Related papers: MAFFT-inspired Quantum Shift-based Sequence Alignm…
Quantum computing promises breakthroughs in simulating and solving complex, classically intractable problems. However, current noisy intermediate-scale quantum (NISQ) devices are relatively small and error-prone, prohibiting large-scale…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…
We present a quantum synthesis algorithm designed to produce short circuits and to scale well in practice. The main contribution is a novel representation of circuits able to encode placement and topology using generic "gates", which allows…
We present QCAM, a quantum analogue of Content-Addressable Memory (CAM), useful for finding matches in two sequences of bit-strings. Our QCAM implementation takes advantage of Grover's search algorithm and proposes a highly-optimized…
Quantum sequential machines (QSMs) are a quantum version of stochastic sequential machines (SSMs). Recently, we showed that two QSMs M_1 and M_2 with n_1 and n_2 states, respectively, are equivalent iff they are (n_1+n_2)^2--equivalent…
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult…
We perform formal verification of quantum circuits by integrating several techniques specialized to particular classes of circuits. Our verification methodology is based on the new notion of a reversible miter that allows one to leverage…
Quantum computing leverages the unique properties of qubits and quantum parallelism to solve problems intractable for classical systems, offering unparalleled computational potential. However, the optimization of quantum circuits remains…
In this paper, we show the design and implementation of a quantum algorithm for industrial shift scheduling (QISS), which uses Grover's adaptive search to tackle a common and important class of valuable, real-world combinatorial…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
The multisilce method is an important algorithm for electron diffraction and image simulations in transmission electron microscopy. We have proposed a quantum algorithm of the multislice method based on quantum circuit model previously. In…
The use of Boolean Satisfiability (SAT) solver for hardware verification incurs exponential run-time in several instances. In this work we have proposed an efficient quantum SAT (qSAT) solver for equivalence checking of Boolean circuits…
The difference between classical and quantum algorithms (QA) is following: problem solved by QA is coded in the structure of the quantum operators. Input to QA in this case is always the same. Output of QA says which problem coded. In some…
Quantum multi-programming is a method utilizing contemporary noisy intermediate-scale quantum computers by executing multiple quantum circuits concurrently. Despite early research on it, the research remains on quantum gates or small-size…
Quantum computing is a hotspot technology for its potential to accelerate specific applications by exploiting quantum parallelism. However, current physical quantum computers are limited to a relatively small scale, simulators based on…
Satisfiability (SAT) is a central problem in computer science, and advances in SAT-solving algorithms have a far-reaching impact across many fields. Recent works have proposed quantum SAT solvers based on Grover's algorithm, a quantum…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…