arXiv subjects

Cheng-Yu Hung

Publications and source records attributed to Cheng-Yu Hung.

5 recordsLinked to original sources

arXiv2020

Cryo-RALib -- a modular library for accelerating alignment in cryo-EM

Thanks to automated cryo-EM and GPU-accelerated processing, single-particle cryo-EM has become a rapid structure determination method that permits capture of dynamical structures of molecules in solution, which has been recently demonstrated by the determination of COVID-19 spike protein in March, shortly after its breakout in late January 2020. This rapidity is critical for vaccine development in response to emerging pandemic. This explains why a 2D classification approach based on multi-reference alignment (MRA) is not as popular as the Bayesian-based approach despite that the former has advantage in differentiating structural variations under low signal-to-noise ratio. This is perhaps because that MRA is a time-consuming process and a modular GPU-acceleration library for MRA is lacking. Here, we introduce a library called Cryo-RALib that expands the functionality of CUDA library used by GPU ISAC. It contains a GPU-accelerated MRA routine for accelerating MRA-based classification algorithms. In addition, we connect the cryo-EM image analysis with the python data science stack so as to make it easier for users to perform data analysis and visualization. Benchmarking on the TaiWan Computing Cloud (TWCC) container shows that our implementation can accelerate the computation by one order of magnitude. The library is available at https://github.com/phonchi/Cryo-RAlib.

q-bio.QM↗

arXiv2020

Incremental Learning Algorithm for Sound Event Detection

This paper presents a new learning strategy for the Sound Event Detection (SED) system to tackle the issues of i) knowledge migration from a pre-trained model to a new target model and ii) learning new sound events without forgetting the previously learned ones without re-training from scratch. In order to migrate the previously learned knowledge from the source model to the target one, a neural adapter is employed on the top of the source model. The source model and the target model are merged via this neural adapter layer. The neural adapter layer facilitates the target model to learn new sound events with minimal training data and maintaining the performance of the previously learned sound events similar to the source model. Our extensive analysis on the DCASE16 and US-SED dataset reveals the effectiveness of the proposed method in transferring knowledge between source and target models without introducing any performance degradation on the previously learned sound events while obtaining a competitive detection performance on the newly learned sound events.

cs.LG↗

arXiv2019

Joint Block Low Rank and Sparse Matrix Recovery in Array Self-Calibration Off-Grid DoA Estimation

This letter addresses the estimation of directions-of-arrival (DoA) by a sensor array using a sparse model in the presence of array calibration errors and off-grid directions. The received signal utilizes previously used models for unknown errors in calibration and structured linear representation of the off-grid effect. A convex optimization problem is formulated with an objective function to promote two-layer joint block-sparsity with its second-order cone programming (SOCP) representation. The performance of the proposed method is demonstrated by numerical simulations and compared with the Cramer-Rao Bound (CRB), and several previously proposed methods.

eess.SP↗

arXiv2019

Linearly Constrained Smoothing Group Sparsity Solvers in Off-grid Model

In compressed sensing, the sensing matrix is assumed perfectly known. However, there exists perturbation in the sensing matrix in reality due to sensor offsets or noise disturbance. Directions-of-arrival (DoA) estimation with off-grid effect satisfies this situation, and can be formulated into a (non)convex optimization problem with linear inequalities constraints, which can be solved by the interior point method (using the CVX tools), but at a large computational cost. In this work, in order to design efficient algorithms, we consider various alternative formulations, such as unconstrained formulation, primal-dual formulation, or conic formulation to develop group-sparsity promoted solvers. First, the consensus alternating direction method of multipliers (C-ADMM) is applied. Then, iterative algorithms for the BPDN formulation is proposed by combining the Nesterov smoothing technique with accelerated proximal gradient method, and the convergence analysis of the method is conducted as well. We also developed a variant of EGT (Excessive Gap Technique)-based primal-dual method to systematically reduce the smoothing parameter sequentially. Finally, we propose algorithms for quadratically constrained L2-L1 mixed norm minimization problem by using the smoothed dual conic optimization (SDCO) and continuation technique. The performance of accuracy and convergence for all the proposed methods are demonstrated in the numerical simulations.

eess.SP↗

arXiv2017

Low Rank Matrix Recovery for Joint Array Self-Calibration and Sparse Model DoA Estimation

In this work, combined calibration and DoA estimation is approached as an extension of the formulation for the Single Measurement Vector (SMV) model of self-calibration to the Multiple Measurement Model (MMV) case. By taking advantage of multiple snapshots, a modified nuclear norm minimization problem is proposed to recover a low-rank larger dimension matrix. We also give the definition of a linear operator for the MMV model, and give its corresponding matrix representation to generate a variant of a convex optimization problem. In order to mitigate the computational complexity of the approach, singular value decomposition (SVD) is applied to reduce the problem size. The performance of the proposed methods are demonstrated by numerical simulations.

eess.SP↗