Geodesic Paths On 3D Surfaces: Survey and Open Problems

This survey gives a brief overview of theoretically and practically relevant algorithms to compute geodesic paths and distances on three-dimensional surfaces. The survey focuses on polyhedral three-dimensional surfaces

The space of ultrametric phylogenetic trees

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.Comment: Minor changes. This version has been published in JTB. 27 pages, 9 figure

Articular human joint modelling

Copyright @ Cambridge University Press 2009.The work reported in this paper encapsulates the theories and algorithms developed to drive the core analysis modules of the software which has been developed to model a musculoskeletal structure of anatomic joints. Due to local bone surface and contact geometry based joint kinematics, newly developed algorithms make the proposed modeller different from currently available modellers. There are many modellers that are capable of modelling gross human body motion. Nevertheless, none of the available modellers offer complete elements of joint modelling. It appears that joint modelling is an extension of their core analysis capability, which, in every case, appears to be musculoskeletal motion dynamics. It is felt that an analysis framework that is focused on human joints would have significant benefit and potential to be used in many orthopaedic applications. The local mobility of joints has a significant influence in human motion analysis, in understanding of joint loading, tissue behaviour and contact forces. However, in order to develop a bone surface based joint modeller, there are a number of major problems, from tissue idealizations to surface geometry discretization and non-linear motion analysis. This paper presents the following: (a) The physical deformation of biological tissues as linear or non-linear viscoelastic deformation, based on spring-dashpot elements. (b) The linear dynamic multibody modelling, where the linear formulation is established for small motions and is particularly useful for calculating the equilibrium position of the joint. This model can also be used for finding small motion behaviour or loading under static conditions. It also has the potential of quantifying the joint laxity. (c) The non-linear dynamic multibody modelling, where a non-matrix and algorithmic formulation is presented. The approach allows handling complex material and geometrical nonlinearity easily. (d) Shortest path algorithms for calculating soft tissue line of action geometries. The developed algorithms are based on calculating minimum ‘surface mass’ and ‘surface covariance’. An improved version of the ‘surface covariance’ algorithm is described as ‘residual covariance’. The resulting path is used to establish the direction of forces and moments acting on joints. This information is needed for linear or non-linear treatment of the joint motion. (e) The final contribution of the paper is the treatment of the collision. In the virtual world, the difficulty in analysing bodies in motion arises due to body interpenetrations. The collision algorithm proposed in the paper involves finding the shortest projected ray from one body to the other. The projection of the body is determined by the resultant forces acting on it due to soft tissue connections under tension. This enables the calculation of collision condition of non-convex objects accurately. After the initial collision detection, the analysis involves attaching special springs (stiffness only normal to the surfaces) at the ‘potentially colliding points’ and motion of bodies is recalculated. The collision algorithm incorporates the rotation as well as translation. The algorithm continues until the joint equilibrium is achieved. Finally, the results obtained based on the software are compared with experimental results obtained using cadaveric joints

Exact algorithms for the order picking problem

Order picking is the problem of collecting a set of products in a warehouse in a minimum amount of time. It is currently a major bottleneck in supply-chain because of its cost in time and labor force. This article presents two exact and effective algorithms for this problem. Firstly, a sparse formulation in mixed-integer programming is strengthened by preprocessing and valid inequalities. Secondly, a dynamic programming approach generalizing known algorithms for two or three cross-aisles is proposed and evaluated experimentally. Performances of these algorithms are reported and compared with the Traveling Salesman Problem (TSP) solver Concorde

Physical Simulation of Inarticulate Robots

In this note we study the structure and the behavior of inarticulate robots. We introduce a robot that moves by successive revolvings. The robot's structure is analyzed, simulated and discussed in detail

Robust network design under polyhedral traffic uncertainty

Ankara : The Department of Industrial Engineering and The Institute of Engineering and Science of Bilkent Univ., 2007.Thesis (Ph.D.) -- Bilkent University, 2007.Includes bibliographical references leaves 160-166.In this thesis, we study the design of networks robust to changes in demand estimates. We consider the case where the set of feasible demands is defined by an arbitrary polyhedron. Our motivation is to determine link capacity or routing configurations, which remain feasible for any realization in the corresponding demand polyhedron. We consider three well-known problems under polyhedral demand uncertainty all of which are posed as semi-infinite mixed integer programming problems. We develop explicit, compact formulations for all three problems as well as alternative formulations and exact solution methods. The first problem arises in the Virtual Private Network (VPN) design field. We present compact linear mixed-integer programming formulations for the problem with the classical hose traffic model and for a new, less conservative, robust variant relying on accessible traffic statistics. Although we can solve these formulations for medium-to-large instances in reasonable times using off-the-shelf MIP solvers, we develop a combined branch-and-price and cutting plane algorithm to handle larger instances. We also provide an extensive discussion of our numerical results. Next, we study the Open Shortest Path First (OSPF) routing enhanced with traffic engineering tools under general demand uncertainty with the motivation to discuss if OSPF could be made comparable to the general unconstrained routing (MPLS) when it is provided with a less restrictive operating environment. To the best of our knowledge, these two routing mechanisms are compared for the first time under such a general setting. We provide compact formulations for both routing types and show that MPLS routing for polyhedral demands can be computed in polynomial time. Moreover, we present a specialized branchand-price algorithm strengthened with the inclusion of cuts as an exact solution tool. Subsequently, we compare the new and more flexible OSPF routing with MPLS as well as the traditional OSPF on several network instances. We observe that the management tools we use in OSPF make it significantly better than the generic OSPF. Moreover, we show that OSPF performance can get closer to that of MPLS in some cases. Finally, we consider the Network Loading Problem (NLP) under a polyhedral uncertainty description of traffic demands. After giving a compact multicommodity formulation of the problem, we prove an unexpected decomposition property obtained from projecting out the flow variables, considerably simplifying the resulting polyhedral analysis and computations by doing away with metric inequalities, an attendant feature of most successful algorithms on NLP. Under the hose model of feasible demands, we study the polyhedral aspects of NLP, used as the basis of an efficient branch-and-cut algorithm supported by a simple heuristic for generating upper bounds. We provide the results of extensive computational experiments on well-known network design instances.Altın, AyşegülPh.D

Continuous Alternation: The Complexity of Pursuit in Continuous Domains

Complexity theory has used a game-theoretic notion, namely alternation, to great advantage in modeling parallelism and in obtaining lower bounds. The usual definition of alternation requires that transitions be made in discrete steps. The study of differential games is a classic area of optimal control, where there is continuous interaction and alternation between the players. Differential games capture many aspects of control theory and optimal control over continuous domains. In this paper, we define a generalization of the notion of alternation which applies to differential games, and which we call "continuous alternation." This approach allows us to obtain the first known complexity-theoretic results for open problems in differential games and optimal control. We concentrate our investigation on an important class of differential games, which we call polyhedral pursuit games. Pursuit games have application to many fundamental problems in autonomous robot control in the presence of an adversary. For example, this problem occurs in manufacturing environments with a single robot moving among a number of autonomous robots with unknown control programs, as well as in automatic automobile control, and collision control among aircraft and boats with unknown or adversary control. We show that in a three-dimensional pursuit game where each player's velocity is bounded (but there is no bound on acceleration), the pursuit game decision problem is hard for exponential time. This lower bound is somewhat surprising due to the sparse nature of the problem: there are only two moving objects (the players), each with only three degrees of freedom. It is also the first provably intractable result for any robotic problem with complete information; previous intractability results have relied on complexity-theoretic assumptions. Fortunately, we can counter our somewhat pessimistic lower bounds with polynomial time upper bounds for obtaining approximate solutions. In particular, we give polynomial time algorithms that approximately solve a very large class of pursuit games with arbitrarily small error. For e > 0, this algorithm finds a winning strategy for the evader provided that there is a winning strategy that always stays at least E distance from the pursuer and all obstacles. If the obstacles are described with n bits, then the algorithm runs in time (n/e)0(1), and applies to several types of pursuit games: either velocity or both acceleration and velocity may be bounded, and the bound may be of either the L2- or L&infin-norm. Our algorithms also generalize to when the obstacles have constant degree algebraic descriptions, and are allowed to have predictable movement