arXiv subjects

Yiliang Yuan

Publications and source records attributed to Yiliang Yuan.

5 recordsLinked to original sources

arXiv2026

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↗

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↗

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↗

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 1Å (2Å) 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↗