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 …

Advancements in federated learning: Models, methods, and privacy

H Chen, H Wang, Q Long, D Jin, Y Li - ACM Computing Surveys, 2024 - dl.acm.org
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 …

[PDF][PDF] Manopt, a Matlab toolbox for optimization on manifolds

N Boumal, B Mishra, PA Absil, R Sepulchre - The Journal of Machine …, 2014 - jmlr.org
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 …

A Broyden class of quasi-Newton methods for Riemannian optimization

W Huang, KA Gallivan, PA Absil - SIAM Journal on Optimization, 2015 - SIAM
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 …

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 …

Quotient geometry with simple geodesics for the manifold of fixed-rank positive-semidefinite matrices

E Massart, PA Absil - SIAM Journal on Matrix Analysis and Applications, 2020 - SIAM
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 …

Riemannian optimization for distance-geometric inverse kinematics

F Marić, M Giamou, AW Hall… - IEEE Transactions …, 2021 - ieeexplore.ieee.org
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 …

[HTML][HTML] Low-rank matrix completion via preconditioned optimization on the Grassmann manifold

N Boumal, PA Absil - Linear Algebra and its Applications, 2015 - Elsevier
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 …

Low-rank optimization with trace norm penalty

B Mishra, G Meyer, F Bach, R Sepulchre - SIAM Journal on Optimization, 2013 - SIAM
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 …

Fixed-rank matrix factorizations and Riemannian low-rank optimization

B Mishra, G Meyer, S Bonnabel, R Sepulchre - Computational Statistics, 2014 - Springer
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 …