7760234
Automated Discovery of Active Motifs in Three Dimensional Molecules
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in three dimensional (3D) molecules. Each node in a molecule is represented by a 3D point in the Euclidean Space and each edge is represented by an undirected line segment connecting two nodes in the molecule. Motifs are rigid substructures which may occur in a molecule after allowing for an arbitrary number of rotations and translations as well as a small number (specified by the user) of node insert/delete operations in the motifs or the molecule. (We call this "approximate occurrence.") The proposed method combines the geometric hashing technique and block detection algorithms for undirected graphs. To demonstrate the utility of our algorithms, we discuss their applications to classifying three families of molecules pertaining to antibacterial sulfa drugs, anti-anxiety agents (benzodiazepines) and antiadrenergic agents (β receptors). Experimental results indicate the good performance of our algorithms and the high quality of the discovered motife.
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).
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.
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.
2079839
Understanding CHOKe
A recently proposed active queue management, CHOKe, is stateless, simple to implement, yet surprisingly effective in protecting TCP from UDP flows. As UDP rate increases, even though the number of UDP packets in the queue rises, its bandwidth share eventually drops to zero, in stark contrast to the behavior of a regular FIFO buffer. We derive a detailed model of CHOKe that accurately predicts this, and other behaviors of CHOKe, and validate the model with simulations. Its key features are the incorporation of the feedback equilibrium of TCP with dropping probability and the spatial characteristics of the queueing process. CHOKe produces a "leaky buffer" where packets can be dropped as they move toward the head of the queue. This leads to a spatially nonuniform distribution of packets and their velocity, and makes it possible for a flow to simultaneously maintain a large number of packets in the queue and receive a vanishingly small bandwidth share. This is the main mechanism through which CHOKe protects TCP from UDP flows.
17604851
Efficient point coverage in wireless sensor networks
We study minimum-cost sensor placement on a bounded 3D sensing field, R, which comprises a number of discrete points that may or may not be grid points. Suppose we have ℓ types of sensors available with different sensing ranges and different costs. We want to find, given an integer σ ≥ 1, a selection of sensors and a subset of points to place these sensors such that every point in R is covered by at least σ sensors and the total cost of the sensors is minimum. This problem is known to be NP-hard. Let ki denote the maximum number of points that can be covered by a sensor of the ith type. We present in this paper a polynomial-time approximation algorithm for this problem with a proven approximation ratio $${\gamma = \sum_{i=1}^{\ell} k_{i} -\sigma+1}$$. In applications where the distance of any two points has a fixed positive lower bound, each ki is a constant, and so we have a polynomial-time approximation algorithms with a constant guarantee. While γ may be large, we note that it is only a worst-case upper bound. In practice the actual approximation ratio is small, even on randomly generated points that do not have a fixed positive minimum distance between them. We provide a number of numerical results for comparing approximation solutions and optimal solutions, and show that the actual approximation ratios in these examples are all less than 3, even though γ is substantially larger.
39144227
Cursive word reference line detection
This paper proposes a novel method in detecting the four reference lines of a cursive word at any skew angle. The proposed method is rotation independent because the detection is based on points determined by their relative positions between the outer contour of a cursive word and its convex hull. Features like bounding box, contour area, convex hull and furthest points are used in detecting and grouping these points. The reference lines are detected by searching for suitable peaks in the Hough transformation space of these points. Encouraging experimental results have been obtained.
18868983
Mobility-Pattern Based Localization Update Algorithms for Mobile Wireless Sensor Networks
In mobile wireless sensor networks, sensors move in the monitored area at any direction and at any speed. Unlike many other networking hosts, sensor nodes do not have global addresses. Very often they are identified by using a location-based addressing scheme. Therefore, it is important to have the knowledge of the sensor location indicating where the data came from. In this paper, we design three mobility-pattern based localization update algorithms. Specifically, we divide sensor movements into three states, Pause, Linear, and Random. Each state adopts different localization update algorithms. Analytical and simulation results are provided to study the localization cost and location accuracy of the proposed localization-update algorithm in different mobility patterns. The analysis to these results indicates that the localization cost is minimized and the location accuracy is improved.
2380687
Packet classification using multidimensional cutting
This paper introduces a classification algorithm called phHyperCuts. Like the previously best known algorithm, HiCuts, HyperCuts is based on a decision tree structure. Unlike HiCuts, however, in which each node in the decision tree represents a hyperplane, each node in the HyperCuts decision tree represents a k--dimensional hypercube. Using this extra degree of freedom and a new set of heuristics to find optimal hypercubes for a given amount of storage, HyperCuts can provide an order of magnitude improvement over existing classification algorithms. HyperCuts uses 2 to 10 times less memory than HiCuts optimized for memory, while the worst case search time of HyperCuts is 50--500% better than that of HiCuts optimized for speed. Compared with another recent scheme, EGT-PC, HyperCuts uses 1.8--7 times less memory space while the worst case search time is up to 5 times smaller. More importantly, unlike EGT-PC, HyperCuts can be fully pipelined to provide one classification result every packet arrival time, and also allows fast updates.