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Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. This paper introduces SpecPCM, an in-memory computing (IMC) accelerator designed to…

This paper presents software implementations of batch computations, dealing with multi-precision integer operations. In this work, we use the Single Instruction Multiple Data (SIMD) AVX512 instruction set of the x86-64 processors, in…

Neural networks with a latency requirement on the order of microseconds, like the ones used at the CERN Large Hadron Collider, are typically deployed on FPGAs fully unrolled and pipelined. A bottleneck for the deployment of such neural…

This paper presents a new distributed-memory algorithm called FastSV for finding connected components in an undirected graph. Our algorithm simplifies the classic Shiloach-Vishkin algorithm and employs several novel and efficient hooking…

Partial differential equations (PDEs) with near singular solutions pose significant challenges for traditional numerical methods, particularly in complex geometries where mesh generation and adaptive refinement become computationally…

In recent years, novel AI accelerators have emerged as promising alternatives to GPU for AI model training and inference tasks. One such accelerator, the Cerebras CS-3, achieves strong performance on large model training as well as…

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…

We introduce FastPM, a highly-scalable approximated particle mesh N-body solver, which implements the particle mesh (PM) scheme enforcing correct linear displacement (1LPT) evolution via modified kick and drift factors. Employing a…

Autoregressive Models (ARMs) have long dominated the landscape of Large Language Models. Recently, a new paradigm has emerged in the form of diffusion-based Large Language Models (dLLMs), which generate text by iteratively denoising masked…

Tensors play a vital role in machine learning (ML) and often exhibit properties best explored while maintaining high-order. Efficiently performing ML computations requires taking advantage of sparsity, but generalized hardware support is…

Smart programmable microgrids (SPM) is an emerging technology for making microgrids more software-defined and less hardware-independent such that converting distributed energy resources (DERs) to networked community microgrids becomes…

Dense linear algebra libraries, such as BLAS and LAPACK, provide a relevant collection of numerical tools for many scientific and engineering applications. While there exist high performance implementations of the BLAS (and LAPACK)…

The $hp$-adaptive finite element method (FEM) - where one independently chooses the mesh size ($h$) and polynomial degree ($p$) to be used on each cell - has long been known to have better theoretical convergence properties than either $h$-…

On modern architectures, the performance of 32-bit operations is often at least twice as fast as the performance of 64-bit operations. By using a combination of 32-bit and 64-bit floating point arithmetic, the performance of many dense and…

Data structures for efficient sampling from a set of weighted items are an important building block of many applications. However, few parallel solutions are known. We close many of these gaps both for shared-memory and distributed-memory…

Sparsity is a growing trend in modern DNN models. Existing Sparse-Sparse Matrix Multiplication (SpMSpM) accelerators are tailored to a particular SpMSpM dataflow (i.e., Inner Product, Outer Product or Gustavsons), that determines their…

We present scalable distributed-memory algorithms for sparse matrix permutation, extraction, and assignment. Our methods follow an Identify-Exchange-Build (IEB) strategy where each process identifies the local nonzeros to be sent, exchanges…

Processing-in-memory (PIM) has emerged as the go to solution for addressing the von Neumann bottleneck in edge AI accelerators. However, state-of-the-art (SoTA) digital PIM approaches suffer from low compute density, primarily due to the…

A machine learning (ML) based equivariant neural network for constructing distributed charge models (DCMs) of arbitrary resolution, DCM-net, is presented. DCMs efficiently and accurately model the anisotropy of the molecular electrostatic…

De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…