Author

K. Provatas

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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 Aug 2026

Derivation of oligonucleotide barcodes that are absent from natural sequences

BarcodesDB is presented, a comprehensive database of synthetic DNA barcodes systematically identified by scanning 403 199 complete organismal genome assemblies across the tree of life, together with 215 Gbp of raw metagenomic sequencing reads spanning marine, soil, polar and host-associated environments, providing maxi...

Michail Patsakis, K. Provatas, I. Mouratidis et al. · Bioinformatics Advances · 0 citations

#machine learning Preprint Sep 2026

Auditing System-1 Models on Biosecurity-Relevant Benchmarks: Calibration, Selective Prediction, and Permutation Instability in a Non-Generative Model

Non-generative"System-1"models return structured probabilistic decisions in a single forward pass, without autoregressive decoding, at a small fraction of the inference cost of a generative model. This makes them of interest as inexpensive components in larger pipelines, but their reliability on biosecurity-relevant ta...

K. Provatas, I. Georgakopoulos-Soares · 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