Jiabao Brad Wang

Jiabao Brad Wang, Xiang Shi, Yiliang Yuan et al.

Automated algorithm selection in continuous black-box optimisation typically relies on fixed landscape descriptors computed under a limited probing budget, yet such descriptors can degrade under problem-split or cross-benchmark evaluation. We propose GeoPAS, a geometric probing approach that represents a problem instance by multiple coarse two-dimensional slices sampled across locations, orientations, and logarithmic scales. A shared validity-aware convolutional encoder maps each slice to an embedding, conditions it on slice-scale and amplitude statistics, and aggregates the resulting features permutation-invariantly for risk-aware solver selection via log-scale performance prediction with an explicit penalty on tail failures. On COCO/BBOB with a 12-solver portfolio in dimensions 2--10, GeoPAS improves over the single best solver under leave-instance-out, grouped random, and leave-problem-out evaluation. These results suggest that multi-scale geometric slices provide a useful transferable static signal for algorithm selection, although a small number of heavy-tail regimes remain and continue to dominate the mean. Our code is available at $\href{https://github.com/BradWangW/GeoPAS}{GitHub}$.

Jiabao Brad Wang, Siyuan Cao, Hongxuan Wu et al.

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, or protocol regimes. We introduce MolAS, a lightweight algorithm selection system that predicts per-algorithm performance from pretrained protein-ligand embeddings using attentional pooling and a shallow residual decoder. With only hundreds to a few thousand labelled complexes, MolAS achieves up to 15% absolute improvement over the single-best solver (SBS) and closes 17-66% of the Virtual Best Solver (VBS)-SBS gap across five diverse docking benchmarks. Analyses of reliability, embedding geometry, and solver-selection patterns show that MolAS succeeds when the oracle landscape exhibits low entropy and separable solver behaviour, but collapses under protocol-induced hierarchy shifts. These findings indicate that the main barrier to robust docking AS is not representational capacity but instability in solver rankings across pose-generation regimes, positioning MolAS as both a practical in-domain selector and a diagnostic tool for assessing when AS is feasible.

Siyuan Cao, Hongxuan Wu, Jiabao Brad Wang et al.

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.