Hybrid Quantum Reinforcement Learning for Sequence Alignment (QLearning)
Annette Zapf, Sabine Wölk
Pairwise sequence alignment is central in bioinformatics for analyzing DNA, RNA, and proteins, revealing similarities that inform evolutionary relationships, gene or protein functions, and disease mechanisms. Classical dynamic programming guarantees optimal alignments but scales poorly, while heuristics reduce runtime at the cost of optimality and still require high resources. Quantum algorithms exploit superposition and entanglement to accelerate optimization or find exact solutions faster. We present a hybrid quantum reinforcement learning (RL) agent based on (Hamann & Wölk, 2022), optimized for NISQ hardware. The agent learns a policy mapping states to action sequences from feedback of an environment. Using a Grover-like subroutine, it evaluates all sequences in parallel, reinforcing those leading to a solution, which reduces environment interactions and can achieve a quadratic speedup over classical RL. To enable execution on current hardware, we introduce a novel Parameterized Quantum Policy embedding entire action sequences, combined with a simplified Grover routine using a black-box oracle. This reduces resource demands but requires prior knowledge and retraining per alignment, limiting generalization. We also outline design ideas for a more general Grover oracle and circuit with broader generalization, which, while not NISQ-compatible, suggest a promising direction for future work.
•Oct 6, 2025•0 citations