Doniyorkhon Obidov, Xiaolong Guo, Yonghui Li, Kaichen Yang
Large Language Models (LLMs) have accelerated drug discovery, particularly in the automated design of antimicrobial peptides (AMPs). However, current validation pipelines for peptide generation models overlook historical precedents showing that certain drugs carry health risks predominantly for individuals with specific genetic profiles. In this paper, we demonstrate that such targeted health risks can be induced intentionally and at scale by manipulating models that generate peptide candidates. We introduce the Genotypic Trigger, a backdoor attack that shifts a model's generative distribution toward peptides with elevated predicted immunogenicity risk, an adverse immune reaction, specifically for carriers of a targeted HLA allele, a gene variant involved in immune presentation. Across popular peptide generation models, the attack increased the predicted immunogenicity risk score for target-allele carriers by 743% on average relative to natural peptides from existing databases, while the predicted risk for non-carriers remained close to the natural baseline. Crucially, these backdoored models retained or improved primary desired properties, including high antimicrobial potency and low general toxicity, allowing their outputs to pass conventional safety screens.
Andy Huang, Chentao Yue, Branka Vucetic, Yonghui Li
Semantic error control coding (SECC) has emerged as a promising paradigm for improving communication reliability by exploiting the inherent structure and semantic dependencies of transmitted information. This paper proposes a semantic successive cancellation list (SCL) decoder for polar codes carrying natural-language text. A fine-tuned byte-level language model provides next-byte priors, which are converted into conditional bit costs and incorporated directly into the SCL path metric before each pruning step. This allows the decoder to jointly exploit channel reliability and source structure while retaining the conventional polar coding framework. The language model can also be invoked only for bytes whose channel decisions are unreliable, trading decoding performance for latency. Simulations for length-512 polar codes show substantial block error rate (BLER) improvements over conventional CRC-aided SCL (CA-SCL) decoding. At rate R=0.75 and list size L=16, the proposed decoder achieves more than 1 dB of gain in BLER compared to CA-SCL with the same L. Moreover, with L=8, it outperforms conventional CA-SCL with L=256 in terms of BLER, while requiring about one quarter of the decoding time of the latter in the evaluated software implementation.