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Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Machine- and deep-learning approaches for biological sequences depend critically on transforming raw DNA, RNA, and protein FASTA files into informative numerical representations. However, this process is often fragmented across multiple…
Quantum state tomography (QST) via local measurements on reduced density matrices (LQST) is a promising approach but becomes impractical for large systems. To tackle this challenge, we developed an efficient quantum state tomography method…
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…
Quarter sampling is a novel sensor design that allows for an acquisition of higher resolution images without increasing the number of pixels. When being used for video data, one out of four pixels is measured in each frame. Effectively,…
For unsupervised data-dependent hashing, the two most important requirements are to preserve similarity in the low-dimensional feature space and to minimize the binary quantization loss. A well-established hashing approach is Iterative…
We present QFAST, a quantum synthesis tool designed to produce short circuits and to scale well in practice. Our contributions are: 1) a novel representation of circuits able to encode placement and topology; 2) a hierarchical approach with…
Homomorphic Encryption (HE), allowing computations on encrypted data (ciphertext) without decrypting it first, enables secure but prohibitively slow Convolutional Neural Network (CNN) inference for privacy-preserving applications in clouds.…
Coreset selection compresses large datasets into compact, representative subsets, reducing the energy and computational burden of training deep neural networks. Existing methods are either: (i) DNN-based, which are tied to model-specific…
Quantum computing promises polynomial and exponential speedups in many domains, such as unstructured search and prime number factoring. However, quantum programs yield probabilistic outputs from exponentially growing distributions and are…
The popular VQ-VAE models reconstruct images through learning a discrete codebook but suffer from a significant issue in the rapid quality degradation of image reconstruction as the compression rate rises. One major reason is that a higher…
Tensor decomposition is an effective tool for learning multi-way structures and heterogeneous features from high-dimensional data, such as the multi-view images and multichannel electroencephalography (EEG) signals, are often represented by…
Approximate Nearest-Neighbor Search (ANNS) is a key technique in retrieval-augmented generation (RAG), enabling rapid identification of the most relevant high-dimensional embeddings from massive vector databases. Modern ANNS engines…
Homomorphic encryption (HE) enables computations on encrypted data by concealing information under noise for security. However, the process of bootstrapping, which resets the noise level in the ciphertext, is computationally expensive and…
The data representation in a machine-learning model strongly influences its performance. This becomes even more important for quantum machine learning models implemented on noisy intermediate scale quantum (NISQ) devices. Encoding high…
High-Order, High-Dimension, and Sparse Tensor (HOHDST) data originates from real industrial applications, i.e., social networks, recommender systems, bio-information, and traffic information. Sparse Tensor Decomposition (STD) can project…
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To…
High-performance learned image compression codecs require flexible probability models to fit latent representations. Gaussian Mixture Models (GMMs) were proposed to satisfy this demand, but suffer from a significant runtime performance…
The Unlimited Sensing Framework (USF) was recently introduced to overcome the sensor saturation bottleneck in conventional digital acquisition systems. At its core, the USF allows for high-dynamic-range (HDR) signal reconstruction by…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…