Integration of Alignment and Phylogeny in the Whole-Genome Era

With the development of new sequencing techniques, whole genomes of many species have become available. This huge amount of data gives rise to new opportunities and challenges. These new sequences provide valuable information on relationships among species, e.g. genome recombination and conservation. One of the principal ways to investigate such information is multiple sequence alignment (MSA). Currently, there is large amount of MSA data on the internet, such as the UCSC genome database, but how to effectively use this information to solve classical and new problems is still an area lacking of exploration. In this thesis, we explored how to use this information in four problems, i.e. sequence orthology search problem, multiple alignment improvement problem, short read mapping problem, and genome rearrangement inference problem. For the first problem, we developed a EM algorithm to iteratively align a query with a multiple alignment database with the information from a phylogeny relating the query species and the species in the multiple alignment. We also infer the query\u27s location in the phylogeny. We showed that by doing alignment and phylogeny inference together, we can improve the accuracies for both problems. For the second problem, we developed an optimization algorithm to iteratively refine the multiple alignment quality. Experiment results showed our algorithm is very stable in term of resulting alignments. The results showed that our method is more accurate than existing methods, i.e. Mafft, Clustal-O, and Mavid, on test data from three sets of species from the UCSC genome database. For the third problem, we developed a model, PhyMap, to align a read to a multiple alignment allowing mismatches and indels. PhyMap computes local alignments of a query sequence against a fixed multiple-genome alignment of closely related species. PhyMap uses a known phylogenetic tree on the species in the multiple alignment to improve the quality of its computed alignments while also estimating the placement of the query on this tree. Both theoretical computation and experiment results show that our model can differentiate between orthologous and paralogous alignments better than other popular short read mapping tools (BWA, BOWTIE and BLAST). For the fourth problem, we gave a simple genome recombination model which can express insertions, deletions, inversions, translocations and inverted translocations on aligned genome segments. We also developed an MCMC algorithm to infer the order of the query segments. We proved that using any Euclidian metrics to measure distance between two sequence orders in the tree optimization goal function will lead to a degenerated solution where the inferred order will be the order of one of the leaf nodes. We also gave a graph-based formulation of the problem which can represent the probability distribution of the order of the query sequences

A Theory of the Policy-Holder\u27s Duty of Disclosure (Chinese)

The implementation of policy-holder\u27s duty of disclosure provides a kind of technical support for the insurer\u27s work, and thus it is vital to the operation of the insurance system in its entirety. This Article analyzes the basic problems in the policy-holder\u27s duty of disclosure, and puts forward some reasonable suggestions for the perfection of the policy-holder\u27s duty of disclosure

A Theory of the Policy-Holder\u27s Duty of Disclosure (Chinese)

The implementation of policy-holder\u27s duty of disclosure provides a kind of technical support for the insurer\u27s work, and thus it is vital to the operation of the insurance system in its entirety. This Article analyzes the basic problems in the policy-holder\u27s duty of disclosure, and puts forward some reasonable suggestions for the perfection of the policy-holder\u27s duty of disclosure

TransGrasp: Grasp Pose Estimation of a Category of Objects by Transferring Grasps from Only One Labeled Instance

Grasp pose estimation is an important issue for robots to interact with the real world. However, most of existing methods require exact 3D object models available beforehand or a large amount of grasp annotations for training. To avoid these problems, we propose TransGrasp, a category-level grasp pose estimation method that predicts grasp poses of a category of objects by labeling only one object instance. Specifically, we perform grasp pose transfer across a category of objects based on their shape correspondences and propose a grasp pose refinement module to further fine-tune grasp pose of grippers so as to ensure successful grasps. Experiments demonstrate the effectiveness of our method on achieving high-quality grasps with the transferred grasp poses. Our code is available at https://github.com/yanjh97/TransGrasp.Comment: Accepted to European Conference on Computer Vision (ECCV) 202

Characterization of ultrathin InSb nanocrystals film deposited on SiO2/Si substrate

Recently, solid-phase recrystallization of ultrathin indium antimonide nanocrystals (InSb NCs (films grown on SiO2/Si substrate is very attractive, because of the rapid development of thermal annealing technique. In this study, the recrystallization behavior of 35 nm indium antimonide film was studied. Through X-ray diffraction (XRD) analysis, it is demonstrated that the InSb film is composed of nanocrystals after high temperature rapid thermal annealing. Scanning electron microscopy shows that the film has a smooth surface and is composed of tightly packed spherical grains, the average grain size is about 12.3 nm according to XRD results. The optical bandgap of the InSb NCs film analyzed by Fourier Transform infrared spectroscopy measurement is around 0.26 eV. According to the current-voltage characteristics of the InSb NCs/SiO2/p-Si heterojunction, the film has the rectifying behavior and the turn-on voltage value is near 1 V

Dual-terminal event triggered control for cyber-physical systems under false data injection attacks

summary:This paper deals with the problem of security-based dynamic output feedback control of cyber-physical systems (CPSs) with the dual-terminal event triggered mechanisms (DT-ETM) under false data injection (FDI) attacks. Considering the limited attack energy, FDI attacks taking place in transmission channels are modeled as extra bounded disturbances for the resulting closed-loop system, thus enabling $H_{\infty}$ performance analysis with a suitable $\varrho$ attenuation level. Then two buffers at the controller and actuator sides are skillfully introduced to cope with the different transmission delays in such a way to facilitate the subsequent security analysis. Next, a dynamic output feedback security control (DOFSC) model based on the DT-ETM schemes under FDI attacks is well constructed. Furthermore, novel criteria for stability analysis and robust stabilization are carefully derived by exploiting Lyapunov-Krasovskii theory and LMIs technique. Finally, an illustrative example is provided to show the effectiveness of the proposed method

Security-based resilient event-triggered control of networked control systems under denial of service attacks

This paper is concerned with the security control problem of the networked control system (NCSs) subjected to denial of service (DoS) attacks. In order to guarantee the security performance, this paper treats the influence of packet dropouts due to DoS attacks as a uncertainty of triggering condition. Firstly, a novel resilient triggering strategy by considering the uncertainty of triggering condition caused by DoS attacks is proposed. Secondly, the event-based security controller under the resilient triggering strategy is designed while the DoS-based security performance is preserved. At last, the simulation results show that the proposed resilient triggering strategy is resilient to DoS attacks while guaranteing the security performance

Resilient control of networked control systems with stochastic denial of service attacks

This paper focuses on resilient control of networked control systems (NCSs) under the denial of service (DoS) attacks characterized by a Markov process. Firstly, based on the game between attack strategies and defense strategies, the packet dropouts induced by DoS attacks are modeled as a Markov process. Secondly, an NCS under DoS attacks is modeled as a Markovian jump linear system. Then, by use of the Lyapunov theory and the derived NCS model, four theorems are given for the system stability analysis and controller design. Finally, a numerical example is used to illustrative the effectiveness of proposed method