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arXiv 2022年

作者： Dawid, Anna Arnold, Julian Requena, Borja Gresch, Alexander Plodzien, Marcin Donatella, Kaelan Nicoli, Kim A. Stornati, Paolo Koch, Rouven Büttner, Miriam Okula, Robert Muñoz–Gil, Gorka Vargas–Hernández, Rodrigo A. Cervera-Lierta, Alba Carrasquilla, Juan Dunjko, Vedran Gabrié, Marylou Huembeli, Patrick van Nieuwenburg, Evert Vicentini, Filippo Wang, Lei Wetzel, Sebastian J. Carleo, Giuseppe Greplová, Eliška Krems, Roman Marquardt, Florian Tomza, Michal Lewenstein, Maciej Dauphin, Alexandre Faculty of Physics University of Warsaw Poland ICFO - Institut de Ciències Fotòniques The Barcelona Institute of Science and Technology Castelldefels Barcelona08860 Spain Center for Computational Quantum Physics Flatiron Institute New York United States Department of Physics University of Basel Switzerland Institute for Theoretical Physics Heinrich Heine University Düsseldorf Germany Institute for Quantum Inspired and Quantum Optimization Hamburg University of Technology Germany Université de Paris CNRS Laboratoire Matériaux et Phénomènes Quantiques France Machine Learning Group Technische Universität Berlin Germany BIFOLD Berlin Institute for the Foundations of Learning and Data Berlin10587 Germany Department of Applied Physics Aalto University Espoo Finland Institute of Physics Albert-Ludwig University of Freiburg Germany International Centre for Theory of Quantum Technologies University of Gdańsk Poland Department of Algorithms and System Modeling Faculty of Electronics Faculty of Electronics Telecommunications and Informatics Gdańsk University of Technology Poland Institute for Theoretical Physics University of Innsbruck Austria Department of Chemistry University of Toronto Canada Vector Institute for Artificial Intelligence MaRS Centre Toronto Canada Department of Chemistry and Chemical Biology McMaster University Hamilton Canada Barcelona Supercomputing Center Spain LIACS Leiden University Netherlands CMAP École Polytechnique France Switzerland Menten AI Inc. Palo AltoCA United States Niels Bohr Institute Copenhagen Denmark CPHT CNRS École Polytechnique Institut Polytechnique de Paris PalaiseauF-91128 France Beijing National Lab for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Songshan Lake Materials Laboratory Dongguan China Perimeter Institute for Theoretical Physics Waterloo Canada Kavli Institute of Nanoscience Delft University of Technology DelftNL-2600 GA Netherlands Department of

In this book, we provide a comprehensive introduction to the most recentadvances in the application of machine learning methods in quantum sciences. Wecover the use of deep learning and kernel methods in supervised, unsupervised,and reinforcement learning algorithms for phase classification, representationof many-body quantum states, quantum feedback control, and quantum circuitsoptimization. Moreover, we introduce and discuss more specialized topics suchas differentiable programming, generative models, statistical approach tomachine learning, and quantum machine learning. © 2022, CC BY.

关键词： Deep learning

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DPA-2: a large atomic model as a multi-task learner

arXiv

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arXiv 2023年

作者： Zhang, Duo Liu, Xinzijian Zhang, Xiangyu Zhang, Chengqian Cai, Chun Bi, Hangrui Du, Yiming Qin, Xuejian Peng, Anyang Huang, Jiameng Li, Bowen Shan, Yifan Zeng, Jinzhe Zhang, Yuzhi Liu, Siyuan Li, Yifan Chang, Junhan Wang, Xinyan Zhou, Shuo Liu, Jianchuan Luo, Xiaoshan Wang, Zhenyu Jiang, Wanrun Wu, Jing Yang, Yudi Yang, Jiyuan Yang, Manyi Gong, Fu-Qiang Zhang, Linshuang Shi, Mengchao Dai, Fu-Zhi York, Darrin M. Liu, Shi Zhu, Tong Zhong, Zhicheng Lv, Jian Cheng, Jun Jia, Weile Chen, Mohan Ke, Guolin Weinan, E. Zhang, Linfeng Wang, Han AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China CAS Key Laboratory of Magnetic Materials and Devices Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of Sciences Ningbo315201 China School of Electronics Engineering and Computer Science Peking University Beijing100871 China Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Chemistry Princeton University PrincetonNJ08540 United States College of Chemistry and Molecular Engineering Peking University Beijing100871 China Yuanpei College Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China State Key Laboratory of Superhard Materials College of Physics Jilin University Changchun130012 China Key Laboratory of Material Simulation Methods & Software of Ministry of Education College of Physics Jilin University Changchun130012 China International Center of Future Science Jilin University Changchun130012 China Key Laboratory for Quantum Materials of Zhejiang Province Department of Physics School of Science Westlake University Zhejiang Hangzhou310030 China Atomistic Simulations Italia

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research. Copyright © 2023, The Authors. All rights reserved.

关键词： Multi-task learning

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Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes

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ImmunoInformatics 2023年 9卷

作者： Christian A Balbin Janelle Nunez-Castilla Vitalii Stebliankin Prabin Baral Masrur Sobhan Trevor Cickovski Ananda Mohan Mondal Giri Narasimhan Prem Chapagain Kalai Mathee Jessica Siltberg-Liberles Department of Biological Sciences College of Arts Science and Education Florida International University Miami United States Bioinformatics Research Group (BioRG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Department of Physics College of Arts Science and Education Florida International University Miami United States Machine Learning and Data Analytics Group (MLDAG) Knight Foundation School of Computing and Information Sciences Florida International University Miami United States Biomolecular Sciences Institute Florida International University Miami United States Department of Human and Molecular Genetics Herbert Wertheim College of Medicine Florida International University Miami United States

Upon infection, foreign antigenic proteins stimulate the host's immune system to produce antibodies targeting the pathogen. These antibodies bind to regions on the antigen called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host proteins or other pathogenic proteins the host has previously encountered can impact the host immune response to the pathogen and may lead to cross-reactive antibodies. The ability to identify potential regions of molecular mimicry in a pathogen can illuminate immune effects which are especially important to pathogen treatment and vaccine design. Here we present Epitopedia, a software pipeline that facilitates the identification of regions that may exhibit potential three-dimensional molecular mimicry between an antigenic pathogen protein and known immune epitopes as catalogued by the Immune Epitope database (IEDB). Epitopedia is open-source software released under the MIT license and is freely available on GitHub, including a Docker container with all other software dependencies preinstalled. We performed an analysis describing how various secondary structure states, identity between pentapeptide pairs, and identity between the parent sequences of pentapeptide pairs affects RMSD. We found that pentapeptides pairs in a helical conformation had considerably lower RMSD values than those in extended or coil conformations. We also found that RMSD is significantly increased when pentapeptide pairs are from non-homologous sequences.

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Why is the Winner the Best?

Why is the Winner the Best?

引用

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

引用

arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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LimeSoDa: A dataset collection for benchmarking of machine learning regressors in digital soil mapping

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Geoderma 2025年 459卷

作者： Schmidinger, Jonas Vogel, Sebastian Barkov, Viacheslav Pham, Anh-Duy Gebbers, Robin Tavakoli, Hamed Correa, Jose Tavares, Tiago R. Filippi, Patrick Jones, Edward J. Lukas, Vojtech Boenecke, Eric Ruehlmann, Joerg Schroeter, Ingmar Kramer, Eckart Paetzold, Stefan Kodaira, Masakazu Wadoux, Alexandre M.J.-C. Bragazza, Luca Metzger, Konrad Huang, Jingyi Valente, Domingos S.M. Safanelli, Jose L. Bottega, Eduardo L. Dalmolin, Ricardo S.D. Farkas, Csilla Steiger, Alexander Horst, Taciara Z. Ramirez-Lopez, Leonardo Scholten, Thomas Stumpf, Felix Rosso, Pablo Costa, Marcelo M. Zandonadi, Rodrigo S. Wetterlind, Johanna Atzmueller, Martin Osnabrück University Joint Lab Artificial Intelligence and Data Science Osnabrück Germany Department of Agromechatronics Potsdam Germany Piracicaba Brazil The University of Sydney Sydney Institute of Agriculture Sydney Australia Mendel University in Brno Department of Agrosystems and Bioclimatology Brno Czech Republic Leibniz Institute of Vegetable and Ornamental Crops Next Generation Horticultural Systems Grossbeeren Germany Eberswalde University for Sustainable Development Landscape Management and Nature Conservation Eberswalde Germany —Soil Science and Soil Ecology Bonn Germany Tokyo University of Agriculture and Technology Institute of Agriculture Tokyo Japan LISAH Univ. Montpellier AgroParisTech INRAE IRD L'Institut Agro Montpellier France Agroscope Field-Crop Systems and Plant Nutrition Nyon Switzerland University of Wisconsin-Madison Department of Soil Science Madison United States Federal University of Viçosa Department of Agricultural Engineering Viçosa Brazil Woodwell Climate Research Center Falmouth United States Academic Coordination Santa Maria Brazil Soil Department Santa Maria Brazil Division of Environment and Natural Resources Aas Norway University of Rostock Chair of Geodesy and Geoinformatics Rostock Germany Federal Technological University of Paraná Dois Vizinhos Brazil BÜCHI Labortechnik AG Data Science Department Flawil Switzerland Imperial College London Imperial College Business School London United Kingdom University of Tübingen Department of Geosciences Tübingen Germany University of Tübingen DFG Cluster of Excellence ‘Machine Learning for Science’ Germany Bern University of Applied Sciences Competence Center for Soils Zollikofen Switzerland Simulation and Data Science Müncheberg Germany Federal University of Jataí Institute of Agricultural Sciences Jatai Brazil Federal University of Mato Grosso Instute of Agricultural and Environmental Scinces Sinop Brazil Department of Soil and Environment Skara S

Digital soil mapping (DSM) relies on a broad pool of statistical methods, yet determining the optimal method for a given context remains challenging and contentious. Benchmarking studies on multiple datasets are needed to reveal strengths and limitations of commonly used methods. Existing DSM studies usually rely on a single dataset with restricted access, leading to incomplete and potentially misleading conclusions. To address these issues, we introduce an open-access dataset collection called Precision Liming Soil datasets (LimeSoDa). LimeSoDa consists of 31 field- and farm-scale datasets from various countries. Each dataset has three target soil properties: (1) soil organic matter or soil organic carbon, (2) clay content and (3) pH, alongside a set of features. Features are dataset-specific and were obtained by optical spectroscopy, proximal- and remote soil sensing. All datasets were aligned to a tabular format and are ready-to-use for modeling. We demonstrated the use of LimeSoDa for benchmarking by comparing the predictive performance of four learning algorithms across all datasets. This comparison included multiple linear regression (MLR), support vector regression (SVR), categorical boosting (CatBoost) and random forest (RF). The results showed that although no single algorithm was universally superior, certain algorithms performed better in specific contexts. MLR and SVR performed better on high-dimensional spectral datasets, likely due to better compatibility with principal components. In contrast, CatBoost and RF exhibited considerably better performances when applied to datasets with a moderate number ( © 2025 The Author(s)

关键词： Random forests

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SimBIG: Field-level Simulation-Based Inference of Galaxy Clustering

arXiv

引用

arXiv 2023年

作者： Lemos, Pablo Parker, Liam Hahn, ChangHoon Ho, Shirley Eickenberg, Michael Hou, Jiamin Massara, Elena Modi, Chirag Dizgah, Azadeh Moradinezhad Blancard, Bruno Régaldo-Saint Spergel, David Department of Physics Université de Montréal 1375 Avenue Thérèse-Lavoie-Roux MontréalQCH2V 0B3 Canada Mila - Quebec Artificial Intelligence Institute 6666 Rue Saint-Urbain MontréalQCH2S 3H1 Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Princeton University PrincetonNJ08544 United States Center for Cosmology and Particle Physics Department of Physics New York University New YorkNY10003 United States Department of Physics Carnegie Mellon University PittsburghPA15213 United States Center for Computational Mathematics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Astronomy University of Florida 211 Bryant Space Science Center GainesvilleFL32611 United States Max-Planck-Institut für Extraterrestrische Physik Postfach 1312 Giessenbachstrasse 1 Garching bei München85748 Germany Waterloo Centre for Astrophysics University of Waterloo 200 University Ave W WaterlooONN2L 3G1 Canada Department of Physics and Astronomy University of Waterloo 200 University Ave W WaterlooONN2L 3G1 Canada Département de Physique Théorique Université de Genève 24 quai Ernest Ansermet Genève 41211 Switzerland

We present the first simulation-based inference (SBI) of cosmological parameters from field-level analysis of galaxy clustering. Standard galaxy clustering analyses rely on analyzing summary statistics, such as the power spectrum, P, with analytic models based on perturbation theory. Consequently, they do not fully exploit the non-linear and non-Gaussian features of the galaxy distribution. To address these limitations, we use the SimBIG forward modelling framework to perform SBI using normalizing flows. We apply SimBIG to a subset of the BOSS CMASS galaxy sample using a convolutional neural network with stochastic weight averaging to perform massive data compression of the galaxy field. We infer constraints on (Equation presented) and (Equation presented). While our constraints on Ωm are in-line with standard P analyses, those on σ8 are 2.65× tighter. Our analysis also provides constraints on the Hubble constant H0 = 64.5 ± 3.8 km/s/Mpc from galaxy clustering alone. This higher constraining power comes from additional non-Gaussian cosmological information, inaccessible with P. We demonstrate the robustness of our analysis by showcasing our ability to infer unbiased cosmological constraints from a series of test simulations that are constructed using different forward models than the one used in our training dataset. This work not only presents competitive cosmological constraints but also introduces novel methods for leveraging additional cosmological information in upcoming galaxy surveys like DESI, PFS, and Euclid. © 2023, CC0.

关键词： Galaxies

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Cosmological N-body simulations: A challenge for scalable generative models

arXiv

引用

arXiv 2019年

作者： Perraudin, Nathanaël Srivastava, Ankit Lucchi, Aurelien Kacprzak, Tomasz Hofmann, Thomas Réfrégier, Alexandre Swiss Data Science Center ETH Zurich Universitätstrasse 25 Zurich8006 Switzerland Institute for Particle Physics and Astrophysics ETH Zurich Wolfgang-Pauli-Str. 27 Zurich8093 Switzerland Institute for Machine Learning ETH Zurich Universitätstrasse 6 Zurich8006 Switzerland

Deep generative models, such as Generative Adversarial Networks (GANs) or Variational Autoencoders (VAs) have been demonstrated to produce images of high visual quality. However, the existing hardware on which these models are trained severely limits the size of the images that can be generated. The rapid growth of high dimensional data in many fields of science therefore poses a significant challenge for generative models. In cosmology, the large-scale, three-dimensional matter distribution, modeled with N-body simulations, plays a crucial role in understanding of evolution of structures in the universe. As these simulations are computationally very expensive, GANs have recently generated interest as a possible method to emulate these datasets, but they have been, so far, mostly limited to two dimensional data. In this work, we introduce a new benchmark for the generation of three dimensional N-body simulations, in order to stimulate new ideas in the machine learning community and move closer to the practical use of generative models in cosmology. As a first benchmark result, we propose a scalable GAN approach for training a generator of N-body three-dimensional cubes. Our technique relies on two key building blocks, (i) splitting the generation of the high-dimensional data into smaller parts, and (ii) using a multi-scale approach that efficiently captures global image features that might otherwise be lost in the splitting process. We evaluate the performance of our model for the generation of N-body samples using various statistical measures commonly used in cosmology. Our results show that the proposed model produces samples of high visual quality, although the statistical analysis reveals that capturing rare features in the data poses significant problems for the generative models. We make the data, quality evaluation routines, and the proposed GAN architecture publicly available at https://***/nperraud/3DcosmoGAN. Copyright © 2019, The Authors. All right

关键词： Cosmology

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Nonparametric density estimation with adversarial losses 18

Nonparametric density estimation with adversarial losses

引用

Proceedings of the 32nd International Conference on Neural Information Processing Systems

作者： Shashank Singh Ananya Uppal Boyue Li Chun-Liang Li Manzil Zaheer Barnabás Póczos Machine Learning Department Carnegie Mellon University and Department of Statistics & Data Science Carnegie Mellon University Department of Mathematical Sciences Carnegie Mellon University Language Technologies Institute Carnegie Mellon University Machine Learning Department Carnegie Mellon University

We study minimax convergence rates of nonparametric density estimation under a large class of loss functions called "adversarial losses", which, besides classical Lp losses, includes maximum mean discrepancy (MMD), Wasserstein distance, and total variation distance. These losses are closely related to the losses encoded by discriminator networks in generative adversarial networks (GANs). In a general framework, we study how the choice of loss and the assumed smoothness of the underlying density together determine the minimax rate. We also discuss implications for training GANs based on deep ReLU networks, and more general connections to learning implicit generative models in a minimax statistical sense.

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An Open-Source Knowledge Graph Ecosystem for the Life sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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