13574031
Mining genes in DNA using GeneScout
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. 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 the good performance of the proposed system and its complementarity to a widely used gene detection system.
14900181
Unordered tree mining with applications to phylogeny
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. 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. Given a tree T, our algorithm finds all interesting cousin pairs of T in O(|T|/sup 2/) time where |T| is the number of nodes in T. Experimental results on synthetic data and phylogenies show the scalability and effectiveness of the proposed technique. To demonstrate the usefulness of our approach, we discuss its applications to locating co-occurring patterns in multiple evolutionary trees, evaluating the consensus of equally parsimonious trees, and finding kernel trees of groups of phylogenies. We also describe extensions of our algorithms for undirected acyclic graphs (or free trees).
2286283
Query result ranking over e-commerce web databases
To deal with the problem of too many results returned from an E-commerce Web database in response to a user query, this paper proposes a novel approach to rank the query results. Based on the user query, we speculate how much the user cares about each attribute and assign a corresponding weight to it. Then, for each tuple in the query result, each attribute value is assigned a score according to its "desirableness" to the user. These attribute value scores are combined according to the attribute weights to get a final ranking score for each tuple. Tuples with the top ranking scores are presented to the user first. Our ranking method is domain independent and requires no user feedback. Experimental results demonstrate that this ranking method can effectively capture a user's preferences.
11616193
Automatic Hierarchical Classification of Structured Deep Web Databases
We present a method that automatically classifies structured deep Web databases according to a pre-defined topic hierarchy. We assume that there are some manually classified databases, i.e., training databases, in every node of the topic hierarchy. Each training database is probed using queries constructed from the node titles of the topic hierarchy and the query result counts reported by the database are used to represent the content of the database. Hence, when adding a new database it can be probed by the same set of queries and classified to a node whose training databases are most similar to the new one. Specifically, a support vector machine classifier is trained on each internal node of the topic hierarchy with these training databases and the new database can be classified into the hierarchy top-down level by level. A feature extension method is proposed to create discriminant features. Experiments run on real structured Web databases collected from the Internet show that this classification method is quite accurate.
236203
New Techniques for DNA Sequence Classification
DNA sequence classification is the activity of determining whether or not an unlabeled sequence S belongs to an existing class C. This paper proposes two new techniques for DNA sequence classification. The first technique works by comparing the unlabeled sequence S with a group of active motifs discovered from the elements of C and by distinction with elements outside of C. The second technique generates and matches gapped fingerprints of S with elements of C. Experimental results obtained by running these algorithms on long and well conserved Alu sequences demonstrate the good performance of the presented methods compared with FASTA. When applied to less conserved and relatively short functional sites such as splice-junctions, a variation of the second technique combining fingerprinting with consensus sequence analysis gives better results than the current classifiers employing text compression and machine learning algorithms.
12680145
Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining
Presents a method for finding patterns in 3D graphs. Each node in a graph is an undecomposable or atomic unit and has a label. Edges are links between the atomic units. Patterns are rigid substructures that may occur in a graph after allowing for an arbitrary number of whole-structure rotations and translations as well as a small number (specified by the user) of edit operations in the patterns or in the graph. (When a pattern appears in a graph only after the graph has been modified, we call that appearance "approximate occurrence.") The edit operations include relabeling a node, deleting a node and inserting a node. The proposed method is based on the geometric hashing technique, which hashes node-triplets of the graphs into a 3D table and compresses the label-triplets in the table. To demonstrate the utility of our algorithms, we discuss two applications of them in scientific data mining. First, we apply the method to locating frequently occurring motifs in two families of proteins pertaining to RNA-directed DNA polymerase and thymidylate synthase and use the motifs to classify the proteins. Then, we apply the method to clustering chemical compounds pertaining to aromatic compounds, bicyclicalkanes and photosynthesis. Experimental results indicate the good performance of our algorithms and high recall and precision rates for both classification and clustering.
37577300
Probabilistic location problems with discrete demand weights
In this article we consider four models for locating a facility on an undirected network with demand weights, which are independent discrete random variables. These problems include the probabilistic versions of two models for locating desirable facilities: the 1-median and 1-minimax problems and two problems for locating undesirable facilities: the 1-antimedian and 1-maximin problems. The article contains analysis of special cases where a solution is determined by solving deterministic versions of the problems and efficient algorithms to solve the problems in general. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 44(1), 47–57 2004
15532439
Scalable and accurate identification of AS-level forwarding paths
Traceroute is used heavily by network operators and researchers to identify the IP forwarding path from a source to a destination. In practice, knowing the autonomous system (AS) associated with each hop in the path is also quite valuable. In previous work we showed that the IP-to-AS mapping extracted from BGP routing tables is not sufficient for determining the AS-level forwarding paths. By comparing BGP and traceroute AS paths from multiple vantage points, Z. Morley Mao et al. (2003) proposed heuristics that identify the root causes of the mismatches and fix the inaccurate IP-to-AS mappings. These heuristics, though effective, are labor-intensive and mostly ad hoc. This paper proposes a systematic way to construct accurate IP-to-AS mappings using dynamic programming and iterative improvement. Our algorithm reduces the initial mismatch ratio of 15% between BGP and traceroute AS paths to 5% while changing only 2.9% of the assignments in the initial IP-to-AS mappings. This is in contrast to the results of Z. Morley Mao et al. (2003), where 10% of the assignments were modified and the mismatch ratio was only reduced to 9%. We show that our algorithm is robust and can yield near-optimal results even when the initial mapping is corrupted or when the number of probing sources or destinations is reduced. Our work is a key step towards building a scalable and accurate AS-level traceroute tool
3235521
Towards an accurate AS-level traceroute tool
Traceroute is widely used to detect routing problems, characterize end-to-end paths, and discover the Internet topology. Providing an accurate list of the Autonomous Systems (ASes) along the forwarding path would make traceroute even more valuable to researchers and network operators. However, conventional approaches to mapping traceroute hops to AS numbers are not accurate enough. Address registries are often incomplete and out-of-date. BGP routing tables provide a better IP-to-AS mapping, though this approach has significant limitations as well. Based on our extensive measurements, about 10% of the traceroute paths have one or more hops that do not map to a unique AS number, and around 15% of the traceroute AS paths have an AS loop. In addition, some traceroute AS paths have extra or missing AS hops due to Internet eXchange Points, sibling ASes managed by the same institution, and ASes that do not advertise routes to their infrastructure. Using the BGP tables as a starting point, we propose techniques for improving the IP-to-AS mapping as an important step toward an AS-level traceroute tool. Our algorithms draw on analysis of traceroute probes, reverse DNS lookups, BGP routing tables, and BGP update messages collected from multiple locations. We also discuss how the improved IP-to-AS mapping allows us to home in on cases where the BGP and traceroute AS paths differ for legitimate reasons.
14219803
A new method to measure the semantic similarity of GO terms
MOTIVATION
Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) (http://www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources.


RESULTS
To address this critical need, we proposed a novel method to encode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO graph and, in turn, designed an algorithm to measure the semantic similarity of GO terms. Based on the semantic similarities of GO terms used for gene annotation, we designed a new algorithm to measure the functional similarity of genes. The results of using our algorithm to measure the functional similarities of genes in pathways retrieved from the saccharomyces genome database (SGD), and the outcomes of clustering these genes based on the similarity values obtained by our algorithm are shown to be consistent with human perspectives. Furthermore, we developed a set of online tools for gene similarity measurement and knowledge discovery.


AVAILABILITY
The online tools are available at: http://bioinformatics.clemson.edu/G-SESAME.


SUPPLEMENTARY INFORMATION
http://bioinformatics.clemson.edu/Publication/Supplement/gsp.htm.
550060
Automatic categorization of figures in scientific documents
Figures are very important non-textual information contained in scientific documents. Current digital libraries do not provide users tools to retrieve documents based on the information available within the figures. We propose architecture for retrieving documents by integrating figures and other information. The initial step in enabling integrated document search is to categorize figures into a set of pre-defined types. We propose several categories of figures based on their functionalities in scholarly articles. We have developed a machine-learning-based approach for automatic categorization of figures. Both global features, such as texture, and part features, such as lines, are utilized in the architecture for discriminating among figure categories. The proposed approach has been evaluated on a testbed document set collected from the CiteSeer scientific literature digital library. Experimental evaluation has demonstrated that our algorithms can produce acceptable results for real- world use. Our tools can be integrated into a scientific-document digital library