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Accelerated pattern matching method on a quantum computing system

Pradeep Niroula

Published Mar 18, 2024• 0 citations
OpenAlex

Abstract

A method of determining a pattern in a sequence of bits using a quantum computing system includes setting a first register of a quantum processor in a superposition of a plurality of string index states, encoding a bit string in a second register of the quantum processor, encoding a bit pattern in a third register of the quantum processor, circularly shifting qubits of the second register conditioned on the first register, amplifying an amplitude of a state combined with the first register in which the circularly shifted qubits of the second register matches qubits of the third register, measuring an amplitude of the first register and determining a string index state of the plurality of string index states associated with the amplified state, and outputting, by use of a classical computer, a string index associated with the first register in the measured state.

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A method of determining a pattern in a sequence of bits using a quantum computing system includes setting a first register of a quantum processor in a superposition of a plurality of string index states, encoding a bit string in a second register of the quantum processor, encoding a bit pattern in a third register of the quantum processor, circularly shifting qubits of the second register conditioned on the first register, amplifying an amplitude of a state combined with the first register in which the circularly shifted qubits of the second register matches qubits of the third register, measuring an amplitude of the first register and determining a string index state of the plurality of string index states associated with the amplified state, and outputting, by use of a classical computer, a string index associated with the first register in the measured state.
A computing system includes a quantum processor with qubits, a classical memory including a quantum program defining a plurality of instructions in a source language, and a classical processor configured to: (i) receive a circuit of gates representing a quantum program for a variational algorithm in which computation is interleaved with compilation; (ii) identify a plurality of blocks, each block includes a subcircuit of gates, leaving one or more remainder subcircuits of the circuit of gates outside of the plurality of blocks; (iii) pre-compile each block of the plurality of blocks with a pulse generation program to generate a plurality of pre-compiled blocks including control pulses configured to perform the associated block on the quantum processor; and (iv) iteratively execute the quantum program using the pre-compiled blocks as static during runtime and recompiling the one or more remainder subcircuits on the classical processor at each iteration of execution.
A quantum computing system includes a quantum processor having a plurality of qubits, a classical memory, and a classical processor. The classical processor is configured to compile a quantum program into logical assembly instructions in an intermediate language, aggregate the logical assembly instructions together into a plurality of logical blocks of instructions, generate a logical schedule for the quantum program based on commutativity between the plurality of logical blocks, generate a tentative physical schedule based on the logical schedule, the tentative physical schedule includes a mapping of the logical assembly instructions in the logical schedule onto the plurality of qubits of the quantum processor, aggregate instructions together within the tentative physical schedule that do not reduce parallelism, thereby generating an updated physical schedule; generate optimized control pulses for the aggregated instructions, and execute the quantum program on the quantum processor with the optimized control pulses and the updated physical schedule.
A quantum computing system includes a quantum processor having a plurality of qubits, a classical memory, and a classical processor. The classical processor is configured to compile a quantum program into logical assembly instructions in an intermediate language, aggregate the logical assembly instructions together into a plurality of logical blocks of instructions, generate a logical schedule for the quantum program based on commutativity between the plurality of logical blocks, generate a tentative physical schedule based on the logical schedule, the tentative physical schedule includes a mapping of the logical assembly instructions in the logical schedule onto the plurality of qubits of the quantum processor, aggregate instructions together within the tentative physical schedule that do not reduce parallelism, thereby generating an updated physical schedule; generate optimized control pulses for the aggregated instructions, and execute the quantum program on the quantum processor with the optimized control pulses and the updated physical schedule.
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors in a few years are expected to scale up and be more robust for efficiently computing important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of data processing for genome sequence reconstruction. This research describes an architecture-aware implementation of a quantum algorithm for sub-sequence alignment. A new algorithm named QiBAM (quantum indexed bidirectional associative memory) is proposed, which uses approximate pattern-matching based on Hamming distances. QiBAM extends the Grover’s search algorithm in two ways, allowing: (1) approximate matches needed for read errors in genomics, and (2) a distributed search for multiple solutions over the quantum encoding of DNA sequences. This approach gives a quadratic speedup over the classical algorithm. A full implementation of the algorithm is provided and verified using the OpenQL compiler and QX Simulator framework. Our implementation represents a first exploration towards a full-stack quantum accelerated genome sequencing pipeline design.
This work-in-progress paper consists of four points which relate to the foundations and physical realization of quantum computing. The first point is that the qubit cannot be taken as the basic unit for quantum computing, because not every superposition of bit-strings of length n can be factored into a string of n-qubits. The second point is that the “No-cloning” theorem does not apply to the copying of one quantum register into another register, because the mathematical representation of this copying is the identity operator, which is manifestly linear. The third point is that quantum parallelism is not destroyed only by environmental decoherence. There are two other forms of decoherence, which we call measurement decoherence and internal decoherence, that can also destroy quantum parallelism. The fourth point is that processing the contents of a quantum register “one qubit at a time” destroys entanglement. Keywords-qubit; entanglement; decoherence; no-cloning theorem; quantum register.
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of big data processing for genome sequence reconstruction. This research describes an architecture-aware implementation of a quantum algorithm for sub-sequence alignment. A new algorithm named QiBAM (quantum indexed bidirectional associative memory) is proposed, that uses approximate pattern-matching based on Hamming distances. QiBAM extends the Grover's search algorithm in two ways to allow for: (1) approximate matches needed for read errors in genomics, and (2) a distributed search for multiple solutions over the quantum encoding of DNA sequences. This approach gives a quadratic speedup over the classical algorithm. A full implementation of the algorithm is provided and verified using the OpenQL compiler and QX simulator framework. This represents a first exploration towards a full-stack quantum accelerated genome sequencing pipeline design. The open-source implementation can be found on https://github.com/prince-ph0en1x/QAGS.