Search results for: Protein homology detection; support vectormachine; string kernel.

Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: Wei Zhang, Su-Yan Tang, Yi-Fan Zhu, Wei-Ping Wang

Abstract:

Support vector regression (SVR) has been regarded as a state-of-the-art method for approximation and regression. The importance of kernel function, which is so-called admissible support vector kernel (SV kernel) in SVR, has motivated many studies on its composition. The Gaussian kernel (RBF) is regarded as a “best" choice of SV kernel used by non-expert in SVR, whereas there is no evidence, except for its superior performance on some practical applications, to prove the statement. Its well-known that reproducing kernel (R.K) is also a SV kernel which possesses many important properties, e.g. positive definiteness, reproducing property and composing complex R.K by simpler ones. However, there are a limited number of R.Ks with explicit forms and consequently few quantitative comparison studies in practice. In this paper, two R.Ks, i.e. SV kernels, composed by the sum and product of a translation invariant kernel in a Sobolev space are proposed. An exploratory study on the performance of SVR based general R.K is presented through a systematic comparison to that of RBF using multiple criteria and synthetic problems. The results show that the R.K is an equivalent or even better SV kernel than RBF for the problems with more input variables (more than 5, especially more than 10) and higher nonlinearity.

Keywords: admissible support vector kernel, reproducing kernel, reproducing kernel Hilbert space, support vector regression.

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Authors: Jamuna Bhandari

Abstract:

String matching also known as pattern matching is one of primary concept for network security. In this area the effectiveness and efficiency of string matching algorithms is important for applications in network security such as network intrusion detection, virus detection, signature matching and web content filtering system. This paper presents brief review on some of string matching techniques used for network security.

Keywords: Filtering, honeypot, network telescope, pattern, string, signature.

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Authors: Assad Maalouf, Lunjin Lu, James Lynott

Abstract:

We design and implement a precise model of string operations using finite state machine transformers and state transformers to approximate the values string variables can take throughout the execution of the program.We use our model to analyze Android program string variables. Our experimental results show that our string analysis is very efficient at detecting the contextual effect of string operations on the string variables. Our model proved to be very useful when it came to verifying statements about the string variables of the program.

Keywords: Abstract interpretation, android, static analysis, string analysis.

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Authors: Andreas Theissler, Ian Dear

Abstract:

The one-class support vector machine “support vector data description” (SVDD) is an ideal approach for anomaly or outlier detection. However, for the applicability of SVDD in real-world applications, the ease of use is crucial. The results of SVDD are massively determined by the choice of the regularisation parameter C and the kernel parameter  of the widely used RBF kernel. While for two-class SVMs the parameters can be tuned using cross-validation based on the confusion matrix, for a one-class SVM this is not possible, because only true positives and false negatives can occur during training. This paper proposes an approach to find the optimal set of parameters for SVDD solely based on a training set from one class and without any user parameterisation. Results on artificial and real data sets are presented, underpinning the usefulness of the approach.

Keywords: Support vector data description, anomaly detection, one-class classification, parameter tuning.

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Authors: Mohamed EL Boujnouni, Mohamed Jedra, Noureddine Zahid

Abstract:

Support Vector Domain Description (SVDD) is one of the best-known one-class support vector learning methods, in which one tries the strategy of using balls defined on the feature space in order to distinguish a set of normal data from all other possible abnormal objects. As all kernel-based learning algorithms its performance depends heavily on the proper choice of the kernel parameter. This paper proposes a new approach to select kernel's parameter based on maximizing the distance between both gravity centers of normal and abnormal classes, and at the same time minimizing the variance within each class. The performance of the proposed algorithm is evaluated on several benchmarks. The experimental results demonstrate the feasibility and the effectiveness of the presented method.

Keywords: Gravity centers, Kernel’s parameter, Support Vector Domain Description, Variance.

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Authors: Wei Zhang, Xin Zhao, Yi-Fan Zhu, Xin-Jian Zhang

Abstract:

Kernel function, which allows the formulation of nonlinear variants of any algorithm that can be cast in terms of dot products, makes the Support Vector Machines (SVM) have been successfully applied in many fields, e.g. classification and regression. The importance of kernel has motivated many studies on its composition. It-s well-known that reproducing kernel (R.K) is a useful kernel function which possesses many properties, e.g. positive definiteness, reproducing property and composing complex R.K by simple operation. There are two popular ways to compute the R.K with explicit form. One is to construct and solve a specific differential equation with boundary value whose handicap is incapable of obtaining a unified form of R.K. The other is using a piecewise integral of the Green function associated with a differential operator L. The latter benefits the computation of a R.K with a unified explicit form and theoretical analysis, whereas there are relatively later studies and fewer practical computations. In this paper, a new algorithm for computing a R.K is presented. It can obtain the unified explicit form of R.K in general reproducing kernel Hilbert space. It avoids constructing and solving the complex differential equations manually and benefits an automatic, flexible and rigorous computation for more general RKHS. In order to validate that the R.K computed by the algorithm can be used in SVM well, some illustrative examples and a comparison between R.K and Gaussian kernel (RBF) in support vector regression are presented. The result shows that the performance of R.K is close or slightly superior to that of RBF.

Keywords: admissible support vector kernel, reproducing kernel, reproducing kernel Hilbert space, Green function, support vectorregression

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Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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Authors: Assad Maalouf, Lunjin Lu, James Lynott

Abstract:

We present a taint analysis that can automatically detect when string operations result in a string that is free of taints, where all the tainted patterns have been removed. This is an improvement on the conservative behavior of previous taint analyzers, where a string operation on a tainted string always leads to a tainted string unless the operation is manually marked as a sanitizer. The taint analysis is built on top of a string analysis that uses finite state automata to approximate the sets of values that string variables can take during the execution of a program. The proposed approach has been implemented as an extension of FlowDroid and experimental results show that the resulting taint analyzer is much more precise than the original FlowDroid.

Keywords: Android, static analysis, string analysis, taint analysis.

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Authors: Z. Altawallbeh

Abstract:

In this paper, an explicit homotopic function is constructed to compute the Hochschild homology of a finite dimensional free k-module V. Because the polynomial algebra is of course fundamental in the computation of the Hochschild homology HH and the cyclic homology CH of commutative algebras, we concentrate our work to compute HH of the polynomial algebra, by providing certain homotopic function.

Keywords: Exterior algebra, free resolution, free and projective modules, Hochschild homology, homotopic function, symmetric algebra.

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Authors: Essam Al Daoud

Abstract:

Intrusion detection is a mechanism used to protect a system and analyse and predict the behaviours of system users. An ideal intrusion detection system is hard to achieve due to nonlinearity, and irrelevant or redundant features. This study introduces a new anomaly-based intrusion detection model. The suggested model is based on particle swarm optimisation and nonlinear, multi-class and multi-kernel support vector machines. Particle swarm optimisation is used for feature selection by applying a new formula to update the position and the velocity of a particle; the support vector machine is used as a classifier. The proposed model is tested and compared with the other methods using the KDD CUP 1999 dataset. The results indicate that this new method achieves better accuracy rates than previous methods.

Keywords: Feature selection, Intrusion detection, Support vector machine, Particle swarm.

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Authors: Rajender Singh Chillar, Barjesh Kochar

Abstract:

All Text processing systems allow their users to search a pattern of string from a given text. String matching is fundamental to database and text processing applications. Every text editor must contain a mechanism to search the current document for arbitrary strings. Spelling checkers scan an input text for words in the dictionary and reject any strings that do not match. We store our information in data bases so that later on we can retrieve the same and this retrieval can be done by using various string matching algorithms. This paper is describing a new string matching algorithm for various applications. A new algorithm has been designed with the help of Rabin Karp Matcher, to improve string matching process.

Keywords: Algorithm, Complexity, Matching-patterns, Pattern, Rabin-Karp, String, text-processing.

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Authors: Bi Kun, Gu Nai-jie, Tu Kun, Liu Xiao-hu, Liu Gang

Abstract:

Traditional parallel single string matching algorithms are always based on PRAM computation model. Those algorithms concentrate on the cost optimal design and the theoretical speed. Based on the distributed string matching algorithm proposed by CHEN, a practical distributed string matching algorithm architecture is proposed in this paper. And also an improved single string matching algorithm based on a variant Boyer-Moore algorithm is presented. We implement our algorithm on the above architecture and the experiments prove that it is really practical and efficient on distributed memory machine. Its computation complexity is O(n/p + m), where n is the length of the text, and m is the length of the pattern, and p is the number of the processors.

Keywords: Boyer-Moore algorithm, distributed algorithm, parallel string matching, string matching.

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Authors: Abhishek Neogi, Jayesh Verma, Pinaki Pratim Acharjya

Abstract:

Image segmentation and edge detection is a fundamental section in image processing. In case of noisy images Edge Detection is very less effective if we use conventional Spatial Filters like Sobel, Prewitt, LOG, Laplacian etc. To overcome this problem we have proposed the use of Stochastic Gradient Mask instead of Spatial Filters for generating gradient images. The present study has shown that the resultant images obtained by applying Stochastic Gradient Masks appear to be much clearer and sharper as per Edge detection is considered.

Keywords: Image segmentation, edge Detection, noisy images, spatialfilters, stochastic gradient kernel.

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Authors: Wei Zhang, Yao-Yu Li, Yi-Fan Zhu, Qun Li, Wei-Ping Wang

Abstract:

It-s known that incorporating prior knowledge into support vector regression (SVR) can help to improve the approximation performance. Most of researches are concerned with the incorporation of knowledge in the form of numerical relationships. Little work, however, has been done to incorporate the prior knowledge on the structural relationships among the variables (referred as to Structural Prior Knowledge, SPK). This paper explores the incorporation of SPK in SVR by constructing appropriate admissible support vector kernel (SV kernel) based on the properties of reproducing kernel (R.K). Three-levels specifications of SPK are studied with the corresponding sub-levels of prior knowledge that can be considered for the method. These include Hierarchical SPK (HSPK), Interactional SPK (ISPK) consisting of independence, global and local interaction, Functional SPK (FSPK) composed of exterior-FSPK and interior-FSPK. A convenient tool for describing the SPK, namely Description Matrix of SPK is introduced. Subsequently, a new SVR, namely Motivated Support Vector Regression (MSVR) whose structure is motivated in part by SPK, is proposed. Synthetic examples show that it is possible to incorporate a wide variety of SPK and helpful to improve the approximation performance in complex cases. The benefits of MSVR are finally shown on a real-life military application, Air-toground battle simulation, which shows great potential for MSVR to the complex military applications.

Keywords: admissible support vector kernel, reproducing kernel, structural prior knowledge, motivated support vector regression

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Authors: Wei Zhang, Yao-Yu Li, Yi-Fan Zhu, Qun Li, Wei-Ping Wang

Abstract:

It-s known that incorporating prior knowledge into support vector regression (SVR) can help to improve the approximation performance. Most of researches are concerned with the incorporation of knowledge in form of numerical relationships. Little work, however, has been done to incorporate the prior knowledge on the structural relationships among the variables (referred as to Structural Prior Knowledge, SPK). This paper explores the incorporation of SPK in SVR by constructing appropriate admissible support vector kernel (SV kernel) based on the properties of reproducing kernel (R.K). Three-levels specifications of SPK are studies with the corresponding sub-levels of prior knowledge that can be considered for the method. These include Hierarchical SPK (HSPK), Interactional SPK (ISPK) consisting of independence, global and local interaction, Functional SPK (FSPK) composed of exterior-FSPK and interior-FSPK. A convenient tool for describing the SPK, namely Description Matrix of SPK is introduced. Subsequently, a new SVR, namely Motivated Support Vector Regression (MSVR) whose structure is motivated in part by SPK, is proposed. Synthetic examples show that it is possible to incorporate a wide variety of SPK and helpful to improve the approximation performance in complex cases. The benefits of MSVR are finally shown on a real-life military application, Air-toground battle simulation, which shows great potential for MSVR to the complex military applications.

Keywords: admissible support vector kernel, reproducing kernel, structural prior knowledge, motivated support vector regression

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Authors: Qi Xiu, Hiromu Hota, Yohsuke Ishii, Takuya Oda

Abstract:

Recently, collectable manufacturing data are rapidly increasing. On the other hand, mega recall is getting serious as a social problem. Under such circumstances, there are increasing needs for preventing mega recalls by defect analysis such as root cause analysis and abnormal detection utilizing manufacturing data. However, the time to classify strings in manufacturing data by traditional method is too long to meet requirement of quick defect analysis. Therefore, we present String Length Distribution Classification method (SLDC) to correctly classify strings in a short time. This method learns character features, especially string length distribution from Product ID, Machine ID in BOM and asset list. By applying the proposal to strings in actual manufacturing data, we verified that the classification time of strings can be reduced by 80%. As a result, it can be estimated that the requirement of quick defect analysis can be fulfilled.

Keywords: Data quality, feature selection, probability distribution, string classification, string length.

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Authors: Tatjana Eitrich, Bruno Lang

Abstract:

This work deals with aspects of support vector machine learning for large-scale data mining tasks. Based on a decomposition algorithm for support vector machine training that can be run in serial as well as shared memory parallel mode we introduce a transformation of the training data that allows for the usage of an expensive generalized kernel without additional costs. We present experiments for the Gaussian kernel, but usage of other kernel functions is possible, too. In order to further speed up the decomposition algorithm we analyze the critical problem of working set selection for large training data sets. In addition, we analyze the influence of the working set sizes onto the scalability of the parallel decomposition scheme. Our tests and conclusions led to several modifications of the algorithm and the improvement of overall support vector machine learning performance. Our method allows for using extensive parameter search methods to optimize classification accuracy.

Keywords: Support Vector Machine Training, Multi-ParameterKernels, Shared Memory Parallel Computing, Large Data

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Authors: Rasmus Engholm, Eva B. Vedel Jensen, Henrik Karstoft

Abstract:

In this paper we present a noise reduction filter for video processing. It is based on the recently proposed two dimensional steering kernel, extended to three dimensions and further augmented to suit the spatial-temporal domain of video processing. Two alternative filters are proposed - the time symmetric kernel and the time asymmetric kernel. The first reduces the noise on single sequences, but to handle the problems at scene shift the asymmetric kernel is introduced. The performance of both are tested on simulated data and on a real video sequence together with the existing steering kernel. The proposed kernels improves the Rooted Mean Squared Error (RMSE) compared to the original steering kernel method on video material.

Keywords: Adaptive image filtering, noise reduction, kernel methods, video processing.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

Abstract:

The P-Bigram method is a string comparison methods base on an internal two characters-based similarity measure. The edit distance between two strings is the minimal number of elementary editing operations required to transform one string into the other. The elementary editing operations include deletion, insertion, substitution two characters. In this paper, we address the P-Bigram method to sole the similarity problem in DNA sequence. This method provided an efficient algorithm that locates all minimum operation in a string. We have been implemented algorithm and found that our program calculated that smaller distance than one string. We develop PBigram edit distance and show that edit distance or the similarity and implementation using dynamic programming. The performance of the proposed approach is evaluated using number edit and percentage similarity measures.

Keywords: Edit distance, String Matching, String Similarity

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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Authors: Kei Kawamorita, Ryouta Kasahara, Yuuki Mochizuki, Kenichiro Noguchi

Abstract:

A separation-kernel-based operating system (OS) has been designed for use in secure embedded systems by applying formal methods to the design of the separation-kernel part. The separation kernel is a small OS kernel that provides an abstract distributed environment on a single CPU. The design of the separation kernel was verified using two formal methods, the B method and the Spin model checker. A newly designed semi-formal method, the extended state transition method, was also applied. An OS comprising the separation-kernel part and additional OS services on top of the separation kernel was prototyped on the Intel IA-32 architecture. Developing and testing of a prototype embedded application, a point-of-sale application, on the prototype OS demonstrated that the proposed architecture and the use of formal methods to design its kernel part are effective for achieving a secure embedded system having a high-assurance separation kernel.

Keywords: B method, embedded systems, extended state transition, formal methods, separation kernel, Spin.

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Authors: S. Deswal, M. Pal

Abstract:

Presently various computational techniques are used in modeling and analyzing environmental engineering data. In the present study, an intra-comparison of polynomial and radial basis kernel functions based on Support Vector Regression and, in turn, an inter-comparison with Multi Linear Regression has been attempted in modeling mass transfer capacity of vertical (θ = 90O) and inclined (θ multiple plunging jets (varying from 1 to 16 numbers). The data set used in this study consists of four input parameters with a total of eighty eight cases, forty four each for vertical and inclined multiple plunging jets. For testing, tenfold cross validation was used. Correlation coefficient values of 0.971 and 0.981 along with corresponding root mean square error values of 0.0025 and 0.0020 were achieved by using polynomial and radial basis kernel functions based Support Vector Regression respectively. An intra-comparison suggests improved performance by radial basis function in comparison to polynomial kernel based Support Vector Regression. Further, an inter-comparison with Multi Linear Regression (correlation coefficient = 0.973 and root mean square error = 0.0024) reveals that radial basis kernel functions based Support Vector Regression performs better in modeling and estimating mass transfer by multiple plunging jets.

Keywords: Mass transfer, multiple plunging jets, polynomial and radial basis kernel functions, Support Vector Regression.

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Authors: Hamza Nejib, Okba Taouali

Abstract:

This paper presents two of the most knowing kernel adaptive filtering (KAF) approaches, the kernel least mean squares and the kernel recursive least squares, in order to predict a new output of nonlinear signal processing. Both of these methods implement a nonlinear transfer function using kernel methods in a particular space named reproducing kernel Hilbert space (RKHS) where the model is a linear combination of kernel functions applied to transform the observed data from the input space to a high dimensional feature space of vectors, this idea known as the kernel trick. Then KAF is the developing filters in RKHS. We use two nonlinear signal processing problems, Mackey Glass chaotic time series prediction and nonlinear channel equalization to figure the performance of the approaches presented and finally to result which of them is the adapted one.

Keywords: KLMS, online prediction, KAF, signal processing, RKHS, Kernel methods, KRLS, KLMS.

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Authors: A. Perolini

Abstract:

Feature and model selection are in the center of attention of many researches because of their impact on classifiers- performance. Both selections are usually performed separately but recent developments suggest using a combined GA-SVM approach to perform them simultaneously. This approach improves the performance of the classifier identifying the best subset of variables and the optimal parameters- values. Although GA-SVM is an effective method it is computationally expensive, thus a rough method can be considered. The paper investigates a joined approach of Genetic Algorithm and kernel matrix criteria to perform simultaneously feature and model selection for SVM classification problem. The purpose of this research is to improve the classification performance of SVM through an efficient approach, the Kernel Matrix Genetic Algorithm method (KMGA).

Keywords: Feature and model selection, Genetic Algorithms, Support Vector Machines, kernel matrix.

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Authors: Omar GACI, Stefan BALEV, Antoine DUTOT

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.

Keywords: interaction network, protein structure, community structure detection.

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Authors: Chouvalit Khancome, Veera Boonjing

Abstract:

This paper proposes a new solution to string matching problem. This solution constructs an inverted list representing a  string pattern to be searched for. It then uses a new algorithm to process an input string in a single pass. The preprocessing phase  takes 1) time complexity O(m) 2) space complexity O(1) where m is  the length of pattern. The searching phase time complexity takes 1)  O(m+α ) in average case 2) O(n/m) in the best case and 3) O(n) in  the worst case, where α is the number of comparing leading to  mismatch and n is the length of input text.

Keywords: String matching, inverted list, inverted index, pattern, algorithm.

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Authors: Chan Weng Howe, Mohd Saberi Mohamad

Abstract:

Protein residue contact map is a compact representation of secondary structure of protein. Due to the information hold in the contact map, attentions from researchers in related field were drawn and plenty of works have been done throughout the past decade. Artificial intelligence approaches have been widely adapted in related works such as neural networks, genetic programming, and Hidden Markov model as well as support vector machine. However, the performance of the prediction was not generalized which probably depends on the data used to train and generate the prediction model. This situation shown the importance of the features or information used in affecting the prediction performance. In this research, support vector machine was used to predict protein residue contact map on different combination of features in order to show and analyze the effectiveness of the features.

Keywords: contact map, protein residue contact, support vector machine, protein structure prediction

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