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Register a new userValidation of non-negative matrix factorization for assessment of atomic pair-distribution function (PDF) data in a real-time streaming context
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We validate the use of matrix factorization for the automatic identification of relevant components from atomic pair distribution function (PDF) data. We also present a newly developed software infrastructure for analyzing the PDF data arriving in streaming manner. We then apply two matrix factorization techniques, Principal Component Analysis (PCA) and Non-negative Matrix Factorization (NMF), to study simulated and experiment datasets in the context of in situ experiment.
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In this article, we study algorithms for nonnegative matrix factorization (NMF) in various applications involving streaming data. Utilizing the continual nature of the data, we develop a fast two-stage algorithm for highly efficient and accurate NMF. In the first stage, an alternating non-negative least squares (ANLS) framework is used, in combination with active set method with warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. The results demonstrate the advantage of our algorithm in finding high-precision solutions.
Many crystalline materials show chemical short range order and relaxation of neighboring atoms. Local structural information can be obtained by analyzing the atomic pair distribution function (PDF) obtained from powder diffraction data. In this paper, we present the successful extraction of chemical short range order parameters from the x-ray PDF of a quenched Cu_3Au sample.
In the non-negative matrix factorization (NMF) problem, the input is an $mtimes n$ matrix $M$ with non-negative entries and the goal is to factorize it as $Mapprox AW$. The $mtimes k$ matrix $A$ and the $ktimes n$ matrix $W$ are both constrained to have non-negative entries. This is in contrast to singular value decomposition, where the matrices $A$ and $W$ can have negative entries but must satisfy the orthogonality constraint: the columns of $A$ are orthogonal and the rows of $W$ are also orthogonal. The orthogonal non-negative matrix factorization (ONMF) problem imposes both the non-negativity and the orthogonality constraints, and previous work showed that it leads to better performances than NMF on many clustering tasks. We give the first constant-factor approximation algorithm for ONMF when one or both of $A$ and $W$ are subject to the orthogonality constraint. We also show an interesting connection to the correlation clustering problem on bipartite graphs. Our experiments on synthetic and real-world data show that our algorithm achieves similar or smaller errors compared to previous ONMF algorithms while ensuring perfect orthogonality (many previous algorithms do not satisfy the hard orthogonality constraint).
We report on the potential for using algorithms for non-negative matrix factorization (NMF) to improve parameter estimation in topic models. While several papers have studied connections between NMF and topic models, none have suggested leveraging these connections to develop new algorithms for fitting topic models. Importantly, NMF avoids the sum-to-one constraints on the topic model parameters, resulting in an optimization problem with simpler structure and more efficient computations. Building on recent advances in optimization algorithms for NMF, we show that first solving the NMF problem then recovering the topic model fit can produce remarkably better fits, and in less time, than standard algorithms for topic models. While we focus primarily on maximum likelihood estimation, we show that this approach also has the potential to improve variational inference for topic models. Our methods are implemented in the R package fastTopics.
In this paper we explore avenues for improving the reliability of dimensionality reduction methods such as Non-Negative Matrix Factorization (NMF) as interpretive exploratory data analysis tools. We first explore the difficulties of the optimization problem underlying NMF, showing for the first time that non-trivial NMF solutions always exist and that the optimization problem is actually convex, by using the theory of Completely Positive Factorization. We subsequently explore four novel approaches to finding globally-optimal NMF solutions using various ideas from convex optimization. We then develop a new method, isometric NMF (isoNMF), which preserves non-negativity while also providing an isometric embedding, simultaneously achieving two properties which are helpful for interpretation. Though it results in a more difficult optimization problem, we show experimentally that the resulting method is scalable and even achieves more compact spectra than standard NMF.
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