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Full-Text Articles in Physical Sciences and Mathematics
Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu
Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu
Computer Science Faculty Publications
We describe our experience porting FUN3D’s CUDA-optimized kernels to Intel oneAPI SYCL.We faced several challenges, including foremost the suboptimal performance of the oneAPI code on Intel’s new data center GPU. Suboptimal performance of the oneAPI code was due primarily to high register spills, memory latency, and poor vectorization. We addressed these issues by implementing the kernels using Intel oneAPI’s Explicit SIMD SYCL extension (ESIMD) API. The ESIMD API enables the writing of explicitly vectorized kernel code, gives more precise control over register usage and prefetching, and better handles thread divergence compared to SYCL. The ESIMD code outperforms the optimized SYCL …
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
Computer Science Faculty Publications
More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …
Theory Entity Extraction For Social And Behavioral Sciences Papers Using Distant Supervision, Xin Wei, Lamia Salsabil, Jian Wu
Theory Entity Extraction For Social And Behavioral Sciences Papers Using Distant Supervision, Xin Wei, Lamia Salsabil, Jian Wu
Computer Science Faculty Publications
Theories and models, which are common in scientific papers in almost all domains, usually provide the foundations of theoretical analysis and experiments. Understanding the use of theories and models can shed light on the credibility and reproducibility of research works. Compared with metadata, such as title, author, keywords, etc., theory extraction in scientific literature is rarely explored, especially for social and behavioral science (SBS) domains. One challenge of applying supervised learning methods is the lack of a large number of labeled samples for training. In this paper, we propose an automated framework based on distant supervision that leverages entity mentions …
Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu
Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu
Computer Science Faculty Publications
Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in …
Automatic Slide Generation For Scientific Papers, Athar Sefid, Jian Wu, Prasenjit Mitra, C. Lee Giles
Automatic Slide Generation For Scientific Papers, Athar Sefid, Jian Wu, Prasenjit Mitra, C. Lee Giles
Computer Science Faculty Publications
We describe our approach for automatically generating presentation slides for scientific papers using deep neural networks. Such slides can help authors have a starting point for their slide generation process. Extractive summarization techniques are applied to rank and select important sentences from the original document. Previous work identified important sentences based only on a limited number of features that were extracted from the position and structure of sentences in the paper. Our method extends previous work by (1) extracting a more comprehensive list of surface features, (2) considering semantic or meaning of the sentence, and (3) using context around the …