scholarly journals Bi-cross validation of spectral clustering hyperparameters

2020 ◽  
Vol 35 (2) ◽  
pp. 112-116
Author(s):  
Sioan Zohar ◽  
Chun Hong Yoon

One challenge impeding the analysis of terabyte scale X-ray scattering data from the Linac Coherent Light Source (LCLS) is determining the number of clusters required for the execution of traditional clustering algorithms. Here, we demonstrate that the previous work using bi-cross validation to determine the number of singular vectors directly maps to the spectral clustering problem of estimating both the number of clusters and hyperparameter values. Applying this method to LCLS X-ray scattering data enables the identification of dropped shots without manually setting boundaries on detector fluence and provides a path toward identifying rare and anomalous events.

2018 ◽  
Vol 122 (45) ◽  
pp. 10320-10329 ◽  
Author(s):  
Amin Sadeghpour ◽  
Marjorie Ladd Parada ◽  
Josélio Vieira ◽  
Megan Povey ◽  
Michael Rappolt

1995 ◽  
Author(s):  
Yibin Zheng ◽  
Peter C. Doerschuk ◽  
John E. Johnson

2020 ◽  
Author(s):  
Steve P. Meisburger ◽  
Da Xu ◽  
Nozomi Ando

AbstractMixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput, or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori. To address this issue, we introduce the REGALS method (REGularized Alternating Least Squares), which incorporates simple expectations about the data as prior knowledge and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, which makes it well-suited for exploring datasets with unknown species. Here we apply REGALS to analyze experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing, and time-resolved temperature jump. Based on its performance with these challenging datasets, we anticipate that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and python and is available freely as an open-source software package.


2008 ◽  
Vol 95 (5) ◽  
pp. 2356-2367 ◽  
Author(s):  
Norbert Kučerka ◽  
John F. Nagle ◽  
Jonathan N. Sachs ◽  
Scott E. Feller ◽  
Jeremy Pencer ◽  
...  

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