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A model to optimize palm oil biomass supply chain by considering production traceability information

AIP Conference Proceedings 2023年第1期2714卷

作者： Heru Pranoto Muhammad Zarlis Syahril Efendi Herman Mawengkang Doctoral Program of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Faculty of Mathematics and Natural Sciences Universitas Sumatera Utara Medan Indonesia

Due to the global situation, it is necessary for an industrial company to integrate production scheduling and traceability planning, in a way to get more reliable stand and to make economics advantages. This paper presents biomass supply chain company which could produce a renewable energy. Traceability is a tracking requirement to check whether the quality of the product is satisfied. The supply chain of biomass planning problem aims to meet customer demand subject to traceability and other restrictions. The problem is modelled as a mixed integer linear program, and then it is solved using neighborhood search approach.

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Minimizing Number of Nodes in Decision Trees with Hypotheses

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Procedia computer science 2021年 192卷 232-240页

作者： Mohammad Azad Igor Chikalov Shahid Hussain Mikhail Moshkov Jouf University College of Computer and Information Sciences Department of Computer Science Sakaka 72441 Saudi Arabia Intel Corporation 5000 W Chandler Blvd Chandler AZ 85226 USA Habib University Dhanani School of Science and Engineering Computer Science Program Karachi 75290 Pakistan King Abdullah University of Science and Technology (KAUST) Computer Electrical and Mathematical Sciences & Engineering Division Thuwal 23955-6900 Saudi Arabia

In this paper, we consider decision trees that use both conventional queries based on one attribute each and queries based on hypotheses about values of all attributes. This approach is similar to one studied in exact learning, where membership and equivalence queries are considered. We propose dynamic programming algorithms for the minimization of the number of nodes in such decision trees and discuss results of computer experiments.

关键词： Decision tree Hypothesis Number of nodes

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technology Roadmap for Flexible Sensors

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ACS NANO 2023年第6期17卷 5211-5295页

作者： Luo, Yifei Abidian, Mohammad Reza Ahn, Jong-Hyun Akinwande, Deji Andrews, Anne M. Antonietti, Markus Bao, Zhenan Berggren, Magnus Berkey, Christopher A. Bettinger, Christopher John Chen, Jun Chen, Peng Cheng, Wenlong Cheng, Xu Choi, Seon-Jin Chortos, Alex Dagdeviren, Canan Dauskardt, Reinhold H. Di, Chong-an Dickey, Michael D. Duan, Xiangfeng Facchetti, Antonio Fan, Zhiyong Fang, Yin Feng, Jianyou Feng, Xue Gao, Huajian Gao, Wei Gong, Xiwen Guo, Chuan Fei Guo, Xiaojun Hartel, Martin C. He, Zihan Ho, John S. Hu, Youfan Huang, Qiyao Huang, Yu Huo, Fengwei Hussain, Muhammad M. Javey, Ali Jeong, Unyong Jiang, Chen Jiang, Xingyu Kang, Jiheong Karnaushenko, Daniil Khademhosseini, Ali Kim, Dae-Hyeong Kim, Il-Doo Kireev, Dmitry Kong, Lingxuan Lee, Chengkuo Lee, Nae-Eung Lee, Pooi See Lee, Tae-Woo Li, Fengyu Li, Jinxing Liang, Cuiyuan Lim, Chwee Teck Lin, Yuanjing Lipomi, Darren J. Liu, Jia Liu, Kai Liu, Nan Liu, Ren Liu, Yuxin Liu, Yuxuan Liu, Zhiyuan Liu, Zhuangjian Loh, Xian Jun Lu, Nanshu Lv, Zhisheng Magdassi, Shlomo Malliaras, George G. Matsuhisa, Naoji Nathan, Arokia Niu, Simiao Pan, Jieming Pang, Changhyun Pei, Qibing Peng, Huisheng Qi, Dianpeng Ren, Huaying Rogers, John A. Rowe, Aaron Schmidt, Oliver G. Sekitani, Tsuyoshi Seo, Dae-Gyo Shen, Guozhen Sheng, Xing Shi, Qiongfeng Someya, Takao Song, Yanlin Stavrinidou, Eleni Su, Meng Sun, Xuemei Takei, Kuniharu Tao, Xiao-Ming Tee, Benjamin C. K. Thean, Aaron Voon-Yew Trung, Tran Quang Wan, Changjin Wang, Huiliang Wang, Joseph Wang, Ming Wang, Sihong Wang, Ting Wang, Zhong Lin Weiss, Paul S. Wen, Hanqi Xu, Sheng Xu, Tailin Yan, Hongping Yan, Xuzhou Yang, Hui Yang, Le Yang, Shuaijian Yin, Lan Yu, Cunjiang Yu, Guihua Yu, Jing Yu, Shu-Hong Yu, Xinge Zamburg, Evgeny Zhang, Haixia Zhang, Xiangyu Zhang, Xiaosheng Zhang, Xueji Zhang, Yihui Zhang, Yu Zhao, Siyuan Zhao, Xuanhe Zheng, Yuanjin Zheng, Yu-Qing Zheng, Zijian Zhou, Tao Zhu, Bowen Zhu, Ming Zhu, Rong Zhu, Yangzhi Zhu, Yong Zou, Guijin Chen, Xiaodong 08-03 Innovis Singapore 138634 Republic of Singapore Innovative Centre for Flexible Devices (iFLEX) School of Materials Science and Engineering Nanyang Technological University Singapore 639798 Singapore Department of Biomedical Engineering University of Houston Houston Texas 77024 United States School of Electrical and Electronic Engineering Yonsei University Seoul 03722 Republic of Korea Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 United States Microelectronics Research Center The University of Texas at Austin Austin Texas 78758 United States Department of Chemistry and Biochemistry California NanoSystems Institute and Department of Psychiatry and Biobehavioral Sciences Semel Institute for Neuroscience and Human Behavior and Hatos Center for Neuropharmacology University of California Los Angeles Los Angeles California 90095 United States Colloid Chemistry Department Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany Department of Chemical Engineering Stanford University Stanford California 94305 United States Laboratory of Organic Electronics Department of Science and Technology Campus Norrköping Linköping University 83 Linköping Sweden Wallenberg Initiative Materials Science for Sustainability (WISE) and Wallenberg Wood Science Center (WWSC) SE-100 44 Stockholm Sweden Department of Materials Science and Engineering Stanford University Stanford California 94301 United States Department of Biomedical Engineering and Department of Materials Science and Engineering Carnegie Mellon University Pittsburgh Pennsylvania 15213 United States Department of Bioengineering University of California Los Angeles Los Angeles California 90095 United States School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore 637457 Singapore Nanobionics Group Department of Chemical and Biological Engineering Monash University Clayton Australia 3800 Monash

Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze continued...challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative

关键词： soft materials mechanics engineering flexible electronics conformable sensors bioelectronics human-machine interfaces body area sensor networks technology translation sustainable electronics

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Survival analysis of Kasturi tobacco plants in Jember district using the stratified cox and extended cox models.

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MethodsX 2025年 14卷

作者： Pratama, Angga Iryanto Rantini, Dwi Ningrum, Ratih Ardiati Ramadan, Arip Othman, Fazidah Data Science Technology Study Program Faculty of Advanced Technology and Multidiscipline Universitas Airlangga Surabaya 60115 Indonesia Research Group of Data-Driven Decision Support System Faculty of Advanced Technology and Multidiscipline Universitas Airlangga Surabaya 60115 Indonesia Information System Study Program School of Industrial and System Engineering Telkom University Surabaya Campus Surabaya 60231 Indonesia Department of Computer System and Technology Faculty of Computer Science and Information Technology University of Malaya Malaya Malaysia

In 2022, tobacco was the top export commodity, generating $106.3 million in sales. East Java Province contributes significantly to Indonesia's tobacco production, with an annual output of 188.6 thousand tons. Jember Regency is the area in East Java Province which is a Kasturi tobacco cultivation area. The productivity of Kasturi tobacco continues to decrease due to several factors that can affect the survival of the tobacco. This study aims to analyze the survival of Kasturi tobacco by creating stratified Cox and extended Cox models in order to handle factors that cannot fulfill the proportional hazard assumption. Based on the results of the analysis, the stratified Cox model is the best model with AIC and BIC values of 798.108 and 805.5748 respectively, while the extended Cox has AIC and BIC values of 840.2186 and 850.1732 respectively. Variables that can significantly affect the survival of Kasturi tobacco are the variable concentration of ZA fertilizer, pesticide concentration. The addition of ZA fertilizer must be appropriate, because if excessive it can cause poisoning of tobacco plants. Likewise with pesticides, if excessive it will cause damage to the leaves. This policy can increase the productivity of Kasturi tobacco. Then, Jember Regency contributes greater export capacity. • This paper aims to determine the factors that affect the survival of Kasturi tobacco plants in Jember • By using the extended Cox model, the best one is obtained using the Heaviside function with AIC and BIC values of 840.2186 and 850.1732, respectively • The stratified Cox model is better than the extended Cox model, which has AIC and BIC values of 798.108 and 805.5748, respectively © 2025 The Author(s)

关键词： Cox proportional hazard Extended cox Kasturi tobacco Productive agriculture Stratified cox

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Supervised Contrastive Learning Enhances MHC-II Peptide Binding Affinity Prediction

SSRN

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SSRN 2024年

作者： Shen, Long-Chen Liu, Yan Liu, Zi Zhang, Yumeng Wang, Zhikang Guo, Yuming Rossjohn, Jamie Song, Jiangning Yu, Dong-Jun School of Computer Science and Engineering Nanjing University of Science and Technology 200 Xiaolingwei Nanjing210094 China Department of Computer Science Yangzhou University Yangzhou225100 China School of Information Enginnering Jingdezhen Ceramic University Jingdezhen333403 China Monash Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVIC3800 Australia Monash Data Futures Institute Monash University MelbourneVIC3800 Australia School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai200240 China Department of Epidemiology and Preventive Medicine Xiangya Hospital China Infection and Immunity Program Netherlands

Accurate prediction of major histocompatibility complex (MHC)-peptide binding affinity can improve our understanding of cellular immune responses and guide personalized immunotherapies. Nevertheless, the existing deep learning-based approaches for predicting MHC-II peptide interactions fall short of satisfactory performance and offer restricted model interpretability. In this study, we propose a novel deep neural network, termed ConBoTNet, to address the above issues by introducing the designed supervised contrastive learning and bottleneck transformer extractors. Specifically, the supervised contrastive learning pre-training enhances the model’s representative and generalizable capabilities on MHC-II peptides by pulling positive pairs closer and pushing negative pairs further in the feature space, while the bottleneck transformer module focuses on MHC-II peptide interactions to precisely identify binding cores and anchor positions in an unsupervised manner. Extensive experiments on benchmark datasets under 5-fold cross-validation, leave-one-molecule-out validation, independent testing, and binding core prediction settings highlighted the superiority of our proposed ConBoTNet over current state-of-the-art methods. Data distribution analysis in the latent feature space demonstrated that supervised contrastive learning can aggregate MHC-II-peptide samples with similar affinity labels and learn common features of similar affinity. Additionally, we interpreted the trained neural network by associating the attention weights with peptides and innovatively find both well-established and potential peptide motifs. This work not only introduces an innovative tool for accurately predicting MHC-II peptide affinity, but also provides new insights into a new paradigm for modeling essential biological interactions, advancing data-driven discovery in biomedicine. © 2024, The Authors. All rights reserved.

关键词： Peptides

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Bayesian multinomial logistic normal models through marginally latent matrix-T processes

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2022年第1期23卷 255-296页

作者： Justin D. Silverman Kimberly Roche Zachary C. Holmes Lawrence A. David Sayan Mukherjee College of Information Science and Technology Department of Statistics and Institute for Computational and Data Science Penn State University University Park PA Program in Computational Biology and Bioinformatics Duke University Durham NC Department of Molecular Genetics and Microbiology Duke University Durham NC Department of Molecular Genetics and Microbiology and Center for Genomic and Computational Biology Duke University Durham NC Departments of Statistical Science Mathematics Computer Science Biostatistics & Bioinformatics Duke University Durham NC

Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing implementations of MLN models are limited to small datasets due to the non-conjugacy of the multinomial and logistic-normal distributions. Motivated by the need to develop efficient inference for Bayesian MLN models, we develop two key ideas. First, we develop the class of Marginally Latent Matrix-T Process (Marginally LTP) models. We demonstrate that many popular MLN models, including those with latent linear, non-linear, and dynamic linear structure are special cases of this class. Second, we develop an efficient inference scheme for Marginally LTP models with specific accelerations for the MLN subclass. Through application to MLN models, we demonstrate that our inference scheme are both highly accurate and often 4-5 orders of magnitude faster than MCMC.

关键词： Bayesian statistics multivariate analysis count data microbiome gene expression

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

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Scientific Reports 2023年第1期13卷 1-10页

作者： Kuo, Tzu-Yun Wang, Jen-Hung Huang, Yung-Wen Sung, Ting-Yi Chen, Ching-Tai Department of Biochemical Science and Technology National Taiwan University Taipei 10617 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Statistical Science Academia Sinica Taipei 11529 Taiwan Institute of Information Science Academia Sinica Taipei 11529 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 11221 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan Department of Bioinformatics and Biomedical Engineering Asia University Taichung 41354 Taiwan Center for Precision Health Research Asia University Taichung 41354 Taiwan

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms;its executable files, user manual, and sample data sets are freely available at https://***/comics/Software_*** . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline. © 2023, Springer Nature Limited.

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A robust optimization approach for measuring efficiency in stochastic DEA

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AIP Conference Proceedings 2023年第1期2714卷

作者： Hengki Tamando Sihotang Syahril Efendi Muhammad Zarlis Herman Mawengkang Doctoral Program Faculty of Computer Science and Information Technology Universitas Sumatera Utara. FEBO Indonesia Faculty of Computer Science and Information Technology Universitas Sumatera Utara. FEBO Indonesia Faculty of Mathematics and Natural Sciences Universitas Sumatera Utara. FEBO Indonesia

The classic data envelopment analysis (DEA) concept assumes that decision making unit (DMU) inputs and outputs can be clearly measured because they have definite values. However, there are times when there is uncertainty in a situation. This study looks at how to build a DEA model with input and output uncertainty. In the DEA model, the uncertainty situation is approached using a stochastic concept. Furthermore, the robust optimization method, which can solve the uncertainty problem, is introduced. As a result, at the conclusion of this study, a robust optimization model based on the Stochastic DEA concept is introduced.

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Framework for tackling stochastic DEA based on data-driven approach

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AIP Conference Proceedings 2023年第1期2714卷

作者： Hengki Tamando Sihotang Syahril Efendi Muhammad Zarlis Herman Mawengkang Doctoral Program Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Faculty of Mathematics and Natural Sciences Universitas Sumatera Utara Medan Indonesia

Data Envelopment Analysis (DEA) is a linear programming-based technique used to evaluate the relative efficiency of multi-input and multi-output decision-making units based on observed data by comparing one decision-making unit (DMU) with another DMU. The efficacy assessment process sometimes involves a stochastic approach due to the uncertainty inherent in many real life problems, so the DEA model discussed in this paper is the stochastic DEA (SDEA) model. Data-driven decision-making is based entirely on the data involved. This paper proposes a framework for the completion of SDEA based on a data-driven approach.

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Economics of Semantic Communication System: An Auction Approach

arXiv

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arXiv 2022年

作者： Liew, Zi Qin Du, Hongyang Yang, Wei Lim, Bryan Xiong, Zehui Niyato, Dusit Miao, Chunyan Kim, Dong In Alibaba-NTU Singapore Joint Research Institute Nanyang Technological Univerity Singapore The School of Computer Science and Engineering The Energy Research Institute NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore The Pillar of Information Systems Technology and Design Singapore University of Technology and Design Singapore The School of Computer Science and Engineering Nanyang Technological University Singapore The School of Computer Science and Engineering Nanyang Technological University Singapore639798 Singapore Nanyang Technological University Singapore639798 Singapore The Department of Electrical and Computer Engineering Sungkyunkwan University Suwon16419 Korea Republic of

Semantic communication technologies enable wireless edge devices to communicate effectively by transmitting semantic meaning of data. Edge components, such as vehicles in next-generation intelligent transport systems, use well-trained semantic models to encode and decode semantic information extracted from raw and sensor data. However, the limitation in computing resources makes it difficult to support the training process of accurate semantic models on edge devices. As such, edge devices can buy the pretrained semantic models from semantic model providers, which is called "semantic model trading". Upon collecting semantic information with the semantic models, the edge devices can then sell the extracted semantic information, e.g., information about urban road conditions or traffic signs, to the interested buyers for profit, which is called "semantic information trading". To facilitate both types of the trades, effective incentive mechanisms should be designed. Thus, in this paper, we propose a hierarchical trading system to support both semantic model trading and semantic information trading jointly. The proposed incentive mechanism helps to maximize the revenue of semantic model providers in the semantic model trading, and effectively incentivizes model providers to participate in the development of semantic communication systems. For semantic information trading, our designed auction approach can support the trading between multiple semantic information sellers and buyers, while ensuring individual rationality, incentive compatibility, and budget balance, and moreover, allowing them achieve higher utilities than the baseline method. Copyright © 2022, The Authors. All rights reserved.

关键词： Commerce

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