9 papers
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…
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…
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…
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…