Antibody lead optimization is inherently a multi-objective challenge in drug discovery. Achieving a balance between different drug-like properties is crucial for the development of viable candidates, and this search becomes exponentially challenging as desired properties grow. The ever-growing zoo of sophisticated in silico tools for predicting antibody properties calls for an efficient joint optimization procedure to overcome resource-intensive sequential filtering pipelines. We present BOAT, a versatile Bayesian optimization framework for multi-property antibody engineering. Our `plug-and-play' framework couples uncertainty-aware surrogate modeling with a genetic algorithm to jointly optimize various predicted antibody traits while enabling efficient exploration of sequence space. Through systematic benchmarking against genetic algorithms and newer generative learning approaches, we demonstrate competitive performance with state-of-the-art methods for multi-objective protein optimization. We identify clear regimes where surrogate-driven optimization outperforms expensive generative approaches and establish practical limits imposed by sequence dimensionality and oracle costs.

In practice, multiple conflicting objectives and costly evaluations (e.g., wet-lab experiments) make the diversity of candidates

To address issues of group-level fairness in machine learning, it is natural to adjust model parameters based on specific fairness objectives over a sensitive-attributed validation set.

Each sublayer adds a skip-connection (ADD) and batch normalization (BN). The decoder sequentially chooses a node according to a probability distribution produced by the node embeddings to construct a solution. The scaled symmetric sampling method is shown in Algorithm 2. The scaled factor The uniform division of the weight space is illustrated as follows. Thus, its approximate Pareto optimal solutions are commonly pursued. V ehicles must serve all the customers and finally return to the depot.