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Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction

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Journal of Integrative Agriculture 2024年第5期23卷 1634-1643页

作者： Keanning Li Bingxing An Mang Liang Tianpeng chang Tianyu Deng Lili Du sheng cao Yueying Du Hongyan Li Lingyang Xu Lupei Zhang Xue Gao Junya LI Huijiang Gao Laboratory of Molecular Biology and Bovine Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China college of computer and Information Engineering Tianjin Agricultural UniversityTianjin 300384China college of Animal science and technology Qingdao Agricultural UniversityQingdao 266109China Tongliao Animal Agriculture Development Service Center Tongliao 028000China

Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction ***,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,*** results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for *** methods also captured more genetic variance than *** study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.

关键词： multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

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Journal of Genetics and Genomics 2024年第4期51卷 443-453页

作者： Shuyu Liang Sicheng Xu Shichong Zhou Cai chang Zhiming Shao Yuanyuan Wang sheng Chen Yunxia Huang Yi Guo Department of Electronic Engineering School of Information Science and TechnologyFudan UniversityShanghai 200433China The Key Laboratory of Medical Imaging Computing and computer Assisted Intervention(MICCAI)of Shanghai Shanghai 200032China Shanghai Key Laboratory of Metabolic Remodeling and Health Institute of Metabolism and Integrative BiologyFudan UniversityShanghai 200433China Department of Ultrasound Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai 200032China Department of Breast Surgery Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai 200032China

Investigating correlations between radiomic and genomic profiling in breast cancer(BC)molecular subtypes is crucial for understanding disease mechanisms and providing personalized *** present a well-designed radiogenomic framework image–gene–gene set(IMAGGS),which detects multi-way associations in BC subtypes by integrating radiomic and genomic *** dataset consists of 721 patients,each of whom has 12 ultrasound(US)images captured from different angles and gene mutation *** better characterize tumor traits,12 multi-angle US images are fused using two distinct ***,we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm,deviating from the prevalent one-to-one relationship pattern observed in previous *** radiomic and genomic features are screened using these *** addition,gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC *** further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and *** together,IMAGGS provides a comprehensive characterization for diseases by associating imaging,genes,and gene sets,paving the way for biological interpretation of radiomics and development of targeted therapy.

关键词： IMAGGS Radiogenomic framework "lmage-gene-geneset"associations Molecular subtypes Breast cancer

An efficient data layout scheme for better I/O balancing in RAID-6 storage systems

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Frontiers of Information technology & Electronic Engineering 2015年第5期16卷 335-345页

作者： Ping xie Jian-zhong HUANG Er-wei DAI qiang cao chang-sheng xie wuhan National Laboratory for Opto Electronics Huazhong University of Science & Technology computer college Qinghai Normal University

Among redundant arrays of independent disks(RAID)-6 codes, maximum distance separable(MDS)based RAID-6 codes are popular because they have the optimal storage efficiency. Although vertical MDS codes exhibit better load balancing compared to horizontal MDS codes in partial stripes, an I/O unbalancing problem still exists in some vertical codes. To address this issue, we propose a novel efficient data layout, uniform P-code(UPC), to support highly balanced I/Os among P-coded disk arrays(i.e., PC). In UPC, the nonuniformly distributed information symbols in each parity chain of P-code are moved along their columns to other rows, thus enabling the parity chain to keep original parity relationships and tolerate double disk failures. The UPC scheme not only achieves optimal storage efficiency, computational complexity, and update complexity, but also supports better I/O balancing in the context of large-scale storage systems. We also conduct a performance study on reconstruction algorithms using an analytical model. Besides extensive theoretical analysis, comparative performance experiments are conducted by replaying real-world workloads under various configurations. Experimental results illustrate that our UPC scheme significantly outperforms the PC scheme in terms of average user response time. In particular, in the case of a 12-disk array, the UPC scheme can improve the access performance of the RAID-6 storage system by29.9% compared to the PC scheme.

关键词： RAID-6 Data availability High performance I/O balancing

Strip-oriented asynchronous prefetching for parallel disk systems

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Journal of Zhejiang university-science C(computers and Electronics) 2012年第11期13卷 799-815页

作者： Yang LIU Jian-zhong HUANG Xiao-dong SHI qiang cao chang-sheng xie wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology Wuhan 430074 China School of computer science and technology Huazhong University of Science and Technology Wuhan 430074 China

Sequential prefetching schemes are widely employed in storage servers to mask disk latency and improve system throughput. However, existing schemes cannot benefit parallel disk systems as expected due to the fact that they ignore the distinct internal characteristics of the parallel disk system, in particular, data striping. Moreover, their aggressive prefetching pattern suffers from premature evictions and prolonged request latencies. In this paper, we propose a strip-oriented asynchronous prefetching (SoAP) technique, which is dedicated to the parallel disk system. It settles the above-mentioned problems by providing multiple novel features, e.g., enhanced prediction accuracy, adaptive prefetching strength, physical data layout awareness, and timely prefetching. To validate SoAP, we implement a prototype by modifying the software redundant arrays of inexpensive disks (RAID) under Linux. Experimental results demonstrate that SoAP can consistently offer improved average response time and throughput to the parallel disk system under non-random workloads compared with STEP, SP, ASP, and Linux-like SEQPs.

关键词： Parallel disk system Strip Sequential prefetching Asynchronous scheduling

一种基于NAS的镜像文件系统的研究及其在Linux下的实现

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计算机科学 2004年第9期31卷 119-123页

作者：谢长生蔡斌曹强刘朝斌黄建忠华中科技大学计算机学院外存储系统国家重点实验室武汉430074

全球数据量快速的增长使得NAS得以广泛应用,但是传统的NAS系统在设备发生故障时数据会丢失,难以满足现代存储对系统的高可用性和高可靠性的要求。本文提出了一种用于实现文件镜像功能的NAS系统框架结构,并且在VFS机制的基础之上,在Linu... 详细信息

全球数据量快速的增长使得NAS得以广泛应用,但是传统的NAS系统在设备发生故障时数据会丢失,难以满足现代存储对系统的高可用性和高可靠性的要求。本文提出了一种用于实现文件镜像功能的NAS系统框架结构,并且在VFS机制的基础之上,在Linux平台下,设计并实现了一种应用于这种结构的镜像文件系统(NASMFS)。它屏蔽了系统底层中各个NAS设备中文件系统的差别,给用户提供了一个安全、可靠的统一的存储目录空间,透明地完成文件镜像功能,在设备发生故障时能够从镜像的文件中恢复数据,从而在可用性、可靠性等方面弥补了传统NAS系统的不足,满足了应用的需要。

关键词： NAS 镜像文件镜像功能文件系统 Linux平台高可用性存储故障 VFS 屏蔽

Exploration of the coupled lattice Boltzmann model based on a multiphase field model:A study of the solid-liquid-gas interaction mechanism in the solidification process

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Chinese Physics B 2024年第3期33卷 638-648页

作者：朱昶胜王利军高梓豪刘硕李广召 college of computer and Communication Lanzhou University of TechnologyLanzhou 730050China State Key Laboratory of Gansu Advanced Processing and Recycling of Non-Ferrous Metal Lanzhou University of TechnologyLanzhou 730050China Institute of Modern Physics Chinese Academy of SciencesLanzhou 730000China

A multiphase field model coupled with a lattice Boltzmann(PF-LBM)model is proposed to simulate the distribution mechanism of bubbles and solutes at the solid-liquid interface,the interaction between dendrites and bubbles,and the effects of different temperatures,anisotropic strengths and tilting angles on the solidified organization of the SCN-0.24wt.%butanedinitrile alloy during the solidification *** model adopts a multiphase field model to simulate the growth of dendrites,calculates the growth motions of dendrites based on the interfacial solute equilibrium;and adopts a lattice Boltzmann model(LBM)based on the Shan-Chen multiphase flow to simulate the growth and motions of bubbles in the liquid phase,which includes the interaction between solid-liquid-gas *** simulation results show that during the directional growth of columnar dendrites,bubbles first precipitate out slowly at the very bottom of the dendrites,and then rise up due to the different solid-liquid densities and pressure *** bubbles will interact with the dendrite in the process of flow migration,such as extrusion,overflow,fusion and *** the case of wide gaps in the dendrite channels,bubbles will fuse to form larger irregular bubbles,and in the case of dense channels,bubbles will deform due to the extrusion of *** the simulated region,as the dendrites converge and diverge,the bubbles precipitate out of the dendrites by compression and diffusion,which also causes physical phenomena such as fusion and spillage of the *** results reveal the physical mechanisms of bubble nucleation,growth and kinematic evolution during solidification and interaction with dendrite growth.

关键词： multiphase field model lattice Boltzmann model(LBM) Shan-Chen multiphase flow solidification organization

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USN安全研究与设计

计算机科学 2003年第9期30卷 107-110页

作者：韩德志耿红琴谢长生胡玉平暨南大学计算机系广州510632 华中科技大学计算机学院武汉430074 河南驻马店师范专科学校河南驻马店453000

1引言随着网络存储的发展,出现了两种非常重要的网络存储技术:NAS(Network Attached Storage)和SAN(StorageArea Network)[1,2].按照存储网络工业协会(SNIA)的定义:NAS是可以直接联到网络上向用户提供文件级服务的存储设备,而SAN是一种... 详细信息

1引言随着网络存储的发展,出现了两种非常重要的网络存储技术:NAS(Network Attached Storage)和SAN(StorageArea Network)[1,2].按照存储网络工业协会(SNIA)的定义:NAS是可以直接联到网络上向用户提供文件级服务的存储设备,而SAN是一种利用Fibre Channel等互联协议连接起来的可以在服务器和存储系统之间直接传送数据的网络.

关键词： USN 存储设备安全网络存储存储系统存储结构

Dynamic-YOLOX:复杂背景下的苹果叶片病害检测模型

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计算机科学与探索 2024年第8期18卷 2118-2129页

作者：盛帅段先华胡维康曹伟杰江苏科技大学计算机学院江苏镇江212100

针对目前苹果叶片数据集的叶片病害种类不全以及图片背景单一等问题,构建了复杂背景下包括苹果叶部六种常见病害的苹果叶片病害数据集。针对目前主流苹果叶片病害检测模型检测精度不高、模型复杂和不满足实时监测等问题,提出了一种基于Y... 详细信息

针对目前苹果叶片数据集的叶片病害种类不全以及图片背景单一等问题,构建了复杂背景下包括苹果叶部六种常见病害的苹果叶片病害数据集。针对目前主流苹果叶片病害检测模型检测精度不高、模型复杂和不满足实时监测等问题,提出了一种基于YOLOX-S(you only look once X-S)改进得到的复杂背景下的苹果叶片病害自适应检测模型Dynamic-YOLOX。设计并使用ECA-SPPFCSPC模块(efficient channel attention cross-stage partial fast spatial pyramid pooling module)更换YOLOX-S模型主干网络尾部Dark5中的空间金字塔池化(SPP)以及跨阶段局部网络(CSPNet)模块来增强模型关注深层语义特征、抑制无用信息的能力,并减少硬件内存开销。设计了动态跨阶段局部网络(ODCSP)模块,并用其更换YOLOX-S模型主干网络中Dark2、Dark3、Dark4部分以及颈部网络中所有的CSPNet模块,使得模型在面对不同输入特征时有更强的自适应性,在减少模型的参数量和计算量的同时提高了模型的平均检测精度。引入Varifocal Loss更换模型中分类置信度损失的BCEWithLogits Loss来提升模型对苹果叶片中密集小目标病害的检测精度。在自制数据集上Dynamic-YOLOX相对原始YOLOX-S模型的mAP提升了4.54个百分点,达到84.63%,同时模型的参数量和计算量分别下降了11.97%和13.45%,检测速度达到44.07 FPS。对比主流苹果叶片病害检测模型,Dynamic-YOLOX具有一定优越性。

关键词：苹果叶部病害目标检测 YOLOX 动态跨阶段局部网络(ODCSP) Varifocal Loss

Boosting家族Boost-by-majority系列代表算法

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计算机科学 2003年第4期30卷 133-135页

作者：涂承胜刁力力鲁明羽陆玉昌重庆三峡学院计算机科学系重庆万州404000 清华大学计算机科学技术系

1 引言 Boosting由Freund和Schapire于1990年提出,是提高预测学习系统预测能力的有效工具,也是组合学习中最具代表性的方法,其代表算法可分为Boost-by-majority和AdaBoost两个系列。Boosting操纵训练例子以产生多个假设。从而建立通过... 详细信息

1 引言 Boosting由Freund和Schapire于1990年提出,是提高预测学习系统预测能力的有效工具,也是组合学习中最具代表性的方法,其代表算法可分为Boost-by-majority和AdaBoost两个系列。Boosting操纵训练例子以产生多个假设。从而建立通过投票结合的预测器集合。Boosting在训练例子上维护一套概率分布。

关键词：学习算法 Boosting算法 Boost-by-majority系列算法组合学习