BLTSA: pseudotime prediction for single cells by branched local tangent space alignment.

Motivation: The development of single-cell RNA sequencing (scRNA-seq) technology makes it possible to study the cellular dynamic processes such as cell cycle and cell differentiation. Due to the difficulties in generating genuine time-series scRNA-seq data, it is of great importance to computationally infer the pseudotime of the cells along differentiation trajectory based on their gene expression patterns. The existing pseudotime prediction methods often suffer from the high level noise of single-cell data, thus it is still necessary to study the single-cell trajectory inference methods.

MicroRNA-disease association prediction by matrix tri-factorization.

Background: Biological evidence has shown that microRNAs(miRNAs) are greatly implicated in various biological progresses involved in human diseases. The identification of miRNA-disease associations(MDAs) is beneficial to disease diagnosis as well as treatment. Due to the high costs of biological experiments, it attracts more and more attention to predict MDAs by computational approaches.

Integrative subspace clustering by common and specific decomposition for applications on cancer subtype identification.

Background: Recent high throughput technologies have been applied for collecting heterogeneous biomedical omics datasets. Computational analysis of the multi-omics datasets could potentially reveal deep insights for a given disease. Most existing clustering methods by multi-omics data assume strong consistency among different sources of datasets, and thus may lose efficacy when the consistency is relatively weak.

Distributed atomic quantum information processing via optical fibers.

The qudit system may offer great flexibilities for quantum information processing. We investigate the possibility of realizing elementary quantum gates between two high-dimensional atoms in distant cavities coupled by an optical fiber. We show that highly reliable special swap gate is achievable by different detuning.

Quantum computation based on photonic systems with two degrees of freedom assisted by the weak cross-Kerr nonlinearity.

Most of previous quantum computations only take use of one degree of freedom (DoF) of photons. An experimental system may possess various DoFs simultaneously. In this paper, with the weak cross-Kerr nonlinearity, we investigate the parallel quantum computation dependent on photonic systems with two DoFs.

Quantum Computation Based on Photons with Three Degrees of Freedom.

Quantum systems are important resources for quantum computer. Different from previous encoding forms using quantum systems with one degree of freedom (DoF) or two DoFs, we investigate the possibility of photon systems encoding with three DoFs consisting of the polarization DoF and two spatial DoFs. By exploring the optical circular birefringence induced by an NV center in a diamond embedded in the photonic crystal cavity, we propose several hybrid controlled-NOT (hybrid CNOT) gates operating on the two-photon or one-photon system.

Photonic ququart logic assisted by the cavity-QED system.

Universal quantum logic gates are important elements for a quantum computer. In contrast to previous constructions of qubit systems, we investigate the possibility of ququart systems (four-dimensional states) dependent on two DOFs of photon systems. We propose some useful one-parameter four-dimensional quantum transformations for the construction of universal ququart logic gates.