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Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data…
NAND flash memory is ubiquitous in everyday life today because its capacity has continuously increased and cost has continuously decreased over decades. This positive growth is a result of two key trends: (1) effective process technology…
Dynamic programming (DP) based algorithms are essential yet compute-intensive parts of numerous bioinformatics pipelines, which typically involve populating a 2-D scoring matrix based on a recursive formula, optionally followed by a…
Solid state disks (SSDs) have advanced to outperform traditional hard drives significantly in both random reads and writes. However, heavy random writes trigger fre- quent garbage collection and decrease the performance of SSDs. In an SSD…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
Deep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become…
Graph neural networks (GNNs) process large-scale graphs consisting of a hundred billion edges. In contrast to traditional deep learning, unique behaviors of the emerging GNNs are engaged with a large set of graphs and embedding data on…
In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates…
Curating, processing, and combining large-scale medical imaging datasets from national studies is a non-trivial task due to the intense computation and data throughput required, variability of acquired data, and associated financial…
Unlike non-volatile memory that resides on the processor memory bus, memory-semantic solid-state drives (SSDs) support both byte and block access granularity via PCIe or CXL interconnects. They provide scalable memory capacity using NAND…
Although NAND flash memory has achieved continuous capacity improvements via advanced 3D stacking and multi-level cell technologies, these innovations introduce new reliability challenges, particularly lateral charge spreading (LCS), absent…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…
Embedded Systems combine one or more processor cores with dedicated logic running on an ASIC or FPGA to meet design goals at reasonable cost. It is achieved by profiling the application with variety of aspects like performance, memory…
Solid-state drives (SSDs) are well suited for near-data processing (NDP) because they: (1) store large application datasets, and (2) support three NDP paradigms: in-storage processing (ISP), processing using DRAM in the SSD (PuD-SSD), and…
Parallel computing is very important to accelerate the performance of software systems. Additionally, considering that a recurring challenge is to process high data volumes continuously, stream processing emerged as a paradigm and software…
During genomics life science research, the data volume of whole genomics and life science algorithm is going bigger and bigger, which is calculated as TB, PB or EB etc. The key problem will be how to store and analyze the data with…
Genetic Programming (GP) is a computationally intensive technique which also has a high degree of natural parallelism. Parallel computing architectures have become commonplace especially with regards Graphics Processing Units (GPU). Hence,…
The advent of dedicated Deep Learning (DL) accelerators and neuromorphic processors has brought on new opportunities for applying both Deep and Spiking Neural Network (SNN) algorithms to healthcare and biomedical applications at the edge.…
Software is a great enabler for a number of projects that otherwise would be impossible to perform. Such projects include Space Exploration, Weather Modeling, Genome Projects, and many others. It is critical that software aiding these…
SSDs are emerging storage devices which unlike HDDs, do not have mechanical parts and therefore, have superior performance compared to HDDs. Due to the high cost of SSDs, entirely replacing HDDs with SSDs is not economically justified.…