A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 40-50. Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spin-off from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work and are publicly available. We also apply our methods to real data

A Multi-objective Perspective for Operator Scheduling using Fine-grained DVS Architecture

The stringent power budget of fine grained power managed digital integrated circuits have driven chip designers to optimize power at the cost of area and delay, which were the traditional cost criteria for circuit optimization. The emerging scenario motivates us to revisit the classical operator scheduling problem under the availability of DVFS enabled functional units that can trade-off cycles with power. We study the design space defined due to this trade-off and present a branch-and-bound(B/B) algorithm to explore this state space and report the pareto-optimal front with respect to area and power. The scheduling also aims at maximum resource sharing and is able to attain sufficient area and power gains for complex benchmarks when timing constraints are relaxed by sufficient amount. Experimental results show that the algorithm that operates without any user constraint(area/power) is able to solve the problem for most available benchmarks, and the use of power budget or area budget constraints leads to significant performance gain.Comment: 18 pages, 6 figures, International journal of VLSI design & Communication Systems (VLSICS

Investigating the impact of image content on the energy efficiency of hardware-accelerated digital spatial filters

Battery-operated low-power portable computing devices are becoming an inseparable part of human daily life. One of the major goals is to achieve the longest battery life in such a device. Additionally, the need for performance in processing multimedia content is ever increasing. Processing image and video content consume more power than other applications. A widely used approach to improving energy efficiency is to implement the computationally intensive functions as digital hardware accelerators. Spatial filtering is one of the most commonly used methods of digital image processing. As per the Fourier theory, an image can be considered as a two-dimensional signal that is composed of spatially extended two-dimensional sinusoidal patterns called gratings. Spatial frequency theory states that sinusoidal gratings can be characterised by its spatial frequency, phase, amplitude, and orientation. This article presents results from our investigation into assessing the impact of these characteristics of a digital image on the energy efficiency of hardware-accelerated spatial filters employed to process the same image. Two greyscale images each of size 128 × 128 pixels comprising two-dimensional sinusoidal gratings at maximum spatial frequency of 64 cycles per image orientated at 0° and 90°, respectively, were processed in a hardware implemented Gaussian smoothing filter. The energy efficiency of the filter was compared with the baseline energy efficiency of processing a featureless plain black image. The results show that energy efficiency of the filter drops to 12.5% when the gratings are orientated at 0° whilst rises to 72.38% at 90°

Better Practical Algorithms for rSPR Distance and Hybridization Number

The problem of computing the rSPR distance of two phylogenetic trees (denoted by RDC) is NP-hard and so is the problem of computing the hybridization number of two phylogenetic trees (denoted by HNC). Since they are important problems in phylogenetics, they have been studied extensively in the literature. Indeed, quite a number of exact or approximation algorithms have been designed and implemented for them. In this paper, we design and implement one exact algorithm for HNC and several approximation algorithms for RDC and HNC. Our experimental results show that the resulting exact program is much faster (namely, more than 80 times faster for the easiest dataset used in the experiments) than the previous best and its superiority in speed becomes even more significant for more difficult instances. Moreover, the resulting approximation programs output much better results than the previous bests; indeed, the outputs are always nearly optimal and often optimal. Of particular interest is the usage of the Monte Carlo tree search (MCTS) method in the design of our approximation algorithms. Our experimental results show that with MCTS, we can often solve HNC exactly within short time