Zhenhong Peng

Junhao Wei, Baili Lu, Zhenhong Peng et al.

Sequence-based deep learning offers a scalable alternative to structure-based scoring for protein-ligand binding affinity prediction. However, progress is hard to interpret when architectural priors are evaluated on canonical PDBbind-style splits that leak similarity classes across folds. We present HonestAffinity, a compact 1D-input predictor to isolate two priors under a leak-aware protocol: frozen ESM-2 (650M) protein embeddings and a learned binary pocket-position marker. We evaluate a multi-scale convolutional/Transformer template in three variants: HonestAffinity-Pocket, HonestAffinity-NoPocket, and HonestAffinity-Pocket-NoESM. All three train on 11,513 LP-PDBBind complexes in ~3 GPU-hours. We benchmark against five baselines on the LP-PDBBind 3-tier no-leak hold-out, CASF-2016, and a CASF-2016 non-train subset. Our central finding is a split-conditioned reversal rather than a uniformly best prior: HonestAffinity-Pocket achieves the best mean Pearson R on validation and CASF-2016 splits, whereas HonestAffinity-Pocket-NoESM achieves the best mean Pearson R on every strict LP no-leak tier (test_cl1-cl3). Both the pocket marker and ESM-2 input improve performance on familiar splits but reduce Pearson R on strict no-leak tiers. We argue models should report paired canonical and leak-proof ablations, and that deployment-regime-matched variants better describe these reversals than a single default. Code and scripts are linked in the footnote; checkpoints will be released upon acceptance.

Yifu Zhao, Xiaofan Zou, Junhao Wei et al.

Learning-assisted algorithm design often has to make reliable search decisions under small evaluation budgets, where committing to a single metaheuristic can be unreliable. We propose WASHH, a Whale-guided Adaptive Selection Hyper-Heuristic for continuous black-box optimization. WASHH uses WOA as the main exploitation backbone, but treats PSO-style memory, GWO-style leader averaging, DE-style variation, local coordinate search, and anchor-guided refinement as selectable search behaviors. An online reward controller allocates evaluations according to observed improvements, while anchor refinement exploits inexpensive reference configurations such as box centers or default model settings without bypassing black-box evaluation. On ten 30-dimensional benchmark functions with 10 independent runs and 12,000 evaluations, WASHH achieves the best average rank, 1.10, and is best or tied best on all ten functions. It strictly improves over WOA on eight functions and ties WOA at the numerical optimum on Rastrigin and Griewank. We further study SVC hyperparameter configuration for breast cancer diagnosis under a 300-evaluation budget. WASHH obtains the lowest mean validation log loss among the compared optimizers, suggesting that anchor-aware selection hyper-heuristics are a practical lightweight direction for LEAD systems.

Junhao Wei, Yanxiao Li, Yifu Zhao et al.

UAV multi-site inspection often reduces to choosing a high-quality visiting order after target sites have been extracted from a map. This paper develops LA-BHH, a landscape-aware bandit hyper-heuristic that learns an operator-selection policy online for this routing layer. LA-BHH treats 2-opt, swap, relocate, and Or-opt moves as low-level arms, builds context from static landscape descriptors and online search-state features, and updates a LinUCB controller from improvement rewards during the same run. Experimental results on 45 generated Euclidean TSP instances show that LA-BHH achieves the best mean final gap and convergence AUC, with 0.0223 and 0.0389 respectively. It reduces final gap by 17.6\% over UCB-HH, 22.6\% over Random-HH, and 68.2\% over nearest-neighbor construction. Ablation results further show that contextual credit assignment, 2-opt repair, and stagnation-aware state use are the main contributors.

Junhao Wei, Yanxiao Li, Yifu Zhao et al.

Learning-assisted hyper-heuristics can select among dispatching rules while preserving the feasibility and interpretability of constructive Job Shop Scheduling Problem (JSSP) heuristics. Their main computational cost lies in label generation rather than model fitting, since each supervised label usually requires rolling out candidate rules from a partial schedule. We study this label-cost problem together with a reliability problem: a learned selector should not switch away from a strong default rule unless the predicted gain is credible. The proposed selector uses regret-normalized rollout labels, a contextual KNN uncertainty estimate, and a gate that acts only when the predicted improvement exceeds an uncertainty-adjusted margin. We also vary rollout depth and breadth to measure the cost-quality trade-off. On synthetic JSSP instances, the gated selector achieves the lowest mean RPD among learned selectors, remains close to the best fixed dispatching rule, and reduces Random-HH mean RPD by more than an order of magnitude.