Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Design

Original Abstract

Generative models can now propose thousands of \emph{de novo} antibody sequences, yet translating these designs into viable therapeutics remains constrained by the cost of biophysical characterization. Here we present CrossAbSense, a framework of property-specific neural oracles that combine frozen protein language model encoders with configurable attention decoders, identified through a systematic hyperparameter campaign totaling over 200 runs per property. On the GDPa1 benchmark of 242 therapeutic IgGs, our oracles achieve notable improvements of 12--20\% over established baselines on three of five developability assays and competitive performance on the remaining two. The central finding is that optimal decoder architectures \emph{invert} our initial biological hypotheses: self-attention alone suffices for aggregation-related properties (hydrophobic interaction chromatography, polyreactivity), where the relevant sequence signatures -- such as CDR-H3 hydrophobic patches -- are already fully resolved within single-chain embeddings by the high-capacity 6B encoder. Bidirectional cross-attention, by contrast, is required for expression yield and thermal stability -- properties that inherently depend on the compatibility between heavy and light chains. Learned chain fusion weights independently confirm heavy-chain dominance in aggregation ($w_H = 0.62$) versus balanced contributions for stability ($w_H = 0.51$). We demonstrate practical utility by deploying CrossAbSense on 100 IgLM-generated antibody designs, illustrating a path toward substantial reduction in experimental screening costs.