Related papers: GenASM: A High-Performance, Low-Power Approximate …

Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…

At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…

Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…

Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…

The continuous shift of computational bottlenecks to the memory access and data transfer, especially for AI applications, poses the urgent needs of re-engineering the computer architecture fundamentals. Many edge computing applications,…

Processing in-memory (PIM) is promising to accelerate neural networks (NNs) because it minimizes data movement and provides large computational parallelism. Similar to machine learning accelerators, application mapping, which determines the…

Graph neural networks (GNNs) have gained significant interest for applications such as citation network analysis and drug discovery due to their ability to apply machine learning techniques on graph-structured data. GNNs typically employ a…

Automated Short Answer Scoring (ASAS) is a critical component in educational assessment. While traditional ASAS systems relied on rule-based algorithms or complex deep learning methods, recent advancements in Generative Language Models…

Similarity search is a key to a variety of applications including content-based search for images and video, recommendation systems, data deduplication, natural language processing, computer vision, databases, computational biology, and…

Processing Using Memory (PUM) accelerators have the potential to perform Deep Neural Network (DNN) inference by using arrays of memory cells as computation engines. Among various memory technologies, ReRAM crossbars show promising…

Low bit-precisions and their bit-slice sparsity have recently been studied to accelerate general matrix-multiplications (GEMM) during large-scale deep neural network (DNN) inferences. While the conventional symmetric quantization…

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…

Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…

We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…

Antibiotic Resistance (AR) is a critical global health challenge that necessitates the development of cost-effective, efficient, and accurate diagnostic tools. Given the genetic basis of AR, techniques such as Polymerase Chain Reaction…

Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…

Approximate nearest neighbor search (ANNS) has become vital to modern AI infrastructure, particularly in retrieval-augmented generation (RAG) applications. Numerous in-browser ANNS engines have emerged to seamlessly integrate with popular…

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…