2694561
Identifying Approximately Common Substructures in Trees Based on a Restricted Edit Distance
In this paper we present a dynamic programming algorithm for identifying the largest approximately common substructures (LACSs) of two ordered labeled trees. We consider a substructure of a tree T to be a connected subgraph of T. Given two trees T1,T2 and an integer d, the LACS problem is to find a substructure U1 of T1 and a substructure U2 of T2 such that U1 is within distance d of U2 and where there does not exist any other substructure V1 of T1 and V2 of T2 such that V1 and V2 satisfy the distance restriction and the sum of the sizes of V1 and V2 is greater than the sum of the sizes of U1 and U2. The distance measure considered in the paper is a restricted edit distance originated from Selkow. The LACS problem is motivated by the studies of program and document comparison. The proposed algorithm solves the problem in time O(d2×|T1|×|T2|), which is as fast as the best known algorithm for calculating Selkow's distance of two trees when the distance allowed in the common substructures is a constant independent of the input trees.
46369194
Mining Frequent Agreement Subtrees in Phylogenetic Databases
32133517
Information Extraction from the Structured Part of Office Documents
The contents of office documents can be divided into structured and unstructured parts. In this paper, we present a sample-based approach to analyzing a document to form its layout and conceptual structures, and then extracting information from the structured part of the office documents. We represent a document's layout structure as an ordered labeled tree structure using nested segmentation, and its conceptual structure as a set of attribute type pairs. The layout similarities between the document to be processed and samples are identified by employing an approximate tree matching method. The conceptual similarities are identified by analyzing document and sample contents, and by measuring the degree of conceptual closeness. Finally, the information is extracted by instantiating the attributes specified in the conceptual structure based on the result of document structure analysis.
17699044
Automated Discovery of Active Motifs in Multiple RNA Secondary Structures
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in multiple RNA secondary structures. The secondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions/insertions. The proposed method consists of two steps: (1) find candidate motifs in a small sample of the secondary structures; (2) search all of the secondary structures to determine how frequently these motifs occur (within the allowed approximation) in the secondary structures. To reduce the running time, we develop two optimization heuristics based on sampling and pattern matching techniques. Experimental results obtained by running these algorithms on both generated data and RNA secondary structures show the good performance of the algorithms. To demonstrate the utility of our algorithms, we discuss their applications to conducting the phylogenetic study of RNA sequences obtained from GenBank.
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.
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).
31564513
Packing of Unequal Spheres and Automated Radiosurgical Treatment Planning
We study an optimization problem of packing unequal spheres into a three-dimensional (3D) bounded region in connection with radiosurgical treatment planning. Given an input (R, V, S, L), where R is a 3D bounded region, V a positive integer, S a multiset of spheres, and L a location constraint on spheres, we want to find a packing of R using the minimum number of spheres in S such that the covered volume is at least V; the location constraint L is satisfied; and the number of points on the boundary of R that are touched by spheres is maximized. Such a packing arrangement corresponds to an optimal radiosurgical treatment planning. Finding an optimal solution to the problem, however, is computationally intractable. In particular, we show that this optimization problem and several related problems are NP-hard. Hence, some form of approximations is needed. One approach is to consider a simplified problem under the assumption that spheres of arbitrary (integral) diameters are available with unlimited supply, and there are no location constraints. This approach has met with certain success in medical applications using a dynamic programming algorithm (Bourland and Wu, 1996; Wu, 1996). We propose in this paper an improvement to the algorithm that can greatly reduce its computation cost.
206541019
An online self-organizing neuro-fuzzy control for autonomous underwater vehicles
Controlling autonomous underwater vehicles (AUVs) in an uncertain and unstructured environment presents many challenging control problems. Model-based control strategies have been used with limited success. The paper presents an online self-organizing neuro-fuzzy control that serves as a better alternative control scheme in controlling AUVs. The proposed self-organizing neuro-fuzzy controller is a six-layer feedforward neural network that is capable of self-constructing and self-restructuring its internal node connectivity and learning the parameters of each node based on incoming training data. Computer simulations have been conducted to validate the performance of the proposed neuro-fuzzy controller and an experimental verification has been scheduled to verify if on ODIN, an autonomous underwater vehicle developed at the University of Hawaii.
123309619
From fragments to salient closed boundaries: an in-depth study
This paper conducts an in-depth study on a classical perceptual-organization problem: finding salient closed boundaries from a set of boundary fragments detected in a noisy image. In this problem, a saliency boundary is formed by identifying and connecting a subset of fragments according to the simple Gestalt laws of closure, continuity, and proximity. Our specific interest is focused on the methods that aim to achieve boundary closure, an important global property of perceptual salient boundaries. In this paper, we analyze and compare three such methods that are developed in recent years: (a) Elder and Zucker's method based on the shortest-path algorithm, (b) Williams and Thornber's method combining the spectral-analysis and the strongly-connected-component algorithms, and (c) Wang, Kubota, and Siskind's method based on ratio-contour algorithm. Both theoretic analysis and experimental study show that, with a unified setting of fragment saliency, Wang, Kubota and Siskind's method more appropriately constrains the search space for the closed boundaries, and usually produces better performance than or at least comparable performance as the other two methods. Particularly, Wang, Kubota, and Siksind's method can always guarantee the boundary closure and simplicity, which may not be always hold in the other two methods. We construct and collect a variety of synthesized and real images for this comparison.
12016558
Constrained motion control of flexible robot manipulators based on recurrent neural networks
In this paper, a neural network approach is presented for the motion control of constrained flexible manipulators, where both the contact force everted by the flexible manipulator and the position of the end-effector contacting with a surface are controlled. The dynamic equations for vibration of flexible link and constrained force are derived. The developed control, scheme can adaptively estimate the underlying dynamics of the manipulator using recurrent neural networks (RNNs). Based on the error dynamics of a feedback controller, a learning rule for updating the connection weights of the adaptive RNN model is obtained. Local stability properties of the control system are discussed. Simulation results are elaborated on for both position and force trajectory tracking tasks in the presence of varying parameters and unknown dynamics, which show that the designed controller performs remarkably well.
28811627
Recognizing depth-first-search trees in parallel
Consider that T. is a given spanning tree of an undirected graph G which contains a vertices and m (/spl ges/n-1) edges. In this paper, we propose an O(m/p+log m)-time parallel algorithm using p processors on the EREW PRAM model to determine whether T is a depth-first-search tree of G. Our algorithm is optimal in time complexity and speed-up.<<ETX>>