RotorMap and Quantum Fingerprints of DNA Sequences via Rotary Position Embeddings
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arXiv
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| Autori principali: | , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2026
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| _version_ | 1866918422804168704 |
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| author | Yakymenko, Danylo Chernyshev, Maksym Savchenko, Illia Strelchuk, Sergii |
| author_facet | Yakymenko, Danylo Chernyshev, Maksym Savchenko, Illia Strelchuk, Sergii |
| contents | For strings of letters from a small alphabet, such as DNA sequences, we present a quantum encoding that empirically provides a strong correlation between the Levenshtein edit distance and the fidelity between quantum states defined by the encodings. It is based on the principles of Rotary Position Embeddings (RoPE), employed in modern large language models. Classically, this encoding yields RotorMap - a GPU-accelerated DNA mapping algorithm that achieves speedups of 50-700x over single-thread Minimap2 in proof-of-concept tests on human and maize genomes. For use on quantum devices, we introduce the Angular encoding, which is built from RoPE and directly outputs state preparation circuits. To verify its properties and utility on NISQ devices, we report results of experiments conducted on quantum computers from Quantinuum: the 56-qubit H2-1, H2-2 and the latest 98-qubit Helios-1. As a potential application, we consider a quantum DNA authentication problem and conjecture that a quantum advantage in one-way communication complexity could be achieved over any comparable classical solution. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2603_22245 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | RotorMap and Quantum Fingerprints of DNA Sequences via Rotary Position Embeddings Yakymenko, Danylo Chernyshev, Maksym Savchenko, Illia Strelchuk, Sergii Quantum Physics 68Q12, 68Q11. 68W05, 81P68, 92-08 For strings of letters from a small alphabet, such as DNA sequences, we present a quantum encoding that empirically provides a strong correlation between the Levenshtein edit distance and the fidelity between quantum states defined by the encodings. It is based on the principles of Rotary Position Embeddings (RoPE), employed in modern large language models. Classically, this encoding yields RotorMap - a GPU-accelerated DNA mapping algorithm that achieves speedups of 50-700x over single-thread Minimap2 in proof-of-concept tests on human and maize genomes. For use on quantum devices, we introduce the Angular encoding, which is built from RoPE and directly outputs state preparation circuits. To verify its properties and utility on NISQ devices, we report results of experiments conducted on quantum computers from Quantinuum: the 56-qubit H2-1, H2-2 and the latest 98-qubit Helios-1. As a potential application, we consider a quantum DNA authentication problem and conjecture that a quantum advantage in one-way communication complexity could be achieved over any comparable classical solution. |
| title | RotorMap and Quantum Fingerprints of DNA Sequences via Rotary Position Embeddings |
| topic | Quantum Physics 68Q12, 68Q11. 68W05, 81P68, 92-08 |
| url | https://arxiv.org/abs/2603.22245 |