arXiv subjects

Ying Cai

Publications and source records attributed to Ying Cai.

21 records · Page 2Linked to original sources

arXiv2021

Parallel finite volume simulation of the spherical shell dynamo with pseudo-vacuum magnetic boundary conditions

In this paper, we study the parallel simulation of the magnetohydrodynamic (MHD) dynamo in a rapidly rotating spherical shell with pseudo-vacuum magnetic boundary conditions. A second-order finite volume scheme based on a collocated quasi-uniform cubed-sphere grid is applied to the spatial discretization of the MHD dynamo equations. To ensure the solenoidal condition of the magnetic field, we adopt a widely-used approach whereby a pseudo-pressure is introduced into the induction equation. The temporal integration is split by a second-order approximate factorization approach, resulting in two linear algebraic systems both solved by a preconditioned Krylov subspace iterative method. A multi-level restricted additive Schwarz preconditioner based on domain decomposition and multigrid method is then designed to improve the efficiency and scalability. Accurate numerical solutions of two benchmark cases are obtained with our code, comparable to the existing local method results. Several large-scale tests performed on the Sunway TaihuLight supercomputer show good strong and weak scalabilities and a noticeable improvement from the multi-level preconditioner with up to 10368 processor cores.

physics.comp-ph↗

arXiv2020

Verifying the Correctness of Analytic Query Results

Data outsourcing is a cost-effective solution for data owners to tackle issues such as large volumes of data, huge number of users, and intensive computation needed for data analysis. They can simply upload their databases to a cloud and let it perform all management works, including query processing. One problem with this service model is how query issuers can verify the query results they receive are indeed correct. This concern is legitimate because, as a third party, clouds may not be fully trustworthy, and as a large data center, clouds are ideal targets for hackers. There has been significant work on query result verification, but most consider only simple queries where query results can be attained by checking the raw data against the query conditions directly. In this paper, we consider the problem of enabling users to verify the correctness of the results of analytic queries. Unlike simple queries, analytic queries involve ranking functions to score a database, which makes it difficult to build data structures for verification purposes. We propose two approaches, namely one-signature and multi-signature, and show that they work well on three representative types of analytic queries, including top-k, range, and KNN queries, through both analysis and experiments.

cs.DB↗

arXiv2012

Utilizing RNA-Seq Data for Cancer Network Inference

An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe the expression levels of the entire set of cancer genes and their transcript isoforms. However, there are onerous statistical and computational issues in interpreting high-dimensional sequencing data and inferring the underlying genetic network. In this study, we analyzed RNA-Seq data from lymphoblastoid cell lines derived from a population of 69 human individuals and implemented a probabilistic framework to construct biologically-relevant genetic networks. In particular, we employed a graphical lasso analysis, motivated by considerations of the maximum entropy formalism, to estimate the sparse inverse covariance matrix of RNA-Seq data. Gene ontology, pathway enrichment and protein-protein path length analysis were all carried out to validate the biological context of the predicted network of interacting cancer gene isoforms.

q-bio.GN↗