Large Language Models (LLMs) such as GPT-4 have demonstrated their ability to understand natural language and generate complex code snippets. This paper introduces a novel Large Language Model Evolutionary Algorithm (LLaMEA) framework, leveraging GPT models for the automated generation and refinement of algorithms. Given a set of criteria and a task definition (the search space), LLaMEA iteratively generates, mutates and selects algorithms based on performance metrics and feedback from runtime evaluations. This framework offers a unique approach to generating optimized algorithms without requiring extensive prior expertise. We show how this framework can be used to generate novel black-box metaheuristic optimization algorithms automatically. LLaMEA generates multiple algorithms that outperform state-of-the-art optimization algorithms (Covariance Matrix Adaptation Evolution Strategy and Differential Evolution) on the five dimensional black box optimization benchmark (BBOB). The algorithms also show competitive performance on the 10- and 20-dimensional instances of the test functions, although they have not seen such instances during the automated generation process. The results demonstrate the feasibility of the framework and identify future directions for automated generation and optimization of algorithms via LLMs.

Cell-penetrating peptides (CPPs) are powerful vectors for the intracellular delivery of a diverse array of therapeutic molecules. Despite their potential, the rational design of CPPs remains a challenging task that often requires extensive experimental efforts and iterations. In this study, we introduce an innovative approach for the de novo design of CPPs, leveraging the strengths of machine learning (ML) and optimization algorithms. Our strategy, named LightCPPgen, integrates a LightGBM-based predictive model with a genetic algorithm (GA), enabling the systematic generation and optimization of CPP sequences. At the core of our methodology is the development of an accurate, efficient, and interpretable predictive model, which utilizes 20 explainable features to shed light on the critical factors influencing CPP translocation capacity. The CPP predictive model works synergistically with an optimization algorithm, which is tuned to enhance computational efficiency while maintaining optimization performance. The GA solutions specifically target the candidate sequences' penetrability score, while trying to maximize similarity with the original non-penetrating peptide in order to retain its original biological and physicochemical properties. By prioritizing the synthesis of only the most promising CPP candidates, LightCPPgen can drastically reduce the time and cost associated with wet lab experiments. In summary, our research makes a substantial contribution to the field of CPP design, offering a robust framework that combines ML and optimization techniques to facilitate the rational design of penetrating peptides, by enhancing the explainability and interpretability of the design process.

We study the addition of shape constraints and their consideration during the parameter estimation step of symbolic regression (SR). Shape constraints serve as a means to introduce prior knowledge about the shape of the otherwise unknown model function into SR. Unlike previous works that have explored shape constraints in SR, we propose minimizing shape constraint violations during parameter estimation using gradient-based numerical optimization. We test three algorithm variants to evaluate their performance in identifying three symbolic expressions from a synthetically generated data set. This paper examines two benchmark scenarios: one with varying noise levels and another with reduced amounts of training data. The results indicate that incorporating shape constraints into the expression search is particularly beneficial when data is scarce. Compared to using shape constraints only in the selection process, our approach of minimizing violations during parameter estimation shows a statistically significant benefit in some of our test cases, without being significantly worse in any instance.

People are remarkably capable of generating their own goals, beginning with child's play and continuing into adulthood. Despite considerable empirical and computational work on goals and goal-oriented behavior, models are still far from capturing the richness of everyday human goals. Here, we bridge this gap by collecting a dataset of human-generated playful goals, modeling them as reward-producing programs, and generating novel human-like goals through program synthesis. Reward-producing programs capture the rich semantics of goals through symbolic operations that compose, add temporal constraints, and allow for program execution on behavioral traces to evaluate progress. To build a generative model of goals, we learn a fitness function over the infinite set of possible goal programs and sample novel goals with a quality-diversity algorithm. Human evaluators found that model-generated goals, when sampled from partitions of program space occupied by human examples, were indistinguishable from human-created games. We also discovered that our model's internal fitness scores predict games that are evaluated as more fun to play and more human-like.

Existing efforts are dedicated to designing many topologies and graph-aware strategies for the graph Transformer, which greatly improve the model's representation capabilities. However, manually determining the suitable Transformer architecture for a specific graph dataset or task requires extensive expert knowledge and laborious trials. This paper proposes an evolutionary graph Transformer architecture search framework (EGTAS) to automate the construction of strong graph Transformers. We build a comprehensive graph Transformer search space with the micro-level and macro-level designs. EGTAS evolves graph Transformer topologies at the macro level and graph-aware strategies at the micro level. Furthermore, a surrogate model based on generic architectural coding is proposed to directly predict the performance of graph Transformers, substantially reducing the evaluation cost of evolutionary search. We demonstrate the efficacy of EGTAS across a range of graph-level and node-level tasks, encompassing both small-scale and large-scale graph datasets. Experimental results and ablation studies show that EGTAS can construct high-performance architectures that rival state-of-the-art manual and automated baselines.

Dynamic Vehicle Routing Problem (DVRP), is an extension of the classic Vehicle Routing Problem (VRP), which is a fundamental problem in logistics and transportation. Typically, DVRPs involve two stakeholders: service providers that deliver services to customers and customers who raise requests from different locations. Many real-world applications can be formulated as DVRP such as ridesharing and non-compliance capture. Apart from original objectives like optimising total utility or efficiency, DVRP should also consider fairness for all parties. Unfairness can induce service providers and customers to give up on the systems, leading to negative financial and social impacts. However, most existing DVRP-related applications focus on improving fairness from a single side, and there have been few works considering two-sided fairness and utility optimisation concurrently. To this end, we propose a novel framework, a Two-sided Fairness-aware Genetic Algorithm (named 2FairGA), which expands the genetic algorithm from the original objective solely focusing on utility to multi-objectives that incorporate two-sided fairness. Subsequently, the impact of injecting two fairness definitions into the utility-focused model and the correlation between any pair of the three objectives are explored. Extensive experiments demonstrate the superiority of our proposed framework compared to the state-of-the-art.

When developing empirical equations, domain experts require these to be accurate and adhere to physical laws. Often, constants with unknown units need to be discovered alongside the equations. Traditional unit-aware genetic programming (GP) approaches cannot be used when unknown constants with undetermined units are included. This paper presents a method for dimensional analysis that propagates unknown units as ''jokers'' and returns the magnitude of unit violations. We propose three methods, namely evolutive culling, a repair mechanism, and a multi-objective approach, to integrate the dimensional analysis in the GP algorithm. Experiments on datasets with ground truth demonstrate comparable performance of evolutive culling and the multi-objective approach to a baseline without dimensional analysis. Extensive analysis of the results on datasets without ground truth reveals that the unit-aware algorithms make only low sacrifices in accuracy, while producing unit-adherent solutions. Overall, we presented a promising novel approach for developing unit-adherent empirical equations.

Institute for Particle Physics Phenomenology, Department of Physics, Durham University, Durham DH1 3LE, U.K. We propose symbolic regression as a powerful tool for studying Beyond the Standard Model physics. As a benchmark model, we consider the so-called Constrained Minimal Supersymmetric Standard Model, which has a four-dimensional parameter space defined at the GUT scale. We provide a set of analytical expressions that reproduce three low-energy observables of interest in terms of the parameters of the theory: the Higgs mass, the contribution to the anomalous magnetic moment of the muon, and the cold dark matter relic density. To demonstrate the power of the approach, we employ the symbolic expressions in a global fits analysis to derive the posterior probability densities of the parameters, which are obtained extremely rapidly in comparison with conventional methods. The chief test of any proposal for Beyond the Standard To avoid this bottleneck, it is natural to turn to Model (BSM) physics is to confront it with experimental machine learning to bypass the computation chain or data.

Swarm robots, inspired by the emergence of animal herds, are robots that assemble a large number of modules and self-organize themselves to form specific morphologies and exhibit specific functions. These modular robots perform relatively simple actions and controls, and create macroscopic morphologies and functions through the interaction of a large number of modular robots. This research focuses on such self-organizing robots or swarm robots. The proposed algorithm is a model that applies the Turing pattern, one of the self-organization models, to make a group of modules accumulate and stay within a certain region. The proposed method utilizes the area within the spots of the Turing pattern as the aggregation region of the modules. Furthermore, it considers the value corresponding to the concentration distribution within the spotted pattern of the Turing pattern model (referred to as the potential value in this research), identifies the center of the region (spotted pattern), and makes it the center of the module group. By controlling the modules in the direction of the higher potential value, it succeeds in maintaining the shape of the module group as a whole while moving. The algorithm was validated using a two-dimensional simulation model. The unit module robot was assumed to have the following properties: 1) limited self-drive, 2) no module identifier, 3) information exchange only with adjacent modules, 4) no coordinate system, and 5) only simple arithmetic and memory functions. Using these modules, the devised algorithm was able to achieve not only the creation of static forms but also the realization of the following movements: 1) modules accumulate and grow, 2) modules move to the light source, 3) exit the gap while maintaining its shape, and 4) self-replication.

Feature interaction selection is a fundamental problem in commercial recommender systems. Most approaches equally enumerate all features and interactions by the same pre-defined operation under expert guidance. Their recommendation is unsatisfactory sometimes due to the following issues: (1)~They cannot ensure the learning abilities of models because their architectures are poorly adaptable to tasks and data; (2)~Useless features and interactions can bring unnecessary noise and complicate the training process. In this paper, we aim to adaptively evolve the model to select appropriate operations, features, and interactions under task guidance. Inspired by the evolution and functioning of natural organisms, we propose a novel \textsl{Cognitive EvoLutionary Learning (CELL)} framework, where cognitive ability refers to a property of organisms that allows them to react and survive in diverse environments. It consists of three stages, i.e., DNA search, genome search, and model functioning. Specifically, if we regard the relationship between models and tasks as the relationship between organisms and natural environments, interactions of feature pairs can be analogous to double-stranded DNA, of which relevant features and interactions can be analogous to genomes. Along this line, we diagnose the fitness of the model on operations, features, and interactions to simulate the survival rates of organisms for natural selection. We show that CELL can adaptively evolve into different models for different tasks and data, which enables practitioners to access off-the-shelf models. Extensive experiments on four real-world datasets demonstrate that CELL significantly outperforms state-of-the-art baselines. Also, we conduct synthetic experiments to ascertain that CELL can consistently discover the pre-defined interaction patterns for feature pairs.