Drawing Binary Tanglegrams: An Experimental Evaluation

A binary tanglegram is a pair of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required that the individual trees are drawn crossing-free. A natural optimization problem, denoted tanglegram layout problem, is thus to minimize the number of crossings between inter-tree edges. The tanglegram layout problem is NP-hard and is currently considered both in application domains and theory. In this paper we present an experimental comparison of a recursive algorithm of Buchin et al., our variant of their algorithm, the algorithm hierarchy sort of Holten and van Wijk, and an integer quadratic program that yields optimal solutions.Comment: see http://www.siam.org/proceedings/alenex/2009/alx09_011_nollenburgm.pd

WARP: Wavelets with adaptive recursive partitioning for multi-dimensional data

Effective identification of asymmetric and local features in images and other data observed on multi-dimensional grids plays a critical role in a wide range of applications including biomedical and natural image processing. Moreover, the ever increasing amount of image data, in terms of both the resolution per image and the number of images processed per application, requires algorithms and methods for such applications to be computationally efficient. We develop a new probabilistic framework for multi-dimensional data to overcome these challenges through incorporating data adaptivity into discrete wavelet transforms, thereby allowing them to adapt to the geometric structure of the data while maintaining the linear computational scalability. By exploiting a connection between the local directionality of wavelet transforms and recursive dyadic partitioning on the grid points of the observation, we obtain the desired adaptivity through adding to the traditional Bayesian wavelet regression framework an additional layer of Bayesian modeling on the space of recursive partitions over the grid points. We derive the corresponding inference recipe in the form of a recursive representation of the exact posterior, and develop a class of efficient recursive message passing algorithms for achieving exact Bayesian inference with a computational complexity linear in the resolution and sample size of the images. While our framework is applicable to a range of problems including multi-dimensional signal processing, compression, and structural learning, we illustrate its work and evaluate its performance in the context of 2D and 3D image reconstruction using real images from the ImageNet database. We also apply the framework to analyze a data set from retinal optical coherence tomography

NXNSAttack: Recursive DNS Inefficiencies and Vulnerabilities

This paper exposes a new vulnerability and introduces a corresponding attack, the NoneXistent Name Server Attack (NXNSAttack), that disrupts and may paralyze the DNS system, making it difficult or impossible for Internet users to access websites, web e-mail, online video chats, or any other online resource. The NXNSAttack generates a storm of packets between DNS resolvers and DNS authoritative name servers. The storm is produced by the response of resolvers to unrestricted referral response messages of authoritative name servers. The attack is significantly more destructive than NXDomain attacks (e.g., the Mirai attack): i) It reaches an amplification factor of more than 1620x on the number of packets exchanged by the recursive resolver. ii) In addition to the negative cache, the attack also saturates the 'NS' section of the resolver caches. To mitigate the attack impact, we propose an enhancement to the recursive resolver algorithm, MaxFetch(k), that prevents unnecessary proactive fetches. We implemented the MaxFetch(1) mitigation enhancement on a BIND resolver and tested it on real-world DNS query datasets. Our results show that MaxFetch(1) degrades neither the recursive resolver throughput nor its latency. Following the discovery of the attack, a responsible disclosure procedure was carried out, and several DNS vendors and public providers have issued a CVE and patched their systems

Task mapping on a dragonfly supercomputer

The dragonfly network topology has recently gained traction in the design of high performance computing (HPC) systems and has been implemented in large-scale supercomputers. The impact of task mapping, i.e., placement of MPI ranks onto compute cores, on the communication performance of applications on dragonfly networks has not been comprehensively investigated on real large-scale systems. This paper demonstrates that task mapping affects the communication overhead significantly in dragonflies and the magnitude of this effect is sensitive to the application, job size, and the OpenMP settings. Among the three task mapping algorithms we study (in-order, random, and recursive coordinate bisection), selecting a suitable task mapper reduces application communication time by up to 47%

Bayesian model averaging over tree-based dependence structures for multivariate extremes

Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue we develop a novel statistical algorithm that describes extremal dependence taking advantage of the inherent hierarchical dependence structure of the max-stable nested logistic distribution and that identifies possible clusters of extreme variables using reversible jump Markov chain Monte Carlo techniques. Parsimonious representations are achieved when clusters of extreme variables are found to be completely independent. Moreover, we significantly decrease the computational complexity of full likelihood inference by deriving a recursive formula for the nested logistic model likelihood. The algorithm performance is verified through extensive simulation experiments which also compare different likelihood procedures. The new methodology is used to investigate the dependence relationships between extreme concentration of multiple pollutants in California and how these pollutants are related to extreme weather conditions. Overall, we show that our approach allows for the representation of complex extremal dependence structures and has valid applications in multivariate data analysis, such as air pollution monitoring, where it can guide policymaking