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Tree edit distance with variables. Measuring the similarity between mathematical formulas

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arXiv 2021年

作者： Akutsu, Tatsuya Mori, Tomoya Nakamura, Naotoshi Kozawa, Satoshi Ueno, Yuhei Sato, Thomas N. Bioinformatics Center Institute for Chemical Research Kyoto University Karydo TherapeutiX Inc. Center for Mathematical Modeling and Data Science Osaka University V-iCliniX Laboratory Nara Medical University

In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas, especially, those appearing in mathematical models of biological systems. We analyze the computational complexities of several variants of this new model. In particular, we show that the problem is NP-complete for ordered trees. We also show for unordered trees that the problem of deciding whether or not the distance is 0 is graph isomorphism complete but can be solved in polynomial time if the maximum outdegree of input trees is bounded by a constant. This distance model is then extended for measuring the difference/similarity between two systems of differential equations, for which results of preliminary computational experiments using biological models are provided. © 2021, CC BY.

关键词： Polynomial approximation

A simple model of edit activity in Wikipedia

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arXiv 2023年

作者： Shimada, Takashi Ogushi, Fumiko Török, János Kertész, János Kaski, Kimmo Department of Systems Innovation Graduate School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-8656 Japan Mathematics and Informatics Center The University of Tokyo 1-3 Machikaneyama Osaka Toyonaka560-8531 Japan Center for Mathematical Modeling and Data Science Osaka University 1-3 Machikaneyama Osaka Toyonaka560-8531 Japan MTA-BME Morphodynamics Research Group Department of Theoretical Physics Budapest University of Technology and Economics Muegyetem Rkp 3 Budapest1111 Hungary Department of Network and Data Science Central European University Vienna Austria Aalto University School of Science Espoo Finland

A simple dynamical model of collective edit activity of Wikipedia articles and their content evolution is introduced. Based on the recent empirical findings, each editor in the model is characterized by an ability to make content edit, i.e., improving the article by adding content and a tendency to make maintenance edit, i.e., dealing with formal aspects and maintaining the edit flow. In addition, each article is characterized by a level of maturity as compared to a potential quality needed to comprehensively cover its topic. This model is found to reproduce the basic structure of the bipartite network between editors and articles of Wikipedia. Furthermore, the relation between the model parameters of editors and articles and the metrics of those calculated from the emergent network turns out to be robust, i.e. depending only on the rate of the introduction of new articles to the editing activity. This results provides us a way to relate observations in the real data to the hidden characteristics of editors and articles. For the nestedness of the networks, systems with weighted parameter distribution gives better match to the empirical one. This suggests the importance of high-dimensional nature of the ability of editors and quality of articles in the real system. Copyright © 2023, The Authors. All rights reserved.

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Sentence Generation from IMU-based Human Whole-Body Motions in Daily Life Behaviors

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Sentence Generation from IMU-based Human Whole-Body Motions ...

IEEE/SICE International Symposium on System Integration

作者： Wataru Takano Center for Mathematical Modeling and Data Science Mathematics and Computer Science Osaka University 1-3 Machikaneyamacho Toyonaka Japan

ISBN: (数字)9781728166674

ISBN: (纸本)9781728166681

This paper presents a probabilistic approach to-ward integrating human whole-body motions with natural language. Human whole-body motions in daily life are recorded by inertial measurement units (IMU) and subsequently encoded into motion symbols. Sentences are manually attached to the human motion primitives for their annotation. Two aspects of semantics and syntactics are represented by probabilistic graphical models. One probabilistic model trains the linking of motion symbols to words, and the other model represents sentence structure as word sequences. These two models are useful toward translating human whole-body motions into descriptions, where multiple words are associated from the human motions by the first model, and the second model searches for syntactically consistent sentences consisting of the associated words. The proposed approach was tested on a large dataset of human whole-body motions and sentences to annotate these motions. The linking of human motions to natural language enables robots to understand observations of human behavior as sentences.

关键词： Probabilistic logic mathematical model Robot sensing systems Graphical models Optical variables measurement Natural languages

Florid – a Nationwide Identification Service for Plants from Photos and Habitat Information

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SSRN

SSRN 2024年

作者： Brun, Philipp de Witte, Lucienne Popp, Manuel Richard Zurell, Damaris Karger, Dirk Nikolaus Descombes, Patrice de Lutio, Riccardo Wegner, Jan Dirk Bornand, Christophe Eggenberg, Stefan Olevski, Tasko Zimmermann, Niklaus E. Swiss Federal Research Institute WSL Birmensdorf8903 Switzerland Musée et jardins botaniques cantonaux Lausanne1007 Switzerland Institute of Biochemistry and Biology University of Potsdam Potsdam14469 Germany EcoVision Lab Photogrammetry and Remote Sensing ETH Zurich Zürich8092 Switzerland Department of Mathematical Modeling and Machine Learning University of Zurich Zürich8057 Switzerland InfoFlora Switzerland Bern3013 Switzerland Swiss Data Science Center ETH Zurich Zürich8092 Switzerland University of Basel Switzerland

Citizen science has become key to biodiversity monitoring but critically depends on accurate quality control that is scalable and tailored to the focal region. We developed FlorID, a free-to-use identification service for all native and many non-native plants of Switzerland. FlorID can identify >3000 species, using vision transformers trained on 1.5M photos, and ecological predictions from multilayer perceptrons, trained on 6.7M occurrence observations and 20 high-resolution environmental variables. Embedded in a free-to-use application programming interface, FlorID can be accessed directly, via webservice, and via FlorApp smartphone application. If multiple images and spatiotemporal location are available, FlorID correctly identifies 93% of field observations and has a top-5 accuracy of 99%. Ecological predictions boost identification success especially for native species with distinct distributions. By evaluating information on appearance and fine-grained ecology, FlorID is a blueprint for similar solutions targeting different taxa or regions, and a basis for developments like automated community inventories. © 2024, The Authors. All rights reserved.

关键词： Blueprints

Clinical Analogy Resolution Performance for Foundation Language Models

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ACM Transactions on Computing for Healthcare 2025年第2期6卷

作者： Villena, Fabián Quiroga, Tamara Dunstan, Jocelyn Department of Computer Science University of Chile Santiago Chile Millennium Institute for Foundation Research on Data Santiago Chile Center for Mathematical Modeling University of Chile Santiago Chile Department of Computer Science Pontificia Universidad Catolica de Chile Santiago Chile Institute for Mathematical and Computational Engineering Pontificia Universidad Catolica de Chile Santiago Chile

Using extensive data sources to create foundation language models has revolutionized the performance of deep learning-based architectures. This remarkable improvement has led to state-of-the-art results for various downstream NLP tasks, including clinical tasks. However, more research is needed to measure model performance intrinsically, especially in the clinical domain. We revisit the use of analogy questions as an effective method to measure the intrinsic performance of language models for the clinical domain in English. We tested multiple Transformer-based language models s over analogy questions constructed from the Unified Medical Language System (UMLS), a massive knowledge graph of clinical concepts. Our results show that large language models are significantly more performant for analogy resolution than small language models. Similarly, domain-specific language models perform better than general domain language models. We also found a correlation between intrinsic and extrinsic performance, validated through PubMedQA extrinsic task. Creating clinical-specific and language-specific language models is essential for advancing biomedical and clinical NLP and will ensure a valid application in clinical practice. Finally, given that our proposed intrinsic test is based on a term graph available in multiple languages, the dataset can be built to measure the performance of models in languages other than English. © 2025 Copyright held by the owner/author(s).

关键词： Foundation Models Clinical NLP Intrinsic Tests

Mass conservative reaction diffusion systems describing cell polarity

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arXiv 2020年

作者： Latos, Evangelos Suzuki, Takashi Institut für Mathematik und Wissenschaftliches Rechnen Heinrichstraße 36 Graz8010 Austria Center for Mathematical Modeling and Data Science Osaka University

A reaction-diffusion system with mass conservation modelling cell polarity is considered. A range of the parameters is found where the solution converges exponentially to the constant equilibrium and the ω-limit set of the solution is spatially homogeneous, containing the constant stationary solution as well as possible spatially homogeneous orbits. Copyright © 2020, The Authors. All rights reserved.

关键词： Dynamic models

The Most Probable Transition Paths of Stochastic Dynamical Systems: A Sufficient and Necessary Characterization

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arXiv 2021年

作者： Huang, Yuanfei Huang, Qiao Duan, Jinqiao School of Mathematics and Statistics Center for Mathematical Sciences Hubei Key Laboratory of Engineering Modeling and Scientific Computing Huazhong University of Science and Technology Wuhan430074 China Department of Statistics and Data Science National University of Singapore 6 Science Drive 2 Singapore117546 Singapore School of Data Science City University of Hong Kong Kowloon Hong Kong Department of Mathematics Faculty of Sciences University of Lisbon Campo Grande Edifício C6 LisboaPT-1749-016 Portugal Division of Mathematical Sciences School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore637371 Singapore The Dongguan Key Laboratory for Data Science and Intelligent Medicine Department of Mathematics Department of Physics Great Bay University Guangdong Dongguan523000 China

The most probable transition paths of a stochastic dynamical system are the global minimizers of the Onsager–Machlup action functional and can be described by a necessary but not sufficient condition, the Euler–Lagrange equation (a second-order differential equation with initial-terminal conditions) from a variational principle. This work is devoted to showing a sufficient and necessary characterization for the most probable transition paths of stochastic dynamical systems with Brownian noise. We prove that, under appropriate conditions, the most probable transition paths are completely determined by a first-order ordinary differential equation. The equivalence is established by showing that the Onsager–Machlup action functional of the original system can be derived from the corresponding Markovian bridge process. For linear stochastic systems and the nonlinear Hongler’s model, the first-order differential equations determining the most probable transition paths are shown analytically to imply the Euler–Lagrange equations of the Onsager–Machlup functional. For general nonlinear systems, the determining first-order differential equations can be approximated, in a short time or for the small noise case. Some numerical experiments are presented to illustrate our results. Copyright © 2021, The Authors. All rights reserved.

关键词： Dynamical systems

ABCSS: A novel approach for increasing the TCP congestion window in a network

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Procedia Computer science 2021年 191卷 437-444页

作者： N.M. Kasoro S.K. Kasereka G.K. Alpha K. Kyamakya University of Kinshasa Faculty of Sciences Mathematics and Computer Science Department Kinshasa Democratic Republic of the Congo Artificial intelligence Big data and modeLing simulation research center (ABIL) Kinshasa Democratic Republic of the Congo Université Libre des Pays des Grands Lacs Faculty of Sciences and Technologies Goma Democratic Republic of the Congo Alpen-Adria-Universitaet Klagenfurt Institute of Smart Systems Technologies Department of Mathematical Sciences Klagenfurt Austria

Congestion control is a useful task to be taken into account in order to maintain a good traffic in a network. In the case of a TCP/IP (Transmission Control Protocol/Internet Protocol) network, congestion creates queues in routers and even packet rejection. It is the reason why research have been conducted to improve congestion control mechanisms. Nowadays, several TCP congestion algorithms have been implemented. However, with the technology evolution and the need in terms of traffic capacity, various mechanisms implemented by these algorithms have shown their limitations and still need to be improved. The aim of this paper is to develop a novel TCP congestion control approach based on two famous algorithms: Appropriate Byte Counting (ABC) and Slow Start (SS). The results obtained show that ABC increases the congestion window appropriately compared to Slow Start. However, the congestion window remains invariant during the first round trips, which causes the TCP burst phenomenon. The TCP splitting can cause buffer overflows and long queues. For theses shortcomings, we propose ABCSS as a novel approach that appropriately increase the TCP congestion window and minimize the TCP splitting problem. The simulations of ABCSS algorithm provide interesting results compared to some known algorithms.

关键词： Congestion TCP ABC Slow Start Congestion window Congestion control ABCSS

Correction to: Pointwise agglomeration in continuous racetrack model

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Portuguese Economic Journal 2021年第2期21卷 237-237页

作者： Ohtake, Kensuke Yagi, Atsushi Center for Mathematical Modeling and Data Science Osaka University Toyonaka Japan Graduate School of Information Science and Technology Osaka University Suita Japan

Incorrect equation 1.

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