arXiv Machine Learning October 16, 2026 By Charalampos Koilakos, Kimon-Antonios Provatas, Michail Patsakis, Candace SY Chan, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares

Poisoning the corpora of protein design systems during pre-training and retrieval

Read the original on arXiv Machine Learning →

The paper reports two data‑only poisoning attacks on protein design systems. In the first, poisoned sequences were added to the pre‑training corpus of large autoregressive language models, causing the models to reliably generate sequences triggered by specific patterns after as few as 200 contaminated examples. The second attack inserted malicious records into a retrieval corpus, enabling a single query‑aware record to dominate retrieval results and, in many cases, alter the generated protein sequence or transfer a new domain via homology.

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