Related papers: GateKeeper: A New Hardware Architecture for Accele…

A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…

The rapidly-changing deep learning landscape presents a unique opportunity for building inference accelerators optimized for specific datacenter-scale workloads. We propose Full-stack Accelerator Search Technique (FAST), a hardware…

The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…

Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as…

Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…

It is usually infeasible to fit and train an entire large deep neural network (DNN) model using a single edge device due to the limited resources. To facilitate intelligent applications across edge devices, researchers have proposed…

We tackle the problem of predicting the performance of MapReduce applications, designing accurate progress indicators that keep programmers informed on the percentage of completed computation time during the execution of a job. Through…

Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…

Recent advances in algorithm-hardware co-design for deep neural networks (DNNs) have demonstrated their potential in automatically designing neural architectures and hardware designs. Nevertheless, it is still a challenging optimization…

This paper presents Bancroft, a computational genomics acceleration platform that provides the illusion of practically infinite on-device memory capacity by compressing genomic data movement over PCIe. Bancroft introduces novel…

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…

Nowadays a diverse range of physiological data can be captured continuously for various applications in particular wellbeing and healthcare. Such data require efficient methods for classification and analysis. Deep learning algorithms have…

The paradigm shift towards local and on-device inference under stringent resource constraints is represented by the tiny machine learning (TinyML) domain. The primary goal of TinyML is to integrate intelligence into tiny, low-cost devices…

Recently, randomized algorithms for low-rank approximation of quaternion matrices have received increasing attention. However, for large-scale problems, existing quaternion orthonormalizations are inefficient, leading to slow rangefinders.…

Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are…

In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…

For strings of letters from a small alphabet, such as DNA sequences, we present a quantum encoding that empirically provides a strong correlation between the Levenshtein edit distance and the fidelity between quantum states defined by the…

Fast item ranking is an important task in recommender systems. In previous works, graph-based Approximate Nearest Neighbor (ANN) approaches have demonstrated good performance on item ranking tasks with generic searching/matching measures…

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…

While the prominent quantum computing architectures are based on superconducting technology, new quantum hardware technologies are emerging, such as Trapped Ions, Neutral Atoms (or FPQAs), Silicon Spin Qubits, etc. This diverse set of…