Visualization of Geometric Spanner Algorithms

It is easier to understand an algorithm when it can be seen in interactive mode. The current study implemented four algorithms to construct geometric spanners; the path-greedy, gap-greedy, Theta-graph and Yao-graph algorithms. The data structure visualization framework (http://www.cs.usfca.edu/~galles/visualization/) developed by David Galles was used. Two features were added to allow its use in spanner algorithm visualization: support point-based algorithms and export of the output to Ipe drawing software format. The interactive animations in the framework make steps of visualization beautiful and media controls are available to manage the animations. Visualization does not require extensions to be installed on the web browser. It is available at http://cs.yazd.ac.ir/cgalg/AlgsVis/

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can computationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important. In this article, we present a spatio-temporal mining approach to analyze protein folding trajectories. It exploits the simplicity of contact maps, while also integrating 3D structural information in the analysis. It characterizes the dynamic folding process by first identifying spatio-temporal association patterns in contact maps, then studying how such patterns evolve along a folding trajectory. We demonstrate that such patterns can be leveraged to summarize folding trajectories, and to facilitate the detection and ordering of important folding events along a folding path. We also show that such patterns can be used to identify a consensus partial folding pathway across multiple folding trajectories. Furthermore, we argue that such patterns can capture both local and global structural topology in a 3D protein conformation, thereby facilitating effective structural comparison amongst conformations. We apply this approach to analyze the folding trajectories of two small synthetic proteins-BBA5 and GSGS (or Beta3S). We show that this approach is promising towards addressing the above issues, namely, folding trajectory summarization, folding events detection and ordering, and consensus partial folding pathway identification across trajectories

Exploration of graphs with excluded minors

We study the online graph exploration problem proposed by Kalyanasundaram and Pruhs (1994) and prove a constant competitive ratio on minor-free graphs. This result encompasses and significantly extends the graph classes that were previously known to admit a constant competitive ratio. The main ingredient of our proof is that we find a connection between the performance of the particular exploration algorithm Blocking and the existence of light spanners. Conversely, we exploit this connection to construct light spanners of bounded genus graphs. In particular, we achieve a lightness that improves on the best known upper bound for genus g>0 and recovers the known tight bound for the planar case (g=0).Comment: to appear at ESA 202

Exploration of Graphs with Excluded Minors

We study the online graph exploration problem proposed by Kalyanasundaram and Pruhs (1994) and prove a constant competitive ratio on minor-free graphs. This result encompasses and significantly extends the graph classes that were previously known to admit a constant competitive ratio. The main ingredient of our proof is that we find a connection between the performance of the particular exploration algorithm Blocking and the existence of light spanners. Conversely, we exploit this connection to construct light spanners of bounded genus graphs. In particular, we achieve a lightness that improves on the best known upper bound for genus g ? 1 and recovers the known tight bound for the planar case (g = 0)

A soft kinetic data structure for lesion border detection

Motivation: The medical imaging and image processing techniques, ranging from microscopic to macroscopic, has become one of the main components of diagnostic procedures to assist dermatologists in their medical decision-making processes. Computer-aided segmentation and border detection on dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermoscopic images have become an important research field mainly because of inter- and intra-observer variations in human interpretations. In this study, a novel approach—graph spanner—for automatic border detection in dermoscopic images is proposed. In this approach, a proximity graph representation of dermoscopic images in order to detect regions and borders in skin lesion is presented

The Role of Mutations in Protein Structural Dynamics and Function: A Multi-scale Computational Approach

abstract: Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.Dissertation/ThesisPh.D. Physics 201

Computing the greedy spanner in near-quadratic time

It is well-known that the greedy algorithm produces high quality spanners and therefore is used in several applications. However, for points in d-dimensional Euclidean space, the greedy algorithm has cubic running time. In this paper we present an algorithm that computes the greedy spanner (spanner computed by the greedy algorithm) for a set of n points from a metric space with bounded doubling dimension in time using space. Since the lower bound for computing such spanners is Ω(n 2), the time complexity of our algorithm is optimal to within a logarithmic factor

Near-Optimal Motion Planning Algorithms Via A Topological and Geometric Perspective

Motion planning is a fundamental problem in robotics, which involves finding a path for an autonomous system, such as a robot, from a given source to a destination while avoiding collisions with obstacles. The properties of the planning space heavily influence the performance of existing motion planning algorithms, which can pose significant challenges in handling complex regions, such as narrow passages or cluttered environments, even for simple objects. The problem of motion planning becomes deterministic if the details of the space are fully known, which is often difficult to achieve in constantly changing environments. Sampling-based algorithms are widely used among motion planning paradigms because they capture the topology of space into a roadmap. These planners have successfully solved high-dimensional planning problems with a probabilistic-complete guarantee, i.e., it guarantees to find a path if one exists as the number of vertices goes to infinity. Despite their progress, these methods have failed to optimize the sub-region information of the environment for reuse by other planners. This results in re-planning overhead at each execution, affecting the performance complexity for computation time and memory space usage. In this research, we address the problem by focusing on the theoretical foundation of the algorithmic approach that leverages the strengths of sampling-based motion planners and the Topological Data Analysis methods to extract intricate properties of the environment. The work contributes a novel algorithm to overcome the performance shortcomings of existing motion planners by capturing and preserving the essential topological and geometric features to generate a homotopy-equivalent roadmap of the environment. This roadmap provides a mathematically rich representation of the environment, including an approximate measure of the collision-free space. In addition, the roadmap graph vertices sampled close to the obstacles exhibit advantages when navigating through narrow passages and cluttered environments, making obstacle-avoidance path planning significantly more efficient. The application of the proposed algorithms solves motion planning problems, such as sub-optimal planning, diverse path planning, and fault-tolerant planning, by demonstrating the improvement in computational performance and path quality. Furthermore, we explore the potential of these algorithms in solving computational biology problems, particularly in finding optimal binding positions for protein-ligand or protein-protein interactions. Overall, our work contributes a new way to classify routes in higher dimensional space and shows promising results for high-dimensional robots, such as articulated linkage robots. The findings of this research provide a comprehensive solution to motion planning problems and offer a new perspective on solving computational biology problems

Collaborative Motion Planning

Planning motion is an essential component for any autonomous robotic system. An intelligent agent must be able to efficiently plan collision-free paths in order to move through its world. Despite its importance, this problem is PSPACE-Hard which means that even planning motions for simple robots is computationally difficult. State-of-the-art approaches trade completeness (always able to provide a solution if one exists or report none exists) for probabilistic completeness (probabilistically guaranteed to find a solution if one exists but cannot report if none exists) and improved efficiency. These methods use sampling-based techniques to design a sequence of motions for the robot. However, as these methods are random in nature, the probability of their success is directly related to the expansiveness, or openness, of the underlying planning space. In other words, narrow passages, complex systems, and various constraints make planning with these methods difficult. On the other hand, humans can often determine approximate solutions for these difficult solutions quickly. In this research, we explore user-guided planning in which a human operator works together with a sampling-based motion planner. By having a human-in-the-loop, a human can steer a sampling-based planner towards a solution. This strategy can provide benefits to many applications such as computer-aided design and virtual prototyping, to name a few. We begin by classifying and creating simple models of common user-guided and heuristic-guided motion planning methods. Our models encompass three forms of user input: configuration-based, path-based, and region-based input. We compare and contrast these approaches and motivate our choice of a region-based collaborative framework. Through this analysis, we gain insight into user-guided planning and further motivate methods that harness low interface complexity and work entirely in workspace, which is most natural to a human operator. Further, we extend the theory of expansiveness to analyze the various types of user inputs. Our novel region-based collaboration framework takes advantage of human intuition by allowing a user to define regions in the workspace to bias and/or constrain the search space of a sampling-based motion planner. This approach allows a user to bias a high dimensional search with low dimensional input, supports intermittent user hints, and empowers a user to customize motion solutions. Finally, we extend region steering to both non-holonomic robotic systems and a human-inspired approach to motion planning. Our results show that this region-based framework can aid many variants of sampling-based planning, reduce computation time, support solution customization, and can be used to develop advanced heuristic methods for solving motion planning problems. We provide experiments exemplifying our approach in planning motions for complex robotic applications such as mobile manipulators, car-like, and free-flying robots