Journal of Machine Learning Research最新文献

{"title":"Minimax Nonparametric Parallelism Test.","authors":"Xin Xing, Meimei Liu, Ping Ma, Wenxuan Zhong","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Testing the hypothesis of parallelism is a fundamental statistical problem arising from many applied sciences. In this paper, we develop a nonparametric parallelism test for inferring whether the trends are parallel in treatment and control groups. In particular, the proposed nonparametric parallelism test is a Wald type test based on a smoothing spline ANOVA (SSANOVA) model which can characterize the complex patterns of the data. We derive that the asymptotic null distribution of the test statistic is a Chi-square distribution, unveiling a new version of Wilks phenomenon. Notably, we establish the minimax sharp lower bound of the distinguishable rate for the nonparametric parallelism test by using the information theory, and further prove that the proposed test is minimax optimal. Simulation studies are conducted to investigate the empirical performance of the proposed test. DNA methylation and neuroimaging studies are presented to illustrate potential applications of the test. The software is available at https://github.com/BioAlgs/Parallelism.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11086968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Provable Convex Co-clustering of Tensors.","authors":"Eric C Chi, Brian R Gaines, Will Wei Sun, Hua Zhou, Jian Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Cluster analysis is a fundamental tool for pattern discovery of complex heterogeneous data. Prevalent clustering methods mainly focus on vector or matrix-variate data and are not applicable to general-order tensors, which arise frequently in modern scientific and business applications. Moreover, there is a gap between statistical guarantees and computational efficiency for existing tensor clustering solutions due to the nature of their non-convex formulations. In this work, we bridge this gap by developing a provable convex formulation of tensor co-clustering. Our convex co-clustering (CoCo) estimator enjoys stability guarantees and its computational and storage costs are polynomial in the size of the data. We further establish a non-asymptotic error bound for the CoCo estimator, which reveals a surprising \"blessing of dimensionality\" phenomenon that does not exist in vector or matrix-variate cluster analysis. Our theoretical findings are supported by extensive simulated studies. Finally, we apply the CoCo estimator to the cluster analysis of advertisement click tensor data from a major online company. Our clustering results provide meaningful business insights to improve advertising effectiveness.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38706545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generalized Score Matching for Non-Negative Data.","authors":"Shiqing Yu,&nbsp;Mathias Drton,&nbsp;Ali Shojaie","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A common challenge in estimating parameters of probability density functions is the intractability of the normalizing constant. While in such cases maximum likelihood estimation may be implemented using numerical integration, the approach becomes computationally intensive. The score matching method of Hyvärinen (2005) avoids direct calculation of the normalizing constant and yields closed-form estimates for exponential families of continuous distributions over <math> <mrow><msup><mi>R</mi> <mi>m</mi></msup> </mrow> </math> . Hyvärinen (2007) extended the approach to distributions supported on the non-negative orthant, <math> <mrow><msubsup><mi>R</mi> <mo>+</mo> <mi>m</mi></msubsup> </mrow> </math> . In this paper, we give a generalized form of score matching for non-negative data that improves estimation efficiency. As an example, we consider a general class of pairwise interaction models. Addressing an overlooked inexistence problem, we generalize the regularized score matching method of Lin et al. (2016) and improve its theoretical guarantees for non-negative Gaussian graphical models.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8291733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39208339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proximal Distance Algorithms: Theory and Practice.","authors":"Kevin L Keys,&nbsp;Hua Zhou,&nbsp;Kenneth Lange","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Proximal distance algorithms combine the classical penalty method of constrained minimization with distance majorization. If <i>f</i>(<i>x</i>) is the loss function, and <i>C</i> is the constraint set in a constrained minimization problem, then the proximal distance principle mandates minimizing the penalized loss <math><mrow><mi>f</mi> <mo>(</mo> <mi>x</mi> <mo>)</mo> <mo>+</mo> <mfrac><mi>ρ</mi> <mn>2</mn></mfrac> <mtext>dist</mtext> <msup> <mrow><mrow><mo>(</mo> <mrow><mi>x</mi> <mo>,</mo> <mi>C</mi></mrow> <mo>)</mo></mrow> </mrow> <mn>2</mn></msup> </mrow> </math> and following the solution <i>x</i> _<i>ρ</i> to its limit as <i>ρ</i> tends to ∞. At each iteration the squared Euclidean distance dist(<i>x,C</i>)² is majorized by the spherical quadratic ‖<i>x</i>- <i>P</i> _<i>C</i> (<i>x</i> _<i>k</i> )‖², where <i>P</i> _<i>C</i> (<i>x</i> _<i>k</i> ) denotes the projection of the current iterate <i>x</i> _<i>k</i> onto <i>C</i>. The minimum of the surrogate function <math><mrow><mi>f</mi> <mo>(</mo> <mi>x</mi> <mo>)</mo> <mo>+</mo> <mfrac><mi>ρ</mi> <mn>2</mn></mfrac> <mo>‖</mo> <mi>x</mi> <mo>-</mo> <msub><mi>P</mi> <mi>C</mi></msub> <mrow><mo>(</mo> <mrow><msub><mi>x</mi> <mi>k</mi></msub> </mrow> <mo>)</mo></mrow> <msup><mo>‖</mo> <mn>2</mn></msup> </mrow> </math> is given by the proximal map prox _<i>ρ</i> -_1<i>f</i> [<i>P</i> _<i>C</i> (<i>x</i> _<i>k</i> )]. The next iterate <i>x</i> _<i>k</i>+1 automatically decreases the original penalized loss for fixed <i>ρ</i>. Since many explicit projections and proximal maps are known, it is straightforward to derive and implement novel optimization algorithms in this setting. These algorithms can take hundreds if not thousands of iterations to converge, but the simple nature of each iteration makes proximal distance algorithms competitive with traditional algorithms. For convex problems, proximal distance algorithms reduce to proximal gradient algorithms and therefore enjoy well understood convergence properties. For nonconvex problems, one can attack convergence by invoking Zangwill's theorem. Our numerical examples demonstrate the utility of proximal distance algorithms in various high-dimensional settings, including a) linear programming, b) constrained least squares, c) projection to the closest kinship matrix, d) projection onto a second-order cone constraint, e) calculation of Horn's copositive matrix index, f) linear complementarity programming, and g) sparse principal components analysis. The proximal distance algorithm in each case is competitive or superior in speed to traditional methods such as the interior point method and the alternating direction method of multipliers (ADMM). Source code for the numerical examples can be found at https://github.com/klkeys/proxdist.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6812563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41219016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Reduced PC-Algorithm: Improved Causal Structure Learning in Large Random Networks.","authors":"Arjun Sondhi, Ali Shojaie","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We consider the task of estimating a high-dimensional directed acyclic graph, given observations from a linear structural equation model with arbitrary noise distribution. By exploiting properties of common random graphs, we develop a new algorithm that requires conditioning only on small sets of variables. The proposed algorithm, which is essentially a modified version of the PC-Algorithm, offers significant gains in both computational complexity and estimation accuracy. In particular, it results in more efficient and accurate estimation in large networks containing hub nodes, which are common in biological systems. We prove the consistency of the proposed algorithm, and show that it also requires a less stringent faithfulness assumption than the PC-Algorithm. Simulations in low and high-dimensional settings are used to illustrate these findings. An application to gene expression data suggests that the proposed algorithm can identify a greater number of clinically relevant genes than current methods.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10552884/pdf/nihms-1885649.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41105823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causal Learning via Manifold Regularization.","authors":"Steven M Hill, Chris J Oates, Duncan A Blythe, Sach Mukherjee","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper frames causal structure estimation as a machine learning task. The idea is to treat indicators of causal relationships between variables as 'labels' and to exploit available data on the variables of interest to provide features for the labelling task. Background scientific knowledge or any available interventional data provide labels on some causal relationships and the remainder are treated as unlabelled. To illustrate the key ideas, we develop a distance-based approach (based on bivariate histograms) within a manifold regularization framework. We present empirical results on three different biological data sets (including examples where causal effects can be verified by experimental intervention), that together demonstrate the efficacy and general nature of the approach as well as its simplicity from a user's point of view.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9142095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"All Models are Wrong, but <i>Many</i> are Useful: Learning a Variable's Importance by Studying an Entire Class of Prediction Models Simultaneously.","authors":"Aaron Fisher,&nbsp;Cynthia Rudin,&nbsp;Francesca Dominici","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Variable importance (VI) tools describe how much covariates contribute to a prediction model's accuracy. However, important variables for one well-performing model (for example, a linear model <i>f</i> (x) = x ^<i>T</i> <i>β</i> with a fixed coefficient vector <i>β</i>) may be unimportant for another model. In this paper, we propose model class reliance (MCR) as the range of VI values across <i>all</i> well-performing model in a prespecified class. Thus, MCR gives a more comprehensive description of importance by accounting for the fact that many prediction models, possibly of different parametric forms, may fit the data well. In the process of deriving MCR, we show several informative results for permutation-based VI estimates, based on the VI measures used in Random Forests. Specifically, we derive connections between permutation importance estimates for a <i>single</i> prediction model, U-statistics, conditional variable importance, conditional causal effects, and linear model coefficients. We then give probabilistic bounds for MCR, using a novel, generalizable technique. We apply MCR to a public data set of Broward County criminal records to study the reliance of recidivism prediction models on sex and race. In this application, MCR can be used to help inform VI for unknown, proprietary models.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8323609/pdf/nihms-1670270.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39264727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determining the Number of Latent Factors in Statistical Multi-Relational Learning.","authors":"Chengchun Shi,&nbsp;Wenbin Lu,&nbsp;Rui Song","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Statistical relational learning is primarily concerned with learning and inferring relationships between entities in large-scale knowledge graphs. Nickel et al. (2011) proposed a RESCAL tensor factorization model for statistical relational learning, which achieves better or at least comparable results on common benchmark data sets when compared to other state-of-the-art methods. Given a positive integer <i>s</i>, RESCAL computes an <i>s</i>-dimensional latent vector for each entity. The latent factors can be further used for solving relational learning tasks, such as collective classification, collective entity resolution and link-based clustering. The focus of this paper is to determine the number of latent factors in the RESCAL model. Due to the structure of the RESCAL model, its log-likelihood function is not concave. As a result, the corresponding maximum likelihood estimators (MLEs) may not be consistent. Nonetheless, we design a specific pseudometric, prove the consistency of the MLEs under this pseudometric and establish its rate of convergence. Based on these results, we propose a general class of information criteria and prove their model selection consistencies when the number of relations is either bounded or diverges at a proper rate of the number of entities. Simulations and real data examples show that our proposed information criteria have good finite sample properties.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37581845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient augmentation and relaxation learning for individualized treatment rules using observational data.","authors":"Ying-Qi Zhao, Eric B Laber, Yang Ning, Sumona Saha, Bruce E Sands","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Individualized treatment rules aim to identify if, when, which, and to whom treatment should be applied. A globally aging population, rising healthcare costs, and increased access to patient-level data have created an urgent need for high-quality estimators of individualized treatment rules that can be applied to observational data. A recent and promising line of research for estimating individualized treatment rules recasts the problem of estimating an optimal treatment rule as a weighted classification problem. We consider a class of estimators for optimal treatment rules that are analogous to convex large-margin classifiers. The proposed class applies to observational data and is doubly-robust in the sense that correct specification of either a propensity or outcome model leads to consistent estimation of the optimal individualized treatment rule. Using techniques from semiparametric efficiency theory, we derive rates of convergence for the proposed estimators and use these rates to characterize the bias-variance trade-off for estimating individualized treatment rules with classification-based methods. Simulation experiments informed by these results demonstrate that it is possible to construct new estimators within the proposed framework that significantly outperform existing ones. We illustrate the proposed methods using data from a labor training program and a study of inflammatory bowel syndrome.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41219015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nonuniformity of P-values Can Occur Early in Diverging Dimensions.","authors":"Yingying Fan,&nbsp;Emre Demirkaya,&nbsp;Jinchi Lv","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Evaluating the joint significance of covariates is of fundamental importance in a wide range of applications. To this end, p-values are frequently employed and produced by algorithms that are powered by classical large-sample asymptotic theory. It is well known that the conventional p-values in Gaussian linear model are valid even when the dimensionality is a non-vanishing fraction of the sample size, but can break down when the design matrix becomes singular in higher dimensions or when the error distribution deviates from Gaussianity. A natural question is when the conventional p-values in generalized linear models become invalid in diverging dimensions. We establish that such a breakdown can occur early in nonlinear models. Our theoretical characterizations are confirmed by simulation studies.</p>","PeriodicalId":50161,"journal":{"name":"Journal of Machine Learning Research","volume":null,"pages":null},"PeriodicalIF":6.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37753218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}