Related papers: Read Mapping Near Non-Volatile Memory

We propose a novel Hamming distance tolerant content-addressable memory (HD-CAM) for energy-efficient in memory approximate matching applications. HD-CAM implements approximate search using matchline charge redistribution rather than its…

The massive interest in deep neural networks (DNNs) for both computer vision and natural language processing has been sparked by the growth in computational power. However, this led to an increase in the memory footprint, to a point where…

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…

Deep neural network learning can be formulated as a non-convex optimization problem. Existing optimization algorithms, e.g., Adam, can learn the models fast, but may get stuck in local optima easily. In this paper, we introduce a novel…

Designing DNA and protein sequences with improved function has the potential to greatly accelerate synthetic biology. Machine learning models that accurately predict biological fitness from sequence are becoming a powerful tool for…

Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…

While memory-augmented neural networks (MANNs) offer an effective solution for few-shot learning (FSL) by integrating deep neural networks with external memory, the capacity requirements and energy overhead of data movement become enormous…

The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural…

Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition,…

In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…

Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost has led to an exponential…

Non-volatile memory (NVM) provides a scalable and power-efficient solution to replace DRAM as main memory. However, because of relatively high latency and low bandwidth of NVM, NVM is often paired with DRAM to build a heterogeneous memory…

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…

We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…

High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit…

In recent years, Approximate Nearest Neighbor Search (ANNS) has played a pivotal role in modern search and recommendation systems, especially in emerging LLM applications like Retrieval-Augmented Generation. There is a growing exploration…

Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…