A distribution-aware and functionally relevant novel framework for generation and discovery of bioactive peptides

Abstract

Recent advances in artificial intelligence have accelerated the discovery of bioactive peptides by enabling computational exploration of the vast peptide sequence space. However, existing peptide generation approaches generally rely on either distribution-learning models, which generate biologically realistic sequences but do not consistently optimize functional activity, or optimization-based methods, which maximize prediction confidence while often deviating from the underlying distribution of experimentally validated peptides. To address this limitation, a two-phase generative–evolutionary framework is proposed that integrates distribution learning with evolutionary optimization. In the first phase, Variational Autoencoders (VAE), Autoregressive Transformers (ART), and Token Diffusion Transformers (TDT) are used to generate biologically plausible seed peptides. In the second phase, these peptides were used as initial seed for Hill Climbing optimization procedure that iteratively improves fitness function score. The proposed two-phase framework was evaluated using a dataset of experimentally validated IL-2-inducing peptides. Evaluation using independent IL-2 prediction models showed that Autoregressive Transformer combined with Hill Climbing achieved the best overall performance, achieving the mean IL-2 induction confidence score of 0.96 while reducing KL divergence from 2.26 for standalone Hill Climbing to 0.75. A case study on an independent IL-13 inducing peptide dataset showed similar trends, with ART initialized Hill Climbing achieving the mean IL-13 induction score of 0.99 while reducing KL divergence from 1.76 to 0.59. Overall, the framework provides a generalizable approach for balancing functional optimization and distributional realism and can be applied to peptide discovery and data augmentation in imbalanced biological datasets thereby generating high confidence peptides for wet lab validation. Highlights Proposed a two-phase framework for bioactive peptide generation with potential to address class imbalance in peptide classification tasks. Performed a systematic comparison of distribution-learning and optimization-based approaches for peptide generation. Combined distribution-learning models for sequence generation with optimization algorithms for improving peptide functional properties. Demonstrated the applicability of the proposed framework across multiple bioactive peptide datasets.