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SRAMM: Short read alignment mapping metrics

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arXiv 2021年

作者： Chon, Alvin Huang, Xiaoqiu Bioinformatics and Computational Biology Graduate Program Iowa State University AmesIA50010 United States Department of Computer Science Iowa State University AmesIA50010 United States

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering process of aligned short reads for various downstream applications. SRAMM is compatible with Python 2.6+ and Python 3.6+ on all operating systems. It works with any short read aligner that generates SAM/BAM/CRAM file outputs and reports 'AS' tags. It is freely available under the MIT license at http://***/achon/sramm. © 2021, CC BY.

关键词： Mapping

Video-Text as Game Players: Hierarchical Banzhaf Interaction for Cross-Modal Representation Learning

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Video-Text as Game Players: Hierarchical Banzhaf Interaction...

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Peng Jin Jinfa Huang Pengfei Xiong Shangxuan Tian Chang Liu Xiangyang Ji Li Yuan Jie Chen School of Electronic and Computer Engineering Peking University Shenzhen China AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Shenzhen China Shopee Shenzhen China Department of Automation and BNRist Tsinghua University Beijing China Peng Cheng Laboratory Shenzhen China

Contrastive learning-based video-language representation learning approaches, e.g., CLIP, have achieved outstanding performance, which pursue semantic interaction upon pre-defined video-text pairs. To clarify this coarse-grained global interaction and move a step further, we have to encounter challenging shell-breaking interactions for fine-grained cross-modal learning. In this paper, we creatively model video-text as game players with multivariate cooperative game theory to wisely handle the uncertainty during fine-grained semantic interaction with diverse granularity, flexible combination, and vague intensity. Concretely, we propose Hierarchical Banzhaf Interaction (HBI) to value possible correspondence between video frames and text words for sensitive and explainable cross-modal contrast. To efficiently realize the cooperative game of multiple video frames and multiple text words, the proposed method clusters the original video frames (text words) and computes the Banzhaf Interaction between the merged tokens. By stacking token merge modules, we achieve cooperative games at different semantic levels. Extensive experiments on commonly used text-video retrieval and video-question answering bench-marks with superior performances justify the efficacy of our HBI. More encouragingly, it can also serve as a visualization tool to promote the understanding of cross-modal interaction, which have a far-reaching impact on the community. Project page is available at https://***/HBI/.

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Measurement of Water Diffusion Coefficient in Cross-Linked Gelatins Using the Terahertz Time-Domain Spectroscopy Technique

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Measurement of Water Diffusion Coefficient in Cross-Linked G...

Conference on Lasers and Electro-Optics (CLEO)

作者： D. Walden D. Chakraborty J. Cheng A. Straksys A. Stirke W. CMA Melo A. Jukna I. Komissarov Roman Sobolewski Department of Physics and Astronomy University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA Materials Science Graduate Program University of Rochester Rochester New York USA State Research Institute Center for Physical Sciences & Technology Vilnius Lithuania Department of Physics Vilnius Gediminas Technical University Vilnius Lithuania Department of Electrical and Computer Engineering University of Rochester Rochester New York USA

A novel method has been developed to evaluate the water diffusion dynamics in gelatin-based gels, based on transient terahertz time-domain spectroscopy measurements. Such gels are widely used models for human skin.

ISBN: (纸本)9798350369311

关键词： Spectroscopy Measurement by laser beam Lasers and electrooptics Laser modes Skin Time-domain analysis Transient analysis Electro-optical waveguides

ACSeg: Adaptive Conceptualization for Unsupervised Semantic Segmentation

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ACSeg: Adaptive Conceptualization for Unsupervised Semantic ...

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Kehan Li Zhennan Wang Zesen Cheng Runyi Yu Yian Zhao Guoli Song Chang Liu Li Yuan Jie Chen School of Electronic and Computer Engineering Peking University Shenzhen China AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Shenzhen China Peng Cheng Laboratory Shenzhen China Dalian University of Technology Department of Automation and BNRist Tsinghua University Beijing China

Recently, self-supervised large-scale visual pre-training models have shown great promise in representing pixel-level semantic relationships, significantly promoting the development of unsupervised dense prediction tasks, e.g., unsupervised semantic segmentation (USS). The extracted relationship among pixel-level representations typically contains rich class-aware information that semantically identical pixel embeddings in the representation space gather together to form sophisticated concepts. However, leveraging the learned models to ascertain semantically consistent pixel groups or regions in the image is non-trivial since over/ under-clustering overwhelms the conceptualization procedure under various semantic distributions of different images. In this work, we investigate the pixel-level semantic aggregation in self-supervised ViT pre-trained models as image Segmentation and propose the Adaptive Conceptualization approach for USS, termed ACSeg. Concretely, we explicitly encode concepts into learnable prototypes and design the Adaptive Concept Generator (ACG), which adaptively maps these prototypes to informative concepts for each image. Meanwhile, considering the scene complexity of different images, we propose the modularity loss to optimize ACG independent of the concept number based on estimating the intensity of pixel pairs belonging to the same concept. Finally, we turn the USS task into classifying the discovered concepts in an unsupervised manner. Extensive experiments with state-of-the-art results demonstrate the effectiveness of the proposed ACSeg.

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Towards the continuum limit of nucleon form factors at the physical point using lattice QCD

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arXiv 2022年

作者： Tsuji, Ryutaro Aoki, Yasumichi Ishikawa, Ken-Ichi Kuramashi, Yoshinobu Sasaki, Shoichi Shintani, Eigo Yamazaki, Takeshi Department of Physics Tohoku University Sendai980-8578 Japan RIKEN Center for Computational Science Kobe650-0047 Japan Core of Research for the Energetic Universe Graduate School of Advanced Science and Engineering Hiroshima University Higashi-Hiroshima739-8526 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Faculty of pure and Applied Sciences University of Tsukuba Tsukuba305-8571 Japan

We present results for the axial charge and root-mean-square (RMS) radii of the nucleon obtained from 2+1 flavor lattice QCD at the physical point with a large spatial extent of about 10 fm. Our calculations are performed with the PACS10 gauge configurations generated by the PACS Collaboration with the six stout-smeared O(a) improved Wilson-clover quark action and Iwasaki gauge action at β = 1.82 and 2.00 corresponding to lattice spacings of 0.085 fm and 0.063 fm respectively. We first evaluate the value of gA/gV , which is not renormalized in the continuum limit and thus ends up with the renormalized axial charge. Moreover, we also calculate the nucleon elastic form factors and determine three kinds of isovector RMS radii such as electric, magnetic and axial ones at the two lattice spacings. We finally discuss the discretization uncertainties on renormalized axial charge and isovector RMS radii towards the continuum limit. Copyright © 2022, The Authors. All rights reserved.

关键词： Gages

Exploring Collaborative Distributed Diffusion-Based AI-Generated Content (AIGC) in Wireless Networks

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arXiv 2023年

作者： Du, Hongyang Zhang, Ruichen Niyato, Dusit Kang, Jiawen Xiong, Zehui Kim, Dong In Shen, Xuemin Poor, H. Vincent The School of Computer Science and Engineering The Energy Research Institute @ NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore The School of Computer Science and Engineering Nanyang Technological University Singapore The School of Computer and Information Technology Beijing Jiaotong University Beijing100044 China The School of Automation Guangdong University of Technology China The Pillar of Information Systems Technology and Design Singapore University of Technology and Design Singapore The Department of Electrical and Computer Engineering Sungkyunkwan University Suwon16419 Korea Republic of The Department of Electrical and Computer Engineering University of Waterloo Canada The Department of Electrical and Computer Engineering Princeton University PrincetonNJ08544 United States

Driven by advances in generative artificial intelligence (AI) techniques and algorithms, the widespread adoption of AI-generated content (AIGC) has emerged, allowing for the generation of diverse and high-quality content. Especially, the diffusion model-based AIGC technique has been widely used to generate content in a variety of modalities. However, the real-world implementation of AIGC models, particularly on resource-constrained devices such as mobile phones, introduces significant challenges related to energy consumption and privacy concerns. To further promote the realization of ubiquitous AIGC services, we propose a novel collaborative distributed diffusion-based AIGC framework. By capitalizing on collaboration among devices in wireless networks, the proposed framework facilitates the efficient execution of AIGC tasks, optimizing edge computation resource utilization. Furthermore, we examine the practical implementation of the denoising steps on mobile phones, the impact of the proposed approach on the wireless network-aided AIGC landscape, and the future opportunities associated with its real-world integration. The contributions of this paper not only offer a promising solution to the existing limitations of AIGC services but also pave the way for future research in device collaboration, resource optimization, and the seamless delivery of AIGC services across various devices. Our code is available at https://***/HongyangDu/DistributedDiffusion. © 2023, CC BY.

关键词： Wireless networks

Steady-state phases and interaction-induced depletion in a driven-dissipative chirally-coupled dissimilar atomic array

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arXiv 2023年

作者： Chung, Shao-Hung Handayana, I. Gusti Ngurah Yudi Tsao, Yi-Lin Wu, Chun-Chi Lin, G.-D. Jen, H.H. Department of Physics Center for Quantum Science and Engineering National Taiwan University Taipei10617 Taiwan Institute of Atomic and Molecular Sciences Academia Sinica Taipei10617 Taiwan Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taiwan Department of Physics National Central University Taoyuan City320317 Taiwan Physics Division National Center for Theoretical Sciences Taipei10617 Taiwan Trapped-Ion Quantum Computing Laboratory Hon Hai Research Institute Taipei11492 Taiwan

A nanophotonic waveguide coupled with an atomic array forms one of the strongly-coupled quantum interfaces to showcase many fascinating collective features of quantum dynamics. In particular for a dissimilar array of two different interparticle spacings with competing photon-mediated dipole-dipole interactions and directionality of couplings, we study the steady-state phases of atomic excitations under a weakly-driven condition of laser field. We identify a partial set of steady-state phases of the driven system composed of combinations of steady-state solutions in a homogeneous array. We also reveal an intricate role of the atom at the interface of the dissimilar array in determining the steady-state phases and find an alteration in the dichotomy of the phases strongly associated with steady-state distributions with crystalline orders. We further investigate in detail the interaction-induced depletion in half of the dissimilar array. This blockaded region results from two contrasting interparticle spacings near the reciprocal coupling regime, which is evidenced from the analytical solutions under the reciprocal coupling. Our results can provide insights in the driven-dissipative quantum phases of atomic excitations with nonreciprocal couplings and pave the avenues toward quantum simulations of exotic many-body states essential for quantum information applications. Copyright © 2023, The Authors. All rights reserved.

关键词： Atoms

Observation of Photonic Chiral Flatbands

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arXiv 2024年

作者： Choi, Minho Alù, Andrea Majumdar, Arka Department of Electrical and Computer Engineering University of Washington SeattleWA98195 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10031 United States Department of Physics University of Washington SeattleWA98195 United States

Distinct selectivity to the spin angular momenta of photons have garnered significant attention in recent years, for their relevance in basic science and for imaging and sensing applications. While nonlocal metasurfaces with strong chiral responses to the incident light have been reported, these responses are typically limited to a narrow range of incident angles. In this study, we demonstrate a nonlocal metasurface that showcases strong chirality, characterized by circular dichroism larger than 0.6, over a wide range of incident angles ±5o. Its quality factor, circular dichroism and resonant frequency can be optimized by design. These findings pave the way to further advance the development of valley-selective optical cavities and augmented reality applications. Copyright © 2024, The Authors. All rights reserved.

关键词： Natural frequencies

Model Decision Support System for Diagnosis COVID-19 Using Forward Chaining: A Case in Indonesia 8

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Model Decision Support System for Diagnosis COVID-19 Using F...

8th International Conference on Cyber and IT Service Management, CITSM 2020

作者： Henderi Maulana, Miftah Warnars, Harco Leslie Hendrie S. Setiyadi, Didik Qurrohman, Taufik University of Raharja Department of Informatics Engineering Tangerang Indonesia Postgraduate of Information Engineering University of Raharja Tangerang Indonesia BINUS Graduate Program Doctor of Computer Science Bina Nusantara University Computer Science Department Jakarta Indonesia Bina Insani University Department of Informatics Engineering Bekasi Indonesia

ISBN: (纸本)9781728177014

The government in Indonesia and its staff work together to make tactical steps to prevent the spread of COVID-19 in the community. From the ministerial level to the heads of the provinces, regencies, and even the government. Therefore, this study aims to make a model decision support system to diagnose patients exposed to Covid-19, such as people in control, patients in oversight, and those who are positive for the Covid-19 Virus. Model decision support system development aims to provide information about the development of COVID- 19 and help the community in diagnosing themselves related to COVID-19 infection. In this study, the authors use the forward chaining method in application to get conclusions from the symptoms of the Covid-19. This research resulted in an application that patients exposed to the Covid-19, and it's also provided a solution for healing from patients. And this could be a reference for patients before consulting further with the doctor. © 2020 IEEE.

关键词： Decision support systems