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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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X0(2866) as a D*K¯* molecular state

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Physical Review D 2020年第9期102卷 091502(R)-091502(R)页

作者： Ming-Zhu Liu Ju-Jun Xie Li-Sheng Geng School of Physics Beihang University Beijing 100191 China Institute of Modern Physics Chinese Academy of Sciences Lanzhou 730000 China School of Nuclear Sciences and Technology University of Chinese Academy of Sciences Beijing 101408 China School of Physics and Microelectronics Zhengzhou University Zhengzhou Henan 450001 China Beijing Key Laboratory of Advanced Nuclear Materials and Physics Beihang University Beijing 100191 China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine and Engineering Beihang University Beijing 100191 China

Very recently the LHCb Collaboration reported the discovery of two open charm tetraquark states, X0(2866) and X1(2904). In the present work, we study the D(*) and K¯(*) interaction in the one-boson exchange model and show that X0(2866) can be understood as a D*K¯* molecule with I(JP)=0(0+), or at least it has a large molecular component. On the other hand, X1(2904) can not be interpreted as a molecular state. Inspired by the discovery of X0(2866) and the fact that the D*K¯* interaction is strong enough to generate a bound state, we also discuss the likely existence of other open charm molecules. In the meson-meson sector, two molecules near the mass thresholds of DD* and D*D* with I(JP)=0(1+) are obtained, and using the heavy quark flavor symmetry their B¯B¯* and B¯*B¯* counterparts are also predicted. In the meson-baryon sector, seven open charm molecules with I=1/2 near the mass thresholds of D(*)Σc(*) naturally appear, as dictated by the heavy quark spin symmetry.

关键词： Bound states Effective field theory Hadron-hadron interactions

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DDK system in finite volume

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Physical Review D 2020年第11期102卷 114515-114515页

作者： Jin-Yi Pang Jia-Jun Wu Li-Sheng Geng College of Science University of Shanghai for Science and Technology Shanghai 200093 China School of Physical Sciences University of Chinese Academy of Sciences Beijing 100049 China School of Physics Beihang University Beijing 100191 China Beijing Key Laboratory of Advanced Nuclear Materials and Physics Beihang University Beijing 100191 China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine School of Medicine and Engineering Beihang University Beijing 100191 China School of Physics and Microelectronics Zhengzhou University Zhengzhou Henan 450001 China

The DDK three-body system is supposed to be bound due to the strongly attractive interaction between the D meson and the K meson in the isospin zero channel. The minimum quark content of this three-body bound state is ccq¯s¯ with q=u, d. It will be an explicitly exotic tetraquark state once discovered. In order to confirm the phenomenological study of the DDK system, we can refer to lattice QCD as a powerful theoretical tool parallel to the experiment measurement. In this paper, a three-body quantization condition scheme is derived via the nonrelativistic effective theory and the particle-dimer picture in a finite volume. The lattice spectrum of this three-body system is calculated within the existing model inputs. The spectrum shows various interesting properties of the DDK system, and it may reveal the nature of the D*(2317). This predicated spectrum is expected to be tested in future lattice simulations.

关键词： Bound states Effective field theory Hadron-hadron interactions Lattice QCD

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Energy Saving Strategy of Power System Cluster Based on Container Virtualization

Energy Saving Strategy of Power System Cluster Based on Cont...

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IEEE Asia Power and Energy engineering Conference (APEEC)

作者： Ran Zheng Hao Wang Hai Jin Dechao Xu Yong Chen Xiaomeng Li Yufei Rao Zhenan Zhang National Engineering Research Center for Big Data Technology and System Services Computing Technology and System Lab Cluster and Grid Computing Lab School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China State Key Laboratory of Power Grid Safety and Energy Conservation China Electric Power Research Institute Haidian District Beijing China State Grid Henan Electric Power Company Electric Power Research Institute Zhengzhou China

ISBN: (数字)9781728167824

ISBN: (纸本)9781728167831

With the continuous development of power grids, the scale of supercomputing clusters has also gradually increased to carry a large number of power system simulation calculations, and the problem of high energy consumption has appeared. To solve this problem, we propose a container virtualization-based supercomputing cluster for power system. We analyze the impact of containers on power simulation calculations and compare the energy consumption effects of various container scheduling and migration algorithms on clusters. Experiments show that compared to virtual machines with hypervisor, which consumes massive resources and reduces performances by 28.4%, the performance degradation of container on power simulation calculation is 1.3%, which can be ignored. The energy consumption of load-concentration or resource-and-load-balance container scheduling algorithms is up to 4.0% lower and at least 2.2% lower than other algorithms. In container migration, the method combining autoregressive model with most-correlation and resource-andload-balance algorithms is better than other methods, which not only minimizes energy consumption, but also has lowest number of migrations and SLA violations. Experiments verify the feasibility and advantages of container migration in power system computing clusters.

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Review of bankruptcy prediction using machine learning and deep learning techniques

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Procedia Computer Science 2019年 162卷 895-899页

作者： Yi Qu Pei Quan Minglong Lei Yong Shi School of Economics and Management University of Chinese Academy of Sciences Beijing 100190 China Research Center on Fictitious Economy & Data Science Chinese Academy of Sciences Beijing 100190 China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing 100190 China Faculty of Information Technology Beijing University of Technology Beijing 100124 China College of Information Science and Technology University of Nebraska at Omaha NE 68182 USA

Bankruptcy prediction has long been a significant issue in finance and management science, which attracts the attention of researchers and practitioners. With the great development of modern information technology, it has evolved into using machine learning or deep learning algorithms to do the prediction, from the initial analysis of financial statements. In this paper, we will review the machine learning or deep learning models used in bankruptcy prediction, including the classical machine learning models such as Multivariant Discriminant Analysis (MDA), Logistic Regression (LR), Ensemble method, Neural Networks (NN) and Support Vector Machines (SVM), and major deep learning methods such as Deep Belief Network (DBN) and Convolutional Neural Network (CNN). In each model, the specific process of experiment and characteristics will be summarized through analyzing some typical articles. Finally, possible innovative changes of bankruptcy prediction and its future trends will be discussed.

关键词： Bankruptcy prediction Machine learning Deep learning

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Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives

arXiv

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arXiv 2025年

作者： Liu, Xiaokun Rastegari, Sayedmohammadreza Huang, Yijun Cheong, Sxe Chang Liu, Weikang Zhao, Wenjie Tian, Qihao Wang, Hongming Zhou, Shuo Guo, Yingjie Tabakhi, Sina Liu, Xianyuan Zhu, Zheqing Sang, Wei Lu, Haiping Institute of Big Data Science and Industry Shanxi University Taiyuan China School of Computer and Information Technology Shanxi University Taiyuan China Key Laboratory of Evolutionary Science Intelligence of Shanxi Province Shanxi Taiyuan China Faculty of Computer Engineering University of Isfahan Isfahan Iran The First Clinical Medical School Shanxi Medical University Taiyuan China School of Medicine & Population Health University of Sheffield Sheffield United Kingdom School of Computer Science University of Sheffield Sheffield United Kingdom Centre for Machine Intelligence University of Sheffield Sheffield United Kingdom Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Shanxi Medical University Taiyuan China Institute of Medical Technology Shanxi Medical University Taiyuan China

In cancer therapeutics, protein-metal binding mechanisms critically govern drug pharmacokinetics and targeting efficacy, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory methods used to study such mechanisms are often costly, low throughput, and limited in capturing dynamic biological processes, machine learning (ML) has emerged as a promising alternative. Despite increasing efforts to develop protein–metal binding datasets and ML algorithms, the application of ML in tumor protein-metal binding remains limited. key challenges include a shortage of high-quality, tumor-specific datasets, insufficient consideration of multiple data modalities, and the complexity of interpreting results due to the "black box" nature of complex ML models. This paper summarizes recent progress and ongoing challenges in using ML to predict tumor protein-metal binding, focusing on data, modeling, and interpretability. We present multimodal protein-metal binding datasets and outline strategies for acquiring, curating, and preprocessing them for training ML models. Moreover, we explore the complementary value provided by different data modalities and examine methods for their integration. We also review approaches for improving model interpretability to support more trustworthy decisions in cancer research. Finally, we offer our perspective on research opportunities and propose strategies to address the scarcity of tumor protein data and the limited number of predictive models for tumor protein–metal binding. We also highlight two promising directions for effective metal-based drug design: integrating protein–protein interaction data to provide structural insights into metal-binding events and predicting structural changes in tumor proteins after metal binding. Copyright © 2025, The Authors. All rights reserved.

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Rethinking loss design for large-scale 3D shape retrieval

arXiv

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arXiv 2019年

作者： Li, Zhaoqun Xu, Cheng Leng, Biao School of Computer Science and Engineering Beihang University Beijing100191 Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Beijing100191 State Key Laboratory of Virtual Reality Technology and Systems Beihang University Beijing100191

Learning discriminative shape representations is a crucial issue for large-scale 3D shape retrieval. In this paper, we propose the Collaborative Inner Product Loss (CIP Loss) to obtain ideal shape embedding that discriminative among different categories and clustered within the same class. Utilizing simple inner product operation, CIP loss explicitly enforces the features of the same class to be clustered in a linear subspace, while inter-class subspaces are constrained to be at least orthogonal. Compared to previous metric loss functions, CIP loss could provide more clear geometric interpretation for the embedding than Euclidean margin, and is easy to implement without normalization operation referring to cosine margin. Moreover, our proposed loss term can combine with other commonly used loss functions and can be easily plugged into existing off-the-shelf architectures. Extensive experiments conducted on the two public 3D object retrieval datasets, ModelNet and ShapeNetCore 55, demonstrate the effectiveness of our proposal, and our method has achieved state-of-the-art results on both datasets. Copyright © 2019, The Authors. All rights reserved.

关键词： Embeddings

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Kiwifruit detection in field images using Faster R-CNN with VGG16

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IFAC-PapersOnLine 2019年第30期52卷 76-81页

作者： Zhenzhen Song Longsheng Fu Jingzhu Wu Zhihao Liu Rui Li Yongjie Cui College of Mechanical and Electronic Engineering Northwest A&F University Yangling 712100 China College of Mechanical and Electronic Engineering Northwest A&F University Yangling 712100 China Key Laboratory of Agricultural Internet of Things Ministry of Agriculture Yangling 712100 China Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent Service Yangling 712100 China Center for Precision & Automated Agricultural Systems Washington State University Prosser WA 99350 USA Beijing Key Laboratory of Big Data Technology for Food Safety Beijing Technology and Business University Beijing 100048 China

Kiwifruit is widely planted in Shaanxi, China, accounting for approximately 70% of the local production, and 33% of the global. Harvesting kiwifruits in China relies mainly on manual picking, and it is labor-intensive. To develop a machine vision system for harvesting robot which can work all day, kiwifruit images were captured in an orchard at different timing, morning, afternoon, and night, with or without flash, respectively. Kiwifruit images of 2400 were divided into training (1440) and testing (960) groups. A Faster R-CNN model implemented by VGG16 were constructed and trained. The average precision of VGG16 model was 87.61%, and the kiwifruit images collected under different timing and lighting conditions were detected well. In the end, the performance of the proposed method was compared with ZFNet in the same image dataset. It suggested that the proposed method achieved higher detection average precision than ZFNet (72.50%). This system is able to detect different categories of fruit in the field effectively and provides strong support for the harvesting robot, which can work all day round during the busy season.

关键词： image detection kiwifruit VGG16 Faster R-CNN ZFNet data augmentation

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Enhancing 2D Representation via Adjacent Views for 3D Shape Retrieval

Enhancing 2D Representation via Adjacent Views for 3D Shape ...

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International Conference on Computer Vision (ICCV)

作者： Cheng Xu Zhaoqun Li Qiang Qiu Biao Leng Jingfei Jiang School of Computer Science & Engineering Beihang University Duke University Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University State Key Laboratory of Virtual Reality Technology and Systems Beihang University National Laboratory for Parallel and Distributed Processing National University of Defense Technology

ISBN: (数字)9781728148038

ISBN: (纸本)9781728148045

Multi-view shape descriptors obtained from various 2D images are commonly adopted in 3D shape retrieval. One major challenge is that significant shape information are discarded during 2D view rendering through projection. In this paper, we propose a convolutional neural network based method, CenterNet, to enhance each individual 2D view using its neighboring ones. By exploiting cross-view correlations, CenterNet learns how adjacent views can be maximally incorporated for an enhanced 2D representation to effectively describe shapes. We observe that a very small amount of, e.g., six, enhanced 2D views, are already sufficient for a panoramic shape description. Thus, by simply aggregating features from six enhanced 2D views, we arrive at a highly compact yet discriminative shape descriptor. The proposed shape descriptor significantly outperforms state-of-the-art 3D shape retrieval methods on the ModelNet and ShapeNetCore55 benchmarks, and also exhibits robustness against object occlusion.

关键词： Shape Three-dimensional displays Correlation Two dimensional displays Feature extraction Solid modeling Computational modeling

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An Adaptive Control Method for Arterial Signal Coordination Based on Deep Reinforcement Learning*

An Adaptive Control Method for Arterial Signal Coordination ...

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International Conference on Intelligent Transportation

作者： Peng Chen Zemao Zhu Guangquan Lu Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control School of Transportation Science and Engineering Beijing Advanced Innovation Center for Big Data and Brain Computing Beihang University Hai Dian District Beijing Beijing Key Laboratory for Cooperative Vehicle Infrastructure Systems and Safety Control School of Transportation Science and Engineering Beihang University Hai Dian District Beijing

ISBN: (纸本)9781538670255

Traffic signal control is a complex problem and it is difficult to determine an optimal strategy to control multi-directional traffic at multiple intersections. Recent years have witnessed numerous successes of deep learning neural networks in the fields of artificial intelligence. Motivated by the dominant performance of neural networks, this study attempts to develop a novel adaptive signal control approach by fusing deep learning (DL) and reinforcement learning (RL), i.e., deep reinforcement learning (DRL), for arterial signal coordination. DRL can considerably improve the ability to deal with large amounts of data processing, systematic perception and expression, which is key to coordinated control of arterial intersections. The proposed algorithm is implemented by utilizing real-time traffic detection data and aims to optimize the hybrid global and local reward functions. The experimental results obtained by traffic simulation software SUMO demonstrate the advantage of the proposed approach, as well as its efficiency and effectiveness compared with fixed-time and actual signal control methods.

关键词： Aerospace electronics Machine learning Adaptive control Traffic control Roads Optimization

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