Proceedings 14th International Conference on Scientific and Statistical Database Management
Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Man... more Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Many of the current techniques for searching phylogenetic repositories allow the user to perform a keyword-type search or an aligned sequence data search, or to browse a hierarchical list of taxa. Here we describe a new search engine that allows the user to present an example phylogeny, or a query tree, and then searches a phylogenetic database for trees that contain the query structure. The presented search engine is fully operational and is available on the World Wide Web.
15th International Conference on Scientific and Statistical Database Management, 2003.
Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order ... more Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order among siblings is unimportant. In this paper we propose a new similarity measure, called TreeRank, for phylogenetic trees and present an algorithm for computing TreeRank scores. Given a query or pattern tree
Solar flare prediction plays an important role in understanding and forecasting space weather. Th... more Solar flare prediction plays an important role in understanding and forecasting space weather. The main goal of the Helioseismic and Magnetic Imager (HMI), one of the instruments on NASA’s Solar Dynamics Observatory, is to study the origin of solar variability and characterize the Sun’s magnetic activity. HMI provides continuous full-disk observations of the solar vector magnetic field with high cadence data that lead to reliable predictive capability; yet, solar flare prediction effort utilizing these data is still limited. In this paper, we present a machine-learning-as-a-service (MLaaS) framework, called DeepSun, for predicting solar flares on the web based on HMI’s data products. Specifically, we construct training data by utilizing the physical parameters provided by the Space-weather HMI Active Region Patch (SHARP) and categorize solar flares into four classes, namely B, C, M and X, according to the X-ray flare catalogs available at the National Centers for Environmental Infor...
IEEE Transactions on Systems, Man, and Cybernetics, 1994
We consider the problem of comparison between unordered trees, i.e., trees for which the order am... more We consider the problem of comparison between unordered trees, i.e., trees for which the order among siblings is unimportant. The criterion for comparison is the distance as measured by a weighted sum of the costs of deletion, insertion and relabel operations on tree nodes. Such comparisons may contribute to pattern recognition efforts in any field (e.g., genetics) where data can naturally be characterized by unordered trees. In companion work, we have shown this problem to be NP-complete. This paper presents an efflcient enumerative algorithm and several heuristics leading to approximate solutions. The algorithms are based on probabilistic hill climbing and bipartite matching techniques. The paper evaluates the accuracy and time efficiency of the heuristics by applying them to a set of trees transformed from industrial parts based on a previously proposed morphological model.
Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc... more Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc.) that possess some important common externally observable properties. You also have a structural description of the entities (e.g., sequence, topological, or geometrical data) and a distance metric. Combinatorial pattern discovery is the activity of finding patterns in the structural data that might explain these common properties based on the metric. This paper presents an example of combinatorial pattern discovery: the discovery of patterns in protein databases. The structural representation we consider are strings and the distance metric is string edit distance permitting variable length don't cares. Our techniques incorporate string matching algorithms and novel heuristics for discovery and optimization, most of which generalize to other combinatorial structures. Experimental results of applying the techniques to both generated data and functionally related protein families obt...
Proceedings. 20th International Conference on Data Engineering
Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in str... more Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in structural data, such as trees and graphs. FSM finds many applications in bioinformatics, XML processing, Web log analysis, and so on. In this paper we present a new FSM technique for finding patterns in rooted unordered labeled trees. The patterns of interest are cousin pairs in these trees. A cousin pair is a pair of nodes sharing the same parent, the same grandparent, or the same great-grandparent, etc.
Proceedings International Conference and Workshop on Engineering of Computer-Based Systems
I n this paper we put forth a vision for organizations to fully embmce computer support. W e prop... more I n this paper we put forth a vision for organizations to fully embmce computer support. W e propose a business-process oriented architecture for Electronic Enterprise Engineering (EEE) that will enable enterprises to manage and evolve all technological and organizational processes efectively; integrate and manage all enterprise information electronically; and empower knowledge workers at all levels with broad decision support Capabilities. Our goal is for the EEE architecture to empower an enterprise to make the best use of its informational assets to operate efectively in thaS new era of electronic commerce. As part of this project we are developing a standard-based, customizable, integrated tool set called the Support Environment for Enterprise Engineering (SEEE). This paper presents the current SEEE architecture and shows how it supports the three EEE goals.
Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent y... more Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases. We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatc...
Proceedings Twenty-First Annual International Computer Software and Applications Conference (COMPSAC'97), 1997
The Van Houten library has removed some of the personal information and all signatures from the a... more The Van Houten library has removed some of the personal information and all signatures from the approval page and biographical sketches of theses and dissertations in order to protect the identity of NJIT graduates and faculty.
As databases become more pervasive through the biological sciences, various data quality issues r... more As databases become more pervasive through the biological sciences, various data quality issues regarding data legacy, data uniformity and data duplication arise. Due to the nature of this data, each of these problems is non-trivial. For biological data to be corrected and standardized, new methods and frameworks must be developed. This paper proposes one such framework, called BIO-AJAX, which uses principles from data cleaning to improve data quality in biological information systems, specifically in TreeBASE.
Defining an EU indexing system to standardize retrieval in the CH domain. (deliverable 1.5). ISAA... more Defining an EU indexing system to standardize retrieval in the CH domain. (deliverable 1.5). ISAAC project. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Advanced Information and Knowledge Processing, 2005
Knowledge discovery and data mining has recently emerged as an important research direction for e... more Knowledge discovery and data mining has recently emerged as an important research direction for extracting useful information from vast repositories of data of various types. This chapter discusses some of the basic concepts and issues involved in this process with special emphasis on different data mining tasks. The major challenges in data mining are mentioned. Finally, the recent trends in data mining are described and an extensive bibliography is provided.
In this paper we present an index structure, called M e t r i cM a p , that takes a set of object... more In this paper we present an index structure, called M e t r i cM a p , that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such a w ay that the distances among objects are approximately preserved. The index structure is a useful tool for clustering and visualization in data intensive applications, because it replaces expensive distance calculations by sum-of-square calculations. This can make clustering in large databases with expensive distance metrics practical. We compare the index structure with another data mining index structure, F a s t M a p , recently proposed by F aloutsos and Lin, according to two criteria: relative error and clustering accuracy. F or relative error, we s h o w that (i) F astMap gives a lower relative error than MetricMap for Euclidean distances, (ii) MetricMap gives a l o wer relative error than F astMap for non-Euclidean distances (i.e., general distance metrics), and (iii) combining the two reduces the error yet further. A similar result is obtained when comparing the accuracy of clustering. These results hold for di erent data sizes. The main qualitative conclusion is that these two index structures capture complementary information about distance metrics and therefore can be used together
International Journal of Information Quality, 2007
As databases become more pervasive through the biological sciences, various data quality concerns... more As databases become more pervasive through the biological sciences, various data quality concerns are emerging. Biological databases tend to develop data quality issues regarding data legacy, data uniformity and data duplication. Due to the nature of this data, each of these problems is non-trivial and can cause many problems for the database. For biological data to be corrected and standardised, methods and frameworks must be developed to handle both structural and traditional data. This paper discusses issues concerning biological data quality with respect to data cleaning. It presents BIO-AJAX, a framework developed to address these issues. It finally describes BIO-JAX for TreeBASE and BIO-AJAX for Lineage Path, two implementations of BIO-AJAX on phylogenetic data sets.
International Journal of Foundations of Computer Science, 1996
We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with node... more We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with nodes being Labeled). This problem is motivated by the study of information retrieval for bio-chemical and molecular databases. Suppose we define the distance between two CUAL graphs G1 and G2 to be the weighted number of edit operations (insert node, delete node and relabel node) to transform G1 to G2. By reduction from exact cover by 3-sets, one can show that finding the distance between two CUAL graphs is NP-complete. In view of the hardness of the problem, we propose a constrained distance metric, called the degree-2 distance, by requiring that any node to be inserted (deleted) have no more than 2 neighbors. With this metric, we present an efficient algorithm to solve the problem. The algorithm runs in time O(N1N2D2) for general weighting edit operations and in time [Formula: see text] for integral weighting edit operations, where Ni, i=1, 2, is the number of nodes in Gi, D=min{d1, d2} a...
International Journal of Computational Intelligence in Bioinformatics and Systems Biology, 2009
In this paper we present the design and implementation of an RNA structural motif database, calle... more In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: • collected manually from the biomedical literature • submitted by scientists around the world • discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB and report its current status. The RmotifDB system is fully operational and accessible on the web at http://datalab.njit.edu/bioinfo/.
This manuscript has been reproduced from the microfilm master. UM I films the text directly from ... more This manuscript has been reproduced from the microfilm master. UM I films the text directly from the original or copy submitted. Thus, som e thesis and dissertation copies are in typewriter face, while others may be from any type o f computer printer. T h e quality o f th is reproduction is dependent upon the quality o f th e copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back o f the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UM I directly to order.
Automated detection or prediction of coding sequences from within genomic DNA has been a major ra... more Automated detection or prediction of coding sequences from within genomic DNA has been a major rate-limiting step in the pursuit of vertebrate genes. Programs currently available are far from being powerful enough to elucidate a gene structure completely. In this paper, we present a new system, called GeneScout, for predicting gene structures in vertebrate genomic DNA. The system contains specially designed hidden Markov models (HMMs) for detecting functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites, etc. An HMM model is also proposed for exon coding potential computation. Our main hypothesis is that, given a vertebrate genomic DNA sequence S, it is always possible to construct a directed acyclic graph G such that the path for the actual coding region of S is in the set of all paths on G. Thus, the gene detection problem is reduced to that of analyzing the paths in the graph G. A dynamic programming algorithm is used to find the optimal path in G. The proposed system is trained using an expectation-maximization (EM) algorithm and its performance on vertebrate gene prediction is evaluated using the 10-way cross-validation method. Experimental results show that the proposed system performs well and is comparable to existing gene discovery tools.
Proceedings 14th International Conference on Scientific and Statistical Database Management
Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Man... more Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Many of the current techniques for searching phylogenetic repositories allow the user to perform a keyword-type search or an aligned sequence data search, or to browse a hierarchical list of taxa. Here we describe a new search engine that allows the user to present an example phylogeny, or a query tree, and then searches a phylogenetic database for trees that contain the query structure. The presented search engine is fully operational and is available on the World Wide Web.
15th International Conference on Scientific and Statistical Database Management, 2003.
Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order ... more Phylogenetic trees are unordered labeled trees in which each leaf node has a label and the order among siblings is unimportant. In this paper we propose a new similarity measure, called TreeRank, for phylogenetic trees and present an algorithm for computing TreeRank scores. Given a query or pattern tree
Solar flare prediction plays an important role in understanding and forecasting space weather. Th... more Solar flare prediction plays an important role in understanding and forecasting space weather. The main goal of the Helioseismic and Magnetic Imager (HMI), one of the instruments on NASA’s Solar Dynamics Observatory, is to study the origin of solar variability and characterize the Sun’s magnetic activity. HMI provides continuous full-disk observations of the solar vector magnetic field with high cadence data that lead to reliable predictive capability; yet, solar flare prediction effort utilizing these data is still limited. In this paper, we present a machine-learning-as-a-service (MLaaS) framework, called DeepSun, for predicting solar flares on the web based on HMI’s data products. Specifically, we construct training data by utilizing the physical parameters provided by the Space-weather HMI Active Region Patch (SHARP) and categorize solar flares into four classes, namely B, C, M and X, according to the X-ray flare catalogs available at the National Centers for Environmental Infor...
IEEE Transactions on Systems, Man, and Cybernetics, 1994
We consider the problem of comparison between unordered trees, i.e., trees for which the order am... more We consider the problem of comparison between unordered trees, i.e., trees for which the order among siblings is unimportant. The criterion for comparison is the distance as measured by a weighted sum of the costs of deletion, insertion and relabel operations on tree nodes. Such comparisons may contribute to pattern recognition efforts in any field (e.g., genetics) where data can naturally be characterized by unordered trees. In companion work, we have shown this problem to be NP-complete. This paper presents an efflcient enumerative algorithm and several heuristics leading to approximate solutions. The algorithms are based on probabilistic hill climbing and bipartite matching techniques. The paper evaluates the accuracy and time efficiency of the heuristics by applying them to a set of trees transformed from industrial parts based on a previously proposed morphological model.
Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc... more Suppose you are given a set of natural entities (e.g., proteins, organisms, weather patterns, etc.) that possess some important common externally observable properties. You also have a structural description of the entities (e.g., sequence, topological, or geometrical data) and a distance metric. Combinatorial pattern discovery is the activity of finding patterns in the structural data that might explain these common properties based on the metric. This paper presents an example of combinatorial pattern discovery: the discovery of patterns in protein databases. The structural representation we consider are strings and the distance metric is string edit distance permitting variable length don't cares. Our techniques incorporate string matching algorithms and novel heuristics for discovery and optimization, most of which generalize to other combinatorial structures. Experimental results of applying the techniques to both generated data and functionally related protein families obt...
Proceedings. 20th International Conference on Data Engineering
Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in str... more Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in structural data, such as trees and graphs. FSM finds many applications in bioinformatics, XML processing, Web log analysis, and so on. In this paper we present a new FSM technique for finding patterns in rooted unordered labeled trees. The patterns of interest are cousin pairs in these trees. A cousin pair is a pair of nodes sharing the same parent, the same grandparent, or the same great-grandparent, etc.
Proceedings International Conference and Workshop on Engineering of Computer-Based Systems
I n this paper we put forth a vision for organizations to fully embmce computer support. W e prop... more I n this paper we put forth a vision for organizations to fully embmce computer support. W e propose a business-process oriented architecture for Electronic Enterprise Engineering (EEE) that will enable enterprises to manage and evolve all technological and organizational processes efectively; integrate and manage all enterprise information electronically; and empower knowledge workers at all levels with broad decision support Capabilities. Our goal is for the EEE architecture to empower an enterprise to make the best use of its informational assets to operate efectively in thaS new era of electronic commerce. As part of this project we are developing a standard-based, customizable, integrated tool set called the Support Environment for Enterprise Engineering (SEEE). This paper presents the current SEEE architecture and shows how it supports the three EEE goals.
Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent y... more Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases. We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatc...
Proceedings Twenty-First Annual International Computer Software and Applications Conference (COMPSAC'97), 1997
The Van Houten library has removed some of the personal information and all signatures from the a... more The Van Houten library has removed some of the personal information and all signatures from the approval page and biographical sketches of theses and dissertations in order to protect the identity of NJIT graduates and faculty.
As databases become more pervasive through the biological sciences, various data quality issues r... more As databases become more pervasive through the biological sciences, various data quality issues regarding data legacy, data uniformity and data duplication arise. Due to the nature of this data, each of these problems is non-trivial. For biological data to be corrected and standardized, new methods and frameworks must be developed. This paper proposes one such framework, called BIO-AJAX, which uses principles from data cleaning to improve data quality in biological information systems, specifically in TreeBASE.
Defining an EU indexing system to standardize retrieval in the CH domain. (deliverable 1.5). ISAA... more Defining an EU indexing system to standardize retrieval in the CH domain. (deliverable 1.5). ISAAC project. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Advanced Information and Knowledge Processing, 2005
Knowledge discovery and data mining has recently emerged as an important research direction for e... more Knowledge discovery and data mining has recently emerged as an important research direction for extracting useful information from vast repositories of data of various types. This chapter discusses some of the basic concepts and issues involved in this process with special emphasis on different data mining tasks. The major challenges in data mining are mentioned. Finally, the recent trends in data mining are described and an extensive bibliography is provided.
In this paper we present an index structure, called M e t r i cM a p , that takes a set of object... more In this paper we present an index structure, called M e t r i cM a p , that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such a w ay that the distances among objects are approximately preserved. The index structure is a useful tool for clustering and visualization in data intensive applications, because it replaces expensive distance calculations by sum-of-square calculations. This can make clustering in large databases with expensive distance metrics practical. We compare the index structure with another data mining index structure, F a s t M a p , recently proposed by F aloutsos and Lin, according to two criteria: relative error and clustering accuracy. F or relative error, we s h o w that (i) F astMap gives a lower relative error than MetricMap for Euclidean distances, (ii) MetricMap gives a l o wer relative error than F astMap for non-Euclidean distances (i.e., general distance metrics), and (iii) combining the two reduces the error yet further. A similar result is obtained when comparing the accuracy of clustering. These results hold for di erent data sizes. The main qualitative conclusion is that these two index structures capture complementary information about distance metrics and therefore can be used together
International Journal of Information Quality, 2007
As databases become more pervasive through the biological sciences, various data quality concerns... more As databases become more pervasive through the biological sciences, various data quality concerns are emerging. Biological databases tend to develop data quality issues regarding data legacy, data uniformity and data duplication. Due to the nature of this data, each of these problems is non-trivial and can cause many problems for the database. For biological data to be corrected and standardised, methods and frameworks must be developed to handle both structural and traditional data. This paper discusses issues concerning biological data quality with respect to data cleaning. It presents BIO-AJAX, a framework developed to address these issues. It finally describes BIO-JAX for TreeBASE and BIO-AJAX for Lineage Path, two implementations of BIO-AJAX on phylogenetic data sets.
International Journal of Foundations of Computer Science, 1996
We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with node... more We consider the problem of comparing CUAL graphs (Connected, Undirected, Acyclic graphs with nodes being Labeled). This problem is motivated by the study of information retrieval for bio-chemical and molecular databases. Suppose we define the distance between two CUAL graphs G1 and G2 to be the weighted number of edit operations (insert node, delete node and relabel node) to transform G1 to G2. By reduction from exact cover by 3-sets, one can show that finding the distance between two CUAL graphs is NP-complete. In view of the hardness of the problem, we propose a constrained distance metric, called the degree-2 distance, by requiring that any node to be inserted (deleted) have no more than 2 neighbors. With this metric, we present an efficient algorithm to solve the problem. The algorithm runs in time O(N1N2D2) for general weighting edit operations and in time [Formula: see text] for integral weighting edit operations, where Ni, i=1, 2, is the number of nodes in Gi, D=min{d1, d2} a...
International Journal of Computational Intelligence in Bioinformatics and Systems Biology, 2009
In this paper we present the design and implementation of an RNA structural motif database, calle... more In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: • collected manually from the biomedical literature • submitted by scientists around the world • discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB and report its current status. The RmotifDB system is fully operational and accessible on the web at http://datalab.njit.edu/bioinfo/.
This manuscript has been reproduced from the microfilm master. UM I films the text directly from ... more This manuscript has been reproduced from the microfilm master. UM I films the text directly from the original or copy submitted. Thus, som e thesis and dissertation copies are in typewriter face, while others may be from any type o f computer printer. T h e quality o f th is reproduction is dependent upon the quality o f th e copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back o f the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UM I directly to order.
Automated detection or prediction of coding sequences from within genomic DNA has been a major ra... more Automated detection or prediction of coding sequences from within genomic DNA has been a major rate-limiting step in the pursuit of vertebrate genes. Programs currently available are far from being powerful enough to elucidate a gene structure completely. In this paper, we present a new system, called GeneScout, for predicting gene structures in vertebrate genomic DNA. The system contains specially designed hidden Markov models (HMMs) for detecting functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites, etc. An HMM model is also proposed for exon coding potential computation. Our main hypothesis is that, given a vertebrate genomic DNA sequence S, it is always possible to construct a directed acyclic graph G such that the path for the actual coding region of S is in the set of all paths on G. Thus, the gene detection problem is reduced to that of analyzing the paths in the graph G. A dynamic programming algorithm is used to find the optimal path in G. The proposed system is trained using an expectation-maximization (EM) algorithm and its performance on vertebrate gene prediction is evaluated using the 10-way cross-validation method. Experimental results show that the proposed system performs well and is comparable to existing gene discovery tools.
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