arXiv subjects

Ana Nikolikj

Publications and source records attributed to Ana Nikolikj.

16 recordsLinked to original sources

arXiv2026

Design Choices That Matter: A Functional ANOVA Analysis for Remote Sensing Multi-Label Classification

Benchmarking deep learning (DL) models for multi-label classification (MLC) of remote sensing images (RSI) typically yields rankings that do not generalize beyond the evaluated datasets. In this work, we move beyond rankings by employing functional analysis of variance (fANOVA) to systematically quantify the contributions of individual design choices and their interactions to performance variability. We conduct two empirical analyses covering 48 and 20 DL models, respectively, spanning design choices such as network architecture, fine-tuning strategy, learning strategy, and initialization. By applying fANOVA across seven MLC RSI datasets, we construct dataset meta-representations that capture design-choice sensitivity profiles. Hierarchical clustering of these meta-representations reveals that datasets naturally group according to how they respond to design decisions, with patterns strongly linked to intrinsic dataset properties such as scale, spatial resolution, and label space complexity. Our findings show that for large-scale datasets, fine-tuning strategy and architecture are dominant factors, while in data-limited regimes, initialization becomes decisive. For intermediate regimes, the interaction between architecture and learning strategy governs performance.

cs.LG↗

arXiv2026

Quantifying the Impact of Modules and Their Interactions in the PSO-X Framework

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.

cs.NE↗

arXiv2025

Longest Filled Common Subsequence for Song Identification from Degraded Audio via Construct--Merge--Solve--Adapt Optimization

This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including exact, metaheuristic, and approximation algorithms, have primarily been evaluated on small instances, which provide limited insight into their scalability. In this work, we introduce a new benchmark dataset with significantly larger instances and demonstrate that existing datasets lack the discriminative power needed to meaningfully assess algorithm performance at scale. To solve large instances efficiently, we utilize an adaptive Construct, Merge, Solve, Adapt (CMSA) framework that iteratively generates promising subproblems via component-based construction and refines them using feedback from prior iterations. Subproblems are solved using an external black-box solver. Extensive experiments on both standard and newly introduced set of large-sized instances prove that the designed adaptive CMSA achieves state-of-the-art performance, outperforming four known approaches. Notably, among 1,510 problem instances with known optimal solutions, our approach matches the proven optimum on 1,486 instances---corresponding to 98.4\% of these instances. These results demonstrate substantially improved scalability on large problem instances. As an engineering contribution, we propose a novel application of LFCS to song identification from degraded audio excerpts, using real-world energy-profile instances derived from popular music. Finally, we conduct an empirical explainability analysis to identify critical feature combinations influencing algorithm performance, revealing the key problem features associated with the success or failure of the approaches across different instance types.

cs.SD↗

arXiv2025

Tracing the Interactions of Modular CMA-ES Configurations Across Problem Landscapes

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.

cs.NE↗

arXiv2025

Customized Exploration of Landscape Features Driving Multi-Objective Combinatorial Optimization Performance

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.

cs.NE↗

arXiv2024

A Learning Search Algorithm for the Restricted Longest Common Subsequence Problem

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.

cs.AI↗

arXiv2024

Instance Selection for Dynamic Algorithm Configuration with Reinforcement Learning: Improving Generalization

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.

cs.LG↗

arXiv2024

A Survey of Features Used for Representing Black-box Single-objective Continuous Optimization

This survey examines key advancements in designing features to represent optimization problem instances, algorithm instances, and their interactions within the context of single-objective continuous black-box optimization. These features support machine learning tasks such as algorithm selection, algorithm configuration, and problem classification, and they are also used to evaluate the complementarity of benchmark problem sets. We provide a comprehensive overview of problem landscape features, algorithm features, high-level problem-algorithm interaction features, and trajectory features, including the latest works from the past five years. We also point out limitations of the current state-of-the-art and suggest directions for future research.

cs.LG↗

arXiv2024

Quantifying Individual and Joint Module Impact in Modular Optimization Frameworks

This study explores the influence of modules on the performance of modular optimization frameworks for continuous single-objective black-box optimization. There is an extensive variety of modules to choose from when designing algorithm variants, however, there is a rather limited understanding of how each module individually influences the algorithm performance and how the modules interact with each other when combined. We use the functional ANOVA (f-ANOVA) framework to quantify the influence of individual modules and module combinations for two algorithms, the modular Covariance Matrix Adaptation (modCMA) and the modular Differential Evolution (modDE). We analyze the performance data from 324 modCMA and 576 modDE variants on the BBOB benchmark collection, for two problem dimensions, and three computational budgets. Noteworthy findings include the identification of important modules that strongly influence the performance of modCMA, such as the~\textit{weights\ option} and~\textit{mirrored} modules for low dimensional problems, and the~\textit{base\ sampler} for high dimensional problems. The large individual influence of the~\textit{lpsr} module makes it very important for the performance of modDE, regardless of the problem dimensionality and the computational budget. When comparing modCMA and modDE, modDE undergoes a shift from individual modules being more influential, to module combinations being more influential, while modCMA follows the opposite pattern, with an increase in problem dimensionality and computational budget.

cs.NE↗

arXiv2024

Generalization Ability of Feature-based Performance Prediction Models: A Statistical Analysis across Benchmarks

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.

cs.LG↗

arXiv2023

PS-AAS: Portfolio Selection for Automated Algorithm Selection in Black-Box Optimization

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.

cs.LG↗

arXiv2023

Algorithm Instance Footprint: Separating Easily Solvable and Challenging Problem Instances

In black-box optimization, it is essential to understand why an algorithm instance works on a set of problem instances while failing on others and provide explanations of its behavior. We propose a methodology for formulating an algorithm instance footprint that consists of a set of problem instances that are easy to be solved and a set of problem instances that are difficult to be solved, for an algorithm instance. This behavior of the algorithm instance is further linked to the landscape properties of the problem instances to provide explanations of which properties make some problem instances easy or challenging. The proposed methodology uses meta-representations that embed the landscape properties of the problem instances and the performance of the algorithm into the same vector space. These meta-representations are obtained by training a supervised machine learning regression model for algorithm performance prediction and applying model explainability techniques to assess the importance of the landscape features to the performance predictions. Next, deterministic clustering of the meta-representations demonstrates that using them captures algorithm performance across the space and detects regions of poor and good algorithm performance, together with an explanation of which landscape properties are leading to it.

cs.NE↗

arXiv2023

Assessing the Generalizability of a Performance Predictive Model

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.

cs.LG↗

arXiv2023

Sensitivity Analysis of RF+clust for Leave-one-problem-out Performance Prediction

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.

cs.LG↗

arXiv2023

RF+clust for Leave-One-Problem-Out Performance Prediction

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.

cs.NE↗

arXiv2022

Improving Nevergrad's Algorithm Selection Wizard NGOpt through Automated Algorithm Configuration

Algorithm selection wizards are effective and versatile tools that automatically select an optimization algorithm given high-level information about the problem and available computational resources, such as number and type of decision variables, maximal number of evaluations, possibility to parallelize evaluations, etc. State-of-the-art algorithm selection wizards are complex and difficult to improve. We propose in this work the use of automated configuration methods for improving their performance by finding better configurations of the algorithms that compose them. In particular, we use elitist iterated racing (irace) to find CMA configurations for specific artificial benchmarks that replace the hand-crafted CMA configurations currently used in the NGOpt wizard provided by the Nevergrad platform. We discuss in detail the setup of irace for the purpose of generating configurations that work well over the diverse set of problem instances within each benchmark. Our approach improves the performance of the NGOpt wizard, even on benchmark suites that were not part of the tuning by irace.

cs.NE↗