Short and long peptidoglycan recognition proteins (PGRPs) in zebrafish, with findings of multiple PGRP homologs in teleost fish

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. Using a database mining approach and RT-PCR, multiple peptidoglycan recognition protein (PGRP) like genes have been discovered in fish including zebrafish Danio rerio, Japanese pufferfish TakiFugu rubripes and spotted green pufferfish Tetraodon nigroviridis. They share the common features of those PGRPs in arthropod and mammals, by containing a conserved PGRP domain. Based on the predicted structures, the identified zebrafish PGRP homologs resemble short and long PGRP members in arthropod and mammals. The identified PGRP genes in T. nigroviridis and TakiFugu rubripes resemble the long PGRPs, and the short PGRP genes have not been found in T. nigroviridis and TakiFugu rubripes databases. Computer modelling of these molecules revealed the presence of three alpha-helices and five or six beta-strands in all fish PGRPs reported in the present study. The long PGRP in teleost fish have multiple alternatively spliced forms, and some of the identified spliced variants, e.g., tnPGRP-L3 and tnPGRP-L4 (in: Tetraodon nigroviridis), exhibited no characters present in the PGRP homologs domain. The coding regions of zfPGRP6 (zf: zebrafish), zfPGRP2-A, zfPGRP2-B and zfPGRP-L contain five exons and four introns; however, the other PGRP-like genes including zfPGRPSC1a, zfPGRPSC2, tnPGRP-L1-, tnPGRP-L2 and frPGRP-L (fr: Takifugu rubripes) contain four exons and three introns. In zebrafish, long and short PGRP genes identified are located in different chromosomes, and an unknown locus containing another long PGRP-like gene has also been found in zebrafish, demonstrating that multiple PGRP loci may be present in fish. In zebrafish, the constitutive expressions of zfPGRP-L, zfPGRP-6 and zfPGRP-SC during ontogeny from unfertilized eggs to larvae, in different organs of adult, and the inductive expression following stimulation by Flavobacterium columnare, were detected by real-time PCR, but the levels and patterns varied for different PGRP genes, implying that different short and long PGRPs may play different roles in innate immune response. (c) 2007 Elsevier Ltd. All rights reserved.

Computer assisted peak recognition for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) in environmental samples

A software has been developed for the peak recognition of 136 polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) after high resolution gas chromatography coupled with mass spectrometry (HRGC/HRMS). Based on the retention times of C-13 labelled 2,3,7,8-substituted PCDD/F internal standards, the retention times of all PCDD and PCDF can be calibrated automatically and accurately. Therefore, it is very convenient to identify the peaks by comparing the retention of samples and the calibrated retention times of their chromatograms. Hence, this approach is very significant because it is impossible to obtain always a standard chromatogram and PCDD/F analysis are very expensive and time consuming. The calibration results can be transferred to Excel for calculation. The approach is a first step to store costly and environmentally relevant data for future application.

A Cancer Recognition Method Based on DNA Microarray

The accurate cancer classification is of great importance in clinical treatment. Recently, the DNA microarray technology provides a promising approach to the diagnosis and prognosis of cancer types. However, it has no perfect method for the multiclass classification problem. The difficulty lies in the fact that the data are of high dimensionality with small sample size. This paper proposed an automatic classification method of multiclass cancers based on Biomimetic pattern recognition (BPR). To the public GCM data set, the average correct classification rate reaches 80% under the condition that the correct rejection rate is 81%.

Study on Closed-set Speaker Identification Based on Biomimetic Pattern Recognition

In this paper, a new classifier of speaker identification has been proposed, which is based on Biomimetic pattern recognition (BPR). Distinguished from traditional speaker recognition methods, such as DWT, HMM, GMM, SVM and so on, the proposed classifier is constructed by some finite sub-space which is reasonable covering of the points in high dimensional space according to distributing characteristic of speech feature points. It has been used in the system of speaker identification. Experiment results show that better effect could be obtained especially with lesser samples. Furthermore, the proposed classifier employs a much simpler modeling structure as compared to the GMM. In addition, the basic idea "cognition" of Biomimetic pattern recognition (BPR) results in no requirement of retraining the old system for enrolling new speakers.

An Automatic Classification Method of Metabolic Cycle Based on Biomimetic Pattern Recognition

Correct classification of different metabolic cycle stages to identification cell cycle is significant in both human development and clinical diagnostics. However, it has no perfect method has been reached in classification of metabolic cycle yet. This paper exploringly puts forward an automatic classification method of metabolic cycle based on Biomimetic pattern recognition (BPR). As to the three phases of yeast metabolic cycle, the correct classification rate reaches 90%, 100% and 100% respectively.

Biomimetic pattern recognition theory and its applications

Biomimetic pattern recogntion (BPR), which is based on "cognition" instead of "classification", is much closer to the function of human being. The basis of BPR is the Principle of homology-continuity (PHC), which means the difference between two samples of the same class must be gradually changed. The aim of BPR is to find an optimal covering in the feature space, which emphasizes the "similarity" among homologous group members, rather than "division" in traditional pattern recognition. Some applications of BPR are surveyed, in which the results of BPR are much better than the results of Support Vector Machine. A novel neuron model, Hyper sausage neuron (HSN), is shown as a kind of covering units in BPR. The mathematical description of HSN is given and the 2-dimensional discriminant boundary of HSN is shown. In two special cases, in which samples are distributed in a line segment and a circle, both the HSN networks and RBF networks are used for covering. The results show that HSN networks act better than RBF networks in generalization, especially for small sample set, which are consonant with the results of the applications of BPR. And a brief explanation of the HSN networks' advantages in covering general distributed samples is also given.

The application of DBF neural networks for object recognition

On the basis of DBF nets proposed by Wang Shoujue, the model and properties of DBF neural network were discussed in this paper. When applied in pattern recognition, the algorithm and implement on hardware were presented respectively. We did experiments on recognition of omnidirectionally oriented rigid objects on the same level, using direction basis function neural networks, which acts by the method of covering the high dimensional geometrical distribution of the sample set in the feature space. Many animal and vehicle models (even with rather similar shapes) were recognized omnidirectionally thousands of times. For total 8800 tests, the correct recognition rate is 98.75%, the error rate and the rejection rate are 0.5% and 1.25% respectively. (C) 2003 Elsevier Inc. All rights reserved.

Digits speech recognition based on geometrical learning

We investigate the use of independent component analysis (ICA) for speech feature extraction in digits speech recognition systems.We observe that this may be true for a recognition tasks based on geometrical learning with little training data. In contrast to image processing, phase information is not essential for digits speech recognition. We therefore propose a new scheme that shows how the phase sensitivity can be removed by using an analytical description of the ICA-adapted basis functions via the Hilbert transform. Furthermore, since the basis functions are not shift invariant, we extend the method to include a frequency-based ICA stage that removes redundant time shift information. The digits speech recognition results show promising accuracy, Experiments show method based on ICA and geometrical learning outperforms HMM in different number of train samples.

Geometrical learning, descriptive geometry, and biomimetic pattern recognition

Studies on learning problems from geometry perspective have attracted an ever increasing attention in machine learning, leaded by achievements on information geometry. This paper proposes a different geometrical learning from the perspective of high-dimensional descriptive geometry. Geometrical properties of high-dimensional structures underlying a set of samples are learned via successive projections from the higher dimension to the lower dimension until two-dimensional Euclidean plane, under guidance of the established properties and theorems in high-dimensional descriptive geometry. Specifically, we introduce a hyper sausage like geometry shape for learning samples and provides a geometrical learning algorithm for specifying the hyper sausage shapes, which is then applied to biomimetic pattern recognition. Experimental results are presented to show that the proposed approach outperforms three types of support vector machines with either a three degree polynomial kernel or a radial basis function kernel, especially in the cases of high-dimensional samples of a finite size. (c) 2005 Elsevier B.V. All rights reserved.

Iris recognition algorithm based on point covering of high-dimensional space and neural network

In this paper, we constructed a Iris recognition algorithm based on point covering of high-dimensional space and Multi-weighted neuron of point covering of high-dimensional space, and proposed a new method for iris recognition based on point covering theory of high-dimensional space. In this method, irises are trained as "cognition" one class by one class, and it doesn't influence the original recognition knowledge for samples of the new added class. The results of experiments show the rejection rate is 98.9%, the correct cognition rate and the error rate are 95.71% and 3.5% respectively. The experimental results demonstrate that the rejection rate of test samples excluded in the training samples class is very high. It proves the proposed method for iris recognition is effective.

Application of multi-weighted neuron for iris recognition

In this paper, from the cognition science point of view, we constructed a neuron of multi-weighted neural network, and proposed a new method for iris recognition based on multi-weighted neuron. In this method, irises are trained as "cognition" one class by one class, and it doesn't influence the original recognition knowledge for samples of the new added class. The results of experiments show the correct rejection rate is 98.9%, the correct cognition rate and the error recognition rate are 95.71% and 3.5% respectively. The experimental results demonstrate that the correct rejection rate of the test samples excluded in the classes of training samples is very high. It proves the proposed method for iris recognition is effective.

Manifold covering theory in biomimetic pattern recognition

We describe a new model which is based on the concept of cognizing theory. The method identifies subsets of the data which are embedded in arbitrary oriented lower dimensional space. We definite manifold covering in biomimetic pattern recognition, and study its property. Furthermore, we propose this manifold covering algorithm based on Biomimetic Pattern Recognition. At last, the experimental results for face recognition demonstrates that the correct rejection rate of the test samples excluded in the classes of training samples is very high and effective.

Information geometry theory of high-dimension space and application for speaker independent continuous digit speech recognition

In the light of descriptive geometry and notions in set theory, this paper re-defines the basic elements in space such as curve and surface and so on, presents some fundamental notions with respect to the point cover based on the High-dimension space (HDS) point covering theory, finally takes points from mapping part of speech signals to HDS, so as to analyze distribution information of these speech points in HDS, and various geometric covering objects for speech points and their relationship. Besides, this paper also proposes a new algorithm for speaker independent continuous digit speech recognition based on the HDS point dynamic searching theory without end-points detection and segmentation. First from the different digit syllables in real continuous digit speech, we establish the covering area in feature space for continuous speech. During recognition, we make use of the point covering dynamic searching theory in HDS to do recognition, and then get the satisfying recognized results. At last, compared to HMM (Hidden Markov models)-based method, from the development trend of the comparing results, as sample amount increasing, the difference of recognition rate between two methods will decrease slowly, while sample amount approaching to be very large, two recognition rates all close to 100% little by little. As seen from the results, the recognition rate of HDS point covering method is higher than that of in HMM (Hidden Markov models) based method, because, the point covering describes the morphological distribution for speech in HDS, whereas HMM-based method is only a probability distribution, whose accuracy is certainly inferior to point covering.

Mandarin speech emotion recognition based on high dimensional geometry theory

In this paper, a novel approach for mandarin speech emotion recognition, that is mandarin speech emotion recognition based on high dimensional geometry theory, is proposed. The human emotions are classified into 6 archetypal classes: fear, anger, happiness, sadness, surprise and disgust. According to the characteristics of these emotional speech signals, the amplitude, pitch frequency and formant are used as the feature parameters for speech emotion recognition. The new method called high dimensional geometry theory is applied for recognition. Compared with traditional GSVM model, the new method has some advantages. It is noted that this method has significant values for researches and applications henceforth.