Using consistent subcuts for detecting stable properties

We present a general protocol for detecting whether a property holds in a distributed system, where the property is a member of a subclass of stable properties we call the locally stable properties. Our protocol is based on a decentralized method for constructing a maximal subset of the local states that are mutually consistent, which in turn is based on a weakened version of vectored time stamps. The structure of our protocol lends itself to refinement, and we demonstrate its utility by deriving some specialized property-detection protocols, including two previously known protocols that are known to be effective

Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

The derivation of distributed termination detection algorithms from garbage collection schemes

It is shown that the termination detection problem for distributed computations can be modelled as an instance of the garbage collection problem. Consequently, algorithms for the termination detection problem are obtained by applying transformations to garbage collection algorithms. The transformation can be applied to collectors of the "mark-and-sweep" type as well as to reference counting garbage collectors. As examples, the scheme is used to transform the distributed reference counting protocol of Lermen and Maurer, the weighted reference counting protocol, the local reference counting protocol, and Ben-Ari's mark-and-sweep collector into termination detection algorithms. Known termination detection algorithms as well as new variants are obtained

Distributed Object Tracking Using a Cluster-Based Kalman Filter in Wireless Camera Networks

Local data aggregation is an effective means to save sensor node energy and prolong the lifespan of wireless sensor networks. However, when a sensor network is used to track moving objects, the task of local data aggregation in the network presents a new set of challenges, such as the necessity to estimate, usually in real time, the constantly changing state of the target based on information acquired by the nodes at different time instants. To address these issues, we propose a distributed object tracking system which employs a cluster-based Kalman filter in a network of wireless cameras. When a target is detected, cameras that can observe the same target interact with one another to form a cluster and elect a cluster head. Local measurements of the target acquired by members of the cluster are sent to the cluster head, which then estimates the target position via Kalman filtering and periodically transmits this information to a base station. The underlying clustering protocol allows the current state and uncertainty of the target position to be easily handed off among clusters as the object is being tracked. This allows Kalman filter-based object tracking to be carried out in a distributed manner. An extended Kalman filter is necessary since measurements acquired by the cameras are related to the actual position of the target by nonlinear transformations. In addition, in order to take into consideration the time uncertainty in the measurements acquired by the different cameras, it is necessary to introduce nonlinearity in the system dynamics. Our object tracking protocol requires the transmission of significantly fewer messages than a centralized tracker that naively transmits all of the local measurements to the base station. It is also more accurate than a decentralized tracker that employs linear interpolation for local data aggregation. Besides, the protocol is able to perform real-time estimation because our implementation takes into consideration the sparsit- - y of the matrices involved in the problem. The experimental results show that our distributed object tracking protocol is able to achieve tracking accuracy comparable to the centralized tracking method, while requiring a significantly smaller number of message transmissions in the network

Arcfinder: An algorithm for the automatic detection of gravitational arcs

We present an efficient algorithm designed for and capable of detecting elongated, thin features such as lines and curves in astronomical images, and its application to the automatic detection of gravitational arcs. The algorithm is sufficiently robust to detect such features even if their surface brightness is near the pixel noise in the image, yet the amount of spurious detections is low. The algorithm subdivides the image into a grid of overlapping cells which are iteratively shifted towards a local centre of brightness in their immediate neighbourhood. It then computes the ellipticity for each cell, and combines cells with correlated ellipticities into objects. These are combined to graphs in a next step, which are then further processed to determine properties of the detected objects. We demonstrate the operation and the efficiency of the algorithm applying it to HST images of galaxy clusters known to contain gravitational arcs. The algorithm completes the analysis of an image with 3000x3000 pixels in about 4 seconds on an ordinary desktop PC. We discuss further applications, the method's remaining problems and possible approaches to their solution.Comment: 12 pages, 12 figure

A Parallelized Implementation of Cut-and-Solve and a Streamlined Mixed-Integer Linear Programming Model for Finding Genetic Patterns Optimally Associated with Complex Diseases

With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as late-onset Alzheimer’s disease (AD), but it has been a challenge to fully uncover the necessary information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases does not involve single markers working alone, but patterns of genetic markers interacting additively or epistatically. But as we move upwards beyond patterns of size two, it quickly becomes computationally infeasible to examine all combinations in the solution space. A common solution to solving this type of combinatorial optimization problem is to model it as a mixed-integer linear program (MIP) and solve it using the algorithm branch-and-cut, implemented by a commercial solver. However, with the trend of using increasing numbers of computing cores to increase computational power, there is a need for a different approach to solving MIPs that can utilize parallel environments. Here we show how a parallelized implementation of an alternative algorithm, cut-and-solve, can be used to solve this genetics problem faster than CPLEX, one of the leading commercial MIP solvers

GPU Acceleration of ADMM for Large-Scale Quadratic Programming

The alternating direction method of multipliers (ADMM) is a powerful operator splitting technique for solving structured convex optimization problems. Due to its relatively low per-iteration computational cost and ability to exploit sparsity in the problem data, it is particularly suitable for large-scale optimization. However, the method may still take prohibitively long to compute solutions to very large problem instances. Although ADMM is known to be parallelizable, this feature is rarely exploited in real implementations. In this paper we exploit the parallel computing architecture of a graphics processing unit (GPU) to accelerate ADMM. We build our solver on top of OSQP, a state-of-the-art implementation of ADMM for quadratic programming. Our open-source CUDA C implementation has been tested on many large-scale problems and was shown to be up to two orders of magnitude faster than the CPU implementation

Automated Verification of Asynchronous Communicating Systems with TLA+

Verifying the compatibility of communicating peers is a crucial issue in critical distributed systems. Unlike the synchronous world, the asynchronous world covers a wide range of message ordering paradigms (e.g. FIFO or causal) that are instrumental to the compatibility of peer compositions. We propose a framework that takes into account the variety of asynchronous communication models and compatibility properties. The notions of peer, communication model, system and compatibility criteria are formalized in TLA+ to benefit from its verification tools. We present an implemented toolchain that generates TLA+ specifications from the behavioral descriptions of peers and checks compatibility of the composition with respect to given communication models and compatibility criteria