSP algorithm and also has only polynomial-space complexity. We also introduce new pseudo-Boolean (PB) and Constraint Satisfaction (CSP) formulations of the WSP with UI constraints which efficiently exploit this new decomposition of the problem and raise the novel issue of how to use general-purpose solvers to tackle FPT problems in a fashion that meets FPT efficiency expectations. In our computational study, we investigate, for the first time, the phase transition (PT) properties of the WSP, under a model for generation of random instances. We show how PT studies can be extended, in a novel fashion, to support empirical evaluation of scaling of FPT algorithms.

Shahriar Asta, Daniel Karapetyan, Ahmed Kheiri et al.

Multi-mode resource and precedence-constrained project scheduling is a well-known challenging real-world optimisation problem. An important variant of the problem requires scheduling of activities for multiple projects considering availability of local and global resources while respecting a range of constraints. A critical aspect of the benchmarks addressed in this paper is that the primary objective is to minimise the sum of the project completion times, with the usual makespan minimisation as a secondary objective. We observe that this leads to an expected different overall structure of good solutions and discuss the effects this has on the algorithm design. This paper presents a carefully designed hybrid of Monte-Carlo tree search, novel neighbourhood moves, memetic algorithms, and hyper-heuristic methods. The implementation is also engineered to increase the speed with which iterations are performed, and to exploit the computing power of multicore machines. Empirical evaluation shows that the resulting information-sharing multi-component algorithm significantly outperforms other solvers on a set of "hidden" instances, i.e. instances not available at the algorithm design phase.