Author

Georgios A. Pavlopoulos

2 papers indexed here

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#machine learning Preprint Oct 2026

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

Protein foundation models increasingly support the generation of novel biological sequences, yet their reliance on large public datasets creates opportunities for adversarial manipulation of the material they learn from and retrieve. We investigate two data-only poisoning attacks against protein design systems, targeti...

Charalampos Koilakos, K. Provatas, Michail Patsakis et al. · 0 citations

Open access Jul 2026

Accelerating inference in genomic and proteomic foundation models via speculative decoding

Abstract Motivation Genomic and protein foundation models (GFMs and PFMs) have demonstrated strong performance in learning the language of DNA and proteins, but their use in large-scale sequence generation is limited by the latency of autoregressive decoding. Because every token triggers a forward pass of a large Trans...

K. Provatas, Aris Karatzikos, Charalampos Koilakos et al. · Bioinform. · 0 citations