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Scientific reports 2020年第1期10卷 11482页

作者： Pavel Kharyuk Dmitry Nazarenko Ivan Oseledets Igor Rodin Oleg Shpigun Andrey Tsitsilin Mikhail Lavrentyev Skolkovo Institute of Science and Technology Center for Computational and Data-Intensive Science and Engineering Moscow 143026 Russia. kharyuk.pavel@***. Institute of Numerical Mathematics of the Russian Academy of Sciences Moscow 119991 Russia. kharyuk.pavel@***. Lomonosov Moscow State University Faculty of Chemistry Moscow 119991 Russia. dmitro.nazarenko@***. Skolkovo Institute of Science and Technology Center for Computational and Data-Intensive Science and Engineering Moscow 143026 Russia. Institute of Numerical Mathematics of the Russian Academy of Sciences Moscow 119991 Russia. Lomonosov Moscow State University Faculty of Chemistry Moscow 119991 Russia. All-Russian Research Institute of Medicinal and Aromatic Plants (VILAR) Moscow 117216 Russia. Saratov State University Department of Botanics and Ecology Saratov 410012 Russia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Heavy metals prediction in coastal marine sediments using hybridized machine learning models with metaheuristic optimization algorithm

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Chemosphere 2024年 352卷 141329页

作者： Yaseen, Zaher Mundher Melini Wan Mohtar, Wan Hanna Homod, Raad Z. Alawi, Omer A. Abba, Sani I. Oudah, Atheer Y. Togun, Hussein Goliatt, Leonardo Ul Hassan Kazmi, Syed Shabi Tao, Hai Civil and Environmental Engineering Department King Fahd University of Petroleum and Minerals Dhahran 31261 Saudi Arabia Interdisciplinary Research Center for Membranes and Water Security King Fahd University of Petroleum & Minerals (KFUPM) Dhahran Saudi Arabia Department of Civil Engineering Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia UKM Selangor Bangi 43600 Malaysia Environmental Management Centre Institute of Climate Change Universiti Kebangsaan Malaysia Selangor UKM Bangi 43600 Malaysia Department of Oil and Gas Engineering Basrah University for Oil and Gas Basra Iraq Department of Thermofluids School of Mechanical Engineering Universiti Teknologi Malaysia UTM Skudai Johor Bahru 81310 Malaysia Department of Computer Sciences College of Education for Pure Science University of Thi-Qar Nasiriyah 64001 Iraq Information and Communication Technology Research Group Scientific Research Center Al-Ayen University Nasiriyah 64001 Iraq Department of Mechanical Engineering College of Engineering University of Baghdad Baghdad Iraq Computational and Applied Mechanics Department Federal University of Juiz de Fora 36036-900 Brazil Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention and Guangdong Provincial Key Laboratory of Marine Biotechnology Shantou University Shantou 515063 China School of Computer and Information Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Institute of Big Data Application and Artificial Intelligence Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Faculty of Data Science and Information Technology INTI International University 71800 Malaysia

This study proposes different standalone models viz: Elman neural network (ENN), Boosted Tree algorithm (BTA), and f relevance vector machine (RVM) for modeling arsenic (As (mg/kg)) and zinc (Zn (mg/kg)) in marine sediments owing to anthropogenic activities. A heuristic algorithm based on the potential of RVM and a flower pollination algorithm (RVM-FPA) was developed to improve the prediction performance. Several evaluation indicators and graphical methods coupled with visualized cumulative probability function (CDF) were used to evaluate the accuracy of the models. Akaike (AIC) and Schwarz (SCI) information criteria based on Dickey-Fuller (ADF) and Philip Perron (PP) tests were introduced to check the reliability and stationarity of the data. The prediction performance in the verification phase indicated that RVM-M2 (PBAIS = -o.0465, MAE = 0.0335) and ENN-M2 (PBAIS = 0.0043, MAE = 0.0322) emerged as the best model for As (mg/kg) and Zn (mg/kg), respectively. In contrast with the standalone approaches, the simulated hybrid RVM-FPA proved merit and the most reliable, with a 5 % and 18 % predictive increase for As (mg/kg) and Zn (mg/kg), respectively. The study's findings validated the potential for estimating complex HMs through intelligent data-driven models and heuristic optimization. The study also generated valuable insights that can inform the decision-makers and stockholders for environmental management strategies. © 2024 Elsevier Ltd

关键词： Artificial intelligence Heavy metals Sensitivity analysis Soil contamination

MOST DISCRIMINATIVE STIMULI FOR FUNCTIONAL CELL TYPE CLUSTERING

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arXiv 2023年

作者： Burg, Max F. Zenkel, Thomas Vystrčilová, Michaela Oesterle, Jonathan Höfling, Larissa Willeke, Konstantin F. Lause, Jan Müller, Sarah Fahey, Paul G. Ding, Zhiwei Restivo, Kelli Sridhar, Shashwat Gollisch, Tim Berens, Philipp Tolias, Andreas S. Euler, Thomas Bethge, Matthias Ecker, Alexander S. International Max Planck Research School for Intelligent Systems Tübingen Germany Institute of Computer Science University of Göttingen Campus Institute Data Science Germany Tübingen AI Center University of Tübingen Germany Institute of Ophthalmic Research University of Tübingen Germany Centre for Integrative Neuroscience University of Tübingen Germany Institute for Bioinformatics and Medical Informatics Tübingen University Germany Hertie Institute for AI in Brain Health University of Tübingen Germany Department of Neuroscience Baylor College of Medicine HoustonTX United States Center for Neuroscience and Artificial Intelligence Baylor College of Medicine HoustonTX United States University Medical Center Göttingen Department of Ophthalmology Germany Bernstein Center for Computational Neuroscience Göttingen Germany University of Göttingen Germany Department of Electrical and Computer Engineering Rice University HoustonTX United States Max Planck Institute for Dynamics and Self-Organization Göttingen Germany

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron. © 2023, CC BY-NC-SA.

关键词： Maximum principle

A practical guide to machine learning interatomic potentials – Status and future

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arXiv 2025年

作者： Jacobs, Ryan Morgan, Dane Attarian, Siamak Meng, Jun Shen, Chen Wu, Zhenghao Xie, Clare Yijia Yang, Julia H. Artrith, Nongnuch Blaiszik, Ben Ceder, Gerbrand Choudhary, Kamal Csanyi, Gabor Cubuk, Ekin Dogus Deng, Bowen Drautz, Ralf Fu, Xiang Godwin, Jonathan Honavar, Vasant Isayev, Olexandr Johansson, Anders Kozinsky, Boris Martiniani, Stefano Ong, Shyue Ping Poltavsky, Igor Schmidt, K.J. Takamoto, So Thompson, Aidan Westermayr, Julia Wood, Brandon M. Department of Materials Science and Engineering University of Wisconsin-Madison MadisonWI55705 United States Harvard University Center for the Environment Harvard University CambridgeMA02138 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States Materials Chemistry and Catalysis Debye Institute for Nanomaterials Science Utrecht University Utrecht3584 CG Netherlands Globus University of Chicago ChicagoIL United States Data Science and Learning Division Argonne National Laboratory LemontIL United States Department of Materials Science and Engineering University of California BerkeleyCA94720 United States Materials Sciences Division Lawrence Berkeley National Laboratory CA94720 United States Material Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Engineering University of Cambridge CambridgeCB2 1PZ United Kingdom Google DeepMind Mountain ViewCA United States Ruhr-Universität Bochum Bochum44780 Germany Meta United States Orbital Materials London United Kingdom Department of Computer Science and Engineering The Pennsylvania State University University ParkPA United States College of Information Sciences and Technology The Pennsylvania State University University ParkPA United States Artificial Intelligence Research Laboratory The Pennsylvania State University University ParkPA United States Center for Artificial Intelligence Foundations and Scientific Applications The Pennsylvania State University University ParkPA United States Department of Chemistry Mellon College of Science Carnegie Mellon University PittsburghPA15213 United States Computational Biology Department School of Computer Science Carnegie Mellon University PittsburghPA15213 United States Courant Institute of Mathematical Sciences New York University New YorkNY10003 United States Center for Soft Matter Research Department of P

The rapid development and large body of literature on machine learning interatomic potentials (MLIPs) can make it difficult to know how to proceed for researchers who are not experts but wish to use these tools. The spirit of this review is to help such researchers by serving as a practical, accessible guide to the state-of-the-art in MLIPs. This review paper covers a broad range of topics related to MLIPs, including (i) central aspects of how and why MLIPs are enablers of many exciting advancements in molecular modeling, (ii) the main underpinnings of different types of MLIPs, including their basic structure and formalism, (iii) the potentially transformative impact of universal MLIPs for both organic and inorganic systems, including an overview of the most recent advances, capabilities, downsides, and potential applications of this nascent class of MLIPs, (iv) a practical guide for estimating and understanding the execution speed of MLIPs, including guidance for users based on hardware availability, type of MLIP used, and prospective simulation size and time, (v) a manual for what MLIP a user should choose for a given application by considering hardware resources, speed requirements, energy and force accuracy requirements, as well as guidance for choosing pre-trained potentials or fitting a new potential from scratch, (vi) discussion around MLIP infrastructure, including sources of training data, pre-trained potentials, and hardware resources for training, (vii) summary of some key limitations of present MLIPs and current approaches to mitigate such limitations, including methods of including long-range interactions, handling magnetic systems, and treatment of excited states, and finally (viii) we finish with some more speculative thoughts on what the future holds for the development and application of MLIPs over the next 3-10+ years. © 2025, CC BY.

关键词： Digital storage

Improving Policy-Oriented Agent-Based Modeling with History Matching: A Case Study

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arXiv 2024年

作者： O’Gara, David Kerr, Cliff C. Klein, Daniel J. Binois, Mickaël Garnett, Roman Hammond, Ross A. Division of Computational and Data Sciences Washington University in St. Louis St. LouisMO United States Institute for Disease Modeling Bill & Melinda Gates Foundation SeattleWA United States Acumes Team Université Côte d’Azur Inria Sophia Antipolis France Department of Computer Science McKelvey School of Engineering Washington University in St. Louis St. LouisMO United States Public Health Brown School Washington University in St. Louis St. LouisMO United States Center on Social Dynamics and Policy Brookings Institution WashingtonDC United States The Santa Fe Institute Santa FeNM United States

Advances in computing power and data availability have led to growing sophistication in mechanistic mathematical models of social dynamics. Increasingly these models are used to inform real-world policy decision-making, often with significant time sensitivity. One such modeling approach is agent-based modeling, which offers particular strengths for capturing spatial and behavioral realism, and for in-silico experiments (varying input parameters and assumptions to explore their downstream impact on key outcomes). To be useful in the real-world, these models must be able to qualitatively or quantitatively capture observed empirical phenomena, forming the starting point for subsequent experimentation. computational constraints often form a significant hurdle to timely calibration and policy analysis in high-resolution agent-based models. In this paper, we present a technical solution to address this bottleneck, substantially increasing efficiency and thus widening the range of utility for policy models. We illustrate our approach with a case study using a previously published and widely used epidemiological model. © 2024, CC BY.

关键词： Digital elevation model

Model Predictive Path Integral Control for Car Driving with Autogenerated Cost map Based on Prior Map and Camera Image

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Model Predictive Path Integral Control for Car Driving with ...

International Conference on Intelligent Transportation

作者： Alexander Buyval Aidar Gabdullin Konstantin Sozykin Alexandr Klimchik Center for Technologies in Robotics and Mechatronics Components Innopolis University Innopolis Russia Skolkovo Institute of Science and Technology (Skoltech) Center for Computational and Data-Intensive Science and Engineering (CDISE) Russia

ISBN: (纸本)9781538670255

Model Predictive Path Integral (MPPI) algorithm is an efficient approach to control an autonomous car. However, it requires a cost map. Preparing a cost map in advance is a task that can be completed only for a static closed unchanging environment, but impossible for real city conditions where the environment is dynamic. In this work, we present a method for automatic creation of the cost map based on map data and image from a camera mounted on a self-driving car. The described approach was tested on the Kia Soul car.

关键词： Cameras Automobiles Fires Roads Image segmentation Prediction algorithms Heuristic algorithms

Parallel Planning:A New Motion Planning Framework for Autonomous Driving

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IEEE/CAA Journal of Automatica Sinica 2019年第1期6卷 236-246页

作者： Long Chen Xuemin Hu Wei Tian Hong Wang Dongpu Cao Fei-Yue Wang IEEE School of Data and Computer Science Sun Yat-sen University the School of Computer Science and Information Engineering Hubei University Institute of Measurement and Control Systems Karlsruhe Institute of Technology Department of Mechanical and Mechatronics Engineering University of Waterloo the State Key Laboratory of Management and Control for Complex Systems.Institute of Automation Chinese Academy of Sciences the Research Center for Military Computational Experiments and Parallel Systems Technology National University of Defense Technology

Motion planning is one of the most significant technologies for autonomous driving. To make motion planning models able to learn from the environment and to deal with emergency situations, a new motion planning framework called as"parallel planning" is proposed in this paper. In order to generate sufficient and various training samples, artificial traffic scenes are firstly constructed based on the knowledge from the reality.A deep planning model which combines a convolutional neural network(CNN) with the Long Short-Term Memory module(LSTM) is developed to make planning decisions in an end-toend mode. This model can learn from both real and artificial traffic scenes and imitate the driving style of human ***, a parallel deep reinforcement learning approach is also presented to improve the robustness of planning model and reduce the error rate. To handle emergency situations, a hybrid generative model including a variational auto-encoder(VAE) and a generative adversarial network(GAN) is utilized to learn from virtual emergencies generated in artificial traffic scenes. While an autonomous vehicle is moving, the hybrid generative model generates multiple video clips in parallel, which correspond to different potential emergency scenarios. Simultaneously, the deep planning model makes planning decisions for both virtual and current real scenes. The final planning decision is determined by analysis of real observations. Leveraging the parallel planning approach, the planner is able to make rational decisions without heavy calculation burden when an emergency occurs.

关键词： Autonomous driving artificial traffic scene deep learning emergencies motion planning parallel planning

MatterChat: A Multi-Modal LLM for Material science

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arXiv 2025年

作者： Tang, Yingheng Xu, Wenbin Cao, Jie Ma, Jianzhu Gao, Weilu Farrell, Steve Erichson, Benjamin Mahoney, Michael W. Nonaka, Andy Yao, Zhi Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA United States NSF National AI Institute for Student-AI Teaming University of Colorado at Boulder Boulder United States Institute for AI Industry Research Tsinghua University Beijing China Department of Electrical and Computer Engineering The University of Utah Salt Lake CityUT United States Scientific Data Division Lawrence Berkeley National Laboratory BerkeleyCA United States International Computer Science Institute BerkeleyCA United States Department of Statistics University of California at Berkeley BerkeleyCA United States

Understanding and predicting the properties of inorganic materials is crucial for accelerating advancements in materials science and driving applications in energy, electronics, and beyond. Integrating material structure data with language-based information through multi-modal large language models (LLMs) offers great potential to support these efforts by enhancing human–AI interaction. However, a key challenge lies in integrating atomic structures at full resolution into LLMs. In this work, we introduce MatterChat, a versatile structure-aware multi-modal LLM that unifies material structural data and textual inputs into a single cohesive model. MatterChat employs a bridging module to effectively align a pretrained machine learning interatomic potential with a pretrained LLM, reducing training costs and enhancing flexibility. Our results demonstrate that MatterChat significantly improves performance in material property prediction and human-AI interaction, surpassing general-purpose LLMs such as GPT-4. We also demonstrate its usefulness in applications such as more advanced scientific reasoning and step-by-step material synthesis. © 2025, CC BY.

关键词： Materials properties

Stability of stochastic gradient descent on nonsmooth convex losses 20

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Stability of stochastic gradient descent on nonsmooth convex...

Proceedings of the 34th International Conference on Neural Information Processing Systems

作者： Raef Bassily Vitaly Feldman Cristóbal Guzmán Kunal Talwar Department of Computer Science & Engineering The Ohio State University Apple Pontificia Universidad Católica de Chile Institute for Mathematical and Computational Engineering ANID – Millennium Science Initiative Program Millennium Nucleus Center for the Discovery of Structures in Complex Data

ISBN: (纸本)9781713829546

Uniform stability is a notion of algorithmic stability that bounds the worst case change in the model output by the algorithm when a single data point in the dataset is replaced. An influential work of Hardt et al. [20] provides strong upper bounds on the uniform stability of the stochastic gradient descent (SGD) algorithm on sufficiently smooth convex losses. These results led to important progress in understanding of the generalization properties of SGD and several applications to differentially private convex optimization for smooth *** work is the first to address uniform stability of SGD on nonsmooth convex losses. Specifically, we provide sharp upper and lower bounds for several forms of SGD and full-batch GD on arbitrary Lipschitz nonsmooth convex losses. Our lower bounds show that, in the nonsmooth case, (S)GD can be inherently less stable than in the smooth case. On the other hand, our upper bounds show that (S)GD is sufficiently stable for deriving new and useful bounds on generalization error. Most notably, we obtain the first dimension-independent generalization bounds for multi-pass SGD in the nonsmooth case. In addition, our bounds allow us to derive a new algorithm for differentially private nonsmooth stochastic convex optimization with optimal excess population risk. Our algorithm is simpler and more efficient than the best known algorithm for the nonsmooth case [16].

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AA-ICP: Iterative closest point with anderson acceleration

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AA-ICP: Iterative closest point with anderson acceleration

2018 IEEE International Conference on Robotics and Automation, ICRA 2018

作者： Pavlov, Artem L. Ovchinnikov, Grigory W.V. Derbyshev, Dmitry Yu. Tsetserukou, Dzmitry Oseledets, Ivan V. Skolkovo Institute of Science and Technology Skolkovo Innovation Center Space Center Moscow143026 Russia Skolkovo Institute of Science and Technology Computational and Data-Intensive Science and Engineering Russia Moscow Institute of Physics and Technology Russia Skolkovo Institute of Science and Technology Space Center Russia Skolkovo Institute of Science and Technology Center for Computational and Data-Intensive Science and Engineering Russia

ISBN: (纸本)9781538630815

Iterative Closest Point (ICP) is a widely used method for performing scan-matching and registration. Being simple and robust, this method is still computationally expensive and may be challenging to use in real-time applications with limited resources on mobile platforms. In this paper we propose a novel effective method for acceleration of ICP which does not require substantial modifications to the existing code. This method is based on an idea of Anderson acceleration which is an iterative procedure for finding a fixed point of contractive mapping. The latter is often faster than a standard Picard iteration, usually used in ICP implementations. We show that ICP, being a fixed point problem, can be significantly accelerated by this method enhanced by heuristics to improve overall robustness. We implement proposed approach into Point Cloud Library (PCL) and make it available online. Benchmarking on the real-world data fully supports our claims. © 2018 IEEE.

关键词： Iterative methods