16171801
Regular Mesh Construction Algorithms using Regular Handles
This paper presents our recent theoretical results on high genus modeling. We introduce a new concept called regular handles. Using regular handles it is possible to increase genus without increasing the number of vertices. Using regular handles a wide variety of mesh structures can be constructed. One of the usages of regular handles is to construct families of regular meshes, which is useful to create a wide variety of high genus mesh structures
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.
3146463
On Strong Menger-Connectivity of Star Graphs
Motivated by parallel routing in networks with faults, we study the following graph theoretical problem. Let G be a d-regular graph. We say that G is strongly Menger-connected if for any copy Gf of G with at most d - 2 nodes removed, every pair of nodes u and v in Gf are connected by min{deg f(u), deg f(v)} node-disjoint paths in Gf, where deg f(u) and deg f(v) are the degrees of the nodes u and v in Gf, respectively. We show that the star graphs, which are a recently proposed attractive alternative to the widely used hypercubes as network models, are strongly Menger-connected. An algorithm of optimal running time is developed that constructs the maximum number of node-disjoint paths of nearly optimal length in star graphs with faults.
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.
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.
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.
12471299
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
MOTIVATION
Small molecules play a fundamental role in organic chemistry and biology. They can be used to probe biological systems and to discover new drugs and other useful compounds. As increasing numbers of large datasets of small molecules become available, it is necessary to develop computational methods that can deal with molecules of variable size and structure and predict their physical, chemical and biological properties.


RESULTS
Here we develop several new classes of kernels for small molecules using their 1D, 2D and 3D representations. In 1D, we consider string kernels based on SMILES strings. In 2D, we introduce several similarity kernels based on conventional or generalized fingerprints. Generalized fingerprints are derived by counting in different ways subpaths contained in the graph of bonds, using depth-first searches. In 3D, we consider similarity measures between histograms of pairwise distances between atom classes. These kernels can be computed efficiently and are applied to problems of classification and prediction of mutagenicity, toxicity and anti-cancer activity on three publicly available datasets. The results derived using cross-validation methods are state-of-the-art. Tradeoffs between various kernels are briefly discussed.


AVAILABILITY
Datasets available from http://www.igb.uci.edu/servers/servers.html
8059419
Asymptotic analysis of MIMO wireless systems with spatial correlation at the receiver
With a unified approach, this paper investigates the asymptotic performance or, equivalently, the large-system properties, of various point-to-point systems with antenna-array-based multiple-input multiple-output (MIMO) channels having spatial correlations. Using the replica method originally developed for statistical physics, we provide analytical solutions to the input-output mutual information of MIMO systems: 1) at the transmit side, with arbitrary inputs, and 2) at the receive side, with either the optimum space-time joint decoding or various suboptimum spatial equalizers followed by a bank of temporal decoders. Important physical meanings revealed though the analytical solutions to those more practical combinations, such as how the input-output mutual information is affected by the channel spatial correlations, are highlighted along our derivation. Moreover, we provide a novel waterfilling algorithm to determine the data-rate-maximizing transmit signal covariance matrix when only the channel long-term spatial correlations are available at the transmitter.
6798576
Locational pricing and scheduling for an integrated energy-reserve market
It is well known that given a network that can become constrained on voltage or real power flows, reserves must also be spatially located in order to handle all credible contingencies. However, to date, there is no credible science-based method for assigning and pricing reserves in this way. Presented in this paper is a new scheduling algorithm incorporating constraints imposed by grid security considerations, which include one base case (intact system) and a list of possible contingencies (line-out, unit-lost, and load-growth) of the system. By following a cost-minimizing co-optimization procedure, both power and reserve are allocated spatially for the combined energy and reserve markets. With the Lagrange multipliers (dual variables) obtained, the scheduling algorithm also reveals the locational shadow prices for the reserve and energy requirements. Unlike other pricing and scheduling methods in use, which are usually ad-hoc and are based on engineering judgment and experience, this proposed formulation is likely to perform better in restructured markets when market power is a potential problem. An illustrative example of a modified IEEE 30-bus system is used to introduce concepts and present results.
33412733
Learning a Hidden Graph Using O(log n) Queries Per Edge
We consider the problem of learning a general graph using edge-detecting queries. In this model, the learner may query whether a set of vertices induces an edge of the hidden graph. This model has been studied for particular classes of graphs by Kucherov and Grebinski [1] and Alon et al.[2], motivated by problems arising in genome sequencing. We give an adaptive deterministic algorithm that learns a general graph with n vertices and m edges using O(m log n) queries, which is tight up to a constant factor for classes of non-dense graphs. Allowing randomness, we give a 5-round Las Vegas algorithm using \(O(m {\rm log}n+\sqrt{m}{\rm log}^{2}n)\) queries in expectation. We give a lower bound of Ω((2m/r) r/2) for learning the class of non-uniform hypergraphs of dimension r with m edges. For the class of r-uniform hypergraphs with bounded degree d, where d≤ n 1/( r− − 1)/(2r 1 + 2/( r− − 1)), we give a non-adaptive Monte Carlo algorithm using O(dnlog n) queries, which succeeds with probability at least 1–n − − c, where c is any constant.
8876890
Overlay mesh construction using interleaved spanning trees
In this paper we evaluate a method of using interleaved spanning trees to compose a resilient, high performance overlay mesh. Though spanning trees of arbitrary type could be used to construct an overlay mesh, we focus on a distributed algorithm that computes k minimum spanning trees on an arbitrary graph. The principal motivation behind this strategy is to provide applications with a k-redundant, high quality mesh suitable for demanding applications like A/V broadcast, video conferencing, data collection, multi-path routing, and file mirroring/transfer. We elaborate details of k-MST, pointing out advantages and potential problem points of the protocol, and then analyze its performance using a variety of metrics with simulation as well as a functional PlanetLab implementation.