12 papers
Tracing model-generated DNA with position-independent watermarking
Kimon Antonios Provatas1, Christos Galanopoulos, Ilias Georgakopoulos-Soares
Genomic language models can write synthetic DNA that carries no record of its origin. A generation-time watermark could provide a provenance signal, if a verifier can detect it usi…
Auditing System-1 Models on Biosecurity-Relevant Benchmarks: Calibration, Selective Prediction, and Permutation Instability in a Non-Generative Model
Kimon Antonios Provatas, Ilias Georgakopoulos-Soares
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…
Feasibility of Homomorphic Inference for a Genomic Foundation Model
Christos Galanopoulos, Kimon Antonios Provatas, Ilias Georgakopoulos-Soares
Human genomic sequences can identify individuals, cannot be replaced after disclosure, and are the inputs that genomic foundation models are designed to interpret. We assess whethe…
bioETH-Beacon: A Confidential On-Chain Genomic Beacon with Encrypted Counts, Filters, and Bounded Noise over a Fully Homomorphic EVM
Christos Galanopoulos, Kimon Antonios Provatas, Ilias Georgakopoulos-Soares
The Global Alliance for Genomics and Health (GA4GH) Beacon protocol lets researchers ask whether a genomic variant has been observed in a participating cohort and receive aggregate…
bioETH-PRS: Confidential Polygenic Risk Scoring without a Trusted Evaluator via Fully Homomorphic Encryption on a Programmable Blockchain
Kimon Antonios Provatas, Christos Galanopoulos, Ilias Georgakopoulos-Soares
Polygenic risk scores (PRSs) aggregate genetic effect estimates to predict disease susceptibility, yet clinical deployment often exposes raw genotype data to third-party compute in…
BioVeil MATRIX: Uncovering and categorizing vulnerabilities of agentic biological AI scientists
Kimon Antonios Provatas, Avery Self, Ioannis Mouratidis +1
Agentic AI scientists equipped with domain-specific tools are rapidly entering scientific workflows across disciplines, with especially strong uptake in the life sciences where the…
Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models
Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares
Foundation models trained on DNA sequences have achieved strong performance across biological tasks including variant effect prediction and genome design. These models rely on mass…
BEDCrypt: Privacy-preserving interval analytics with homomorphic encryption
Kimon Antonios Provatas, Ilias Georgakopoulos-Soares
Motivation. Genomic data and derived interval datasets can carry sensitive information, and the analysis itself can reveal an analyst's intent. As genomic workloads are increasingl…
Investigating DNA words and their distributions across the tree of life
Charalampos Koilakos, Kimonas Provatas, Michail Patsakis +2
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural la…
MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files
Michail Patsakis, Kimonas Provatas, Ioannis Mouratidis +1
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These al…
Zimin patterns in genomes
Nikol Chantzi, Ioannis Mouratidis, Ilias Georgakopoulos-Soares
Zimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first tim…
MAFin: Motif Detection in Multiple Alignment Files
Michail Patsakis, Kimonas Provatas, Fotis A. Baltoumas +4
Motivation: Genome and Proteome Alignments, represented by the Multiple Alignment File (MAF) format, have become a standard approach in the field of comparative genomics and proteo…