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In this work we propose a highly optimized version of a simulated annealing (SA) algorithm adapted to the more recently developed Graphic Processor Units (GPUs). The programming has been carried out with CUDA toolkit, specially designed for…
State space models (SSMs) like Mamba have recently attracted much attention. Compared to Transformer-based large language models (LLMs), Mamba achieves linear computation complexity with the sequence length and demonstrates superior…
A projection-based immersed boundary method is dominated by sparse linear algebra routines. Using the open-source Cusp library, we observe a speedup (with respect to a single CPU core) which reflects the constraints of a bandwidth-dominated…
Recent quantum-inspired methods based on the Simulated Annealing (SA) algorithm have shown strong potential for solving combinatorial optimization problems. However, Grover's algorithm [1] in gate-based quantum computing offers only a…
State Space Model (SSM)-based machine learning architectures have recently gained significant attention for processing sequential data. Mamba, a recent sequence-to-sequence SSM, offers competitive accuracy with superior computational…
Synthetic data generation has become an increasingly popular way of training models without the need for large, manually labeled datasets. For tasks like text embedding, synthetic data offers diverse and scalable training examples,…
We present SymPhas 2.0, a major update of the compile-time symbolic algebra simulation framework SymPhas for phase-field and reaction-diffusion models. This release introduces significant expansions and enhancements that enable the…
The reduction of a banded matrix to bidiagonal form is a critical step in the calculation of Singular Values, a cornerstone of scientific computing and AI. Although inherently parallel, this step has traditionally been considered unsuitable…
Principal component analysis (PCA) is a statistical technique commonly used in multivariate data analysis. However, PCA can be difficult to interpret and explain since the principal components (PCs) are linear combinations of the original…
In-memory database query processing frequently involves substantial data transfers between the CPU and memory, leading to inefficiencies due to Von Neumann bottleneck. Processing-in-Memory (PIM) architectures offer a viable solution to…
With the growing number of data-intensive workloads, GPU, which is the state-of-the-art single-instruction-multiple-thread (SIMT) processor, is hindered by the memory bandwidth wall. To alleviate this bottleneck, previously proposed…
Matlab is very widely used in scientific computing, but Matlab computational efficiency is lower than C language program. In order to improve the computing speed, some toolbox can use GPU to accelerate the computation. This paper describes…
Graph Neural Networks (GNNs) are becoming a promising technique in various domains due to their excellent capabilities in modeling non-Euclidean data. Although a spectrum of accelerators has been proposed to accelerate the inference of…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
$\textit{De Novo}$ Genome assembly is one of the most important tasks in computational biology. ELBA is the state-of-the-art distributed-memory parallel algorithm for overlap detection and layout simplification steps of $\textit{De Novo}$…
Developing efficient GPU kernels can be difficult because of the complexity of GPU architectures and programming models. Existing performance tools only provide coarse-grained suggestions at the kernel level, if any. In this paper, we…
Synthetic data augmentation helps language models learn new knowledge in data-constrained domains. However, naively scaling existing synthetic data methods by training on more synthetic tokens or using stronger generators yields diminishing…
Efficient parallelization of algorithms on general-purpose GPUs is essential in many areas today. However, it is a non-trivial task for software engineers to utilize GPUs to improve the performance of high-level programs in general.…
Modern GPUs are able to perform significantly more arithmetic operations than transfers of a single word to or from global memory. Hence, many GPU kernels are limited by memory bandwidth and cannot exploit the arithmetic power of GPUs.…
With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…