Author

Aris Karatzikos

The University of Texas at AustinORCID 0009-0005-2655-2422Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:DNA methylation· 1 Assay:proteomics· 1 Research Focus:sequence-to-function modeling· 1 Approach:statistical model· 1 Approach:transformer / foundation model· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Ilias Georgakopoulos‐SoaresiD· 2 shared Ioannis MouratidisiD· 2 shared Aggeliki Vasilopoulou· 1 shared Akshatha NayakiD· 1 shared Alexandros Tzanakakis· 1 shared Candace S. Y. ChaniD· 1 shared Charalampos Koilakos· 1 shared Evangelos Avgoulas· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersGenomics

Ilias Georgakopoulos‐SoaresORCID

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2 papers

Recent·Most cited

GenomicsBioinformaticsPeer-reviewedJul 30, 2026

Accelerating Inference in Genomic Foundation Models via Speculative Decoding

Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos…·Ilias Georgakopoulos‐Soares

This paper introduces speculative decoding to accelerate genomic and proteomic sequence generation using foundation models without compromising prediction quality.

DOI 10.1093/bioinformatics/btag579

DNA methylationproteomics

𝕏 PostBluesky

BioinformaticsbioRxivPreprintJul 10, 2026

Safeguarding open-weight genomic foundation models through weight locking

Aris Karatzikos, Aggeliki Vasilopoulou, Candace S. Y. Chan…·Ilias Georgakopoulos‐Soares

The paper evaluates weight-locking techniques to prevent fine-tuning of genomic foundation models, finding that naive attacks fail but informed attacks can partially bypass the lock.

DOI 10.64898/2026.07.07.736795

whole-genome sequencingstatistical model

𝕏 PostBluesky