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Protocol to explain support vector machine predictions via exact Shapley value computation

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STAR Protocols 2024年第2期5卷 103010页

作者： Mastropietro, Andrea Bajorath, Jürgen Deparment of Computer Control and Management Engineering “Antonio Ruberti” Sapienza University of Rome Via Ariosto 25 Rome 00185 Italy Department of Life Science Informatics and Data Science B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry Rheinische Friedrich-Wilhelms-Universität Friedrich-Hirzebruch-Allee 5/6 Bonn 53115 Germany Lamarr Institute for Machine Learning and Artificial Intelligence Friedrich-Hirzebruch-Allee 5/6 Bonn 53115 Germany

Shapley values from cooperative game theory are adapted for explaining machine learning predictions. For large feature sets used in machine learning, Shapley values are approximated. We present a protocol for two techniques for explaining support vector machine predictions with exact Shapley value computation. We detail the application of these algorithms and provide ready-to-use Python scripts and custom code. The final output of the protocol includes quantitative feature analysis and mapping of important features for visualization. For complete details on the use and execution of this protocol, please refer to Feldmann and Bajorath¹ and Mastropietro et al.² © 2024 The Author(s)

关键词： Bioinformatics Chemistry Computer sciences

A NOVEL APPROACH FOR DEFECT DETECTION OF WIND TURBINE BLADE USING VIRTUAL REALITY AND DEEP LEARNING

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arXiv 2023年

作者： Rabbi, Md Fazle Emon, Solayman Hossain Nishat, Ehtesham Mahmud Tseng, Tzu-Liang Ferdoushi, Atira Huang, Chun-Che Rahman, Md Fashiar Department of Industrial Manufacturing and Systems Engineering The University of Texas El PasoTX79968 United States Data Science Program The University of Texas at El Paso El PasoTX79968 United States Khulna9203 Bangladesh University of Rajshahi Rajshahi6205 Bangladesh National Chi Nan University Pu-Li Taiwan

Wind turbines are subjected to continuous rotational stresses and unusual external forces such as storms, lightning, strikes by flying objects, etc., which may cause defects in turbine blades. Hence, it requires a periodical inspection to ensure proper functionality and avoid catastrophic failure. The task of inspection is challenging due to the remote location and inconvenient reachability by human inspection. Researchers used images with cropped defects from the wind turbine in the literature. They neglected possible background biases, which may hinder real-time and autonomous defect detection using aerial vehicles such as drones or others. To overcome such challenges, in this paper, we experiment with defect detection accuracy by having the defects with the background using a two-step deep-learning methodology. In the first step, we develop virtual models of wind turbines to synthesize the near-reality images for four types of common defects - cracks, leading edge erosion, bending, and light striking damage. The Unity® perception package is used to generate wind turbine blade defects images with variations in background, randomness, camera angle, and light effects. In the second step, a customized U-Net architecture is trained to classify and segment the defect in turbine blades. The outcomes of U-Net architecture have been thoroughly tested and compared with 5-fold validation datasets. The proposed methodology provides reasonable defect detection accuracy, making it suitable for autonomous and remote inspection through aerial vehicles. © 2023, CC BY.

关键词： Turbomachine blades

A NEURAL NETWORK KERNEL DECOMPOSITION FOR LEARNING MULTIPLE STEADY STATES IN PARAMETERIZED DYNAMICAL SYSTEMSa

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arXiv 2023年

作者： Zhang, Yimeng Cloninger, Alexander Li, Bo Tian, Xiaochuan Department of Mathematics University of California San DiegoCA92093 United States Halicioglu Data Science Institute University of California San Diego Lo Jolla CA92093 United States Ph.D. Program in Quantitative Biology University of California San Diego Lo Jolla CA92093 United States

We develop a data-driven machine learning approach to identifying parameters with steady-state solutions, locating such solutions, and determining their linear stability for systems of ordinary differential equations and dynamical systems with parameters. Our approach first constructs target functions for these tasks, then designs a parameter-solution neural network (PSNN) that couples a parameter neural network and a solution neural network to approximate the target functions. We further develop efficient algorithms to train the PSNN and locate steady-state solutions. An approximation theory for the target functions with PSNN is developed based on kernel decomposition. Numerical results are reported to show that our approach is robust in finding solutions, identifying phase boundaries, and classifying solution stability across parameter regions. These numerical results also validate our analysis. While this study focuses on steady states of parameterized dynamical systems, our approach is equation-free and is applicable generally to finding solutions for parameterized nonlinear systems of algebraic equations. Some potential improvements and future work are discussed. Copyright © 2023, The Authors. All rights reserved.

关键词： Nonlinear dynamical systems

A Kanban-based Approach to Manage Machine Learning Projects in Manufacturing

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Procedia CIRP 2025年 134卷 109-114页

作者： Ulf Schreier Peter Reimann Bernhard Mitschang Business Information Systems - Furtwangen University of Applied Science Robert-Gerwig-Platz 1 D-78120 Furtwangen Germany Graduate School of advanced Manufacturing Engineering (GSaME) University of Stuttgart Nobelstr. 12 D-70569 Stuttgart Germany Institute for Program Structures and Data Organization (IPD) Karlsruhe Institute of Technology (KIT) Am Fasanengarten 5 D-76131 Karlsruhe Germany Institute of Parallel and Distributed Systems (IPVS) University of Stuttgart Universitätsstr. 38 D-70569 Stuttgart Germany

A growing number of machine learning (ML) projects in manufacturing require the collaboration of various experts. In addition to data scientists, stakeholders with production engineering knowledge have to specify and prioritize individual project tasks. data engineers prepare input data, while machine learning operations (MLOps) engineers ensure that trained models are deployed and monitored within IT landscapes. Existing project management approaches, e.g., Scrum, have problems for ML projects, as they do not consider various expert roles or ML project stages. We propose a project management approach defining a Kanban workflow by readjusting stages of ML development lifecycles, e.g., CRISP DM. This makes it possible to map expert roles to stages of the Kanban workflow. An adapted Kanban board allows visualizing and reviewing the status of all project tasks. We validate our approach with specific use cases, showing that it facilitates ML project management in manufacturing.

关键词： Machine learning (ML) ML project management machine learning operations (MLOps) Kanban Scrum

Meteorological parameters for PV installations in Indonesia

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AIP Conference Proceedings 2024年第1期3026卷

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Reza Rahutomo Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Many countries are still dependent on fossil fuels as their primary energy supply. However, there is a growing concern about the sustainability and the environmental issue of fossil fuels. Therefore, it is important to utilize renewable resources as the energy supply, such as solar energy. As a country with a tropical climate, Indonesia has a great potential to use solar energy, due to the abundance of sunlight exposure. The present study aims to analyze several meteorological parameters for the installation of photovoltaic (PV) technology in Jakarta, Indonesia. The meteorological data provided by the Ministry of Environment and Forestry, Indonesia from 2008-2021 were used at three different locations in Jakarta. data visualizations were used to show the difference between each variable in different locations. In addition, the statistical difference between the variables in the three locations was also examined using the Mann-Whitney U test. The test shows that all parameters are evenly distributed in the three locations except for a moderate difference in air temperature in the two locations. Furthermore, the monthly analysis of the parameters also indicates that the dry season, especially from August to September, would be the optimal time to utilize PV technology. Hence, this study would be useful to give preliminary insight regarding a site-specified assessment of PV plants in Jakarta based on local meteorological data.

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An analysis of reconstruction noise from undersampled 4D flow MRI

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arXiv 2022年

作者： Partin, Lauren Schiavazzi, Daniele E. Long, Carlos A. Sing Department Of Applied And Computational Mathematics And Statistics University Of Notre Dame Notre DameIN United States Institute For Mathematical And Computational Engineering Institute For Biological And Medical Engineering Pontificia Universidad Católica De Chile Santiago Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For The Discovery Of Structures In Complex Data Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For Cardiovascular Magnetic Resonance Chile

Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction methods from undersampled measurements are routinely used, that leverage representations designed to increase image compressibility. Reconstructed anatomical and hemodynamic images may present visual artifacts. Although some of these artifact are essentially reconstruction errors, and thus a consequence of undersampling, others may be due to measurement noise or the random choice of the sampled frequencies. Said otherwise, a reconstructed image becomes a random variable, and both its bias and its covariance can lead to visual artifacts;the latter leads to spatial correlations that may be misconstrued for visual information. Although the nature of the former has been studied in the literature, the latter has not received as much attention. In this study, we investigate the theoretical properties of the random perturbations arising from the reconstruction process, and perform a number of numerical experiments on simulated and MR aortic flow. Our results show that the correlation length remains limited to two to three pixels when a Gaussian undersampling pattern is combined with recovery algorithms based on 1-norm minimization. However, the correlation length may increase significantly for other undersampling patterns, higher undersampling factors (i.e., 8× or 16× compression), and different reconstruction methods. © 2022, CC BY-NC-ND.

关键词： Magnetic resonance

Comparison of multivariate adaptive Poisson Regression spline and multivariate adaptive generalized Poisson Regression spline

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AIP Conference Proceedings 2023年第1期2536卷

作者： Septia Devi Prihastuti Yasmirullah Bambang Widjanarko Otok Jerry Dwi Trijoyo Purnomo Dedy Dwi Prastyo Data Science Technology Study Program Faculty of Advanced Technology and Multidiscipline Universitas Airlangga Surabaya 60115 Indonesia Department of Statistics Faculty of Science and Data Analytics Institut Teknologi Sepuluh Nopember Surabaya 60111 Indonesia

The multivariate adaptive regression (MARS) spline is a statistical method introduced by Friedman in 1991. The MARS method has several advantages, especially for data that consider the potential nonlinear pattern. These produce a continuous model on knots where the knot selection process is performed via adaptive procedures, capturing additive effects and interactions between predictor variables, and applied to data modeling with numerical and categorical responses. However, the analyzed data is not only numerical or categorical data, but also count type data. Count type data is often found in the health sector, for example, the number of data on tuberculosis. It invites to modify the MARS model with Poisson regression and generalized Poisson regression, i.e. Multivariate Adaptive Poisson Regression Spline (MAPRS) and Multivariate Adaptive Generalized Poisson Regression Spline (MAGPRS) . In addition, this study aimed to compare MAPRS and MAGPRS when applied to tuberculosis data. By applying MAPRS and MAGPRS to model the number of tuberculosis in Lamongan regency, the MAPRS method outperforms the MAGPRS method. The MAPRS method has a lower RMSE value than the MAGPRS method.

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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A Guide to Tracking Phylogenies in Parallel and Distributed Agent-based Evolution Models

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arXiv 2024年

作者： Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among simulated agents. Such phylogenies can provide insight into evolutionary dynamics within these simulations. Existing work generally tracks lineages directly, yielding an exact phylogenetic record of evolutionary history. However, direct tracking can be inefficient for large-scale, many-processor evolutionary simulations. An alternate approach to extracting phylogenetic information from simulation that scales more favorably is post hoc estimation, akin to how bioinformaticians build phylogenies by assessing genetic similarities between organisms. Recently introduced "hereditary stratigraphy" algorithms provide means for efficient inference of phylogenetic history from non-coding annotations on simulated organisms' genomes. A number of options exist in configuring hereditary stratigraphy methodology, but no work has yet tested how they impact reconstruction quality. To address this question, we surveyed reconstruction accuracy under alternate configurations across a matrix of evolutionary conditions varying in selection pressure, spatial structure, and ecological dynamics. We synthesize results from these experiments to suggest a prescriptive system of best practices for work with hereditary stratigraphy, ultimately guiding researchers in choosing appropriate instrumentation for large-scale simulation studies. Copyright © 2024, The Authors. All rights reserved.

关键词： Biotic