Estimating matching affinity matrices under low-rank constraints

2019 ◽  
Vol 8 (4) ◽  
pp. 677-689
Author(s):  
Arnaud Dupuy ◽  
Alfred Galichon ◽  
Yifei Sun

Abstract In this paper, we address the problem of estimating transport surplus (a.k.a. matching affinity) in high-dimensional optimal transport problems. Classical optimal transport theory specifies the matching affinity and determines the optimal joint distribution. In contrast, we study the inverse problem of estimating matching affinity based on the observation of the joint distribution, using an entropic regularization of the problem. To accommodate high dimensionality of the data, we propose a novel method that incorporates a nuclear norm regularization that effectively enforces a rank constraint on the affinity matrix. The low-rank matrix estimated in this way reveals the main factors that are relevant for matching.

Author(s):  
Daniel Povey ◽  
Gaofeng Cheng ◽  
Yiming Wang ◽  
Ke Li ◽  
Hainan Xu ◽  
...  

2019 ◽  
Vol 37 (4) ◽  
pp. 1-34 ◽  
Author(s):  
Huafeng Liu ◽  
Liping Jing ◽  
Yuhua Qian ◽  
Jian Yu

Author(s):  
Yinlei Hu ◽  
Bin Li ◽  
Falai Chen ◽  
Kun Qu

Abstract Unsupervised clustering is a fundamental step of single-cell RNA sequencing data analysis. This issue has inspired several clustering methods to classify cells in single-cell RNA sequencing data. However, accurate prediction of the cell clusters remains a substantial challenge. In this study, we propose a new algorithm for single-cell RNA sequencing data clustering based on Sparse Optimization and low-rank matrix factorization (scSO). We applied our scSO algorithm to analyze multiple benchmark datasets and showed that the cluster number predicted by scSO was close to the number of reference cell types and that most cells were correctly classified. Our scSO algorithm is available at https://github.com/QuKunLab/scSO. Overall, this study demonstrates a potent cell clustering approach that can help researchers distinguish cell types in single-cell RNA sequencing data.


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