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Quantum Machine Intelligence

Implementation of a Hamming distance–like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne

Kunal Kathuria, Aakrosh Ratan, Michael J. McConnell, Stefan Bekiranov

Published Jun 1, 2020• 24 citations
Publisher

Abstract

Abstract Motivated by the problem of classifying individuals with a disease versus controls using a functional genomic attribute as input, we present relatively efficient general purpose inner product–based kernel classifiers to classify the test as a normal or disease sample. We encode each training sample as a string of 1 s (presence) and 0 s (absence) representing the attribute’s existence across ordered physical blocks of the subdivided genome. Having binary-valued features allows for highly efficient data encoding in the computational basis for classifiers relying on binary operations. Given that a natural distance between binary strings is Hamming distance, which shares properties with bit-string inner products, our two classifiers apply different inner product measures for classification. The active inner product (AIP) is a direct dot product–based classifier whereas the symmetric inner product (SIP) classifies upon scoring correspondingly matching genomic attributes. SIP is a strongly Hamming distance–based classifier generally applicable to binary attribute-matching problems whereas AIP has general applications as a simple dot product–based classifier. The classifiers implement an inner product betweenN= 2ndimension test and train vectors usingnFredkin gates while the training sets are respectively entangled with the class-label qubit, without use of an ancilla. Moreover, each training class can be composed of an arbitrary numbermof samples that can be classically summed into one input string to effectively execute all test–train inner products simultaneously. Thus, our circuits require the same number of qubits for any number of training samples and are $O(\log {N})$ O(logN) in gate complexity after the states are prepared. Our classifiers were implemented on ibmqx2 (IBM-Q-team 2019b) and ibmq_16_melbourne (IBM-Q-team 2019a). The latter allowed encoding of 64 training features across the genome.

DOI
10.1007/s42484-020-00017-7

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Abstract Motivated by the problem of classifying individuals with a disease versus controls using a functional genomic attribute as input, we present relatively efficient general purpose inner product–based kernel classifiers to classify the test as a normal or disease sample. We encode each training sample as a string of 1 s (presence) and 0 s (absence) representing the attribute’s existence across ordered physical blocks of the subdivided genome. Having binary-valued features allows for highly efficient data encoding in the computational basis for classifiers relying on binary operations. Given that a natural distance between binary strings is Hamming distance, which shares properties with bit-string inner products, our two classifiers apply different inner product measures for classification. The active inner product (AIP) is a direct dot product–based classifier whereas the symmetric inner product (SIP) classifies upon scoring correspondingly matching genomic attributes. SIP is a strongly Hamming distance–based classifier generally applicable to binary attribute-matching problems whereas AIP has general applications as a simple dot product–based classifier. The classifiers implement an inner product betweenN= 2ndimension test and train vectors usingnFredkin gates while the training sets are respectively entangled with the class-label qubit, without use of an ancilla. Moreover, each training class can be composed of an arbitrary numbermof samples that can be classically summed into one input string to effectively execute all test–train inner products simultaneously. Thus, our circuits require the same number of qubits for any number of training samples and are O(log⁡N)O(\log {N})O(logN) O(logN) in gate complexity after the states are prepared. Our classifiers were implemented on ibmqx2 (IBM-Q-team 2019b) and ibmq_16_melbourne (IBM-Q-team 2019a). The latter allowed encoding of 64 training features across the genome.
Motivated by the problem of classifying individuals with a disease versus controls using functional genomic attributes as input, we encode the input as a string of 1s (presence) or 0s (absence) of the genomic attribute across the genome. Blocks of physical regions in the subdivided genome serve as the feature dimensions, which takes full advantage of remaining in the computational basis of a quantum computer. Given that a natural distance between two binary strings is the Hamming distance and that this distance shares properties with an inner product between qubits, we developed two Hamming-distance-like classifiers which apply two different kinds of inner products ("active" and "symmetric") to directly and efficiently classify a test input into either of two training classes. To account for multiple disease and control samples, each train class can be composed of an arbitrary number of bit strings (i.e., number of samples) that can be compressed into one input string per class. Thus, our circuits require the same number of qubits regardless of the number of training samples. These algorithms, which implement a training bisection decision plane, were simulated and implemented on IBMQX4 and IBMQX16. The latter allowed for encoding of 646464 training features across the genome for 222 (disease and control) training classes.
Abstract Quantum computing opens exciting opportunities for kernel-based machine learning methods, which have broad applications in data analysis. Recent works show that quantum computers can efficiently construct a model of a classifier by engineering the quantum interference effect to carry out the kernel evaluation in parallel. For practical applications of these quantum machine learning methods, an important issue is to minimize the size of quantum circuits. We present the simplest quantum circuit for constructing a kernel-based binary classifier. This is achieved by generalizing the interference circuit to encode data labels in the relative phases of the quantum state and by introducing compact amplitude encoding, which encodes two training data vectors into one quantum register. When compared to the simplest known quantum binary classifier, the number of qubits is reduced by two and the number of steps is reduced linearly with respect to the number of training data. The two-qubit measurement with post-selection required in the previous method is simplified to single-qubit measurement. Furthermore, the final quantum state has a smaller amount of entanglement than that of the previous method, which advocates the cost-effectiveness of our method. Our design also provides a straightforward way to handle an imbalanced data set, which is often encountered in many machine learning problems.
Quantum machine learning has experienced significant progress in both software and hardware development in the recent years and has emerged as an applicable area of near-term quantum computers. In this work, we investigate the feasibility of utilizing quantum machine learning (QML) on real clinical datasets. We propose two QML algorithms for data classification on IBM quantum hardware: a quantum distance classifier (qDS) and a simplified quantum-kernel support vector machine (sqKSVM). We utilize these different methods using the linear time quantum data encoding technique ([Formula: see text]) for embedding classical data into quantum states and estimating the inner product on the 15-qubit IBMQ Melbourne quantum computer. We match the predictive performance of our QML approaches with prior QML methods and with their classical counterpart algorithms for three open-access clinical datasets. Our results imply that the qDS in small sample and feature count datasets outperforms kernel-based methods. In contrast, quantum kernel approaches outperform qDS in high sample and feature count datasets. We demonstrate that the [Formula: see text] encoding increases predictive performance with up to + 2% area under the receiver operator characteristics curve across all quantum machine learning approaches, thus, making it ideal for machine learning tasks executed in Noisy Intermediate Scale Quantum computers.
Machine learning (ML) classification tasks can be carried out on a quantum computer (QC) using probabilistic quantum memory (PQM) and its extension, parametric PQM (P-PQM), by calculating the Hamming distance between an input pattern and a database ofrrrpatterns containingzzzfeatures withaaadistinct attributes. For PQM and P-PQM to correctly compute the Hamming distance, the feature must be encoded using one-hot encoding, which is memory intensive for multiattribute datasets witha>2a>2a>2. We can represent multiattribute data more compactly by replacing one-hot encoding with label encoding; both encodings yield the same Hamming distance. Implementing this replacement on a classical computer is trivial. However, replacing these encoding schemes on a QC is not straightforward because PQM and P-PQM operate at the bit level, rather than at the feature level (a feature is represented by a binary string of 0’s and 1’s). We present an enhanced P-PQM, called efficient P-PQM (EP-PQM), that allows label encoding of data stored in a PQM data structure and reduces the circuit depth of the data storage and retrieval procedures. We show implementations for an ideal QC and a noisy intermediate-scale quantum (NISQ) device. Our complexity analysis shows that the EP-PQM approach requiresO(zlog⁡2(a))O(z \log _{2}(a))O(zlog2​(a))qubits as opposed toO(za)O(za)O(za)qubits for P-PQM. EP-PQM also requires fewer gates, reducing gate count fromO(rza)O(rza)O(rza)toO(rzlog⁡2(a))O(rz\log _{2}(a))O(rzlog2​(a)). For five datasets, we demonstrate that training an ML classification model using EP-PQM requires 48% to 77% fewer qubits than P-PQM for datasets witha>2a>2a>2. EP-PQM reduces circuit depth in the range of 60% to 96%, depending on the dataset. The depth decreases further with a decomposed circuit, ranging between 94% and 99%. EP-PQM requires less space; thus, it can train on and classify larger datasets than previous PQM implementations on NISQ devices. Furthermore, reducing the number of gates speeds up the classification and reduces the noise associated with deep quantum circuits. Thus, EP-PQM brings us closer to scalable ML on an NISQ device.
Abstract Kernel methods have a wide spectrum of applications in machine learning. Recently, a link between quantum computing and kernel theory has been formally established, opening up opportunities for quantum techniques to enhance various existing machine-learning methods. We present a distance-based quantum classifier whose kernel is based on the quantum state fidelity between training and test data. The quantum kernel can be tailored systematically with a quantum circuit to raise the kernel to an arbitrary power and to assign arbitrary weights to each training data. Given a specific input state, our protocol calculates the weighted power sum of fidelities of quantum data in quantum parallel via a swap-test circuit followed by two single-qubit measurements, requiring only a constant number of repetitions regardless of the number of data. We also show that our classifier is equivalent to measuring the expectation value of a Helstrom operator, from which the well-known optimal quantum state discrimination can be derived. We demonstrate the performance of our classifier via classical simulations with a realistic noise model and proof-of-principle experiments using the IBM quantum cloud platform.
Machine learning is a powerful tool which, when given the availability of comprehensive datasets, required training iterations and the necessary resources to support them, can achieve impressive results in a variety of classification tasks. In this paper, we put forward a quantum alternative for users that do not posses the ability to gather and store large amounts of data to be used subsequently in lengthy training iterations. A light-weight probabilistic quantum binary classifier can be built by encoding the two chosen class representatives (images) into quantum vectors, such that a Principal Component decomposition can express the differences between them only along one dimension (basis vector). A standard measurement in the computational basis will then project any transformed input sample along one of the two classes. The classifier accepts quantum representations of images as input, which require exponentially fewer number of quantum bits compared with the number of classical bits used to store an image. The technique is illustrated on a "proof of concept" example, in which a quantum character recognizer is built to label any input sample image as either letter {\bf A} or {\bf P}. The quantum classifier can be tuned to "favor" any of the two classes and the measurement probabilities follow closely how far an input sample is from the two class representatives. Despite its relative simplicity, the quantum classifier can distinguish between the standard letter {\bf A} and the standard letter {\bf P} with 98%98\%98% accuracy. In principle, the procedure can be applied to any image classification task, including gray-scale and color images, as well as classification problems in which an input sample is characterized by a collection of properties given by their values.