Inferring Large-Scale Gene Regulatory Networks Using a Randomized Algorithm Based on Singular Value Decomposition

2019 ◽  
Vol 16 (6) ◽  
pp. 1997-2008
Author(s):  
Anjing Fan ◽  
Haitao Wang ◽  
Hua Xiang ◽  
Xiufen Zou
PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e51141 ◽  
Author(s):  
Ming Zheng ◽  
Jia-nan Wu ◽  
Yan-xin Huang ◽  
Gui-xia Liu ◽  
You Zhou ◽  
...  

2021 ◽  
Author(s):  
Shalin Shah

Recommender systems aim to personalize the experience of user by suggesting items to the user based on the preferences of a user. The preferences are learned from the user’s interaction history or through explicit ratings that the user has given to the items. The system could be part of a retail website, an online bookstore, a movie rental service or an online education portal and so on. In this paper, I will focus on matrix factorization algorithms as applied to recommender systems and discuss the singular value decomposition, gradient descent-based matrix factorization and parallelizing matrix factorization for large scale applications.


2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Jengnan Tzeng

The singular value decomposition (SVD) is a fundamental matrix decomposition in linear algebra. It is widely applied in many modern techniques, for example, high- dimensional data visualization, dimension reduction, data mining, latent semantic analysis, and so forth. Although the SVD plays an essential role in these fields, its apparent weakness is the order three computational cost. This order three computational cost makes many modern applications infeasible, especially when the scale of the data is huge and growing. Therefore, it is imperative to develop a fast SVD method in modern era. If the rank of matrix is much smaller than the matrix size, there are already some fast SVD approaches. In this paper, we focus on this case but with the additional condition that the data is considerably huge to be stored as a matrix form. We will demonstrate that this fast SVD result is sufficiently accurate, and most importantly it can be derived immediately. Using this fast method, many infeasible modern techniques based on the SVD will become viable.


Cell Reports ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. 2290-2303 ◽  
Author(s):  
Delphine Potier ◽  
Kristofer Davie ◽  
Gert Hulselmans ◽  
Marina Naval Sanchez ◽  
Lotte Haagen ◽  
...  

Geophysics ◽  
2018 ◽  
Vol 83 (4) ◽  
pp. G25-G34 ◽  
Author(s):  
Saeed Vatankhah ◽  
Rosemary Anne Renaut ◽  
Vahid Ebrahimzadeh Ardestani

We develop a fast algorithm for solving the under-determined 3D linear gravity inverse problem based on randomized singular-value decomposition (RSVD). The algorithm combines an iteratively reweighted approach for [Formula: see text]-norm regularization with the RSVD methodology in which the large-scale linear system at each iteration is replaced with a much smaller linear system. Although the optimal choice for the low-rank approximation of the system matrix with [Formula: see text] rows is [Formula: see text], acceptable results are achievable with [Formula: see text]. In contrast to the use of the iterative LSQR algorithm for the solution of linear systems at each iteration, the singular values generated using RSVD yield a good approximation of the dominant singular values of the large-scale system matrix. Thus, the regularization parameter found for the small system at each iteration is dependent on the dominant singular values of the large-scale system matrix and appropriately regularizes the dominant singular space of the large-scale problem. The results achieved are comparable with those obtained using the LSQR algorithm for solving each linear system, but they are obtained at a reduced computational cost. The method has been tested on synthetic models along with real gravity data from the Morro do Engenho complex in central Brazil.


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