It is a well-known story that theoretical computer science and biology have been drawing inspiration from each other for decades. While computer science has tried to mimic the functioning of living systems to develop computing models, including automata, artificial neural networks, and evolutionary algorithms, biology has used computing as a metaphor to explain the functioning of living systems.4 For example, biologists have used Boolean logic to conceptualize gene regulation since early 1970s, when Jacques Monod wrote the inspirational statement "… like the workings of computers."40 This article contends that information processing is the link between computer science and molecular biology. In computer science, a model of computation such as finite state machines or Turing machines defines how to generate output from a set of inputs and a set of rules or instructions.

Clustering in dynamic environments is of increasing importance, with broad applications ranging from real-time data analysis and online unsupervised learning to dynamic facility location problems. While meta-heuristics have shown promising effectiveness in static clustering tasks, their application for tracking optimal clustering solutions or robust clustering over time in dynamic environments remains largely underexplored. This is partly due to a lack of dynamic datasets with diverse, controllable, and realistic dynamic characteristics, hindering systematic performance evaluations of clustering algorithms in various dynamic scenarios. This deficiency leads to a gap in our understanding and capability to effectively design algorithms for clustering in dynamic environments. To bridge this gap, this paper introduces the Dynamic Dataset Generator (DDG). DDG features multiple dynamic Gaussian components integrated with a range of heterogeneous, local, and global changes. These changes vary in spatial and temporal severity, patterns, and domain of influence, providing a comprehensive tool for simulating a wide range of dynamic scenarios.

Real-world optimization problems often involve stochastic and dynamic components. Evolutionary algorithms are particularly effective in these scenarios, as they can easily adapt to uncertain and changing environments but often uncertainty and dynamic changes are studied in isolation. In this paper, we explore the use of 3-objective evolutionary algorithms for the chance constrained knapsack problem with dynamic constraints. In our setting, the weights of the items are stochastic and the knapsack's capacity changes over time. We introduce a 3-objective formulation that is able to deal with the stochastic and dynamic components at the same time and is independent of the confidence level required for the constraint. This new approach is then compared to the 2-objective formulation which is limited to a single confidence level. We evaluate the approach using two different multi-objective evolutionary algorithms (MOEAs), namely the global simple evolutionary multi-objective optimizer (GSEMO) and the multi-objective evolutionary algorithm based on decomposition (MOEA/D), across various benchmark scenarios. Our analysis highlights the advantages of the 3-objective formulation over the 2-objective formulation in addressing the dynamic chance constrained knapsack problem.

The paper presents an experimental study of resilient path planning for con-tinuum robots taking into account the multi-objective optimisation problem. To do this, we used two well-known algorithms, namely Genetic algorithm and A* algorithm, for path planning and the Analytical Hierarchy Process al-gorithm for paths evaluation. In our experiment Analytical Hierarchy Process algorithm considers four different criteria, i.e. distance, motors damage, me-chanical damage and accuracy each considered to contribute to the resilience of a continuum robot. The use of different criteria is necessary to increasing the time to maintenance operations of the robot. The experiment shows that on the one hand both algorithms can be used in combination with Analytical Hierarchy Process algorithm for multi criteria path-planning, while Genetic algorithm shows superior performance in the comparison of the two algo-rithms.

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.

The Grey Wolf Optimizer (GWO) is recognized as a novel meta-heuristic algorithm inspired by the social leadership hierarchy and hunting mechanism of grey wolves. It is well-known for its simple parameter setting, fast convergence speed, and strong optimization capability. In the original GWO, there are two significant design flaws in its fundamental optimization mechanisms. Problem (1): the algorithm fails to inherit from elite positions from the last iteration when generating the next positions of the wolf population, potentially leading to suboptimal solutions. Problem (2): the positions of the population are updated based on the central position of the three leading wolves (alpha, beta, delta), without a balanced mechanism between local and global search. To tackle these problems, an enhanced Grey Wolf Optimizer with Elite Inheritance Mechanism and Balance Search Mechanism, named as EBGWO, is proposed to improve the effectiveness of the position updating and the quality of the convergence solutions. The IEEE CEC 2014 benchmark functions suite and a series of simulation tests are employed to evaluate the performance of the proposed algorithm. The simulation tests involve a comparative study between EBGWO, three GWO variants, GWO and two well-known meta-heuristic algorithms. The experimental results demonstrate that the proposed EBGWO algorithm outperforms other meta-heuristic algorithms in both accuracy and convergence speed. Three engineering optimization problems are adopted to prove its capability in processing real-world problems. The results indicate that the proposed EBGWO outperforms several popular algorithms.

Symbolic regression (SR) searches for parametric models that accurately fit a dataset, prioritizing simplicity and interpretability. Despite this secondary objective, studies point out that the models are often overly complex due to redundant operations, introns, and bloat that arise during the iterative process, and can hinder the search with repeated exploration of bloated segments. Applying a fast heuristic algebraic simplification may not fully simplify the expression and exact methods can be infeasible depending on size or complexity of the expressions. We propose a novel agnostic simplification and bloat control for SR employing an efficient memoization with locality-sensitive hashing (LHS). The idea is that expressions and their sub-expressions traversed during the iterative simplification process are stored in a dictionary using LHS, enabling efficient retrieval of similar structures. We iterate through the expression, replacing subtrees with others of same hash if they result in a smaller expression. Empirical results shows that applying this simplification during evolution performs equal or better than without simplification in minimization of error, significantly reducing the number of nonlinear functions. This technique can learn simplification rules that work in general or for a specific problem, and improves convergence while reducing model complexity.

For autonomous crane lifting, optimal trajectories of the crane are required as reference inputs to the crane controller to facilitate feedforward control. Reducing the unactuated payload motion is a crucial issue for under-actuated tower cranes with spherical pendulum dynamics. The planned trajectory should be optimal in terms of both operating time and energy consumption, to facilitate optimum output spending optimum effort. This article proposes an anti-swing tower crane trajectory planner that can provide time-energy optimal solutions for the Computer-Aided Lift Planning (CALP) system developed at Nanyang Technological University, which facilitates collision-free lifting path planning of robotized tower cranes in autonomous construction sites. The current work introduces a trajectory planning module to the system that utilizes the geometric outputs from the path planning module and optimally scales them with time information. Firstly, analyzing the non-linear dynamics of the crane operations, the tower crane is established as differentially flat. Subsequently, the multi-objective trajectory optimization problems for all the crane operations are formulated in the flat output space through consideration of the mechanical and safety constraints. Two multi-objective evolutionary algorithms, namely Non-dominated Sorting Genetic Algorithm (NSGA-II) and Generalized Differential Evolution 3 (GDE3), are extensively compared via statistical measures based on the closeness of solutions to the Pareto front, distribution of solutions in the solution space and the runtime, to select the optimization engine of the planner. Finally, the crane operation trajectories are obtained via the corresponding planned flat output trajectories. Studies simulating real-world lifting scenarios are conducted to verify the effectiveness and reliability of the proposed module of the lift planning system.

The choice of input-data used to train algorithm-selection models is recognised as being a critical part of the model success. Recently, feature-free methods for algorithm-selection that use short trajectories obtained from running a solver as input have shown promise. However, it is unclear to what extent these trajectories reliably discriminate between solvers. We propose a meta approach to generating discriminatory trajectories with respect to a portfolio of solvers. The algorithm-configuration tool irace is used to tune the parameters of a simple Simulated Annealing algorithm (SA) to produce trajectories that maximise the performance metrics of ML models trained on this data. We show that when the trajectories obtained from the tuned SA algorithm are used in ML models for algorithm-selection and performance prediction, we obtain significantly improved performance metrics compared to models trained both on raw trajectory data and on exploratory landscape features.

There is growing interest in engineering unconventional computing devices that leverage the intrinsic dynamics of physical substrates to perform fast and energy-efficient computations. Granular metamaterials are one such substrate that has emerged as a promising platform for building wave-based information processing devices with the potential to integrate sensing, actuation, and computation. Their high-dimensional and nonlinear dynamics result in nontrivial and sometimes counter-intuitive wave responses that can be shaped by the material properties, geometry, and configuration of individual grains. Such highly tunable rich dynamics can be utilized for mechanical computing in special-purpose applications. However, there are currently no general frameworks for the inverse design of large-scale granular materials. Here, we build upon the similarity between the spatiotemporal dynamics of wave propagation in material and the computational dynamics of Recurrent Neural Networks to develop a gradient-based optimization framework for harmonically driven granular crystals. We showcase how our framework can be utilized to design basic logic gates where mechanical vibrations carry the information at predetermined frequencies. We compare our design methodology with classic gradient-free methods and find that our approach discovers higher-performing configurations with less computational effort. Our findings show that a gradient-based optimization method can greatly expand the design space of metamaterials and provide the opportunity to systematically traverse the parameter space to find materials with the desired functionalities.