Molecular Mechanics Simulation of Recognition Identity of tRNA~(His/GUG)

本文选用经过实验验证的碱基序列 ,用简化的方式 ,构建了被水分子和镁离子修饰的核酸序列的分子模型 ,应用分子力学模拟方法对序列进行能量优化 ,对优化后序列的构象参数、成键状况和能量数据等进行了分析。对tRNAHHis GUG的识别特性作了初步的探索 ,得到了和实验结果相近的结论。此外 ,还从能力学的角度讨论了溶剂 -溶质 -溶剂相互作用形成的网状氢键网络对核酸结构稳定性的影响 ,探讨了非Crick_WatsonGU、UU配对的能力学特征并存在于被水分子和镁离子修饰的核酸序列中的GU、UU配对情况。

Biologically-inspired object recognition system with features from complex wavelets

In this paper, a novel cortex-inspired feed-forward hierarchical object recognition system based on complex wavelets is proposed and tested. Complex wavelets contain three key properties for object representation: shift invariance, which enables the extraction of stable local features; good directional selectivity, which simplifies the determination of image orientations; and limited redundancy, which allows for efficient signal analysis using the multi-resolution decomposition offered by complex wavelets. In this paper, we propose a complete cortex-inspired object recognition system based on complex wavelets. We find that the implementation of the HMAX model for object recognition in [1, 2] is rather over-complete and includes too much redundant information and processing. We have optimized the structure of the model to make it more efficient. Specifically, we have used the Caltech 5 standard dataset to compare with Serre's model in [2] (which employs Gabor filter bands). Results demonstrate that the complex wavelet model achieves a speed improvement of about 4 times over the Serre model and gives comparable recognition performance. © 2011 IEEE.

Live 3D shape reconstruction, recognition and registration

We present a video-based system which interactively captures the geometry of a 3D object in the form of a point cloud, then recognizes and registers known objects in this point cloud in a matter of seconds (fig. 1). In order to achieve interactive speed, we exploit both efficient inference algorithms and parallel computation, often on a GPU. The system can be broken down into two distinct phases: geometry capture, and object inference. We now discuss these in further detail. © 2011 IEEE.

A new distance for scale-invariant 3D shape recognition and registration

This paper presents a method for vote-based 3D shape recognition and registration, in particular using mean shift on 3D pose votes in the space of direct similarity transforms for the first time. We introduce a new distance between poses in this spacethe SRT distance. It is left-invariant, unlike Euclidean distance, and has a unique, closed-form mean, in contrast to Riemannian distance, so is fast to compute. We demonstrate improved performance over the state of the art in both recognition and registration on a real and challenging dataset, by comparing our distance with others in a mean shift framework, as well as with the commonly used Hough voting approach. © 2011 IEEE.

A possible mode of the specific recognition of nucleic acids by proteins

Seven sets of protein target sites, which occur in several gene promoters, have been analyzed. The results suggest that there is a possible mode of specific recognition of double-helical nucleic acids by proteins, This recognition mode is related to a spe

A variational perspective on noise-robust speech recognition

Model compensation methods for noise-robust speech recognition have shown good performance. Predictive linear transformations can approximate these methods to balance computational complexity and compensation accuracy. This paper examines both of these approaches from a variational perspective. Using a matched-pair approximation at the component level yields a number of standard forms of model compensation and predictive linear transformations. However, a tighter bound can be obtained by using variational approximations at the state level. Both model-based and predictive linear transform schemes can be implemented in this framework. Preliminary results show that the tighter bound obtained from the state-level variational approach can yield improved performance over standard schemes. © 2011 IEEE.

Improving reverberant VTS for hands-free robust speech recognition

Model-based approaches to handling additive background noise and channel distortion, such as Vector Taylor Series (VTS), have been intensively studied and extended in a number of ways. In previous work, VTS has been extended to handle both reverberant and background noise, yielding the Reverberant VTS (RVTS) scheme. In this work, rather than assuming the observation vector is generated by the reverberation of a sequence of background noise corrupted speech vectors, as in RVTS, the observation vector is modelled as a superposition of the background noise and the reverberation of clean speech. This yields a new compensation scheme RVTS Joint (RVTSJ), which allows an easy formulation for joint estimation of both additive and reverberation noise parameters. These two compensation schemes were evaluated and compared on a simulated reverberant noise corrupted AURORA4 task. Both yielded large gains over VTS baseline system, with RVTSJ outperforming the previous RVTS scheme. © 2011 IEEE.

Extending noise robust structured support vector machines to larger vocabulary tasks

This paper describes a structured SVM framework suitable for noise-robust medium/large vocabulary speech recognition. Several theoretical and practical extensions to previous work on small vocabulary tasks are detailed. The joint feature space based on word models is extended to allow context-dependent triphone models to be used. By interpreting the structured SVM as a large margin log-linear model, illustrates that there is an implicit assumption that the prior of the discriminative parameter is a zero mean Gaussian. However, depending on the definition of likelihood feature space, a non-zero prior may be more appropriate. A general Gaussian prior is incorporated into the large margin training criterion in a form that allows the cutting plan algorithm to be directly applied. To further speed up the training process, 1-slack algorithm, caching competing hypothesis and parallelization strategies are also proposed. The performance of structured SVMs is evaluated on noise corrupted medium vocabulary speech recognition task: AURORA 4. © 2011 IEEE.

Morphological decomposition in Arabic ASR systems

In recent years, the use of morphological decomposition strategies for Arabic Automatic Speech Recognition (ASR) has become increasingly popular. Systems trained on morphologically decomposed data are often used in combination with standard word-based approaches, and they have been found to yield consistent performance improvements. The present article contributes to this ongoing research endeavour by exploring the use of the 'Morphological Analysis and Disambiguation for Arabic' (MADA) tools for this purpose. System integration issues concerning language modelling and dictionary construction, as well as the estimation of pronunciation probabilities, are discussed. In particular, a novel solution for morpheme-to-word conversion is presented which makes use of an N-gram Statistical Machine Translation (SMT) approach. System performance is investigated within a multi-pass adaptation/combination framework. All the systems described in this paper are evaluated on an Arabic large vocabulary speech recognition task which includes both Broadcast News and Broadcast Conversation test data. It is shown that the use of MADA-based systems, in combination with word-based systems, can reduce the Word Error Rates by up to 8.1 relative. © 2012 Elsevier Ltd. All rights reserved.

Interfacial recognition of human prostate-specific antigen by immobilized monoclonal antibody: effects of solution conditions and surface chemistry.

The specific recognition between monoclonal antibody (anti-human prostate-specific antigen, anti-hPSA) and its antigen (human prostate-specific antigen, hPSA) has promising applications in prostate cancer diagnostics and other biosensor applications. However, because of steric constraints associated with interfacial packing and molecular orientations, the binding efficiency is often very low. In this study, spectroscopic ellipsometry and neutron reflection have been used to investigate how solution pH, salt concentration and surface chemistry affect antibody adsorption and subsequent antigen binding. The adsorbed amount of antibody was found to vary with pH and the maximum adsorption occurred between pH 5 and 6, close to the isoelectric point of the antibody. By contrast, the highest antigen binding efficiency occurred close to the neutral pH. Increasing the ionic strength reduced antibody adsorbed amount at the silica-water interface but had little effect on antigen binding. Further studies of antibody adsorption on hydrophobic C8 (octyltrimethoxysilane) surface and chemical attachment of antibody on (3-mercaptopropyl)trimethoxysilane/4-maleimidobutyric acid N-hydroxysuccinimide ester-modified surface have also been undertaken. It was found that on all surfaces studied, the antibody predominantly adopted the 'flat on' orientation, and antigen-binding capabilities were comparable. The results indicate that antibody immobilization via appropriate physical adsorption can replace elaborate interfacial molecular engineering involving complex covalent attachments.

Compression techniques applied to multiple speech recognition systems

Speech recognition systems typically contain many Gaussian distributions, and hence a large number of parameters. This makes them both slow to decode speech, and large to store. Techniques have been proposed to decrease the number of parameters. One approach is to share parameters between multiple Gaussians, thus reducing the total number of parameters and allowing for shared likelihood calculation. Gaussian tying and subspace clustering are two related techniques which take this approach to system compression. These techniques can decrease the number of parameters with no noticeable drop in performance for single systems. However, multiple acoustic models are often used in real speech recognition systems. This paper considers the application of Gaussian tying and subspace compression to multiple systems. Results show that two speech recognition systems can be modelled using the same number of Gaussians as just one system, with little effect on individual system performance. Copyright © 2009 ISCA.

Silhouette-based object phenotype recognition using 3D shape priors

This paper tackles the novel challenging problem of 3D object phenotype recognition from a single 2D silhouette. To bridge the large pose (articulation or deformation) and camera viewpoint changes between the gallery images and query image, we propose a novel probabilistic inference algorithm based on 3D shape priors. Our approach combines both generative and discriminative learning. We use latent probabilistic generative models to capture 3D shape and pose variations from a set of 3D mesh models. Based on these 3D shape priors, we generate a large number of projections for different phenotype classes, poses, and camera viewpoints, and implement Random Forests to efficiently solve the shape and pose inference problems. By model selection in terms of the silhouette coherency between the query and the projections of 3D shapes synthesized using the galleries, we achieve the phenotype recognition result as well as a fast approximate 3D reconstruction of the query. To verify the efficacy of the proposed approach, we present new datasets which contain over 500 images of various human and shark phenotypes and motions. The experimental results clearly show the benefits of using the 3D priors in the proposed method over previous 2D-based methods. © 2011 IEEE.