An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data
O Oluwadare, M Highsmith, J Cheng - Biological procedures online, 2019 - Springer
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and
genome structures have proliferated. This has been primarily due to the development of high …
genome structures have proliferated. This has been primarily due to the development of high …
Advancements in federated learning: Models, methods, and privacy
Federated learning (FL) is a promising technique for resolving the rising privacy and security
concerns. Its main ingredient is to cooperatively learn the model among the distributed …
concerns. Its main ingredient is to cooperatively learn the model among the distributed …
[PDF][PDF] Manopt, a Matlab toolbox for optimization on manifolds
Optimization on manifolds is a rapidly developing branch of nonlinear optimization. Its focus
is on problems where the smooth geometry of the search space can be leveraged to design …
is on problems where the smooth geometry of the search space can be leveraged to design …
A Broyden class of quasi-Newton methods for Riemannian optimization
This paper develops and analyzes a generalization of the Broyden class of quasi-Newton
methods to the problem of minimizing a smooth objective function f on a Riemannian …
methods to the problem of minimizing a smooth objective function f on a Riemannian …
Dropping convexity for faster semi-definite optimization
S Bhojanapalli, A Kyrillidis… - Conference on Learning …, 2016 - proceedings.mlr.press
We study the minimization of a convex function f (X) over the set of n\times n positive semi-
definite matrices, but when the problem is recast as\min_U g (U):= f (UU^⊤), with …
definite matrices, but when the problem is recast as\min_U g (U):= f (UU^⊤), with …
Quotient geometry with simple geodesics for the manifold of fixed-rank positive-semidefinite matrices
This paper explores the well-known identification of the manifold of rank p positive-
semidefinite matrices of size n with the quotient of the set of full-rank n-by-p matrices by the …
semidefinite matrices of size n with the quotient of the set of full-rank n-by-p matrices by the …
Riemannian optimization for distance-geometric inverse kinematics
Solving the inverse kinematics problem is a fundamental challenge in motion planning,
control, and calibration for articulated robots. Kinematic models for these robots are typically …
control, and calibration for articulated robots. Kinematic models for these robots are typically …
[HTML][HTML] Low-rank matrix completion via preconditioned optimization on the Grassmann manifold
We address the numerical problem of recovering large matrices of low rank when most of
the entries are unknown. We exploit the geometry of the low-rank constraint to recast the …
the entries are unknown. We exploit the geometry of the low-rank constraint to recast the …
Low-rank optimization with trace norm penalty
The paper addresses the problem of low-rank trace norm minimization. We propose an
algorithm that alternates between fixed-rank optimization and rank-one updates. The fixed …
algorithm that alternates between fixed-rank optimization and rank-one updates. The fixed …
Fixed-rank matrix factorizations and Riemannian low-rank optimization
Motivated by the problem of learning a linear regression model whose parameter is a large
fixed-rank non-symmetric matrix, we consider the optimization of a smooth cost function …
fixed-rank non-symmetric matrix, we consider the optimization of a smooth cost function …