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Quantum computing (QC) has opened the door to advancements in machine learning (ML) tasks that are currently implemented in the classical domain. Convolutional neural networks (CNNs) are classical ML architectures that exploit data locality and possess a simpler structure than a fully connected multi-layer perceptrons (MLPs) without compromising the accuracy of classification. However, the concept of preserving data locality is usually overlooked in the existing quantum counterparts of CNNs, particularly for extracting multifeatures in multidimensional data. In this paper, we present an multidimensional quantum convolutional classifier (MQCC) that performs multidimensional and multifeature quantum convolution with average and Euclidean pooling, thus adapting the CNN structure to a variational quantum algorithm (VQA). The experimental work was conducted using multidimensional data to validate the correctness and demonstrate the scalability of the proposed method utilizing both noisy and noise-free quantum simulations. We evaluated the MQCC model with reference to reported work on state-of-the-art quantum simulators from IBM Quantum and Xanadu using a variety of standard ML datasets. The experimental results show the favorable characteristics of our proposed techniques compared with existing work with respect to a number of quantitative metrics, such as the number of training parameters, cross-entropy loss, classification accuracy, circuit depth, and quantum gate count. 

Convolutional neural networks (CNNs) have proven to be a very efficient class of machine learning (ML) architectures for handling multidimensional data by maintaining data locality, especially in the field of computer vision. Data pooling, a major component of CNNs, plays a crucial role in extracting important features of the input data and downsampling its dimensionality. Multidimensional pooling, however, is not efficiently implemented in existing ML algorithms. In particular, quantum machine learning (QML) algorithms have a tendency to ignore data locality for higher dimensions by representing/flattening multidimensional data as simple one-dimensional data. In this work, we propose using the quantum Haar transform (QHT) and quantum partial measurement for performing generalized pooling operations on multidimensional data. We present the corresponding decoherence-optimized quantum circuits for the proposed techniques along with their theoretical circuit depth analysis. Our experimental work was conducted using multidimensional data, ranging from 1-D audio data to 2-D image data to 3-D hyperspectral data, to demonstrate the scalability of the proposed methods. In our experiments, we utilized both noisy and noise-free quantum simulations on a state-of-the-art quantum simulator from IBM Quantum. We also show the efficiency of our proposed techniques for multidimensional data by reporting the fidelity of results. 

The convolution operation plays a vital role in a wide range of critical algorithms across various domains, such as digital image processing, convolutional neural networks, and quantum machine learning. In existing implementations, particularly in quantum neural networks, convolution operations are usually approximated by the application of filters with data strides that are equal to the filter window sizes. One challenge with these implementations is preserving the spatial and temporal localities of the input features, specifically for data with higher dimensions. In addition, the deep circuits required to perform quantum convolution with a unity stride, especially for multidimensional data, increase the risk of violating decoherence constraints. In this work, we propose depth-optimized circuits for performing generalized multidimensional quantum convolution operations with unity stride targeting applications that process data with high dimensions, such as hyperspectral imagery and remote sensing. We experimentally evaluate and demonstrate the applicability of the proposed techniques by using real-world, high-resolution, multidimensional image data on a state-of-the-art quantum simulator from IBM Quantum. 

Abstract Recombination has been shown to contribute to human immunodeficiency virus-1 (HIV-1) evolution in vivo, but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models to in vitro experimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission 1, increasing infection multiplicity; 2, promoting the co-transmission of different virus strains from cell to cell; and 3, increasing the rate at which point mutations are generated as a result of more reverse transcription events. This study further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of three viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV evolution. 

Abstract CD4 + T cells are central mediators of adaptive and innate immune responses and constitute a major reservoir for human immunodeficiency virus (HIV) in vivo. Detailed investigations of resting human CD4 + T cells have been precluded by the absence of efficient approaches for genetic manipulation limiting our understanding of HIV replication and restricting efforts to find a cure. Here we report a method for rapid, efficient, activation-neutral gene editing of resting, polyclonal human CD4 + T cells using optimized cell cultivation and nucleofection conditions of Cas9–guide RNA ribonucleoprotein complexes. Up to six genes, including HIV dependency and restriction factors, were knocked out individually or simultaneously and functionally characterized. Moreover, we demonstrate the knock in of double-stranded DNA donor templates into different endogenous loci, enabling the study of the physiological interplay of cellular and viral components at single-cell resolution. Together, this technique allows improved molecular and functional characterizations of HIV biology and general immune functions in resting CD4 + T cells.