Feature transformation aims to reconstruct the feature space of raw features to enhance the performance of downstream models. However, the exponential growth in the combinations of features and operations poses a challenge, making it difficult for existing methods to efficiently explore a wide space. Additionally, their optimization is solely driven by the accuracy of downstream models in specific domains, neglecting the acquisition of general feature knowledge. To fill this research gap, we propose an evolutionary LLM framework for automated feature transformation. This framework consists of two parts: 1) constructing a multi-population database through an RL data collector while utilizing evolutionary algorithm strategies for database maintenance, and 2) utilizing the ability of Large Language Model (LLM) in sequence understanding, we employ few-shot prompts to guide LLM in generating superior samples based on feature transformation sequence distinction. Leveraging the multi-population database initially provides a wide search scope to discover excellent populations. Through culling and evolution, the high-quality populations are afforded greater opportunities, thereby furthering the pursuit of optimal individuals. Through the integration of LLMs with evolutionary algorithms, we achieve efficient exploration within a vast space, while harnessing feature knowledge to propel optimization, thus realizing a more adaptable search paradigm. Finally, we empirically demonstrate the effectiveness and generality of our proposed method.
Surrogate-assisted Evolutionary Algorithm (SAEA) is an essential method for solving expensive expensive problems. Utilizing surrogate models to substitute the optimization function can significantly reduce reliance on the function evaluations during the search process, thereby lowering the optimization costs. The construction of surrogate models is a critical component in SAEAs, with numerous machine learning algorithms playing a pivotal role in the model-building phase. This paper introduces Kolmogorov-Arnold Networks (KANs) as surrogate models within SAEAs, examining their application and effectiveness. We employ KANs for regression and classification tasks, focusing on the selection of promising solutions during the search process, which consequently reduces the number of expensive function evaluations. Experimental results indicate that KANs demonstrate commendable performance within SAEAs, effectively decreasing the number of function calls and enhancing the optimization efficiency. The relevant code is publicly accessible and can be found in the GitHub repository.
Contemporary bioinformatics has seen in profound new visibility into the composition, structure, and history of the natural world around us. Arguably, the central pillar of bioinformatics is phylogenetics -- the study of hereditary relatedness among organisms. Insight from phylogenetic analysis has touched nearly every corner of biology. Examples range across natural history, population genetics and phylogeography, conservation biology, public health, medicine, in vivo and in silico experimental evolution, application-oriented evolutionary algorithms, and beyond. High-throughput genetic and phenotypic data has realized groundbreaking results, in large part, through conjunction with open-source software used to process and analyze it. Indeed, the preceding decades have ushered in a flourishing ecosystem of bioinformatics software applications and libraries. Over the course of its nearly fifteen-year history, the DendroPy library for phylogenetic computation in Python has established a generalist niche in serving the bioinformatics community. Here, we report on the recent major release of the library, DendroPy version 5. The software release represents a major milestone in transitioning the library to a sustainable long-term development and maintenance trajectory. As such, this work positions DendroPy to continue fulfilling a key supporting role in phyloinformatics infrastructure.
To solve real-world expensive constrained multi-objective optimization problems (ECMOPs), surrogate/approximation models are commonly incorporated in evolutionary algorithms to pre-select promising candidate solutions for evaluation. However, the performance of existing approaches are highly dependent on the relative position of unconstrained and constrained Pareto fronts (UPF and CPF, respectively). In addition, the uncertainty information of surrogate models is often ignored, which can misguide the search. To mitigate these key issues (among others), an efficient probabilistic selection based constrained multi-objective EA is proposed, referred to as PSCMOEA. It comprises novel elements such as (a) an adaptive search bound identification scheme based on the feasibility and convergence status of evaluated solutions (b) a probabilistic selection method backed by theoretical formulations of model mean and uncertainties to conduct search in the predicted space to identify promising solutions (c) an efficient single infill sampling approach to balance feasibility, convergence and diversity across different stages of the search and (d) an adaptive switch to unconstrained search based on certain search conditions. Numerical experiments are conducted on an extensive range of challenging constrained problems using low evaluation budgets to simulate ECMOPs. The performance of PSCMOEA is benchmarked against five competitive state-of-the-art algorithms, to demonstrate its competitive and consistent performance.
The Influence Maximization (IM) problem is a well-known NP-hard combinatorial problem over graphs whose goal is to find the set of nodes in a network that spreads influence at most. Among the various methods for solving the IM problem, evolutionary algorithms (EAs) have been shown to be particularly effective. While the literature on the topic is particularly ample, only a few attempts have been made at solving the IM problem over higher-order networks, namely extensions of standard graphs that can capture interactions that involve more than two nodes. Hypergraphs are a valuable tool for modeling complex interaction networks in various domains; however, they require rethinking of several graph-based problems, including IM. In this work, we propose a multi-objective EA for the IM problem over hypergraphs that leverages smart initialization and hypergraph-aware mutation. While the existing methods rely on greedy or heuristic methods, to our best knowledge this is the first attempt at applying EAs to this problem. Our results over nine real-world datasets and three propagation models, compared with five baseline algorithms, reveal that our method achieves in most cases state-of-the-art results in terms of hypervolume and solution diversity.
This paper explores the seamless integration of Generative AI (GenAI) and Evolutionary Algorithms (EAs) within the domain of large-scale multi-objective optimization. Focusing on the transformative role of Large Language Models (LLMs), our study investigates the potential of LLM-Assisted Inference to automate and enhance decision-making processes. Specifically, we highlight its effectiveness in illuminating key decision variables in evolutionarily optimized solutions while articulating contextual trade-offs. Tailored to address the challenges inherent in inferring complex multi-objective optimization solutions at scale, our approach emphasizes the adaptive nature of LLMs, allowing them to provide nuanced explanations and align their language with diverse stakeholder expertise levels and domain preferences. Empirical studies underscore the practical applicability and impact of LLM-Assisted Inference in real-world decision-making scenarios.
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its compatibility with realistic membrane proteins, for example, modeled within the Martini coarse-grained (CG) model, as well as with the widely used GROMACS software for molecular simulations. Our objective is to parameterize this ultra-CG model to accurately reproduce the experimentally observed structural and thermodynamic properties of PC membranes in real units, including properties such as area per lipid, area compressibility, bending modulus, line tension, phase transition temperature, density profile, and radial distribution function. In our example, we specifically focus on the properties of a POPC membrane, although the developed membrane model could be perceived as a generic model of lipid membranes. To optimize the performance of the model (the fitness), we conduct a series of evolutionary runs with diverse random initial population sizes (ranging from 96 to 384). We demonstrate that the ultra-CG membrane model we developed exhibits authentic lipid membrane behaviors, encompassing self-assembly into bilayers, vesicle formation, membrane fusion, and gel phase formation. Moreover, we demonstrate compatibility with the Martini coarse-grained model by successfully reproducing the behavior of a transmembrane domain embedded within a lipid bilayer. This facilitates the simulation of realistic membrane proteins within an ultra-CG bilayer membrane, enhancing the accuracy and applicability of our model in biophysical studies.
Evolutionary algorithms excel in solving complex optimization problems, especially those with multiple objectives. However, their stochastic nature can sometimes hinder rapid convergence to the global optima, particularly in scenarios involving constraints. In this study, we employ a large language model (LLM) to enhance evolutionary search for solving constrained multi-objective optimization problems. Our aim is to speed up the convergence of the evolutionary population. To achieve this, we finetune the LLM through tailored prompt engineering, integrating information concerning both objective values and constraint violations of solutions. This process enables the LLM to grasp the relationship between well-performing and poorly performing solutions based on the provided input data. Solution's quality is assessed based on their constraint violations and objective-based performance. By leveraging the refined LLM, it can be used as a search operator to generate superior-quality solutions. Experimental evaluations across various test benchmarks illustrate that LLM-aided evolutionary search can significantly accelerate the population's convergence speed and stands out competitively against cutting-edge evolutionary algorithms.
A common goal in evolutionary multi-objective optimization is to find suitable finite-size approximations of the Pareto front of a given multi-objective optimization problem. While many multi-objective evolutionary algorithms have proven to be very efficient in finding good Pareto front approximations, they may need quite a few resources or may even fail to obtain optimal or nearly approximations. Hereby, optimality is implicitly defined by the chosen performance indicator. In this work, we propose a set-based Newton method for Hausdorff approximations of the Pareto front to be used within multi-objective evolutionary algorithms. To this end, we first generalize the previously proposed Newton step for the performance indicator for the treatment of constrained problems for general reference sets. To approximate the target Pareto front, we propose a particular strategy for generating the reference set that utilizes the data gathered by the evolutionary algorithm during its run. Finally, we show the benefit of the Newton method as a post-processing step on several benchmark test functions and different base evolutionary algorithms.
Evolutionary Algorithms (EA) have been successfully used for the optimization of neural networks for policy search, but they still remain sample inefficient and underperforming in some cases compared to gradient-based reinforcement learning (RL). Various methods combine the two approaches, many of them training a RL algorithm on data from EA evaluations and injecting the RL actor into the EA population. However, when using Evolution Strategies (ES) as the EA, the RL actor can drift genetically far from the the ES distribution and injection can cause a collapse of the ES performance. Here, we highlight the phenomenon of genetic drift where the actor genome and the ES population distribution progressively drift apart, leading to injection having a negative impact on the ES. We introduce Genetic Drift Regularization (GDR), a simple regularization method in the actor training loss that prevents the actor genome from drifting away from the ES. We show that GDR can improve ES convergence on problems where RL learns well, but also helps RL training on other tasks, , fixes the injection issues better than previous controlled injection methods.
Zero-shot optimization involves optimizing a target task that was not seen during training, aiming to provide the optimal solution without or with minimal adjustments to the optimizer. It is crucial to ensure reliable and robust performance in various applications. Current optimizers often struggle with zero-shot optimization and require intricate hyperparameter tuning to adapt to new tasks. To address this, we propose a Pretrained Optimization Model (POM) that leverages knowledge gained from optimizing diverse tasks, offering efficient solutions to zero-shot optimization through direct application or fine-tuning with few-shot samples. Evaluation on the BBOB benchmark and two robot control tasks demonstrates that POM outperforms state-of-the-art black-box optimization methods, especially for high-dimensional tasks. Fine-tuning POM with a small number of samples and budget yields significant performance improvements. Moreover, POM demonstrates robust generalization across diverse task distributions, dimensions, population sizes, and optimization horizons. For code implementation, see https://github.com/ninja-wm/POM/.
Recently, there has been an increasing interest in the application of multiobjective optimization (MOO) in machine learning (ML). This interest is driven by the numerous real-life situations where multiple objectives must be optimized simultaneously. A key aspect of MOO is the existence of a Pareto set, rather than a single optimal solution, which represents the optimal trade-offs between different objectives. Despite its potential, there is a noticeable lack of satisfactory literature serving as an entry-level guide for ML practitioners aiming to apply MOO effectively. In this paper, our goal is to provide such a resource and highlight pitfalls to avoid. We begin by establishing the groundwork for MOO, focusing on well-known approaches such as the weighted sum (WS) method, alongside more advanced techniques like the multiobjective gradient descent algorithm (MGDA). We critically review existing studies across various ML fields where MOO has been applied and identify challenges that can lead to incorrect interpretations. One of these fields is physics informed neural networks (PINNs), which we use as a guiding example to carefully construct experiments illustrating these pitfalls. By comparing WS and MGDA with one of the most common evolutionary algorithms, NSGA-II, we demonstrate that difficulties can arise regardless of the specific MOO method used. We emphasize the importance of understanding the specific problem, the objective space, and the selected MOO method, while also noting that neglecting factors such as convergence criteria can result in misleading experiments.
Computer aided drug design is a promising approach to reduce the tremendous costs, i.e. time and resources, for developing new medicinal drugs. It finds application in aiding the traversal of the vast chemical space of potentially useful compounds. In this paper, we deploy multi-objective evolutionary algorithms, namely NSGA-II, NSGA-III, and MOEA/D, for this purpose. At the same time, we used the SELFIES string representation method. In addition to the QED and SA score, we optimize compounds using the GuacaMol benchmark multi-objective task sets. Our results indicate that all three algorithms show converging behavior and successfully optimize the defined criteria whilst differing mainly in the number of potential solutions found. We observe that novel and promising candidates for synthesis are discovered among obtained compounds in the Pareto-sets.
This research introduces an innovative method for Traffic Sign Recognition (TSR) by leveraging deep learning techniques, with a particular emphasis on Vision Transformers. TSR holds a vital role in advancing driver assistance systems and autonomous vehicles. Traditional TSR approaches, reliant on manual feature extraction, have proven to be labor-intensive and costly. Moreover, methods based on shape and color have inherent limitations, including susceptibility to various factors and changes in lighting conditions. This study explores three variants of Vision Transformers (PVT, TNT, LNL) and six convolutional neural networks (AlexNet, ResNet, VGG16, MobileNet, EfficientNet, GoogleNet) as baseline models. To address the shortcomings of traditional methods, a novel pyramid EATFormer backbone is proposed, amalgamating Evolutionary Algorithms (EAs) with the Transformer architecture. The introduced EA-based Transformer block captures multi-scale, interactive, and individual information through its components: Feed-Forward Network, Global and Local Interaction, and Multi-Scale Region Aggregation modules. Furthermore, a Modulated Deformable MSA module is introduced to dynamically model irregular locations. Experimental evaluations on the GTSRB and BelgiumTS datasets demonstrate the efficacy of the proposed approach in enhancing both prediction speed and accuracy. This study concludes that Vision Transformers hold significant promise in traffic sign classification and contributes a fresh algorithmic framework for TSR. These findings set the stage for the development of precise and dependable TSR algorithms, benefiting driver assistance systems and autonomous vehicles.
Game economy design significantly shapes the player experience and progression speed. Modern game economies are becoming increasingly complex and can be very sensitive to even minor numerical adjustments, which may have an unexpected impact on the overall gaming experience. Consequently, thorough manual testing and fine-tuning during development are essential. Unlike existing works that address algorithmic balancing for specific games or genres, this work adopts a more abstract approach, focusing on game balancing through its economy, detached from a specific game. We propose GEEvo (Game Economy Evolution), a framework to generate graph-based game economies and balancing both, newly generated or existing economies. GEEvo uses a two-step approach where evolutionary algorithms are used to first generate an economy and then balance it based on specified objectives, such as generated resources or damage dealt over time. We define different objectives by differently parameterizing the fitness function using data from multiple simulation runs of the economy. To support this, we define a lightweight and flexible game economy simulation framework. Our method is tested and benchmarked with various balancing objectives on a generated dataset, and we conduct a case study evaluating damage balancing for two fictional economies of two popular game character classes.
As one of the emerging challenges in Automated Machine Learning, the Hardware-aware Neural Architecture Search (HW-NAS) tasks can be treated as black-box multi-objective optimization problems (MOPs). An important application of HW-NAS is real-time semantic segmentation, which plays a pivotal role in autonomous driving scenarios. The HW-NAS for real-time semantic segmentation inherently needs to balance multiple optimization objectives, including model accuracy, inference speed, and hardware-specific considerations. Despite its importance, benchmarks have yet to be developed to frame such a challenging task as multi-objective optimization. To bridge the gap, we introduce a tailored streamline to transform the task of HW-NAS for real-time semantic segmentation into standard MOPs. Building upon the streamline, we present a benchmark test suite, CitySeg/MOP, comprising fifteen MOPs derived from the Cityscapes dataset. The CitySeg/MOP test suite is integrated into the EvoXBench platform to provide seamless interfaces with various programming languages (e.g., Python and MATLAB) for instant fitness evaluations. We comprehensively assessed the CitySeg/MOP test suite on various multi-objective evolutionary algorithms, showcasing its versatility and practicality. Source codes are available at https://github.com/EMI-Group/evoxbench.
This paper presents the second part of the two-part survey series on decomposition-based evolutionary multi-objective optimization where we mainly focus on discussing the literature related to multi-objective evolutionary algorithms based on decomposition (MOEA/D). Complementary to the first part, here we employ a series of advanced data mining approaches to provide a comprehensive anatomy of the enormous landscape of MOEA/D research, which is far beyond the capacity of classic manual literature review protocol. In doing so, we construct a heterogeneous knowledge graph that encapsulates more than 5,400 papers, 10,000 authors, 400 venues, and 1,600 institutions for MOEA/D research. We start our analysis with basic descriptive statistics. Then we delve into prominent research/application topics pertaining to MOEA/D with state-of-the-art topic modeling techniques and interrogate their sptial-temporal and bilateral relationships. We also explored the collaboration and citation networks of MOEA/D, uncovering hidden patterns in the growth of literature as well as collaboration between researchers. Our data mining results here, combined with the expert review in Part I, together offer a holistic view of the MOEA/D research, and demonstrate the potential of an exciting new paradigm for conducting scientific surveys from a data science perspective.
Evolutionary Algorithms and Generative Deep Learning have been two of the most powerful tools for sound generation tasks. However, they have limitations: Evolutionary Algorithms require complicated designs, posing challenges in control and achieving realistic sound generation. Generative Deep Learning models often copy from the dataset and lack creativity. In this paper, we propose LVNS-RAVE, a method to combine Evolutionary Algorithms and Generative Deep Learning to produce realistic and novel sounds. We use the RAVE model as the sound generator and the VGGish model as a novelty evaluator in the Latent Vector Novelty Search (LVNS) algorithm. The reported experiments show that the method can successfully generate diversified, novel audio samples under different mutation setups using different pre-trained RAVE models. The characteristics of the generation process can be easily controlled with the mutation parameters. The proposed algorithm can be a creative tool for sound artists and musicians.
Despite significant progress in the field of mathematical runtime analysis of multi-objective evolutionary algorithms (MOEAs), the performance of MOEAs on discrete many-objective problems is little understood. In particular, the few existing bounds for the SEMO, global SEMO, and SMS-EMOA algorithms on classic benchmarks are all roughly quadratic in the size of the Pareto front. In this work, we prove near-tight runtime guarantees for these three algorithms on the four most common benchmark problems OneMinMax, CountingOnesCountingZeros, LeadingOnesTrailingZeros, and OneJumpZeroJump, and this for arbitrary numbers of objectives. Our bounds depend only linearly on the Pareto front size, showing that these MOEAs on these benchmarks cope much better with many objectives than what previous works suggested. Our bounds are tight apart from small polynomial factors in the number of objectives and length of bitstrings. This is the first time that such tight bounds are proven for many-objective uses of these MOEAs. While it is known that such results cannot hold for the NSGA-II, we do show that our bounds, via a recent structural result, transfer to the NSGA-III algorithm.
The one-fifth rule and its generalizations are a classical parameter control mechanism in discrete domains. They have also been transferred to control the offspring population size of the $(1, \lambda)$-EA. This has been shown to work very well for hill-climbing, and combined with a restart mechanism it was recently shown by Hevia Fajardo and Sudholt to improve performance on the multi-modal problem Cliff drastically. In this work we show that the positive results do not extend to other types of local optima. On the distorted OneMax benchmark, the self-adjusting $(1, \lambda)$-EA is slowed down just as elitist algorithms because self-adaptation prevents the algorithm from escaping from local optima. This makes the self-adaptive algorithm considerably worse than good static parameter choices, which do allow to escape from local optima efficiently. We show this theoretically and complement the result with empirical runtime results.