Machine learning models increasingly map biological sequence-fitness landscapes to predict mutational effects. Effective evaluation of these models requires benchmarks curated from empirical data. Despite their impressive scales, existing benchmarks lack topographical information regarding the underlying fitness landscapes, which hampers interpretation and comparison of model performance beyond averaged scores. Here, we introduce GraphFLA, a Python framework that constructs and analyzes fitness landscapes from mutagensis data in diverse modalities (e.g., DNA, RNA, protein, and beyond) with up to millions of mutants. GraphFLA calculates 20 biologically relevant features that characterize 4 fundamental aspects of landscape topography. By applying GraphFLA to over 5,300 landscapes from ProteinGym, RNAGym, and CIS-BP, we demonstrate its utility in interpreting and comparing the performance of dozens of fitness prediction models, highlighting factors influencing model accuracy and respective advantages of different models. In addition, we release 155 combinatorially complete empirical fitness landscapes, encompassing over 2.2 million sequences across various modalities. All the codes and datasets are available at https://github.com/COLA-Laboratory/GraphFLA.

To efficiently tune configuration for better system performance (e.g., latency), many tuners have leveraged a surrogate model to expedite the process instead of solely relying on the profoundly expensive system measurement. As such, it is naturally believed that we need more accurate models. However, the fact of accuracy can lie-a somewhat surprising finding from prior work-has left us many unanswered questions regarding what role the surrogate model plays in configuration tuning. This paper provides the very first systematic exploration and discussion, together with a resolution proposal, to disclose the many faces of surrogate models for configuration tuning, through the novel perspective of fitness landscape analysis. We present a theory as an alternative to accuracy for assessing the model usefulness in tuning, based on which we conduct an extensive empirical study involving up to 27,000 cases. Drawing on the above, we propose Model4Tune, an automated predictive tool that estimates which model-tuner pairs are the best for an unforeseen system without expensive tuner profiling. Our results suggest that Moldel4Tune, as one of the first of its kind, performs significantly better than random guessing in 79%-82% of the cases. Our results not only shed light on the possible future research directions but also offer a practical resolution that can assist practitioners in evaluating the most useful model for configuration tuning.

The Nearest-Better Network (NBN) is a powerful method to visualize sampled data for continuous optimization problems while preserving multiple landscape features. However, the calculation of NBN is very time-consuming, and the extension of the method to combinatorial optimization problems is challenging but very important for analyzing the algorithm's behavior. This paper provides a straightforward theoretical derivation showing that the NBN network essentially functions as the maximum probability transition network for algorithms. This paper also presents an efficient NBN computation method with logarithmic linear time complexity to address the time-consuming issue. By applying this efficient NBN algorithm to the OneMax problem and the Traveling Salesman Problem (TSP), we have made several remarkable discoveries for the first time: The fitness landscape of OneMax exhibits neutrality, ruggedness, and modality features. The primary challenges of TSP problems are ruggedness, modality, and deception. Two state-of-the-art TSP algorithms (i.e., EAX and LKH) have limitations when addressing challenges related to modality and deception, respectively. LKH, based on local search operators, fails when there are deceptive solutions near global optima. EAX, which is based on a single population, can efficiently maintain diversity. However, when multiple attraction basins exist, EAX retains individuals within multiple basins simultaneously, reducing inter-basin interaction efficiency and leading to algorithm's stagnation.

Due to climate-induced changes, many habitats are experiencing range shifts away from their traditional geographic locations (Piguet, 2011). We propose a solution to accurately model whether bird species are present in a specific habitat through the combination of Convolutional Neural Networks (CNNs) (O'Shea, 2015) and tabular data. Our approach makes use of satellite imagery and environmental features (e.g., temperature, precipitation, elevation) to predict bird presence across various climates. The CNN model captures spatial characteristics of landscapes such as forestation, water bodies, and urbanization, whereas the tabular method uses ecological and geographic data. Both systems predict the distribution of birds with an average accuracy of 85%, offering a scalable but reliable method to understand bird migration.

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.

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.

Multimodal aerial data are used to monitor natural systems, and machine learning can significantly accelerate the classification of landscape features within such imagery to benefit ecology and conservation. It remains under-explored, however, how these multiple modalities ought to be fused in a deep learning model. As a step towards filling this gap, we study three strategies (Early fusion, Late fusion, and Mixture of Experts) for fusing thermal, RGB, and LiDAR imagery using a dataset of spatially-aligned orthomosaics in these three modalities. In particular, we aim to map three ecologically-relevant biophysical landscape features in African savanna ecosystems: rhino middens, termite mounds, and water. The three fusion strategies differ in whether the modalities are fused early or late, and if late, whether the model learns fixed weights per modality for each class or generates weights for each class adaptively, based on the input. Overall, the three methods have similar macro-averaged performance with Late fusion achieving an AUC of 0.698, but their per-class performance varies strongly, with Early fusion achieving the best recall for middens and water and Mixture of Experts achieving the best recall for mounds.

Recent research in Meta-Black-Box Optimization (MetaBBO) have shown that meta-trained neural networks can effectively guide the design of black-box optimizers, significantly reducing the need for expert tuning and delivering robust performance across complex problem distributions. Despite their success, a paradox remains: MetaBBO still rely on human-crafted Exploratory Landscape Analysis features to inform the meta-level agent about the low-level optimization progress. To address the gap, this paper proposes Neural Exploratory Landscape Analysis (NeurELA), a novel framework that dynamically profiles landscape features through a two-stage, attention-based neural network, executed in an entirely end-to-end fashion. NeurELA is pre-trained over a variety of MetaBBO algorithms using a multi-task neuroevolution strategy. Extensive experiments show that NeurELA achieves consistently superior performance when integrated into different and even unseen MetaBBO tasks and can be efficiently fine-tuned for further performance boost. This advancement marks a pivotal step in making MetaBBO algorithms more autonomous and broadly applicable.

Landscape analysis aims to characterise optimisation problems based on their objective (or fitness) function landscape properties. The problem search space is typically sampled, and various landscape features are estimated based on the samples. One particularly salient set of features is information content, which requires the samples to be sequences of neighbouring solutions, such that the local relationships between consecutive sample points are preserved. Generating such spatially correlated samples that also provide good search space coverage is challenging. It is therefore common to first obtain an unordered sample with good search space coverage, and then apply an ordering algorithm such as the nearest neighbour to minimise the distance between consecutive points in the sample. However, the nearest neighbour algorithm becomes computationally prohibitive in higher dimensions, thus there is a need for more efficient alternatives. In this study, Hilbert space-filling curves are proposed as a method to efficiently obtain high-quality ordered samples. Hilbert curves are a special case of fractal curves, and guarantee uniform coverage of a bounded search space while providing a spatially correlated sample. We study the effectiveness of Hilbert curves as samplers, and discover that they are capable of extracting salient features at a fraction of the computational cost compared to Latin hypercube sampling with post-factum ordering. Further, we investigate the use of Hilbert curves as an ordering strategy, and find that they order the sample significantly faster than the nearest neighbour ordering, without sacrificing the saliency of the extracted features.

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.