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DeeReCT-APA:Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

Genomics, Proteomics & Bioinformatics 2022年第3期20卷 483-495页

作者： Zhongxiao Li Yisheng Li Bin Zhang Yu Li Yongkang Long Juexiao Zhou Xudong Zou Min Zhang Yuhui Hu Wei Chen Xin Gao King Abdullah University of Science and Technology(KAUST) Computational Bioscience Research Center(CBRC)ComputerElectrical and Mathematical Sciences and Engineering(CEMSE)DivisionThuwal 23955-6900Saudi Arabia Department of Biology Southern University of Science and Technology(SUSTech)Shenzhen 518055China Cancer Science Institute of Singapore Singapore 117599Singapore

Alternative polyadenylation(APA)is a crucial step in post-transcriptional *** bioinformatic studies have mainly focused on the recognition of polyadenylation sites(PASs)in a given genomic sequence,which is a binary classification ***,computational methods for predicting the usage level of alternative PASs in the same gene have been ***,all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into *** address this,here we propose a deep learning architecture,Deep Regulatory Code and Tools for Alternative Polyadenylation(DeeReCT-APA),to quantitatively predict the usage of all alternative PASs of a given *** accommodate different genes with potentially different numbers of PASs,DeeReCT-APA treats the problem as a regression task with a variable-length *** on a convolutional neural network-long short-term memory(CNN-LSTM)architecture,DeeReCT-APA extracts sequence features with CNN layers,uses bidirectional LSTM to explicitly model the interactions among competing PASs,and outputs percentage scores representing the usage levels of all PASs of a *** addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene,we show that our method consistently outperforms other existing methods on three different tasks for which they are trained:pairwise comparison task,highest usage prediction task,and ranking ***,we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA *** code and data are available at https://***/lzx325/DeeReCT-APA-repo.

关键词： Polyadenylation Gene regulation Sequence analysis Deep learning Bioinformatics

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Ultra-flexible semitransparent organic photovoltaics

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npj Flexible Electronics 2023年第1期7卷 274-282页

作者： Hanbee Lee Soyeong Jeong Jae-Hyun Kim Yong-Ryun Jo Hyeong Ju Eun Byoungwook Park Sung Cheol Yoon Jong H.Kim Seung-Hoon Lee Sungjun Park Department of Electrical and Computer Engineering Ajou UniversitySuwon 16499Republic of Korea Department of Chemistry and Centre for Processable Electronics Imperial College LondonWhite City W120BZUK Department of Intelligence Semiconductor Engineering Ajou UniversitySuwon 16499Republic of Korea Advanced Photonics Research Institute(APRI) Gwangju Institute of Science and Technology(GIST)Gwangju 61005Republic of Korea Division of Molecular Science and Technology Ajou UniversitySuwon 16499Republic of Korea Division of Advanced Materials Korea Research Institute of Chemical Technology(KRICT)Daejeon 34114Republic of Korea Division of Advanced materials Engineering Kongju National University1223-24 Cheonan-daeroSeobuk-guCheonan-siChungcheongnam-doRepublic of Korea

Ultra-flexible organic photovoltaics(OPVs)are promising candidates for next-generation power sources owing to their low weight,transparency,and ***,obtaining ultra-flexibility under extreme repetitive mechanical stress while maintaining optical transparency remains challenging because of the intrinsic brittleness of transparent ***,we introduce straindurable ultra-flexible semitransparent OPVs with a thickness below 2μ*** conformal surface coverage of nanoscale thin metal electrodes(<10 nm)is achieved,resulting in extremely low flexural rigidity and high strain ***-depth optical and electrical analyses on ultrathin metal electrodes showed that the devices maintain over 73%of their initial efficiency after 1000 cycles of repetitive compression and release at 66%compressive strain,and the average visible light transmittances remain higher than 30%.To our knowledge,this is the first systematical study on mechanical behaviors of strain-durable ultra-flexible ST-OPVs through precise adjustment of each ultrathin electrode thickness toward the emergence of next-generation flexible power sources.

关键词： transparency durability rigidity

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Anomaly-Resistant Decentralized State Estimation Under Minimum Error Entropy With Fiducial Points for Wide-Area Power Systems

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IEEE/CAA Journal of Automatica Sinica 2024年第1期11卷 74-87页

作者： Bogang Qu Zidong Wang Bo Shen Hongli Dong Hongjian Liu the College of Automation Engineering Shanghai University of Electric PowerShanghai 200090China IEEE the Department of Computer Science Brunel University LondonUxbridgeMiddiesex UB83PHUK the College of Information Science and Technology Donghua UniversityShanghai 200051 the Engineering Research Center of Digitalized Textile and Fashion Technology Ministry of EducationShanghai 201620China the Artificial Intelligence Energy Research Institute Northeast Petroleum UniversityDaqing 163318 the Heilongjiang Provincial Key Laboratory of Networking and Intelligent Control Northeast PetroleumDaqing 163318 the Sanya Offshore Oil&Gas Research Institute Northeast Petroleum UniversitySanya 572024China the Key Laboratory of Advanced Perception and Intelligent Control of High-End Equipment Ministry of EducationAnhui Polytechnic UniversityWuhu 2410000 the School of Mathematics and Physics Anhui Polytechnic UniversityWuhu 241000China

This paper investigates the anomaly-resistant decentralized state estimation(SE) problem for a class of wide-area power systems which are divided into several non-overlapping areas connected through transmission lines. Two classes of measurements(i.e., local measurements and edge measurements) are obtained, respectively, from the individual area and the transmission lines. A decentralized state estimator, whose performance is resistant against measurement with anomalies, is designed based on the minimum error entropy with fiducial points(MEEF) criterion. Specifically, 1) An augmented model, which incorporates the local prediction and local measurement, is developed by resorting to the unscented transformation approach and the statistical linearization approach;2) Using the augmented model, an MEEF-based cost function is designed that reflects the local prediction errors of the state and the measurement;and 3) The local estimate is first obtained by minimizing the MEEF-based cost function through a fixed-point iteration and then updated by using the edge measuring information. Finally, simulation experiments with three scenarios are carried out on the IEEE 14-bus system to illustrate the validity of the proposed anomaly-resistant decentralized SE scheme.

关键词： Decentralized state estimation(SE) measurements with anomalies minimum error entropy unscented Kalman filter wide-area power systems

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GastroFuse-Net: an ensemble deep learning framework designed for gastrointestinal abnormality detection in endoscopic images

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Mathematical Biosciences and engineering 2024年第8期21卷 6847-6869页

作者： Aggarwal, Sonam Gupta, Isha Kumar, Ashok Kautish, Sandeep Almazyad, Abdulaziz S. Mohamed, Ali Wagdy Werner, Frank Shokouhifar, Mohammad Chitkara University Institute of Engineering and Technology Chitkara University Punjab India Model Institute of Engineering and Technology J&K Jammu India Chandigarh University Punjab Mohali140413 India Department of Computer Engineering College of Computer and Information Sciences King Saud University P.O. Box 51178 Riyadh11543 Saudi Arabia Operations Research Department Faculty of Graduate Studies for Statistical Research Cairo University Giza12613 Egypt Applied Science Research Center Applied Science Private University Amman11931 Jordan Faculty of Mathematics Otto-von-Guericke University Magdeburg39016 Germany Institute of Research and Development Duy Tan University Da Nang550000 Viet Nam

Convolutional Neural Networks (CNNs) have received substantial attention as a highly effective tool for analyzing medical images, notably in interpreting endoscopic images, due to their capacity to provide results equivalent to or exceeding those of medical specialists. This capability is particularly crucial in the realm of gastrointestinal disorders, where even experienced gastroenterologists find the automatic diagnosis of such conditions using endoscopic pictures to be a challenging endeavor. Currently, gastrointestinal findings in medical diagnosis are primarily determined by manual inspection by competent gastrointestinal endoscopists. This evaluation procedure is labor-intensive, time-consuming, and frequently results in high variability between laboratories. To address these challenges, we introduced a specialized CNN-based architecture called GastroFuse-Net, designed to recognize human gastrointestinal diseases from endoscopic images. GastroFuse-Net was developed by combining features extracted from two different CNN models with different numbers of layers, integrating shallow and deep representations to capture diverse aspects of the abnormalities. The Kvasir dataset was used to thoroughly test the proposed deep learning model. This dataset contained images that were classified according to structures (cecum, z-line, pylorus), diseases (ulcerative colitis, esophagitis, polyps), or surgical operations (dyed resection margins, dyed lifted polyps). The proposed model was evaluated using various measures, including specificity, recall, precision, F1-score, Mathew’s Correlation Coefficient (MCC), and accuracy. The proposed model GastroFuse-Net exhibited exceptional performance, achieving a precision of 0.985, recall of 0.985, specificity of 0.984, F1-score of 0.997, MCC of 0.982, and an accuracy of 98.5%. ©2024 the Author(s), licensee AIMS Press.

关键词： Endoscopy

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Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 959-973页

作者： Juexiao Zhou Bin Zhang Haoyang Li Longxi Zhou Zhongxiao Li Yongkang Long Wenkai Han Mengran Wang Huanhuan Cui Jingjing Li Wei Chen Xin Gao Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China

The accurate annotation of transcription start sites(TSSs)and their usage are critical for the mechanistic understanding of gene regulation in different biological *** fulfill this,specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner,and various computational tools have also been developed for in silico prediction of TSSs solely based on genomic *** of these computational tools cast the problem as a binary classification task on a balanced dataset,thus resulting in drastic false positive predictions when applied on the genome ***,we present Dee Re CT-TSS,a deep learningbased method that is capable of identifying TSSs across the whole genome based on both DNA sequence and conventional RNA sequencing *** show that by effectively incorporating these two sources of information,Dee Re CT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell ***,we develop a meta-learning-based extension for simultaneous TSS annotations on 10 cell types,which enables the identification of cell type-specific ***,we demonstrate the high precision of DeeReCT-TSS on two independent datasets by correlating our predicted TSSs with experimentally defined TSS chromatin *** source code for Dee Re CT-TSS is available at https://github.-com/Joshua Chou2018/Dee Re CT-TSS_release and https://***/biocode/tools/BT007316.

关键词： Transcription start site Machine learning Deep learning Meta-learning RNA sequencing

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Patch Target Guided Dual-Branch Deep Multiple Instance Learning for 3D MRI Analysis

Patch Target Guided Dual-Branch Deep Multiple Instance Learn...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Dai, Mingzhe Shi, Xiaoshuang Zhu, Xiaofeng Pan, Tingrui Li, Kang University of Science and Technology of China School of Software Engineering Hefei China West China Hospital of Sichuan University West China Biomedical Big Data Center Chengdu China University of Electronic Science and Technology of China School of Computer Science and Engineering Chengdu China Sichuan Artificial Intelligence Research Institute Yibin China University of Science and Technology of China Suzhou Institute for Advanced Research Suzhou China Shanghai Artificial Intelligence Laboratory Shanghai China

ISBN: (纸本)9798350386226

Deep multiple instance learning (MIL) has attracted considerable attention in medical image analysis, since it only requires image-level labels for model training without using fine-grained (or patch) annotations. Unfortunately, MIL-based methods might lose some significant patch features. Although pseudo-label-based methods, which assign a pre-defined label to each patch, can explore more patch-level features, they might bring label noise and make the patch-level features lose diversity, thereby possibly restricting the model performance. To overcome this issue, we propose a novel gradient-based patch target generation (PTG) module to dynamically produce a feature vector for each patch as its target. Additionally, based on the PTG module, we propose a patch-target guided dual-branch deep MIL framework for 3D MRI data analysis, where both the two branches consist of a CNN model to extract patch-level features, an attention module to interpret the significance of patches, and a bag-level classifier, while the second branch also contains the PTG module to generate patch targets of patches. Moreover, the two branches are alternatively updated in our framework, resulting in a bi-level optimization problem, and thus we design a bi-level optimization algorithm to solve our proposed objective function. Extensive experiments demonstrate the superior classification and interpretation performance of the proposed framework over recent state-of-the-art methods. Codes are available at https://***/daimz1213/mil2024. © 2024 IEEE.

关键词： Image annotation

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Distributed Secure Storage Scheme Based on Sharding Blockchain

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computers, Materials & Continua 2022年第3期70卷 4485-4502页

作者： Jin Wang Chenchen Han Xiaofeng Yu Yongjun Ren R.Simon Sherratt School of Computer Science and Mathematics Fujian University of TechnologyFuzhou350118China School of Computer&Communication Engineering Changsha University of Science&TechnologyChangsha410004China School of Business Nanjing UniversityNanjing210093China School of Computer School of SoftwareSchool of Cyberspace SecurityEngineering Research Center of Digital ForensicsMinistry of EducationNanjing University of Information Science&TechnologyNanjing210044China Department of Biomedical Engineering University of ReadingRG66AYUK

Distributed storage can store data in multiple devices or servers to improve data ***,in today’s explosive growth of network data,traditional distributed storage scheme is faced with some severe challenges such as insufficient performance,data tampering,and data lose.A distributed storage scheme based on blockchain has been proposed to improve security and efficiency of traditional distributed *** this scheme,the following improvements have been made in this *** paper first analyzes the problems faced by distributed *** proposed to build a new distributed storage blockchain scheme with sharding *** proposed scheme realizes the partitioning of the network and nodes by means of blockchain sharding technology,which can improve the efficiency of data verification between *** addition,this paper uses polynomial commitment to construct a new verifiable secret share scheme called *** new scheme is one of the foundations for building our improved distributed storage blockchain *** with the previous scheme,our new scheme does not require a trusted third party and has some new features such as homomorphic and batch *** security of VSS can be further *** comparisons show that the proposed scheme significantly reduces storage and communication costs.

关键词： Blockchain distributed storage verifiable secret share polynomial commitment

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Reconfigurable Mott electronics for homogeneous neuromorphic platform

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Chinese Physics B 2023年第12期32卷 67-72页

作者：杨振路英明杨玉超 Beijing Advanced Innovation Center for Integrated Circuit School of Integrated CircuitsPeking UniversityBeijing 100871China School of Electronic and Computer Engineering Peking UniversityShenzhen 518055China Center for Brain Inspired Chips Institute for Artificial IntelligenceFrontiers Science Center for Nano-optoelectronicsPeking UniversityBeijing 100871China Center for Brain Inspired Intelligence Chinese Institute for Brain ResearchBeijing 102206China

To simplify the fabrication process and increase the versatility of neuromorphic systems,the reconfiguration concept has attracted much ***,we developed a novel electrochemical VO_(2)(EC-VO_(2))device,which can be reconfigured as synapses or LIF *** ionic dynamic doping contributed to the resistance changes of VO_(2),which enables the reversible modulation of device *** analog resistance switching and tunable LIF functions were both measured based on the same device to demonstrate the capacity of *** on the reconfigurable EC-VO_(2),the simulated spiking neural network model exhibited excellent performances by using low-precision weights and tunable output neurons,whose final accuracy reached 91.92%.

关键词： Mott electronics reconfigurable neuromorphic computing VO_(2)

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Design,synthesis,and biological evaluation of 1,2,4-triazole derivatives as potent antitubercular agents

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Chinese Chemical Letters 2024年第3期35卷 326-331页

作者： Yu Wen Shichun Lun Yuxue Jiao Wei Zhang Tianyu Hu Ting Liu Fan Yang Jie Tang Bing Zhang William R.Bishai Li-Fang Yu Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062China Center for Tuberculosis Research Department of MedicineDivision of Infectious DiseaseJohns Hopkins School of MedicineBaltimoreMD21231-1044United States Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Shanghai Key Laboratory of Green Chemistry and Chemical Process School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062China

Inhibition of mycobacterial membrane protein large 3(MmpL3)thereby affecting the mycolic acid biosynthetic pathway has been proven to be an effective strategy for developing antitubercular *** on the X-ray crystal structure of MmpL3 inhibitor complexes,a series of novel 1,2,4-triazole derivatives were designed,synthesized and evaluated antitubercular activity against Mtb strain *** structure–activity relationship exploration resulted in the identification of compounds 21 and 28,which possess potent antitubercular activity against Mtb strain H37Rv[minimum inhibitory concentration(MIC)=0.03–0.13μg/mL]and the clinical isolates of multidrug resistance(MDR)and extensive drug resistance(XDR)tuberculosis(MIC=0.06–1.0μg/mL).Moreover,compounds 21 and 28 showed neglectable cytotoxicity(IC_(50)≥32μg/mL)to the mammalian Vero cells and favorable physicochemical and pharmacokinetic properties according to the in silico absorption,distribution,metabolism and excretion(ADME)***,the potential target of representative 1,2,4-triazole 28 was identified to be MmpL3 using a microscale thermophoresis(MST)assay.

关键词： Tuberculosis MDR and XDR-TB MmpL3 inhibitor 1 2 4-Triazole Structure-based drug design

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HIET:Hybrid Information Enhancement Transformer Network for Single-Photon Image Reconstruction

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Journal of Beijing Institute of Technology 2025年第1期34卷 1-17页

作者： Yiming Liu Xuri Yao Tao Zhang Yifei Sun Ying Fu School of Computer Science and Technology Beijing Institute of TechnologyBeijing 100081China Center for Quantum Technology Research and Key Laboratory of Advanced Optoelec-tronic Quantum Architecture and Measurements(MOE) School of PhysicsBeijing Institute of TechnologyBeijing 100081China School of Communication Engineering Hangzhou Dianzi UniversityHangzhou 310018China Uniview Technology Hangzhou 310056China

Single-photon sensors are novel devices with extremely high single-photon sensitivity and temporal ***,these advantages also make them highly susceptible to ***,single-photon cameras face severe quantization as low as 1 bit/*** factors make it a daunting task to recover high-quality scene information from noisy single-photon *** current image reconstruction methods for single-photon data are mathematical approaches,which limits information utilization and algorithm *** this work,we propose a hybrid information enhancement model which can significantly enhance the efficiency of information utilization by leveraging attention mechanisms from both spatial and channel ***,we introduce a structural feature enhance module for the FFN of the transformer,which explicitly improves the model's ability to extract and enhance high-frequency structural information through two symmetric convolution ***,we propose a single-photon data simulation pipeline based on RAW images to address the challenge of the lack of single-photon *** results show that the proposed method outperforms state-of-the-art methods in various noise levels and exhibits a more efficient capability for recovering high-frequency structures and extracting information.

关键词： single-photon images hybrid information enhancement structual feature enhancement data simulation pipeline

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