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Systematic evaluation of the isolated effect of tissue environment on the transcriptome using a single-cell RNA-seq atlas dataset

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BMC Genomics 2025年第1期26卷 1-14页

作者： Okada, Daigo Zhu, Jianshen Shota, Kan Nishimura, Yuuki Haraguchi, Kazuya Center for Genomic Medicine Graduate School of Medicine Kyoto University Kyoto 606 - 8507 Japan Discrete Mathematics Laboratory Applied Mathematics and Physics Course Graduate School of Informatics Kyoto University Kyoto 606 - 8501 Japan Institute for Advanced Study Gifu University Gifu 501 - 1193 Japan

Background: Understanding cellular diversity throughout the body is essential for elucidating the complex functions of biological systems. Recently, large-scale single-cell omics datasets, known as omics atlases, have become available. These atlases encompass data from diverse tissues and cell-types, providing insights into the landscape of cell-type-specific gene expression. However, the isolated effect of the tissue environment has not been thoroughly investigated. Evaluating this isolated effect is challenging due to statistical confounding with cell-type effects, which arises from the highly limited subset of tissue-cell-type combinations that are biologically realized compared to the vast number of theoretical possibilities. Results: This study introduces a novel data analysis framework, named the Combinatorial Sub-dataset Extraction for Confounding Reduction (COSER), which addresses statistical confounding by using graph theory to enumerate appropriate sub-datasets. COSER enables the assessment of isolated effects of discrete variables in single cells. Applying COSER to the Tabula Muris Senis single-cell transcriptome atlas, we characterized the isolated impact of tissue environments. Our findings demonstrate that some genes are markedly affected by the tissue environment, particularly in modulating intercellular diversity in immune responses and their age-related changes. Conclusion: COSER provides a robust, general-purpose framework for evaluating the isolated effects of discrete variables from large-scale data mining. This approach reveals critical insights into the interplay between tissue environments and gene expression. © The Author(s) 2025.

关键词： Effect of tissue environment Graph theory Maximal biclique enumeration Single cell RNA-seq

Local convergence analysis of a stabilized sequential quadratic programming method for optimization problems in Banach spaces

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arXiv 2025年

作者： Yamakawa, Yuya Applied Mathematics and Physics Course Graduate School of Informatics Kyoto University Yoshida-Honmachi Sakyo-ku Kyoto606-8501 Japan

This paper presents a stabilized sequential quadratic programming (SQP) method for solving optimization problems in Banach spaces. The optimization problem considered in this study has a general form that enables us to represent various types of optimization problems. Several SQP methods have been proposed for optimization problems in Banach spaces with specific structures;however, research on the local analysis of SQP-type methods for general problems, such as those considered in this study, is limited. We focus on the local behavior of the proposed stabilized SQP method and prove its local quadratic convergence under reasonable assumptions, without including any constraint qualifications. Finally, numerical experiments are performed to confirm the theoretical properties shown in the local analysis. Copyright © 2025, The Authors. All rights reserved.

关键词： Banach spaces

The Use of Machine Learning Algorithms for Evaluating Water Quality Index: A Survey and Perspective

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The Use of Machine Learning Algorithms for Evaluating Water ...

2022 International Conference on Multimedia Analysis and Pattern Recognition, MAPR 2022

作者： Nguyen, Huu Du Nguyen, Tai Quang Dinh Thi, Hien Nguyen Lap, Bui Quoc Phan, Thi-Thu-Hong Hanoi University of Sciences and Technology School of Applied Mathematics and Informatics Hanoi Viet Nam Hanoi University of Sciences and Technology Undergraduate Course of School of Applied Mathematics and Informatics Hanoi Viet Nam Le Quy Don Technical University Hanoi Viet Nam Thuyloi University Faculty of Chemistry & Environment Hanoi Viet Nam Fpt University Department of Information Technology Danang Viet Nam

ISBN: (数字)9781665474108

ISBN: (纸本)9781665474108

The quality of water is determined by its components, called the water parameters. The effect of each parameter on the water quality is different. To assess the water quality, sampling and measuring the value of these parameters are required. The water quality index (WQI) is a special indicator that integrates the value of many parameters into a single value. This value can be used to reflect effectively the quality of water. In this study, we present a survey on the application of machine learning (ML) method to estimate the WQI. A case study is also conducted to illustrate the use of the ML algorithm in the context. © 2022 IEEE.

关键词： Surveys

Second moments of work and heat for a single particle stochastic heat engine in a breathing harmonic potential

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arXiv 2021年

作者： Iida, Shinji Negoro, Koki Yamada, Kanta Applied Mathematics and Informatics Course Faculty of Advanced Science and Technology Ryukoku University Shiga Otsu520-2194 Japan

We consider a simple model of a stochastic heat engine, which consists of a single Brownian particle moving in a one-dimensional periodically breathing harmonic potential Overdamped limit is assumed Expressions of second moments (variances and covariances) of heat and work are obtained in the form of integrals, whose integrands contain functions satisfying certain differential equations The results in the quasi-static limit are simple functions of temperatures of hot and cold thermal baths The coefficient of variation of the work is suggested to give an approximate probability for the work to exceeds a given threshold During derivation, we get the expression of the cumulant-generating function. Copyright © 2021, The Authors. All rights reserved.

关键词： Stochastic systems

Systematic evaluation of the isolated effect of tissue environment on the transcriptome using a single-cell RNA-seq atlas dataset

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arXiv 2024年

作者： Okada, Daigo Zhu, Jianshen Shota, Kan Nishimura, Yuuki Haraguchi, Kazuya Center for Genomic Medicine Graduate School of Medicine Kyoto University Kyoto606-8507 Japan Discrete Mathematics Laboratory Applied Mathematics and Physics Course Graduate School of Informatics Kyoto University Kyoto606-8501 Japan

Background: Understanding cellular diversity throughout the body is essential for elucidating the complex functions of biological systems. Recently, large-scale single-cell omics datasets, known as omics atlases, have become available. These atlases encompass data from diverse tissues and cell-types, providing insights into the landscape of cell-type-specific gene expression. However, the isolated effect of the tissue environment has not been thoroughly investigated. Evaluating this isolated effect is challenging due to statistical confounding with cell-type effects, arising from significant biases in the combinations of tissues and cell-types within the body. Results: This study introduces a novel data analysis framework, named the Combinatorial Sub-dataset Extraction for Confounding Reduction (COSER), which addresses statistical confounding by using graph theory to enumerate appropriate sub-datasets. COSER enables the assessment of isolated effects of discrete variables in single cells. Applying COSER to the Tabula Muris Senis single-cell transcriptome atlas, we characterized the isolated impact of tissue environments. Our findings demonstrate that some of genes are markedly affected by the tissue environment, particularly in modulating intercellular diversity in immune responses and their age-related changes. Conclusion: COSER provides a robust, general-purpose framework for evaluating the isolated effects of discrete variables from large-scale data mining. This approach reveals critical insights into the interplay between tissue environments and gene expression. © 2024, CC BY-NC-ND.

关键词： Tissue

An unsupervised auditory scene analysis system using incremental low-dimensional embedding

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An unsupervised auditory scene analysis system using increme...

IEEE/SICE International Symposium on System Integration

作者： Kenta Shinzato Ryosuke Kojima Undergraduate School of Informatics and Mathematical Science Undergraduate Course Program of Applied Mathematics and Physics Kyoto University 54 Kawahara-cho Shogoin Sakyo-ku Kyoto Japan Graduate School of Medicine Kyoto University 54 Kawahara-cho Shogoin Sakyo-ku Kyoto Japan

ISBN: (数字)9781728176581

ISBN: (纸本)9781728176598

This paper addresses the low-dimensional embedding of sounds towards unsupervised auditory scene analysis. Summarizing long-time recordings by mapping them into low-dimensional space is an essential task in long-time environmental monitoring. In this paper, we propose a novel low-dimensional embedding system using an incremental embedding algorithm. To analyze long-time recordings, we design an incremental system consisting of recording, feature extraction, low-dimensional embedding, and visualization. Recently, many low-dimensional embedding methods for acoustic scenes have been studied; however, applicability of these methods to the long-time recording is not adequately evaluated. Thus, this paper describes the construction of the scene analysis system and evaluates the performance of this system. In this paper, we especially focus on two important viewpoints in long-time monitoring: incremental methods and effects of noisy data. To realize an incremental system, we use Self-Organizing Nebulous Growths (SONG), which can incrementally construct a low-dimensional embedding space. Also, in our experiments, we apply our system to bird song analysis under noise conditions. By the preliminary experiments using benchmark datasets, we discover noise sensitivity of our system and applicability to environmental monitoring.

关键词： Training Image analysis Feature extraction Birds Real-time systems Environmental monitoring Task analysis

Fundamental solution to the heat equation with a dynamical boundary condition

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arXiv 2024年

作者： Ishige, Kazuhiro Katayama, Sho Kawakami, Tatsuki Graduate School of Mathematical Sciences The University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo153-8914 Japan Applied Mathematics and Informatics Course Faculty of Advanced Science and Technology Ryukoku University 1-5 Yokotani Seta Oe-cho Shiga Otsu520-2194 Japan

We give an explicit representation of the fundamental solution to the heat equation on a half-space of RN with the homogeneous dynamical boundary condition, and obtain upper and lower estimates of the fundamental solution. These enable us to obtain sharp decay estimates of solutions to the heat equation with the homogeneous dynamical boundary condition. Furthermore, as an application of our decay estimates, we identify the so-called Fujita exponent for a semilinear heat equation on the half-space of RN with the homogeneous dynamical boundary condition. Copyright © 2024, The Authors. All rights reserved.

关键词： Boundary conditions

Refined asymptotic expansions of solutions to fractional diffusion equations

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arXiv 2021年

作者： Ishige, Kazuhiro Kawakami, Tatsuki Graduate School of Mathematical Sciences The University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo153-8914 Japan Applied Mathematics and Informatics Course Faculty of Advanced Science and Technology Ryukoku University 1-5 Yokotani Seta Oe-cho Shiga Otsu520-2194 Japan

In this paper, as an improvement of the paper [K. Ishige, T. Kawakami and H. Michihisa, SIAM J. Math. Anal. 49 (2017) pp. 2167–2190], we obtain the higher order asymptotic expansions of the large time behavior of the solution to the Cauchy problem for inhomogeneous fractional diffusion equations and nonlinear fractional diffusion equations. Copyright © 2021, The Authors. All rights reserved.

关键词： Asymptotic analysis

On weak solutions to a fractional Hardy–Hénon equation: Part I: Nonexistence

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arXiv 2020年

作者： Hasegawa, Shoichi Ikoma, Norihisa Kawakami, Tatsuki Department of Mathematics School of Fundamental Science and Engineering Waseda University 3-4-1 Okubo Shinjuku-ku Tokyo169-8555 Japan Department of Mathematics Faculty of Science and Technology Keio University 3-14-1 Hiyoshi Kohoku-ku Kanagawa Yokohama223-8522 Japan Applied Mathematics and Informatics Course Faculty of Advanced Science and Technology Ryukoku University 1-5 Yokotani Seta Oe-cho Otsu Shiga520-2194 Japan

This paper and [20] treat the existence and nonexistence of stable (resp. outside stable) weak solutions to a fractional Hardy–Hénon equation (-∆)su = |x|`|u|p-1u in RN, where 0 -2s, p > 1, N ≥ 1 and N > 2s. In this paper, the nonexistence part is proved for the Joseph–Lundgren subcritical *** Codes 35R11, 35J61, 35B33, 35B53, 35D30 Copyright © 2020, The Authors. All rights reserved.

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