FastJet user manual

FastJet is a C++ package that provides a broad range of jet finding and analysis tools. It includes efficient native implementations of all widely used 2-to-1 sequential recombination jet algorithms for pp and e+e- collisions, as well as access to 3rd party jet algorithms through a plugin mechanism, including all currently used cone algorithms. FastJet also provides means to facilitate the manipulation of jet substructure, including some common boosted heavy-object taggers, as well as tools for estimation of pileup and underlying-event noise levels, determination of jet areas and subtraction or suppression of noise in jets.Comment: 69 pages. FastJet 3 is available from http://fastjet.fr

Partial mixture model for tight clustering of gene expression time-course

Background: Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On the other hand, there has been extensive use of maximum likelihood techniques for model parameter estimation. By contrast, the minimum distance estimator has been largely ignored. Results: In this paper we show the inherent robustness of the minimum distance estimator that makes it a powerful tool for parameter estimation in model-based time-course clustering. To apply minimum distance estimation, a partial mixture model that can naturally incorporate replicate information and allow scattered genes is formulated. We provide experimental results of simulated data fitting, where the minimum distance estimator demonstrates superior performance to the maximum likelihood estimator. Both biological and statistical validations are conducted on a simulated dataset and two real gene expression datasets. Our proposed partial regression clustering algorithm scores top in Gene Ontology driven evaluation, in comparison with four other popular clustering algorithms. Conclusion: For the first time partial mixture model is successfully extended to time-course data analysis. The robustness of our partial regression clustering algorithm proves the suitability of the ombination of both partial mixture model and minimum distance estimator in this field. We show that tight clustering not only is capable to generate more profound understanding of the dataset under study well in accordance to established biological knowledge, but also presents interesting new hypotheses during interpretation of clustering results. In particular, we provide biological evidences that scattered genes can be relevant and are interesting subjects for study, in contrast to prevailing opinion

Modeling and Energy Optimization of LDPC Decoder Circuits with Timing Violations

This paper proposes a "quasi-synchronous" design approach for signal processing circuits, in which timing violations are permitted, but without the need for a hardware compensation mechanism. The case of a low-density parity-check (LDPC) decoder is studied, and a method for accurately modeling the effect of timing violations at a high level of abstraction is presented. The error-correction performance of code ensembles is then evaluated using density evolution while taking into account the effect of timing faults. Following this, several quasi-synchronous LDPC decoder circuits based on the offset min-sum algorithm are optimized, providing a 23%-40% reduction in energy consumption or energy-delay product, while achieving the same performance and occupying the same area as conventional synchronous circuits.Comment: To appear in IEEE Transactions on Communication

Towards automatic Markov reliability modeling of computer architectures

The analysis and evaluation of reliability measures using time-varying Markov models is required for Processor-Memory-Switch (PMS) structures that have competing processes such as standby redundancy and repair, or renewal processes such as transient or intermittent faults. The task of generating these models is tedious and prone to human error due to the large number of states and transitions involved in any reasonable system. Therefore model formulation is a major analysis bottleneck, and model verification is a major validation problem. The general unfamiliarity of computer architects with Markov modeling techniques further increases the necessity of automating the model formulation. This paper presents an overview of the Automated Reliability Modeling (ARM) program, under development at NASA Langley Research Center. ARM will accept as input a description of the PMS interconnection graph, the behavior of the PMS components, the fault-tolerant strategies, and the operational requirements. The output of ARM will be the reliability of availability Markov model formulated for direct use by evaluation programs. The advantages of such an approach are (a) utility to a large class of users, not necessarily expert in reliability analysis, and (b) a lower probability of human error in the computation

Longitudinal image analysis of tumour–healthy brain change in contrast uptake induced by radiation

The work is motivated by a quantitative magnetic resonance imaging study of the differential tumour–healthy tissue change in contrast uptake induced by radiation. The goal is to determine the time in which there is maximal contrast uptake (a surrogate for permeability) in the tumour relative to healthy tissue. A notable feature of the data is its spatial heterogeneity. Zhang and co-workers have discussed two parallel approaches to ‘denoise’ a single image of change in contrast uptake from baseline to one follow-up visit of interest. In this work we extend the image model to explore the longitudinal profile of the tumour–healthy tissue contrast uptake in multiple images over time. We fit a two-stage model. First, we propose a longitudinal image model for each subject. This model simultaneously accounts for the spatial and temporal correlation and denoises the observed images by borrowing strength both across neighbouring pixels and over time. We propose to use the Mann–Whitney U -statistic to summarize the tumour contrast uptake relative to healthy tissue. In the second stage, we fit a population model to the U -statistic and estimate when it achieves its maximum. Our initial findings suggest that the maximal contrast uptake of the tumour core relative to healthy tissue peaks around 3 weeks after initiation of radiotherapy, though this warrants further investigation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79255/1/j.1467-9876.2010.00718.x.pd