34139794
Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding
The problem of finding conserved motifs given a set of DNA sequences is among the most fundamental problems in computational biology, with important applications in locating regulatory sites from co-expressed genes. Traditionally, two classes of approaches are used to address the problem: sample-driven approaches focus on finding the locations of the motif instances directly, while pattern-driven approaches focus on finding a consensus string or a profile directly to model the motif. We propose an integrated approach by formulating the motif finding problem as the problem of finding large cliques in k-partite graphs, with the additional requirement that there exists a string s (which may not appear in the given sample) that is close to every motif instance included in such a clique. In this formulation, each clique represents the locations of the motif instances, while the existence of string s ensures that these instances are derived from a common motif pattern. The combined approach provides a better formulation to model motifs than using cliques alone, and the use of k-partite graphs allows the development of a fast and exact divide-and-conquer approach to handle the cases when almost every sequence contains a motif instance. Computational experiments show that this approach is feasible even on the most difficult motif finding problems of moderate size. When many sequences do not contain a motif instance, we complement the above approach by an optimized branch-and-bound algorithm that is much faster than standard clique finding approaches. We will discuss how to further generalize the formulation to better model biological reality.
16331940
Optimal Parallel Routing in Star Networks
Star networks have recently been proposed as attractive alternatives to the popular hypercube for interconnecting processors on a parallel computer. In this paper, we present an efficient algorithm that constructs an optimal parallel routing in star networks. Our result improves previous results for the problem.
5242879
Interactive rind modeling
In this paper, we describe a technique, with roots in topological graph theory, that we call rind modeling. It provides for the easy creation of surfaces resembling peeled and punctured rinds. We show how the method's two main steps of: 1) creation of a shell or crust like the rind of an orange, and 2) opening holes in the crust by punching or peeling can be encapsulated into a real time semi-automatic interactive algorithm. We include a number of worked examples, some by students in a first modeling course, that demonstrate the ease with which a large variety of intricate rind shapes can be created.
1021255
A minimal and complete set of operators for the development of robust manifold mesh modelers
In this paper, we identify a minimal and complete set of fundamental operators, which is necessary and sufficient for performing all homeomorphic and topological operations on 2- manifold mesh structures. Efficient algorithms are developed for the implementation of these operators. We also developed a set of powerful, user-friendly, and effective operators at the level of user-interface. Using these operators, we have developed a prototype system for robust, interactive, and user-friendly modeling of orientable 2-manifold meshes. Users of our system can perform a large set of homeomorphic and topological changes with these user-interface level operators. Our system is topologically robust in the sense that users will never create invalid 2-manifold mesh structure with these operators. In our system, the homeomorphic and topological surgery operations can be applied alternatively on 2-manifold meshes. With our system, users can blend surfaces, construct rinds, and open holes on these rind shapes. With our system, the shapes that look like solid, non-manifold, or 2-manifold with boundary can be manipulated. The system also provides automatic texture mapping during topology changes.
2261180
Graph Ear Decompositions and Graph Embeddings
Ear decomposition of a graph has been extensively studied in relation to graph connectivity. In this paper, a connection of ear decomposition to graph embeddings is exhibited. It is shown that constructing a maximum-paired ear decomposition of a graph and constructing a maximum-genus embedding of the graph are polynomial-time equivalent. Applications of this connection are discussed.
31382426
Strong Fault-Tolerance: Parallel Routing in Networks with Faults
A d-regular network G is strongly fault-tolerant if for any copy Gf of G with at most d - 2 faulty nodes, every pair of nonfaulty nodes u and v in Gf admits min{df(u), df (v)} node-disjoint paths in Gf from u to v, where df(u) and df(v) are the degrees of the nodes u and v in Gf. We show that popular network structures, such as hypercube and star networks, are strongly fault-tolerant. We develop efficient algorithms that construct the maximum number of node-disjoint paths of optimal or nearly optimal length in these networks with faulty nodes. Our algorithms are optimal in terms of their running time.
2525582
Shape sensitivity of constructive representations
Most solid models are archived using boundary representations, but they are created, edited, and optimized using high level constructive methods that rely on parameterized Boolean set operations and feature-based techniques. Downstream applications often require optimization of integral-valued performance measures over such models that include volume, mass, and energy properties, as well as more general distributed fields (stress, temperature, etc.). A key computational utility in all such applications is the computation of the sensitivity of the performance measure with respect to the parameters in the solid's construction history.
 We show that for a class of performance measures defined as domain integrals, the sensitivity with respect to a parameter requires integration over a subset of the solid's boundaries that is affected by that parameter. In contrast to earlier methods, the proposed approach for computing sensitivities does not require solid's boundary to remain homeomorphic, and may be used with most types of constructive representations, including CSG and feature-based representations, where the defining Boolean expression may not be known. Simplicity and effectiveness of the proposed technique are illustrated on several common shape optimization problems.
2164421
Generating a configuration space representation for assembly tasks from demonstration
Removing suboptimal actions that can exist in a demonstration is a key problem to be solved in robot programming by demonstration. In this paper we present the first step of an approach for solving this problem. We present how the configuration space (C-space) of a task can be derived from demonstration. A demonstration traces out paths on a number of C-surfaces in C-space. The idea is to use statistical regression analysis on data from these paths to determine the unknown equation parameters of a C-surface. Experimental results show the validity of the approach. Accurate parameter estimates were obtained so long as a sufficiently rich set of demonstrated paths existed on the C-surface. The approach has the advantage that it tends to provide accurate parameter estimates for C-surfaces where they were most needed; that is, for C-surfaces (i) critical to task completion, and (ii) whose paths contained suboptimal actions.
6192242
Computing Maximum-Scoring Segments in Almost Linear Time
Given a sequence, the problem studied in this paper is to find a set of k disjoint continuous subsequences such that the total sum of all elements in the set is maximized. This problem arises naturally in the analysis of DNA sequences. The previous best known algorithm requires Θ(n log n) time in the worst case. For a given sequence of length n, we present an almost linear-time algorithm for this problem. Our algorithm uses a disjoint-set data structure and requires O(nα(n, n)) time in the worst case, where α(n, n) is the inverse Ackermann function.
2426986
Quantifying Privacy Leakage through Answering Database Queries
We assume a database consists of records of individuals with private or sensitive fields. Queries on the distribution of a sensitive field within a selected population in the database can be submitted to the data center. The answers to the queries leak private information of individuals though no identification information is provided. Inspired by decision theory, we present a quantitative model for the privacy protection problem in such a database query or linkage environment in this paper. In the model, the value of information is estimated from the viewpoint of the querier.To estimate the value, we define the information state of the data user by a class of probability distributions on the set of possible confidential values. We further define the usefulness of information based on how easy the data user can locate individuals that fit the description given in the queries. These states and the usefulness of information can be modified and refined by the user's knowledge acquisition actions. The value of information is then defined as the expected gain of the privacy receiver and the privacy is protected by imposing costs on the answers of the queries for balancing the gain.
6316461
Partitioned optimization algorithms for multiple sequence alignment
Multiple sequence alignment is an important and difficult problem in molecular biology and bioinformatics. In this paper, we propose a partitioning approach that significantly improves the solution time and quality by utilizing the locality structure of the problem. The algorithm solves the multiple sequence alignment in three stages. First, an automated and suboptimal partitioning strategy is used to divide the set of sequences into several subsections. Then a multiple sequence alignment algorithm based on ant colony optimization is used to align the sequences of each subsection. Finally, the alignment of original sequences can be obtained by assembling the result of each subsection. The ant colony algorithm is highly optimized in order to avoid local optimal traps and converge to global optimal efficiently. Experimental results show that the algorithm can significantly reduce the running time and improve the solution quality on large-scale multiple sequence alignment benchmarks.