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Graph neural networks (GNNs) leverage the connectivity and structure of real-world graphs to learn intricate properties and relationships between nodes. Many real-world graphs exceed the memory capacity of a GPU due to their sheer size, and…

Alignment-based conformance checking is the state-of-the-art approach for comparing observed process executions with normative process models. The standard exact solution relies on an A*-based heuristic search, which can exhibit exponential…

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…

Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…

Gaussian Process Regression (GPR) is an important type of supervised machine learning model with inherent uncertainty measure in its predictions. We propose a new framework, nuGPR, to address the well-known challenge of high computation…

The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…

Most parallel neural network training methods assume homogeneous computing resources. For example, synchronous data-parallel SGD suffers from significant synchronization overhead under heterogeneous workloads, often forcing practitioners to…

3D Gaussian splatting (3DGS) is a transformative technique with profound implications on novel view synthesis and real-time rendering. Given its importance, there have been many attempts to improve its performance. However, with the…

Uncertainty quantification for forward and inverse problems is a central challenge across physical and biomedical disciplines. We address this challenge for the problem of modeling subsurface flow at the Hanford Site by combining stochastic…

Achieving efficient task parallelism on many-core architectures is an important challenge. The widely used GNU OpenMP implementation of the popular OpenMP parallel programming model incurs high overhead for fine-grained, short-running tasks…

Graph-based Retrieval-augmented generation (RAG) has become a widely studied approach for improving the reasoning, accuracy, and factuality of Large Language Models (LLMs). However, many existing graph-based RAG systems overlook the high…

Low-Rank Adaptation (LoRA) has become the de facto method for parameter-efficient fine-tuning of large language models (LLMs), enabling rapid adaptation to diverse domains. In production, LoRA-based models are served at scale, creating…

Achieving high performance for GPU codes requires developers to have significant knowledge in parallel programming and GPU architectures, and in-depth understanding of the application. This combination makes it challenging to find…

Growing heterogeneity and configurability in HPC architectures has made auto-tuning applications and runtime parameters on these systems very complex. Users are presented with a multitude of options to configure parameters. In addition to…

Generative adversarial networks (GANs) have proven successful in image generation tasks. However, GAN training is inherently unstable. Although many works try to stabilize it by manually modifying GAN architecture, it requires much…

The global scarcity of GPUs necessitates more sophisticated strategies for Deep Learning jobs in shared cluster environments. Accurate estimation of how much GPU memory a job will require is fundamental to enabling advanced scheduling and…

The deployment of Large Language Models (LLMs) in recommender systems for predicting Click-Through Rates (CTR) necessitates a delicate balance between computational efficiency and predictive accuracy. This paper presents an optimization…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

Graph neural networks (GNNs) have extended the success of deep neural networks (DNNs) to non-Euclidean graph data, achieving ground-breaking performance on various tasks such as node classification and graph property prediction.…