Segmenting DNA sequence into words based on statistical language model

This paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA “words” is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised ‘probability approach to word segmentation’ method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last

Modeling Temporal Dynamics and Spatial Configurations of Actions Using Two-Stream Recurrent Neural Networks

Recently, skeleton based action recognition gains more popularity due to cost-effective depth sensors coupled with real-time skeleton estimation algorithms. Traditional approaches based on handcrafted features are limited to represent the complexity of motion patterns. Recent methods that use Recurrent Neural Networks (RNN) to handle raw skeletons only focus on the contextual dependency in the temporal domain and neglect the spatial configurations of articulated skeletons. In this paper, we propose a novel two-stream RNN architecture to model both temporal dynamics and spatial configurations for skeleton based action recognition. We explore two different structures for the temporal stream: stacked RNN and hierarchical RNN. Hierarchical RNN is designed according to human body kinematics. We also propose two effective methods to model the spatial structure by converting the spatial graph into a sequence of joints. To improve generalization of our model, we further exploit 3D transformation based data augmentation techniques including rotation and scaling transformation to transform the 3D coordinates of skeletons during training. Experiments on 3D action recognition benchmark datasets show that our method brings a considerable improvement for a variety of actions, i.e., generic actions, interaction activities and gestures.Comment: Accepted to IEEE International Conference on Computer Vision and Pattern Recognition (CVPR) 201

A delay fractioning approach to global synchronization of delayed complex networks with stochastic disturbances

This is the post print version of the article. The official published version can be obtained from the link - Copyright 2008 Elsevier LtdIn this Letter, the synchronization problem is investigated for a class of stochastic complex networks with time delays. By utilizing a new Lyapunov functional form based on the idea of ‘delay fractioning’, we employ the stochastic analysis techniques and the properties of Kronecker product to establish delay-dependent synchronization criteria that guarantee the globally asymptotically mean-square synchronization of the addressed delayed networks with stochastic disturbances. These sufficient conditions, which are formulated in terms of linear matrix inequalities (LMIs), can be solved efficiently by the LMI toolbox in Matlab. The main results are proved to be much less conservative and the conservatism could be reduced further as the number of delay fractioning gets bigger. A simulation example is exploited to demonstrate the advantage and applicability of the proposed result.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grants GR/S27658/01, an International Joint Project sponsored by the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany

On robust stability of stochastic genetic regulatory networks with time delays: A delay fractioning approach

Copyright [2009] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.Robust stability serves as an important regulation mechanism in system biology and synthetic biology. In this paper, the robust stability analysis problem is investigated for a class of nonlinear delayed genetic regulatory networks with parameter uncertainties and stochastic perturbations. The nonlinear function describing the feedback regulation satisfies the sector condition, the time delays exist in both translation and feedback regulation processes, and the state-dependent Brownian motions are introduced to reflect the inherent intrinsic and extrinsic noise perturbations. The purpose of the addressed stability analysis problem is to establish some easy-to-verify conditions under which the dynamics of the true concentrations of the messenger ribonucleic acid (mRNA) and protein is asymptotically stable irrespective of the norm-bounded modeling errors. By utilizing a new Lyapunov functional based on the idea of “delay fractioning”, we employ the linear matrix inequality (LMI) technique to derive delay-dependent sufficient conditions ensuring the robust stability of the gene regulatory networks. Note that the obtained results are formulated in terms of LMIs that can easily be solved using standard software packages. Simulation examples are exploited to illustrate the effectiveness of the proposed design procedures

Irregular Convolutional Neural Networks

Convolutional kernels are basic and vital components of deep Convolutional Neural Networks (CNN). In this paper, we equip convolutional kernels with shape attributes to generate the deep Irregular Convolutional Neural Networks (ICNN). Compared to traditional CNN applying regular convolutional kernels like ${3\times3}$, our approach trains irregular kernel shapes to better fit the geometric variations of input features. In other words, shapes are learnable parameters in addition to weights. The kernel shapes and weights are learned simultaneously during end-to-end training with the standard back-propagation algorithm. Experiments for semantic segmentation are implemented to validate the effectiveness of our proposed ICNN.Comment: 7 pages, 5 figures, 3 table