Efficient algorithm to study interconnected networks

Interconnected networks have been shown to be much more vulnerable to random and targeted failures than isolated ones, raising several interesting questions regarding the identification and mitigation of their risk. The paradigm to address these questions is the percolation model, where the resilience of the system is quantified by the dependence of the size of the largest cluster on the number of failures. Numerically, the major challenge is the identification of this cluster and the calculation of its size. Here, we propose an efficient algorithm to tackle this problem. We show that the algorithm scales as O(N log N), where N is the number of nodes in the network, a significant improvement compared to O(N^2) for a greedy algorithm, what permits studying much larger networks. Our new strategy can be applied to any network topology and distribution of interdependencies, as well as any sequence of failures.Comment: 5 pages, 6 figure

Detection of Complex Networks Modularity by Dynamical Clustering

Based on cluster de-synchronization properties of phase oscillators, we introduce an efficient method for the detection and identification of modules in complex networks. The performance of the algorithm is tested on computer generated and real-world networks whose modular structure is already known or has been studied by means of other methods. The algorithm attains a high level of precision, especially when the modular units are very mixed and hardly detectable by the other methods, with a computational effort ${\cal O}(KN)$ on a generic graph with $N$ nodes and $K$ links.Comment: 5 pages, 2 figures. Version accepted for publication on PRE Rapid Communications: figures changed and text adde

An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

Learning Personalized Models with Clustered System Identification

We address the problem of learning linear system models from observing multiple trajectories from different system dynamics. This framework encompasses a collaborative scenario where several systems seeking to estimate their dynamics are partitioned into clusters according to their system similarity. Thus, the systems within the same cluster can benefit from the observations made by the others. Considering this framework, we present an algorithm where each system alternately estimates its cluster identity and performs an estimation of its dynamics. This is then aggregated to update the model of each cluster. We show that under mild assumptions, our algorithm correctly estimates the cluster identities and achieves an approximate sample complexity that scales inversely with the number of systems in the cluster, thus facilitating a more efficient and personalized system identification process

A Holistic Methodology for Improved RFID Network Lifetime by Advanced Cluster Head Selection using Dragonfly Algorithm

Radio Frequency Identification (RFID) networks usually require many tags along with readers and computation facilities. Those networks have limitations with respect to computing power and energy consumption. Thus, for saving energy and to make the best use of the resources, networks should operate and be able to recover in an efficient way. This will also reduce the energy expenditure of RFID readers. In this work, the RFID network life span will be enlarged through an energy-efficient cluster-based protocol used together with the Dragonfly algorithm. There are two stages in the processing of the clustering system: the cluster formation from the whole structure and the election of a cluster leader. After completing those procedures, the cluster leader controls the other nodes that are not leaders. The system works with a large energy node that provides an amount of energy while transmitting aggregated data near a base station

Particle identification with the cluster counting technique for the IDEA drift chamber

IDEA (Innovative Detector for an Electron-positron Accelerator) is a general-purpose detector concept, designed to study electron-positron collisions in a wide energy range from a very large circular leptonic collider. Its drift chamber is designed to provide an efficient tracking, a high precision momentum measurement and an excellent particle identification by exploiting the application of the cluster counting technique. To investigate the potential of the cluster counting techniques on physics events, a simulation of the ionization clusters generation is needed, therefore we developed an algorithm which can use the energy deposit information provided by Geant4 toolkit to reproduce, in a fast and convenient way, the clusters number distribution and the cluster size distribution. The results obtained confirm that the cluster counting technique allows to reach a resolution 2 times better than the traditional dE/dx method. A beam test has been performed during November 2021 at CERN on the H8 to validate the simulations results, to define the limiting effects for a fully efficient cluster counting and to count the number of electron clusters released by an ionizing track at a fixed $\beta\gamma$ as a function of the track angle. The simulation and the beam test results will be described briefly in this issue.Comment: 2 pages, 4 figures, Proceedings of: PM202

Connected component identification and cluster update on GPU

Cluster identification tasks occur in a multitude of contexts in physics and engineering such as, for instance, cluster algorithms for simulating spin models, percolation simulations, segmentation problems in image processing, or network analysis. While it has been shown that graphics processing units (GPUs) can result in speedups of two to three orders of magnitude as compared to serial codes on CPUs for the case of local and thus naturally parallelized problems such as single-spin flip update simulations of spin models, the situation is considerably more complicated for the non-local problem of cluster or connected component identification. I discuss the suitability of different approaches of parallelization of cluster labeling and cluster update algorithms for calculations on GPU and compare to the performance of serial implementations.Comment: 15 pages, 14 figures, one table, submitted to PR

GARLIC: GAmma Reconstruction at a LInear Collider experiment

The precise measurement of hadronic jet energy is crucial to maximise the physics reach of a future Linear Collider. An important ingredient required to achieve this is the efficient identification of photons within hadronic showers. One configuration of the ILD detector concept employs a highly granular silicon-tungsten sampling calorimeter to identify and measure photons, and the GARLIC algorithm described in this paper has been developed to identify photons in such a calorimeter. We describe the algorithm and characterise its performance using events fully simulated in a model of the ILD detector

Multimodal nested sampling: an efficient and robust alternative to MCMC methods for astronomical data analysis

In performing a Bayesian analysis of astronomical data, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multimodal or exhibit pronounced (curving) degeneracies, which can cause problems for traditional MCMC sampling methods. Second, in selecting between a set of competing models, calculation of the Bayesian evidence for each model is computationally expensive. The nested sampling method introduced by Skilling (2004), has greatly reduced the computational expense of calculating evidences and also produces posterior inferences as a by-product. This method has been applied successfully in cosmological applications by Mukherjee et al. (2006), but their implementation was efficient only for unimodal distributions without pronounced degeneracies. Shaw et al. (2007), recently introduced a clustered nested sampling method which is significantly more efficient in sampling from multimodal posteriors and also determines the expectation and variance of the final evidence from a single run of the algorithm, hence providing a further increase in efficiency. In this paper, we build on the work of Shaw et al. and present three new methods for sampling and evidence evaluation from distributions that may contain multiple modes and significant degeneracies; we also present an even more efficient technique for estimating the uncertainty on the evaluated evidence. These methods lead to a further substantial improvement in sampling efficiency and robustness, and are applied to toy problems to demonstrate the accuracy and economy of the evidence calculation and parameter estimation. Finally, we discuss the use of these methods in performing Bayesian object detection in astronomical datasets.Comment: 14 pages, 11 figures, submitted to MNRAS, some major additions to the previous version in response to the referee's comment