Related papers: EXMA: A Genomics Accelerator for Exact-Matching
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…
Research into Few-shot Semantic Segmentation (FSS) has attracted great attention, with the goal to segment target objects in a query image given only a few annotated support images of the target class. A key to this challenging task is to…
Emerging machine learning (ML) models (e.g., transformers) involve memory pin bandwidth-bound matrix-vector (MV) computation in inference. By avoiding pin crossings, processing in memory (PIM) can improve performance and energy for…
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…
Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. However, current computational methods often struggle with suboptimal performance due to…
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…
Approximate nearest neighbor search (ANNS) plays an indispensable role in a wide variety of applications, including recommendation systems, information retrieval, and semantic search. Among the cutting-edge ANNS algorithms, graph-based…
Arbitrary-precision integer multiplication is the core kernel of many applications in simulation, cryptography, etc. Existing acceleration of arbitrary-precision integer multiplication includes CPUs, GPUs, FPGAs, and ASICs. Among these…
Medical imaging is an essential tool for diagnosing and treating diseases. However, lacking medical images can lead to inaccurate diagnoses and ineffective treatments. Generative models offer a promising solution for addressing medical…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Large matrix multiplication is a cornerstone of modern machine learning workloads, yet traditional approaches suffer from cubic computational complexity (e.g., $\mathcal{O}(n^3)$ for a matrix of size $n\times n$). We present Low-Rank GEMM,…
Weight-only quantization has emerged as a promising solution to the deployment challenges of large language models (LLMs). However, it necessitates FP-INT operations, which make implementation on general-purpose hardware like GPUs…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Large language models (LLMs) have demonstrated exceptional proficiency in understanding and generating human language, but efficient inference on resource-constrained embedded devices remains challenging due to large model sizes and…
Time series analysis is a key technique for extracting and predicting events in domains as diverse as epidemiology, genomics, neuroscience, environmental sciences, economics, and more. Matrix profile, the state-of-the-art algorithm to…
Time series analysis is a key technique for extracting and predicting events in domains as diverse as epidemiology, genomics, neuroscience, environmental sciences, economics, and more. Matrix profile, the state-of-the-art algorithm to…
Performance optimization is the art of continuous seeking a harmonious mapping between the application domain and hardware. Recent years have witnessed a surge of deep learning (DL) applications in industry. Conventional wisdom for…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…