Saturating counters: application and design alternatives

Koren, Israel; Koren, Y.; Oomman, B.G.

doi:10.1109/arith.2003.1207683

Cited by 2 publications

(1 citation statement)

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“…Therefore, we can implement O = by using a subtracter, followed by a multiple controlled-NOT (CNOT) gate activated if and only if all the bits of x − y are 0, and at last a NOT gate. Moreover, we can implement O comp by combining a substacter with a CNOT gate activated if and only if the most significant bit of x − y is 0; this is because, if we adopt 2’s complement method to represent negative numbers, the most significant bit represents the sign of a number [27].…”

Section: Preliminarymentioning

confidence: 99%

Quantum algorithm for position weight matrix matching

Miyamoto

Yamamoto

Sakakibara

2023

Preprint

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We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The two proposed algorithms, the naive iteration method and the Monte-Carlo-based method, output matched segments, given the oracular accesses to the entries in the biological sequence and the PWM. The former uses quantum amplitude amplification (QAA) for sequence motif search, resulting in the query complexity scaling on the sequence length n, the sequence motif length m and the number of the PWMs K as Õ(m√Kn), which means speedup over existing classical algorithms with respect to n and K. The latter also uses QAA, and further, quantum Monte Carlo integration for segment score calculation, instead of iteratively operating quantum circuits for arithmetic in the naive iteration method; then it provides the additional speedup with respect to m in some situation. As a drawback, these algorithms use quantum random access memories and their initialization takes O(n) time. Nevertheless, our algorithms keep the advantage especially when we search matches in a sequence for many PWMs in parallel.

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Section: Preliminarymentioning

confidence: 99%