Tome Eftimov

Gjorgjina Cenikj, Jakub Kudela, Eva Tuba et al.

Algorithm Selection (AS) aims to automatically identify the most suitable optimization algorithm for a given problem instance by leveraging measurable problem characteristics and historical performance data. In this study, we investigate the generalization ability of AS models across both synthetic and real-world optimization landscapes. We consider two widely used academic benchmark suites (BBOB and CEC) and two real-world problem sets (robotics trajectory optimization tasks and unmanned aerial vehicle path-planning problems). Through a systematic cross-benchmark evaluation, we analyze how AS models transfer between domains, identify where generalization succeeds or breaks down, and highlight the challenges that arise when applying AS in realistic, domain-specific contexts. Our findings provide insights into the robustness of current AS approaches and inform the development of more reliable, broadly applicable AS systems for real-world optimization.

Denica Kjorvezir, Marko Djukanović, Ana Gjorgjevikj et al.

Evaluating large language models (LLMs) across comprehensive benchmarks is expensive and time-consuming. We propose a graph-based prompt selection framework that models each benchmark as a similarity graph -- nodes are prompts connected if their embedding-space distance falls above a configurable threshold -- and applies Maximum Independent Set (MIS) algorithms to select a maximally diverse, non-redundant subset. We evaluate four MIS solvers (CPLEX, GREEDY, Online-MIS, ReduMIS) across six embedding models, three distance measures, six percentile thresholds, and four benchmarks (GPQA, IFEval, MMLU-Pro, Omni-MATH) covering 66 LLMs. Our central hypothesis -- that repeated selection under different random seeds yields consistent LLM rankings that may also differ from the full-benchmark baseline -- is strongly confirmed: Kendall's $W \geq 0.90$ in 99.2\% of stochastic configurations (mean $W = 0.997 \pm 0.008$), while at higher percentile thresholds selected subsets achieve 25--48\% prompt reduction on average. Ranking divergence from the full benchmark ($ρ< 0.95$) occurs in only 15.95\% of configurations, concentrated at low thresholds ($p_{10}$--$p_{20}$) and benchmarks (GPQA, IFEval), identifying overly dense graphs as the primary failure mode.

Ana Kostovska, Diederick Vermetten, Sašo Džeroski et al.

Selecting the most suitable algorithm and determining its hyperparameters for a given optimization problem is a challenging task. Accurately predicting how well a certain algorithm could solve the problem is hence desirable. Recent studies in single-objective numerical optimization show that supervised machine learning methods can predict algorithm performance using landscape features extracted from the problem instances. Existing approaches typically treat the algorithms as black-boxes, without consideration of their characteristics. To investigate in this work if a selection of landscape features that depends on algorithms properties could further improve regression accuracy, we regard the modular CMA-ES framework and estimate how much each landscape feature contributes to the best algorithm performance regression models. Exploratory data analysis performed on this data indicate that the set of most relevant features does not depend on the configuration of individual modules, but the influence that these features have on regression accuracy does. In addition, we have shown that by using classifiers that take the features relevance on the model accuracy, we are able to predict the status of individual modules in the CMA-ES configurations.

Ana Kostovska, Diederick Vermetten, Carola Doerr et al.

Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates the identification of relevant datasets, their interpretation, and their interoperability. Therefore, a semantically rich, ontology-based, machine-readable data model that can be used by different platforms is highly desirable. In this paper, we report on the development of such an ontology, which we call OPTION (OPTImization algorithm benchmarking ONtology). Our ontology provides the vocabulary needed for semantic annotation of the core entities involved in the benchmarking process, such as algorithms, problems, and evaluation measures. It also provides means for automatic data integration, improved interoperability, and powerful querying capabilities, thereby increasing the value of the benchmarking data. We demonstrate the utility of OPTION, by annotating and querying a corpus of benchmark performance data from the BBOB collection of the COCO framework and from the Yet Another Black-Box Optimization Benchmark (YABBOB) family of the Nevergrad environment. In addition, we integrate features of the BBOB functional performance landscape into the OPTION knowledge base using publicly available datasets with exploratory landscape analysis. Finally, we integrate the OPTION knowledge base into the IOHprofiler environment and provide users with the ability to perform meta-analysis of performance data.

Ana Kostovska, Diederick Vermetten, Sašo Džeroski et al.

Empirical data plays an important role in evolutionary computation research. To make better use of the available data, ontologies have been proposed in the literature to organize their storage in a structured way. However, the full potential of these formal methods to capture our domain knowledge has yet to be demonstrated. In this work, we evaluate a performance prediction model built on top of the extension of the recently proposed OPTION ontology. More specifically, we first extend the OPTION ontology with the vocabulary needed to represent modular black-box optimization algorithms. Then, we use the extended OPTION ontology, to create knowledge graphs with fixed-budget performance data for two modular algorithm frameworks, modCMA, and modDE, for the 24 noiseless BBOB benchmark functions. We build the performance prediction model using a knowledge graph embedding-based methodology. Using a number of different evaluation scenarios, we show that a triple classification approach, a fairly standard predictive modeling task in the context of knowledge graphs, can correctly predict whether a given algorithm instance will be able to achieve a certain target precision for a given problem instance. This approach requires feature representation of algorithms and problems. While the latter is already well developed, we hope that our work will motivate the community to collaborate on appropriate algorithm representations.

Ana Gjorgjevikj, Barbara Koroušić Seljak, Tome Eftimov

Large-scale multilingual text embedding models play crucial role in both research and industry, yet their behavior in language-specific, multi-task settings remains insufficiently understood. Although benchmarking platforms such as MTEB report results across more than 250 languages, conclusions about model superiority often depend on implicit choices of dataset compositions and performance aggregation methods. To address this gap, we present a meta-study of multilingual model performance robustness in MTEB, applying a diverse set of multi-criteria decision-making ranking schemes and introducing two robustness indicators: dataset-composition robustness (sensitivity of rankings to changing dataset compositions) and ranking-scheme robustness (sensitivity to aggregation method change). They enable systematic sensitivity analysis of whether benchmarking conclusions remain stable under different evaluation designs. We conduct an in-depth analysis on five languages (English, French, German, Hindi, and Spanish) across nine tasks (e.g., classification, clustering, retrieval) and release results for approximately 230 additional languages. The task-specific analyses show that large-scale LLM-based models are often robust top performers, though not uniformly (e.g., in retrieval task), while task-agnostic results reveal that only a small subset of models remains consistently strong across tasks, ranking schemes, and data subsamples.

Risto Trajanov, Stefan Dimeski, Martin Popovski et al.

Predicting the performance of an optimization algorithm on a new problem instance is crucial in order to select the most appropriate algorithm for solving that problem instance. For this purpose, recent studies learn a supervised machine learning (ML) model using a set of problem landscape features linked to the performance achieved by the optimization algorithm. However, these models are black-box with the only goal of achieving good predictive performance, without providing explanations which landscape features contribute the most to the prediction of the performance achieved by the optimization algorithm. In this study, we investigate the expressiveness of problem landscape features utilized by different supervised ML models in automated algorithm performance prediction. The experimental results point out that the selection of the supervised ML method is crucial, since different supervised ML regression models utilize the problem landscape features differently and there is no common pattern with regard to which landscape features are the most informative.

Gjorgjina Cenikj, Gašper Petelin, Carola Doerr et al.

The application of machine learning (ML) models to the analysis of optimization algorithms requires the representation of optimization problems using numerical features. These features can be used as input for ML models that are trained to select or to configure a suitable algorithm for the problem at hand. Since in pure black-box optimization information about the problem instance can only be obtained through function evaluation, a common approach is to dedicate some function evaluations for feature extraction, e.g., using random sampling. This approach has two key downsides: (1) It reduces the budget left for the actual optimization phase, and (2) it neglects valuable information that could be obtained from a problem-solver interaction. In this paper, we propose a feature extraction method that describes the trajectories of optimization algorithms using simple descriptive statistics. We evaluate the generated features for the task of classifying problem classes from the Black Box Optimization Benchmarking (BBOB) suite. We demonstrate that the proposed DynamoRep features capture enough information to identify the problem class on which the optimization algorithm is running, achieving a mean classification accuracy of 95% across all experiments.

Ana Kostovska, Carola Doerr, Sašo Džeroski et al.

Multi-label classification (MLC) is an ML task of predictive modeling in which a data instance can simultaneously belong to multiple classes. MLC is increasingly gaining interest in different application domains such as text mining, computer vision, and bioinformatics. Several MLC algorithms have been proposed in the literature, resulting in a meta-optimization problem that the user needs to address: which MLC approach to select for a given dataset? To address this algorithm selection problem, we investigate in this work the quality of an automated approach that uses characteristics of the datasets - so-called features - and a trained algorithm selector to choose which algorithm to apply for a given task. For our empirical evaluation, we use a portfolio of 38 datasets. We consider eight MLC algorithms, whose quality we evaluate using six different performance metrics. We show that our automated algorithm selector outperforms any of the single MLC algorithms, and this is for all evaluated performance measures. Our selection approach is explainable, a characteristic that we exploit to investigate which meta-features have the largest influence on the decisions made by the algorithm selector. Finally, we also quantify the importance of the most significant meta-features for various domains.

Carolin Benjamins, Gjorgjina Cenikj, Ana Nikolikj et al.

Dynamic Algorithm Configuration (DAC) addresses the challenge of dynamically setting hyperparameters of an algorithm for a diverse set of instances rather than focusing solely on individual tasks. Agents trained with Deep Reinforcement Learning (RL) offer a pathway to solve such settings. However, the limited generalization performance of these agents has significantly hindered the application in DAC. Our hypothesis is that a potential bias in the training instances limits generalization capabilities. We take a step towards mitigating this by selecting a representative subset of training instances to overcome overrepresentation and then retraining the agent on this subset to improve its generalization performance. For constructing the meta-features for the subset selection, we particularly account for the dynamic nature of the RL agent by computing time series features on trajectories of actions and rewards generated by the agent's interaction with the environment. Through empirical evaluations on the Sigmoid and CMA-ES benchmarks from the standard benchmark library for DAC, called DACBench, we discuss the potentials of our selection technique compared to training on the entire instance set. Our results highlight the efficacy of instance selection in refining DAC policies for diverse instance spaces.

Sara Gjorgjieva, Eva Tuba, Barbara Koroušić Seljak et al.

Landscape feature representations play a central role in automated algorithm selection and meta-learning for black-box optimization, yet little is known about how different representations agree (or disagree) in the structures they impose on problem spaces. This paper presents a systematic unsupervised evaluation of four state-of-the-art representations (ELA, DeepELA, TransOptAS, and DoE2Vec) using a diverse set of affine combinations of BBOB functions (MA-BBOB). By applying extensive clustering analyses, coverage-based stability measures, and cross-representation similarity assessments, we show that each representation organizes the same problems in markedly different ways: ELA and TransOptAS form compact geometric structures, DeepELA provides a balanced intermediate view, and DoE2Vec achieves strong semantic alignment but with substantial fragmentation. Our results reveal that no single representation dominates; rather, they capture complementary aspects of the underlying landscapes. These findings highlight the importance of multi-view analyses for understanding representation behavior and offer guidance on selecting or combining representations in downstream meta-learning and algorithm selection tasks. In addition, across two different algorithm families (Differential Evolution and Particle Swarm Optimization), we show that landscape representations face an inherent trade-off in how well they align structural landscape descriptions with observed performance, indicating that no single representation can fully capture algorithm performance.

Sara Gjorgjieva, Eva Tuba, Tome Eftimov

In large-scale benchmarking of stochastic optimization algorithms, the key challenge is no longer whether repeated runs are needed for reliability, but how to determine when sufficient evidence has been collected without incurring unnecessary computational cost. We study a learning-based extension of a recent empirical online heuristic that adaptively estimates the required number of runs using outlier handling and skewness-based symmetry checks. Using annotated outcomes from 132{,}000 Nevergrad runs on COCO (24 problems in 20 dimensions, 10 instances each, 11 optimizers), we train classifiers on 23 statistical, energy-free, and shape and stability features to predict whether a run-number estimate is reliable, prioritizing detection of incorrect estimates via minority-class recall. We evaluate reliability prediction using a within-configuration learning setup, where models are trained and tested on data sharing the same optimizer. The results show that run-number reliability can be learned in a within-configuration scenario, enabling detection of unreliable estimates with high minority-class recall, although performance remains limited by the restricted data diversity within fixed configurations.

Christian L. Camacho-Villalón, Ana Nikolikj, Katharina Dost et al.

The PSO-X framework incorporates dozens of modules that have been proposed for solving single-objective continuous optimization problems using particle swarm optimization. While modular frameworks enable users to automatically generate and configure algorithms tailored to specific optimization problems, the complexity of this process increases with the number of modules in the framework and the degrees of freedom defined for their interaction. Understanding how modules affect the performance of algorithms for different problems is critical to making the process of finding effective implementations more efficient and identifying promising areas for further investigation. Despite their practical applications and scientific relevance, there is a lack of empirical studies investigating which modules matter most in modular optimization frameworks and how they interact. In this paper, we analyze the performance of 1424 particle swarm optimization algorithms instantiated from the PSO-X framework on the 25 functions in the CEC'05 benchmark suite with 10 and 30 dimensions. We use functional ANOVA to quantify the impact of modules and their combinations on performance in different problem classes. In practice, this allows us to identify which modules have greater influence on PSO-X performance depending on problem features such as multimodality, mathematical transformations and varying dimensionality. We then perform a cluster analysis to identify groups of problem classes that share similar module effect patterns. Our results show low variability in the importance of modules in all problem classes, suggesting that particle swarm optimization performance is driven by a few influential modules.

Ana Nikolikj, Carola Doerr, Tome Eftimov

Per-instance automated algorithm configuration and selection are gaining significant moments in evolutionary computation in recent years. Two crucial, sometimes implicit, ingredients for these automated machine learning (AutoML) methods are 1) feature-based representations of the problem instances and 2) performance prediction methods that take the features as input to estimate how well a specific algorithm instance will perform on a given problem instance. Non-surprisingly, common machine learning models fail to make predictions for instances whose feature-based representation is underrepresented or not covered in the training data, resulting in poor generalization ability of the models for problems not seen during training.In this work, we study leave-one-problem-out (LOPO) performance prediction. We analyze whether standard random forest (RF) model predictions can be improved by calibrating them with a weighted average of performance values obtained by the algorithm on problem instances that are sufficiently close to the problem for which a performance prediction is sought, measured by cosine similarity in feature space. While our RF+clust approach obtains more accurate performance prediction for several problems, its predictive power crucially depends on the chosen similarity threshold as well as on the feature portfolio for which the cosine similarity is measured, thereby opening a new angle for feature selection in a zero-shot learning setting, as LOPO is termed in machine learning.

Gjorgjina Cenikj, Gašper Petelin, Tome Eftimov

We propose a representation of optimization problem instances using a transformer-based neural network architecture trained for the task of problem classification of the 24 problem classes from the Black-box Optimization Benchmarking (BBOB) benchmark. We show that transformer-based methods can be trained to recognize problem classes with accuracies in the range of 70\%-80\% for different problem dimensions, suggesting the possible application of transformer architectures in acquiring representations for black-box optimization problems.

Ana Kostovska, Gjorgjina Cenikj, Diederick Vermetten et al.

The performance of automated algorithm selection (AAS) strongly depends on the portfolio of algorithms to choose from. Selecting the portfolio is a non-trivial task that requires balancing the trade-off between the higher flexibility of large portfolios with the increased complexity of the AAS task. In practice, probably the most common way to choose the algorithms for the portfolio is a greedy selection of the algorithms that perform well in some reference tasks of interest. We set out in this work to investigate alternative, data-driven portfolio selection techniques. Our proposed method creates algorithm behavior meta-representations, constructs a graph from a set of algorithms based on their meta-representation similarity, and applies a graph algorithm to select a final portfolio of diverse, representative, and non-redundant algorithms. We evaluate two distinct meta-representation techniques (SHAP and performance2vec) for selecting complementary portfolios from a total of 324 different variants of CMA-ES for the task of optimizing the BBOB single-objective problems in dimensionalities 5 and 30 with different cut-off budgets. We test two types of portfolios: one related to overall algorithm behavior and the `personalized' one (related to algorithm behavior per each problem separately). We observe that the approach built on the performance2vec-based representations favors small portfolios with negligible error in the AAS task relative to the virtual best solver from the selected portfolio, whereas the portfolios built from the SHAP-based representations gain from higher flexibility at the cost of decreased performance of the AAS. Across most considered scenarios, personalized portfolios yield comparable or slightly better performance than the classical greedy approach. They outperform the full portfolio in all scenarios.

Gordana Ispirova, Tome Eftimov, Barbara Koroušić Seljak

Although recipe data are very easy to come by nowadays, it is really hard to find a complete recipe dataset - with a list of ingredients, nutrient values per ingredient, and per recipe, allergens, etc. Recipe datasets are usually collected from social media websites where users post and publish recipes. Usually written with little to no structure, using both standardized and non-standardized units of measurement. We collect six different recipe datasets, publicly available, in different formats, and some including data in different languages. Bringing all of these datasets to the needed format for applying a machine learning (ML) pipeline for nutrient prediction [1], [2], includes data normalization using dictionary-based named entity recognition (NER), rule-based NER, as well as conversions using external domain-specific resources. From the list of ingredients, domain-specific embeddings are created using the same embedding space for all recipes - one ingredient dataset is generated. The result from this normalization process is two corpora - one with predefined ingredient embeddings and one with predefined recipe embeddings. On all six recipe datasets, the ML pipeline is evaluated. The results from this use case also confirm that the embeddings merged using the domain heuristic yield better results than the baselines.

Jan Drole, Ana Gjorgjevikj, Barbara Korouši'c Seljak et al.

Standardizing food terms from product labels and menus into ontology concepts is a prerequisite for trustworthy dietary assessment and safety reporting. The dominant approach to Named Entity Linking (NEL) in the food and nutrition domains fine-tunes Large Language Models (LLMs) on task-specific corpora. Although effective, fine-tuning incurs substantial computational cost, ties models to a particular ontology snapshot (i.e., version), and degrades under ontology drift. This paper presents FoodOntoRAG, a model- and ontology-agnostic pipeline that performs few-shot NEL by retrieving candidate entities from domain ontologies and conditioning an LLM on structured evidence (food labels, synonyms, definitions, and relations). A hybrid lexical--semantic retriever enumerates candidates; a selector agent chooses a best match with rationale; a separate scorer agent calibrates confidence; and, when confidence falls below a threshold, a synonym generator agent proposes reformulations to re-enter the loop. The pipeline approaches state-of-the-art accuracy while revealing gaps and inconsistencies in existing annotations. The design avoids fine-tuning, improves robustness to ontology evolution, and yields interpretable decisions through grounded justifications.

Maks Požarnik Vavken, Matevž Ogrinc, Tome Eftimov et al.

In this article, we evaluate four Large Language Models (LLMs) and their effectiveness at retrieving data within a specialized Retrieval-Augmented Generation (RAG) system, using a comprehensive food composition database. Our method is focused on the LLMs ability to translate natural language queries into structured metadata filters, enabling efficient retrieval via a Chroma vector database. By achieving high accuracy in this critical retrieval step, we demonstrate that LLMs can serve as an accessible, high-performance tool, drastically reducing the manual effort and technical expertise previously required for domain experts, such as food compilers and nutritionists, to leverage complex food and nutrition data. However, despite the high performance on easy and moderately complex queries, our analysis of difficult questions reveals that reliable retrieval remains challenging when queries involve non-expressible constraints. These findings demonstrate that LLM-driven metadata filtering excels when constraints can be explicitly expressed, but struggles when queries exceed the representational scope of the metadata format.

Denica Kjorvezir, Danilo Najkov, Eva Valencič et al.

This research focuses on developing advanced methods for assessing similarity between recipes by combining different sources of information and analytical approaches. We explore the semantic, lexical, and domain similarity of food recipes, evaluated through the analysis of ingredients, preparation methods, and nutritional attributes. A web-based interface was developed to allow domain experts to validate the combined similarity results. After evaluating 318 recipe pairs, experts agreed on 255 (80%). The evaluation of expert assessments enables the estimation of which similarity aspects--lexical, semantic, or nutritional--are most influential in expert decision-making. The application of these methods has broad implications in the food industry and supports the development of personalized diets, nutrition recommendations, and automated recipe generation systems.

Ana Gjorgjevikj, Matej Martinc, Gjorgjina Cenikj et al.

This paper introduces FoodSEM, a state-of-the-art fine-tuned open-source large language model (LLM) for named-entity linking (NEL) to food-related ontologies. To the best of our knowledge, food NEL is a task that cannot be accurately solved by state-of-the-art general-purpose (large) language models or custom domain-specific models/systems. Through an instruction-response (IR) scenario, FoodSEM links food-related entities mentioned in a text to several ontologies, including FoodOn, SNOMED-CT, and the Hansard taxonomy. The FoodSEM model achieves state-of-the-art performance compared to related models/systems, with F1 scores even reaching 98% on some ontologies and datasets. The presented comparative analyses against zero-shot, one-shot, and few-shot LLM prompting baselines further highlight FoodSEM's superior performance over its non-fine-tuned version. By making FoodSEM and its related resources publicly available, the main contributions of this article include (1) publishing a food-annotated corpora into an IR format suitable for LLM fine-tuning/evaluation, (2) publishing a robust model to advance the semantic understanding of text in the food domain, and (3) providing a strong baseline on food NEL for future benchmarking.

Gjorgjina Cenikj, Gašper Petelin, Moritz Seiler et al.

%% Text of abstract The process of identifying the most suitable optimization algorithm for a specific problem, referred to as algorithm selection (AS), entails training models that leverage problem landscape features to forecast algorithm performance. A significant challenge in this domain is ensuring that AS models can generalize effectively to novel, unseen problems. This study evaluates the generalizability of AS models based on different problem representations in the context of single-objective continuous optimization. In particular, it considers the most widely used Exploratory Landscape Analysis features, as well as recently proposed Topological Landscape Analysis features, and features based on deep learning, such as DeepELA, TransOptAS and Doe2Vec. Our results indicate that when presented with out-of-distribution evaluation data, none of the feature-based AS models outperform a simple baseline model, i.e., a Single Best Solver.

Ana Nikolikj, Ana Kostovska, Gjorgjina Cenikj et al.

This study examines the generalization ability of algorithm performance prediction models across various benchmark suites. Comparing the statistical similarity between the problem collections with the accuracy of performance prediction models that are based on exploratory landscape analysis features, we observe that there is a positive correlation between these two measures. Specifically, when the high-dimensional feature value distributions between training and testing suites lack statistical significance, the model tends to generalize well, in the sense that the testing errors are in the same range as the training errors. Two experiments validate these findings: one involving the standard benchmark suites, the BBOB and CEC collections, and another using five collections of affine combinations of BBOB problem instances.

Marko Djukanović, Jaume Reixach, Ana Nikolikj et al.

This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for identifying similarities and discovering mutual patterns and important motifs among DNA, RNA, and protein sequences. Building on recent advancements in solving this problem through a general search framework, this paper introduces two novel heuristic approaches designed to enhance the search process by steering it towards promising regions in the search space. The first heuristic employs a probabilistic model to evaluate partial solutions during the search process. The second heuristic is based on a neural network model trained offline using a genetic algorithm. A key aspect of this approach is extracting problem-specific features of partial solutions and the complete problem instance. An effective hybrid method, referred to as the learning beam search, is developed by combining the trained neural network model with a beam search framework. An important contribution of this paper is found in the generation of real-world instances where scientific abstracts serve as input strings, and a set of frequently occurring academic words from the literature are used as restricted patterns. Comprehensive experimental evaluations demonstrate the effectiveness of the proposed approaches in solving the RLCS problem. Finally, an empirical explainability analysis is applied to the obtained results. In this way, key feature combinations and their respective contributions to the success or failure of the algorithms across different problem types are identified.

Ana Nikolikj, Gabriela Ochoa, Tome Eftimov

We present an analysis of landscape features for predicting the performance of multi-objective combinatorial optimization algorithms. We consider features from the recently proposed compressed Pareto Local Optimal Solutions Networks (C-PLOS-net) model of combinatorial landscapes. The benchmark instances are a set of rmnk-landscapes with 2 and 3 objectives and various levels of ruggedness and objective correlation. We consider the performance of three algorithms -- Pareto Local Search (PLS), Global Simple EMO Optimizer (GSEMO), and Non-dominated Sorting Genetic Algorithm (NSGA-II) - using the resolution and hypervolume metrics. Our tailored analysis reveals feature combinations that influence algorithm performance specific to certain landscapes. This study provides deeper insights into feature importance, tailored to specific rmnk-landscapes and algorithms.

Gjorgjina Cenikj, Gašper Petelin, Tome Eftimov

Understanding the behavior of numerical metaheuristic optimization algorithms is critical for advancing their development and application. Traditional visualization techniques, such as convergence plots, trajectory mapping, and fitness landscape analysis, often fall short in illustrating the structural dynamics of the search process, especially in high-dimensional or complex solution spaces. To address this, we propose a novel representation and visualization methodology that clusters solution candidates explored by the algorithm and tracks the evolution of cluster memberships across iterations, offering a dynamic and interpretable view of the search process. Additionally, we introduce two metrics - algorithm stability and algorithm similarity- to quantify the consistency of search trajectories across runs of an individual algorithm and the similarity between different algorithms, respectively. We apply this methodology to a set of ten numerical metaheuristic algorithms, revealing insights into their stability and comparative behaviors, thereby providing a deeper understanding of their search dynamics.

Ana Nikolikj, Mario Andrés Muñoz, Eva Tuba et al.

This paper leverages the recently introduced concept of algorithm footprints to investigate the interplay between algorithm configurations and problem characteristics. Performance footprints are calculated for six modular variants of the CMA-ES algorithm (modCMA), evaluated on 24 benchmark problems from the BBOB suite, across two-dimensional settings: 5-dimensional and 30-dimensional. These footprints provide insights into why different configurations of the same algorithm exhibit varying performance and identify the problem features influencing these outcomes. Our analysis uncovers shared behavioral patterns across configurations due to common interactions with problem properties, as well as distinct behaviors on the same problem driven by differing problem features. The results demonstrate the effectiveness of algorithm footprints in enhancing interpretability and guiding configuration choices.

Gjorgjina Cenikj, Gašper Petelin, Tome Eftimov

The field of numerical optimization has recently seen a surge in the development of "novel" metaheuristic algorithms, inspired by metaphors derived from natural or human-made processes, which have been widely criticized for obscuring meaningful innovations and failing to distinguish themselves from existing approaches. Aiming to address these concerns, we investigate the applicability of statistical tests for comparing algorithms based on their search behavior. We utilize the cross-match statistical test to compare multivariate distributions and assess the solutions produced by 114 algorithms from the MEALPY library. These findings are incorporated into an empirical analysis aiming to identify algorithms with similar search behaviors.

Ana Kostovska, Carola Doerr, Sašo Džeroski et al.

Automated algorithm performance prediction in numerical blackbox optimization often relies on problem characterizations, such as exploratory landscape analysis features. These features are typically used as inputs to machine learning models and are represented in a tabular format. However, such approaches often overlook algorithm configurations, a key factor influencing performance. The relationships between algorithm operators, parameters, problem characteristics, and performance outcomes form a complex structure best represented as a graph. This work explores the use of heterogeneous graph data structures and graph neural networks to predict the performance of optimization algorithms by capturing the complex dependencies between problems, algorithm configurations, and performance outcomes. We focus on two modular frameworks, modCMA-ES and modDE, which decompose two widely used derivative-free optimization algorithms: the covariance matrix adaptation evolution strategy (CMA-ES) and differential evolution (DE). We evaluate 324 modCMA-ES and 576 modDE variants on 24 BBOB problems across six runtime budgets and two problem dimensions. Achieving up to 36.6% improvement in MSE over traditional tabular-based methods, this work highlights the potential of geometric learning in black-box optimization.

Gjorgjina Cenikj, Ana Nikolikj, Gašper Petelin et al.

The selection of the most appropriate algorithm to solve a given problem instance, known as algorithm selection, is driven by the potential to capitalize on the complementary performance of different algorithms across sets of problem instances. However, determining the optimal algorithm for an unseen problem instance has been shown to be a challenging task, which has garnered significant attention from researchers in recent years. In this survey, we conduct an overview of the key contributions to algorithm selection in the field of single-objective continuous black-box optimization. We present ongoing work in representation learning of meta-features for optimization problem instances, algorithm instances, and their interactions. We also study machine learning models for automated algorithm selection, configuration, and performance prediction. Through this analysis, we identify gaps in the state of the art, based on which we present ideas for further development of meta-feature representations.

Ana Nikolikj, Gjorgjina Cenikj, Gordana Ispirova et al.

A key component of automated algorithm selection and configuration, which in most cases are performed using supervised machine learning (ML) methods is a good-performing predictive model. The predictive model uses the feature representation of a set of problem instances as input data and predicts the algorithm performance achieved on them. Common machine learning models struggle to make predictions for instances with feature representations not covered by the training data, resulting in poor generalization to unseen problems. In this study, we propose a workflow to estimate the generalizability of a predictive model for algorithm performance, trained on one benchmark suite to another. The workflow has been tested by training predictive models across benchmark suites and the results show that generalizability patterns in the landscape feature space are reflected in the performance space.

Ana Nikolikj, Michal Pluháček, Carola Doerr et al.

Leave-one-problem-out (LOPO) performance prediction requires machine learning (ML) models to extrapolate algorithms' performance from a set of training problems to a previously unseen problem. LOPO is a very challenging task even for state-of-the-art approaches. Models that work well in the easier leave-one-instance-out scenario often fail to generalize well to the LOPO setting. To address the LOPO problem, recent work suggested enriching standard random forest (RF) performance regression models with a weighted average of algorithms' performance on training problems that are considered similar to a test problem. More precisely, in this RF+clust approach, the weights are chosen proportionally to the distances of the problems in some feature space. Here in this work, we extend the RF+clust approach by adjusting the distance-based weights with the importance of the features for performance regression. That is, instead of considering cosine distance in the feature space, we consider a weighted distance measure, with weights depending on the relevance of the feature for the regression model. Our empirical evaluation of the modified RF+clust approach on the CEC 2014 benchmark suite confirms its advantages over the naive distance measure. However, we also observe room for improvement, in particular with respect to more expressive feature portfolios.

Risto Trajanov, Stefan Dimeski, Martin Popovski et al.

Efficient solving of an unseen optimization problem is related to appropriate selection of an optimization algorithm and its hyper-parameters. For this purpose, automated algorithm performance prediction should be performed that in most commonly-applied practices involves training a supervised ML algorithm using a set of problem landscape features. However, the main issue of training such models is their limited explainability since they only provide information about the joint impact of the set of landscape features to the end prediction results. In this study, we are investigating explainable landscape-aware regression models where the contribution of each landscape feature to the prediction of the optimization algorithm performance is estimated on a global and local level. The global level provides information about the impact of the feature across all benchmark problems' instances, while the local level provides information about the impact on a specific problem instance. The experimental results are obtained using the COCO benchmark problems and three differently configured modular CMA-ESs. The results show a proof of concept that different set of features are important for different problem instances, which indicates that further personalization of the landscape space is required when training an automated algorithm performance prediction model.

Gjorgjina Cenikj, Barbara Koroušić Seljak, Tome Eftimov

In this paper, we present FoodChem, a new Relation Extraction (RE) model for identifying chemicals present in the composition of food entities, based on textual information provided in biomedical peer-reviewed scientific literature. The RE task is treated as a binary classification problem, aimed at identifying whether the contains relation exists between a food-chemical entity pair. This is accomplished by fine-tuning BERT, BioBERT and RoBERTa transformer models. For evaluation purposes, a novel dataset with annotated contains relations in food-chemical entity pairs is generated, in a golden and silver version. The models are integrated into a voting scheme in order to produce the silver version of the dataset which we use for augmenting the individual models, while the manually annotated golden version is used for their evaluation. Out of the three evaluated models, the BioBERT model achieves the best results, with a macro averaged F1 score of 0.902 in the unbalanced augmentation setting.

Urban Škvorc, Tome Eftimov, Peter Korošec

When designing a benchmark problem set, it is important to create a set of benchmark problems that are a good generalization of the set of all possible problems. One possible way of easing this difficult task is by using artificially generated problems. In this paper, one such single-objective continuous problem generation approach is analyzed and compared with the COCO benchmark problem set, a well know problem set for benchmarking numerical optimization algorithms. Using Exploratory Landscape Analysis and Singular Value Decomposition, we show that such representations allow us to further explore the relations between the problems by applying visualization and correlation analysis techniques, with the goal of decreasing the bias in benchmark problem assessment.

Ana Kostovska, Diederick Vermetten, Carola Doerr et al.

Many platforms for benchmarking optimization algorithms offer users the possibility of sharing their experimental data with the purpose of promoting reproducible and reusable research. However, different platforms use different data models and formats, which drastically inhibits identification of relevant data sets, their interpretation, and their interoperability. Consequently, a semantically rich, ontology-based, machine-readable data model is highly desired. We report in this paper on the development of such an ontology, which we name OPTION (OPTImization algorithm benchmarking ONtology). Our ontology provides the vocabulary needed for semantic annotation of the core entities involved in the benchmarking process, such as algorithms, problems, and evaluation measures. It also provides means for automated data integration, improved interoperability, powerful querying capabilities and reasoning, thereby enriching the value of the benchmark data. We demonstrate the utility of OPTION by annotating and querying a corpus of benchmark performance data from the BBOB workshop data - a use case which can be easily extended to cover other benchmarking data collections.

Tome Eftimov, Anja Jankovic, Gorjan Popovski et al.

Accurately predicting the performance of different optimization algorithms for previously unseen problem instances is crucial for high-performing algorithm selection and configuration techniques. In the context of numerical optimization, supervised regression approaches built on top of exploratory landscape analysis are becoming very popular. From the point of view of Machine Learning (ML), however, the approaches are often rather naive, using default regression or classification techniques without proper investigation of the suitability of the ML tools. With this work, we bring to the attention of our community the possibility to personalize regression models to specific types of optimization problems. Instead of aiming for a single model that works well across a whole set of possibly diverse problems, our personalized regression approach acknowledges that different models may suite different types of problems. Going one step further, we also investigate the impact of selecting not a single regression model per problem, but personalized ensembles. We test our approach on predicting the performance of numerical optimization heuristics on the BBOB benchmark collection.

Anja Jankovic, Gorjan Popovski, Tome Eftimov et al.

Automated algorithm selection and configuration methods that build on exploratory landscape analysis (ELA) are becoming very popular in Evolutionary Computation. However, despite a significantly growing number of applications, the underlying machine learning models are often chosen in an ad-hoc manner. We show in this work that three classical regression methods are able to achieve meaningful results for ELA-based algorithm selection. For those three models -- random forests, decision trees, and bagging decision trees -- the quality of the regression models is highly impacted by the chosen hyper-parameters. This has significant effects also on the quality of the algorithm selectors that are built on top of these regressions. By comparing a total number of 30 different models, each coupled with 2 complementary regression strategies, we derive guidelines for the tuning of the regression models and provide general recommendations for a more systematic use of classical machine learning models in landscape-aware algorithm selection. We point out that a choice of the machine learning model merits to be carefully undertaken and further investigated.

Anja Jankovic, Tome Eftimov, Carola Doerr

Black-box optimization is a very active area of research, with many new algorithms being developed every year. This variety is needed, on the one hand, since different algorithms are most suitable for different types of optimization problems. But the variety also poses a meta-problem: which algorithm to choose for a given problem at hand? Past research has shown that per-instance algorithm selection based on exploratory landscape analysis (ELA) can be an efficient mean to tackle this meta-problem. Existing approaches, however, require the approximation of problem features based on a significant number of samples, which are typically selected through uniform sampling or Latin Hypercube Designs. The evaluation of these points is costly, and the benefit of an ELA-based algorithm selection over a default algorithm must therefore be significant in order to pay off. One could hope to by-pass the evaluations for the feature approximations by using the samples that a default algorithm would anyway perform, i.e., by using the points of the default algorithm's trajectory. We analyze in this paper how well such an approach can work. Concretely, we test how accurately trajectory-based ELA approaches can predict the final solution quality of the CMA-ES after a fixed budget of function evaluations. We observe that the loss of trajectory-based predictions can be surprisingly small compared to the classical global sampling approach, if the remaining budget for which solution quality shall be predicted is not too large. Feature selection, in contrast, did not show any advantage in our experiments and rather led to worsened prediction accuracy. The inclusion of state variables of CMA-ES only has a moderate effect on the prediction accuracy.

Hao Wang, Carlos Igncio Hernández Castellanos, Tome Eftimov

Assessing the empirical performance of Multi-Objective Evolutionary Algorithms (MOEAs) is vital when we extensively test a set of MOEAs and aim to determine a proper ranking thereof. Multiple performance indicators, e.g., the generational distance and the hypervolume, are frequently applied when reporting the experimental data, where typically the data on each indicator is analyzed independently from other indicators. Such a treatment brings conceptual difficulties in aggregating the result on all performance indicators, and it might fail to discover significant differences among algorithms if the marginal distributions of the performance indicator overlap. Therefore, in this paper, we propose to conduct a multivariate $\mathcal{E}$-test on the joint empirical distribution of performance indicators to detect the potential difference in the data, followed by a post-hoc procedure that utilizes the linear discriminative analysis to determine the superiority between algorithms. This performance analysis's effectiveness is supported by an experimentation conducted on four algorithms, 16 problems, and 6 different numbers of objectives.

Tome Eftimov, Gorjan Popovski, Quentin Renau et al.

Automated per-instance algorithm selection and configuration have shown promising performances for a number of classic optimization problems, including satisfiability, AI planning, and TSP. The techniques often rely on a set of features that measure some characteristics of the problem instance at hand. In the context of black-box optimization, these features have to be derived from a set of $(x,f(x))$ samples. A number of different features have been proposed in the literature, measuring, for example, the modality, the separability, or the ruggedness of the instance at hand. Several of the commonly used features, however, are highly correlated. While state-of-the-art machine learning techniques can routinely filter such correlations, they hinder explainability of the derived algorithm design techniques. We therefore propose in this work to pre-process the measured (raw) landscape features through representation learning. More precisely, we show that a linear dimensionality reduction via matrix factorization significantly contributes towards a better detection of correlation between different problem instances -- a key prerequisite for successful automated algorithm design.

Thomas Bartz-Beielstein, Carola Doerr, Daan van den Berg et al.

This survey compiles ideas and recommendations from more than a dozen researchers with different backgrounds and from different institutes around the world. Promoting best practice in benchmarking is its main goal. The article discusses eight essential topics in benchmarking: clearly stated goals, well-specified problems, suitable algorithms, adequate performance measures, thoughtful analysis, effective and efficient designs, comprehensible presentations, and guaranteed reproducibility. The final goal is to provide well-accepted guidelines (rules) that might be useful for authors and reviewers. As benchmarking in optimization is an active and evolving field of research this manuscript is meant to co-evolve over time by means of periodic updates.

Khushbu Agarwal, Tome Eftimov, Raghavendra Addanki et al.

Representation learning methods that transform encoded data (e.g., diagnosis and drug codes) into continuous vector spaces (i.e., vector embeddings) are critical for the application of deep learning in healthcare. Initial work in this area explored the use of variants of the word2vec algorithm to learn embeddings for medical concepts from electronic health records or medical claims datasets. We propose learning embeddings for medical concepts by using graph-based representation learning methods on SNOMED-CT, a widely popular knowledge graph in the healthcare domain with numerous operational and research applications. Current work presents an empirical analysis of various embedding methods, including the evaluation of their performance on multiple tasks of biomedical relevance (node classification, link prediction, and patient state prediction). Our results show that concept embeddings derived from the SNOMED-CT knowledge graph significantly outperform state-of-the-art embeddings, showing 5-6x improvement in ``concept similarity" and 6-20\% improvement in patient diagnosis.

Maulik R. Kamdar, Tymor Hamamsy, Shea Shelton et al.

The United States is in the midst of an opioid epidemic with recent estimates indicating that more than 130 people die every day due to drug overdose. The over-prescription and addiction to opioid painkillers, heroin, and synthetic opioids, has led to a public health crisis and created a huge social and economic burden. Statistical learning methods that use data from multiple clinical centers across the US to detect opioid over-prescribing trends and predict possible opioid misuse are required. However, the semantic heterogeneity in the representation of clinical data across different centers makes the development and evaluation of such methods difficult and non-trivial. We create the Opioid Drug Knowledge Graph (ODKG) -- a network of opioid-related drugs, active ingredients, formulations, combinations, and brand names. We use the ODKG to normalize drug strings in a clinical data warehouse consisting of patient data from over 400 healthcare facilities in 42 different states. We showcase the use of ODKG to generate summary statistics of opioid prescription trends across US regions. These methods and resources can aid the development of advanced and scalable models to monitor the opioid epidemic and to detect illicit opioid misuse behavior. Our work is relevant to policymakers and pain researchers who wish to systematically assess factors that contribute to opioid over-prescribing and iatrogenic opioid addiction in the US.