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The GEneral Matrix Multiplication (GEMM) is one of the essential algorithms in scientific computing. Single-thread GEMM implementations are well-optimised with techniques like blocking and autotuning. However, due to the complexity of…
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…
Probabilistic reasoning is an essential tool for robust decision-making systems because of its ability to explicitly handle real-world uncertainty, constraints and causal relations. Consequently, researchers are developing hybrid models by…
Coordinating the design of sampling and sparse-dense matrix multiplication (SpMM) is crucial for accelerating graph neural networks (GNNs). However, due to irrational sampling strategies, existing methods face a trade-off between accuracy…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Neural networks are an increasingly attractive algorithm for natural language processing and pattern recognition. Deep networks with >50M parameters are made possible by modern GPU clusters operating at <50 pJ per op and more recently,…
Future computing systems, from handhelds to supercomputers, will undoubtedly be more parallel and heterogeneous than todays systems to provide more performance and energy efficiency. Thus, GPUs are increasingly being used to accelerate…
Transformer-based models have made tremendous impacts in natural language generation. However the inference speed is a bottleneck due to large model size and intensive computing involved in auto-regressive decoding process. We develop…
We assess the potential of quantum computing to accelerate computation of central tasks in genomics, focusing on often-neglected theoretical limitations. We discuss state-of-the-art challenges of quantum search, optimization, and machine…
Glioblastoma is a highly aggressive form of brain cancer characterized by rapid progression and poor prognosis. Despite advances in treatment, the underlying genetic mechanisms driving this aggressiveness remain poorly understood. In this…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Deep neural networks are widely deployed in many fields. Due to the in-situ computation (known as processing in memory) capacity of the Resistive Random Access Memory (ReRAM) crossbar, ReRAM-based accelerator shows potential in accelerating…
Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
This paper proposes a fast system technology co-optimization (STCO) framework that optimizes power, performance, and area (PPA) for next-generation IC design, addressing the challenges and opportunities presented by novel materials and…
As AI workloads drive increasing memory requirements, domain-specific accelerators need higher-density on-chip memory beyond what current SRAM scaling trends can provide. Simultaneously, the vast amounts of short-lived data in these…
Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…