Neural Filters for Jet Analysis

We study the efficiency of a neural-net filter and deconvolution method for estimating jet energies and spectra in high-background reactions such as nuclear collisions at the relativistic heavy-ion collider and the large hadron collider. The optimal network is shown to be surprisingly close but not identical to a linear high-pass filter. A suitably constrained deconvolution method is shown to uncover accurately the underlying jet distribution in spite of the broad network response. Finally, we show that possible changes of the jet spectrum in nuclear collisions can be analyzed quantitatively, in terms of an effective energy loss with the proposed method. {} {Dong D W and Gyulassy M 1993}{Neural filters for jet analysis} {(LBL-31560) Physical Review E Vol~47(4) pp~2913-2922}Comment: 21 pages of Postscript, (LBL-31560

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

Studying the Functional Genomics of Stress Responses in Loblolly Pine With the Expresso Microarray Experiment Management System

Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress

Associative Decorrelation Dynamics: A Theory of Self-Organization and Optimization in Feedback Networks

This paper outlines a dynamic theory of development and adaptation in neural networks with feedback connections. Given input ensemble, the connections change in strength according to an associative learning rule and approach a stable state where the neuronal outputs are decorrelated. We apply this theory to primary visual cortex and examine the implications of the dynamical decorrelation of the activities of orientation selective cells by the intracortical connections. The theory gives a unified and quantitative explanation of the psychophysical experiments on orientation contrast and orientation adaptation. Using only one parameter, we achieve good agreements between the theoretical predictions and the experimental data. 1 Introduction The mammalian visual system is very effective in detecting the orientations of lines and most neurons in primary visual cortex selectively respond to oriented lines and form orientation columns [1]. Why is the visual system organized as suc..

Associative Decorrelation Dynamics in Visual Cortex

This paper outlines a dynamic theory of development and adaptation in neural networks with feedback connections. Given input ensemble, the connections change in strength according to an associative learning rule and approach a stable state where the neuronal outputs are decorrelated. We apply this theory to primary visual cortex and examine the implications of the dynamical decorrelation of the activities of cortical cells. The orientation selective columns are developed with both feedforward and feedback connection changes and with natural images as inputs. The feedback connections form columnar structures which regulate the development of orientation selectivity of feedforward connections. The theory gives a unified and quantitative account of the development of both feedforward and feedback connections of orientation selective cells which are shown to be able to explain the psychophysical experiments on orientation contrast and orientation adaptation. Using only one parameter, we ac..

Spatiotemporal Coupling and Scaling of Natural Images and Human Visual Sensitivities

We study the spatiotemporal correlation in natural time-varying images and explore the hypothesis that the visual system is concerned with the optimal coding of visual representation through spatiotemporal decorrelation of the input signal. Based on the measured spatiotemporal power spectrum, the transform needed to decorrelate input signal is derived analytically and then compared with the actual processing observed in psychophysical experiments