arXiv subjects

Mustafa Misir

Publications and source records attributed to Mustafa Misir.

8 recordsLinked to original sources

arXiv2026

EEG-AS: Instance-Level Foundation Model Selection for EEG Foundation Models via Behavior Reconstruction

Electroencephalography (EEG) is a non-invasive technique for measuring neural activity and has been widely used in neuroscience applications. Recent advances in EEG foundation models have enabled strong performance across diverse neural decoding tasks. However, no single foundation model consistently performs best across datasets or individual EEG instances, while instance-level model selection remains largely unexplored. To address this limitation, we formulate EEG foundation model selection as an instance-level Algorithm Selection (AS) problem. We propose \textbf{EEG-AS}, an instance-level algorithm selection framework that characterizes each EEG instance using inference-available latent EEG embeddings, handcrafted neurophysiological features, and an anchor foundation model. During training, EEG-AS learns to reconstruct unavailable foundation-model behaviors from privileged prediction tokens conditioned on an anchor foundation model, while during inference it estimates these behaviors without executing the entire model portfolio, enabling efficient selection from seven EEG foundation models. Experiments on seven public EEG benchmarks demonstrate that EEG-AS substantially narrows the gap between the Single Best Solver (SBS) and the oracle upper bound for each instance. These results highlight the effectiveness of instance-level AS for adaptive deployment of EEG foundation models.

cs.LG↗

arXiv2026

Graph Neural Network-based Algorithm Selection for the Traveling Salesman Problem: A Systematic Study of Cost and Rank Losses under Distinct Budget Regimes

Automated Algorithm Selection (AS) aims to improve problem-solving performance by selecting, for each problem instance, the most suitable algorithm from a predefined portfolio. This is particularly relevant to the Traveling Salesman Problem (TSP), where solver performance is strongly instance-dependent. We introduce GNNAS-TSP, a Graph Neural Network (GNN)-based AS framework that learns TSP instance representations directly from raw graph data, avoiding manual feature engineering. GNNAS-TSP formulates AS as a joint cost-prediction and ranking task. We evaluate cost-based (mean squared error (MSE), mean absolute error (MAE), and Huber), rank-based (RankNet, ListNet, and LambdaRank), and hybrid learning objectives for a portfolio comprising Chained Lin-Kernighan, Edge Assembly Crossover, Lin-Kernighan-Helsgaun, Multiagent Optimization System, and Concorde. Experiments use fixed computational budgets of 10 and 60 seconds. On the held-out test set, the selected configurations improve on the Single Best Solver (SBS) in normalized solution cost at both budgets. For the 10s budget, AS achieves substantial and statistically significant cost improvement over SBS. Overall, the results suggest that GNNAS-TSP is a useful meta-solving strategy when exploitable variation exists across solver performance.

cs.LG↗

arXiv2026

Beyond Numerical Features: CNN-Driven Algorithm Selection via Contour Plots for Continuous Black-Box Optimization

The present paper introduces a new representation-driven approach to per-instance algorithm selection, applied to black-box optimization, for automatically choosing the most promising solver from a fixed portfolio. Prior work in continuous optimization largely relies on numerical descriptors, including Exploratory Landscape Analysis features and learned embeddings such as Deep-ELA. This work studies a complementary representation: contour-map visualizations of probed landscapes. A CNN regressor takes multiple instance-specific contour views (stacked or encoded per view and aggregated) and predicts per-solver performance, enabling selection by the predicted best value. On the standard BBOB 2009 single-objective protocol, the resulting selectors significantly outperform the single best solver (SBS) and are competitive with feature-based baselines. A subsequent bi-objective evaluation under the DeepELA setting further indicates that the same image-based principle can be competitive when using windowed contour views. Overall, the results suggest that simple vision models can exploit spatial structure in probed landscapes for algorithm selection without handcrafted ELA features.

cs.LG↗

arXiv2026

GeoPAS: Geometric Probing for Algorithm Selection in Continuous Black-Box Optimization

Automated algorithm selection for continuous black-box optimization depends on representing problem information under limited probing and selecting solvers under heavy-tailed performance distributions. This paper proposes a geometric probing framework that represents each problem instance by randomly sampled multi-scale two-dimensional slices of the objective landscape. The slices are encoded with validity-mask-aware visual pooling and aggregated into an instance representation. Solver selection is then performed by a logarithmic composite score combining a learned instance-conditioned estimate with an algorithm-side empirical prior. The framework is evaluated on a standard single-objective black-box optimization benchmark suite with a portfolio of twelve solvers under instance-level, grouped random, and problem-level transfer protocols. Under the two within-suite protocols, it reduces aggregate mean relative expected running time from 30.37 for the single best solver to 3.14 and 3.61, while also improving median and upper-tail performance. Under problem-level transfer, the canonical adaptive setting improves typical and moderate-tail performance but leaves the mean dominated by rare extreme failures; a prior-heavy scoring variant mitigates this failure mode, although its robustness may be benchmark-dependent. The results suggest that coarse geometric probes provide useful solver-relevant information, while robust cross-problem selection also depends on metric-aligned decision scoring.

cs.LG↗

arXiv2025

Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, and protocol regimes. MolAS is a lightweight algorithm-selection model that predicts per-algorithm performance from pretrained protein and ligand embeddings using attentional pooling and a shallow residual decoder. With hundreds to a few thousand labelled complexes, MolAS achieves up to a 15 percentage-point absolute improvement over the single-best solver (SBS) and closes 17--66\% of the Virtual Best Solver (VBS)--SBS gap across five docking benchmarks. Analyses of selection frequencies, margin-conditioned reliability, and benchmark-level oracle structure indicate that MolAS is most effective when the workflow-defined oracle landscape has low winner entropy and a reasonably separable top-solver region, but degrades under protocol mismatch that shifts solver rankings and changes the induced labels. These results suggest that, in the evaluated regime, robustness is limited less by representational capacity than by workflow- and protocol-induced instability in solver hierarchies, positioning MolAS as an in-domain selector for fixed pipelines and as a diagnostic tool for assessing when docking algorithm selection is well-posed.

q-bio.QM↗

arXiv2025

MC-GNNAS-Dock: Multi-criteria GNN-based Algorithm Selection for Molecular Docking

Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as performance varies by context. To overcome this challenge, algorithm selection frameworks such as GNNAS-Dock, built on graph neural networks, have been proposed. This study introduces an enhanced system, MC-GNNAS-Dock, with three key advances. First, a multi-criteria evaluation integrates binding-pose accuracy (RMSD) with validity checks from PoseBusters, offering a more rigorous assessment. Second, architectural refinements by inclusion of residual connections strengthen predictive robustness. Third, rank-aware loss functions are incorporated to sharpen rank learning. Extensive experiments are performed on a curated dataset containing approximately 3200 protein-ligand complexes from PDBBind. MC-GNNAS-Dock demonstrates consistently superior performance, achieving up to 5.4% (3.4%) gains under composite criteria of RMSD below 1\AA{} (2\AA{}) with PoseBuster-validity compared to the single best solver (SBS) Uni-Mol Docking V2.

cs.AI↗

arXiv2024

GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking

Molecular docking is a major element in drug discovery and design. It enables the prediction of ligand-protein interactions by simulating the binding of small molecules to proteins. Despite the availability of numerous docking algorithms, there is no single algorithm consistently outperforms the others across a diverse set of docking scenarios. This paper introduces GNNAS-Dock, a novel Graph Neural Network (GNN)-based automated algorithm selection system for molecular docking in blind docking situations. GNNs are accommodated to process the complex structural data of both ligands and proteins. They benefit from the inherent graph-like properties to predict the performance of various docking algorithms under different conditions. The present study pursues two main objectives: 1) predict the performance of each candidate docking algorithm, in terms of Root Mean Square Deviation (RMSD), thereby identifying the most accurate method for specific scenarios; and 2) choose the best computationally efficient docking algorithm for each docking case, aiming to reduce the time required for docking while maintaining high accuracy. We validate our approach on PDBBind 2020 refined set, which contains about 5,300 pairs of protein-ligand complexes.

q-bio.BM↗

arXiv2016

A case study of algorithm selection for the traveling thief problem

Many real-world problems are composed of several interacting components. In order to facilitate research on such interactions, the Traveling Thief Problem (TTP) was created in 2013 as the combination of two well-understood combinatorial optimization problems. With this article, we contribute in four ways. First, we create a comprehensive dataset that comprises the performance data of 21 TTP algorithms on the full original set of 9720 TTP instances. Second, we define 55 characteristics for all TPP instances that can be used to select the best algorithm on a per-instance basis. Third, we use these algorithms and features to construct the first algorithm portfolios for TTP, clearly outperforming the single best algorithm. Finally, we study which algorithms contribute most to this portfolio.

cs.AI↗