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Bayesian inference of chaotic dynamics by merging data assimilation, machine learning and expectation-maximization 融合数据同化、机器学习和期望最大化的混沌动力学贝叶斯推理
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-17 DOI: 10.3934/fods.2020004
M. Bocquet, J. Brajard, A. Carrassi, Laurent Bertino
{"title":"Bayesian inference of chaotic dynamics by merging data assimilation, machine learning and expectation-maximization","authors":"M. Bocquet, J. Brajard, A. Carrassi, Laurent Bertino","doi":"10.3934/fods.2020004","DOIUrl":"https://doi.org/10.3934/fods.2020004","url":null,"abstract":"The reconstruction from observations of high-dimensional chaotic dynamics such as geophysical flows is hampered by (i) the partial and noisy observations that can realistically be obtained, (ii) the need to learn from long time series of data, and (iii) the unstable nature of the dynamics. To achieve such inference from the observations over long time series, it has been suggested to combine data assimilation and machine learning in several ways. We show how to unify these approaches from a Bayesian perspective using expectation-maximization and coordinate descents. In doing so, the model, the state trajectory and model error statistics are estimated all together. Implementations and approximations of these methods are discussed. Finally, we numerically and successfully test the approach on two relevant low-order chaotic models with distinct identifiability.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49478111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 75
Mean-field and kinetic descriptions of neural differential equations 神经微分方程的平均场和动力学描述
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-07 DOI: 10.3934/fods.2022007
M. Herty, T. Trimborn, G. Visconti
{"title":"Mean-field and kinetic descriptions of neural differential equations","authors":"M. Herty, T. Trimborn, G. Visconti","doi":"10.3934/fods.2022007","DOIUrl":"https://doi.org/10.3934/fods.2022007","url":null,"abstract":"Nowadays, neural networks are widely used in many applications as artificial intelligence models for learning tasks. Since typically neural networks process a very large amount of data, it is convenient to formulate them within the mean-field and kinetic theory. In this work we focus on a particular class of neural networks, i.e. the residual neural networks, assuming that each layer is characterized by the same number of neurons begin{document}$ N $end{document}, which is fixed by the dimension of the data. This assumption allows to interpret the residual neural network as a time-discretized ordinary differential equation, in analogy with neural differential equations. The mean-field description is then obtained in the limit of infinitely many input data. This leads to a Vlasov-type partial differential equation which describes the evolution of the distribution of the input data. We analyze steady states and sensitivity with respect to the parameters of the network, namely the weights and the bias. In the simple setting of a linear activation function and one-dimensional input data, the study of the moments provides insights on the choice of the parameters of the network. Furthermore, a modification of the microscopic dynamics, inspired by stochastic residual neural networks, leads to a Fokker-Planck formulation of the network, in which the concept of network training is replaced by the task of fitting distributions. The performed analysis is validated by artificial numerical simulations. In particular, results on classification and regression problems are presented.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42109967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Topological reconstruction of sub-cellular motion with Ensemble Kalman velocimetry 基于集合卡尔曼速度法的亚细胞运动拓扑重建
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-01 DOI: 10.3934/fods.2020007
Le Yin, Ioannis Sgouralis, V. Maroulas
{"title":"Topological reconstruction of sub-cellular motion with Ensemble Kalman velocimetry","authors":"Le Yin, Ioannis Sgouralis, V. Maroulas","doi":"10.3934/fods.2020007","DOIUrl":"https://doi.org/10.3934/fods.2020007","url":null,"abstract":"Microscopy imaging of plant cells allows the elaborate analysis of sub-cellular motions of organelles. The large video data set can be efficiently analyzed by automated algorithms. We develop a novel, data-oriented algorithm, which can track organelle movements and reconstruct their trajectories on stacks of image data. Our method proceeds with three steps: (ⅰ) identification, (ⅱ) localization, and (ⅲ) linking. This method combines topological data analysis and Ensemble Kalman Filtering, and does not assume a specific motion model. Application of this method on simulated data sets shows an agreement with ground truth. We also successfully test our method on real microscopy data.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70247921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stochastic gradient descent algorithm for stochastic optimization in solving analytic continuation problems 求解解析延拓问题的随机优化的随机梯度下降算法
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-01 DOI: 10.3934/fods.2020001
F. Bao, T. Maier
{"title":"Stochastic gradient descent algorithm for stochastic optimization in solving analytic continuation problems","authors":"F. Bao, T. Maier","doi":"10.3934/fods.2020001","DOIUrl":"https://doi.org/10.3934/fods.2020001","url":null,"abstract":"We propose a stochastic gradient descent based optimization algorithm to solve the analytic continuation problem in which we extract real frequency spectra from imaginary time Quantum Monte Carlo data. The procedure of analytic continuation is an ill-posed inverse problem which is usually solved by regularized optimization methods, such like the Maximum Entropy method, or stochastic optimization methods. The main contribution of this work is to improve the performance of stochastic optimization approaches by introducing a supervised stochastic gradient descent algorithm to solve a flipped inverse system which processes the random solutions obtained by a type of Fast and Efficient Stochastic Optimization Method.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70247865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Hierarchical approximations for data reduction and learning at multiple scales 多尺度下数据约简和学习的层次近似
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-01 DOI: 10.3934/fods.2020008
P. Shekhar, A. Patra
{"title":"Hierarchical approximations for data reduction and learning at multiple scales","authors":"P. Shekhar, A. Patra","doi":"10.3934/fods.2020008","DOIUrl":"https://doi.org/10.3934/fods.2020008","url":null,"abstract":"This paper describes a hierarchical learning strategy for generating sparse representations of multivariate datasets. The hierarchy arises from approximation spaces considered at successively finer scales. A detailed analysis of stability, convergence and behavior of error functionals associated with the approximations are presented, along with a well chosen set of applications. Results show the performance of the approach as a data reduction mechanism for both synthetic (univariate and multivariate) and a real dataset (geo-spatial). The sparse representation generated is shown to efficiently reconstruct data and minimize error in prediction. The approach is also shown to generalize well to unseen samples, extending its prospective application to statistical learning problems.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70247939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Random Walks and Markov Chains 随机漫步和马尔可夫链
Foundations of data science (Springfield, Mo.) Pub Date : 2020-01-01 DOI: 10.1017/9781108755528.004
Avrim Blum, J. Hopcroft, R. Kannan
{"title":"Random Walks and Markov Chains","authors":"Avrim Blum, J. Hopcroft, R. Kannan","doi":"10.1017/9781108755528.004","DOIUrl":"https://doi.org/10.1017/9781108755528.004","url":null,"abstract":"","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/9781108755528.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"56925823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Stability of non-linear filter for deterministic dynamics 确定性动力学中非线性滤波器的稳定性
Foundations of data science (Springfield, Mo.) Pub Date : 2019-10-31 DOI: 10.3934/fods.2021025
A. Reddy, A. Apte
{"title":"Stability of non-linear filter for deterministic dynamics","authors":"A. Reddy, A. Apte","doi":"10.3934/fods.2021025","DOIUrl":"https://doi.org/10.3934/fods.2021025","url":null,"abstract":"This papers shows that nonlinear filter in the case of deterministic dynamics is stable with respect to the initial conditions under the conditions that observations are sufficiently rich, both in the context of continuous and discrete time filters. Earlier works on the stability of the nonlinear filters are in the context of stochastic dynamics and assume conditions like compact state space or time independent observation model, whereas we prove filter stability for deterministic dynamics with more general assumptions on the state space and observation process. We give several examples of systems that satisfy these assumptions. We also show that the asymptotic structure of the filtering distribution is related to the dynamical properties of the signal.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46089690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
A Bayesian nonparametric test for conditional independence 条件独立性的贝叶斯非参数检验
Foundations of data science (Springfield, Mo.) Pub Date : 2019-10-24 DOI: 10.3934/FODS.2020009
Onur Teymur, S. Filippi
{"title":"A Bayesian nonparametric test for conditional independence","authors":"Onur Teymur, S. Filippi","doi":"10.3934/FODS.2020009","DOIUrl":"https://doi.org/10.3934/FODS.2020009","url":null,"abstract":"This article introduces a Bayesian nonparametric method for quantifying the relative evidence in a dataset in favour of the dependence or independence of two variables conditional on a third. The approach uses Polya tree priors on spaces of conditional probability densities, accounting for uncertainty in the form of the underlying distributions in a nonparametric way. The Bayesian perspective provides an inherently symmetric probability measure of conditional dependence or independence, a feature particularly advantageous in causal discovery and not employed in existing procedures of this type.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43943702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Modelling dynamic network evolution as a Pitman-Yor process 将动态网络演化建模为Pitman-Yor过程
Foundations of data science (Springfield, Mo.) Pub Date : 2019-08-28 DOI: 10.3934/fods.2019013
Francesco Sanna Passino, N. Heard
{"title":"Modelling dynamic network evolution as a Pitman-Yor process","authors":"Francesco Sanna Passino, N. Heard","doi":"10.3934/fods.2019013","DOIUrl":"https://doi.org/10.3934/fods.2019013","url":null,"abstract":"Dynamic interaction networks frequently arise in biology, communications technology and the social sciences, representing, for example, neuronal connectivity in the brain, internet connections between computers and human interactions within social networks. The evolution and strengthening of the links in such networks can be observed through sequences of connection events occurring between network nodes over time. In some of these applications, the identity and size of the network may be unknown a priori and may change over time. In this article, a model for the evolution of dynamic networks based on the Pitman-Yor process is proposed. This model explicitly admits power-laws in the number of connections on each edge, often present in real world networks, and, for careful choices of the parameters, power-laws for the degree distribution of the nodes. A novel empirical method for the estimation of the hyperparameters of the Pitman-Yor process is proposed, and some necessary corrections for uniform discrete base distributions are carefully addressed. The methodology is tested on synthetic data and in an anomaly detection study on the enterprise computer network of the Los Alamos National Laboratory, and successfully detects connections from a red-team penetration test.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48066324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Bayesian inference for latent chain graphs 潜链图的贝叶斯推理
Foundations of data science (Springfield, Mo.) Pub Date : 2019-08-12 DOI: 10.3934/fods.2020003
Deng Lu, M. Iorio, A. Jasra, G. Rosner
{"title":"Bayesian inference for latent chain graphs","authors":"Deng Lu, M. Iorio, A. Jasra, G. Rosner","doi":"10.3934/fods.2020003","DOIUrl":"https://doi.org/10.3934/fods.2020003","url":null,"abstract":"In this article we consider Bayesian inference for partially observed Andersson-Madigan-Perlman (AMP) Gaussian chain graph (CG) models. Such models are of particular interest in applications such as biological networks and financial time series. The model itself features a variety of constraints which make both prior modeling and computational inference challenging. We develop a framework for the aforementioned challenges, using a sequential Monte Carlo (SMC) method for statistical inference. Our approach is illustrated on both simulated data as well as real case studies from university graduation rates and a pharmacokinetics study.","PeriodicalId":73054,"journal":{"name":"Foundations of data science (Springfield, Mo.)","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46556258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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