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Recommended Reading

Below is some recommended reading in advance of the Conference. It is arranged in the 4 categories of Astrophysics, Photon Science, Particle Physics and Statistics. Please do not feel obliged to read every article

  • "Statistics, Handle with Care: Detecting Multiple Model Components with the Likelihood Ration Test"
    Protassov, R. et al., 2002, ApJ, 571, 545
  • "On Computing Upper Limits to Source Intensities"
    Kashyap, Vinay L.; van Dyk, David A.; Connors, Alanna; Freeman, Peter E.; Siemiginowska, Aneta; Xu, Jin; Zezas, Andreas
  • "Optimizing Automated Classification of Periodic Variable Stars in New Synoptic Surveys"
    James P. Long, Noureddine El Karoui, John A. Rice, Joseph W. Richards, Joshua S. Bloom
  • "Automating Discovery and Classification of Transients and Variable Stars in the Synoptic Survey Era"
    J. S. Bloom, J. W. Richards (UC Berkeley), P. E. Nugent (UC Berkeley, Lawrence Berkeley National Laboratory), R. M. Quimby, M. M. Kasliwal (Caltech), D. L. Starr (UC Berkeley), D. Poznanski (UC Berkeley, Lawrence Berkeley National Laboratory), E. O. Ofek (Caltech), S. B. Cenko, N. R. Butler (UC Berkeley), S. R. Kulkarni (Caltech), A. Gal-Yam (Weizmann Institute of Science), N. Law (Dunlap Institute, University of Toronto)
  • "Accounting for Calibration Uncertainties in X-ray Analysis: Effective Areas in Spectral Fitting"
    Lee, Hyunsook; Kashyap, Vinay L.; van Dyk, David A.; Connors, Alanna; Drake, Jeremy J.; Izem, Rima; Meng, Xiao-Li; Min, Shandong; Park, Taeyoung; Ratzlaff, Pete; Siemiginowska, Aneta; Zezas, Andreas, 2011, ApJ, 731, 126.
  • "Multimodal nested sampling: an efficient and robust alternative to Markov Chain Monte Carlo methods for astronomical data analysis"
    Feroz, F. & Hobson, M. P., 2008, MNRAS, 384, 449
  • Photon Science

    Diffraction Imaging

  • Comprehensive review of diffraction imaging
    P. Thibault, V. Elser.
    X-ray diffraction microscopy.
    Annual Reviews in Condensed Matter Physics. 1:5.1-5.19 (2010).
  • Key elements of diffraction imaging: P. Thibault, et al.
    Reconstruction of a yeast cell from X-ray diffraction data. ActaCrystallographica Section A62, 248-261 (2006).
  • Comprehensive review of searches in phasing: S. Marchesini.
    A unified evaluation of iterative projection algorithms for phase retrieval. Review of Scientific Instruments 78, 011301 (2007).
  • Large datasets for 3D imaging

  • Statistics of basic correlation in cryptotomograpy: G. Huldt, et. al. Diffraction imaging of single particles and biomolecules. Journal of Structural Biology.144, 219-227 (2003).
  • Mutual information description of feasibility of cryptotomography: V. Elser. Noise limits on reconstructing diffraction signals from random tomographs. IEEE Transactions on Information Theory, 55(10), 4715-4722 (2009).
  • EMC algorithm showing single reconstructions using 1 million diffraction data each; paper also has sparse implementation if data compression succeeds: N.D. Loh, V. Elser. Reconstruction algorithm for single-particle diffraction imaging experiments Physical Review E 80, 026705 (2009).
  • GTM algorithm: C.M. Bishop, M. Svensen, C.K.I. Williams. The generative topographic map.Neural Computation 10, 215-234 (1998).
  • Diffusion maps: R. Coifman, S. Lafon. Diffusion maps. Applied and Computational Harmonic Analysis 21, 5-30 (2006).
  • Spatial correlation analysis: Z. Kam. Determination of macromolecular structure in solution by spatial correlation of scattering functions.Macromolecules 10(5), Sep.-Oct. (1977).
  • Application of diffusion maps to single molecule imaging: P. Schwander, et. al. Mapping the conformations of biological assemblies. New Journal of Physics 12, 035007(2010).
  • Largest published 3D merging of LCLS dataset: H. Chapman, et. al.Femtosecond x-ray protein nanocrystallographyNature 470, 73-78 (2011).
  • Particle Physics
  • L.Lyons, "Methods for comparing two hypotheses",
  • CMS Collaboration, "Combined results of searches for the Standard Model Higgs boson in pp collisions at sqrt(s) = 7 TeV" (2012),
  • E. Gross and O. Vitells, "Trial factors for the look elsewhere effect in high energy physics",
  • Statistics
  • B. Efron and A. Gous, "Scales of evidence for model selection: Fisher versus Jeffreys"
  • T. Hastie, R. Tibshirani and J. Friedman J (2009) "Elements of Statistical Learning" Section 8.7 on "bagging".
  • B. Efron and R. Tibshirani (1996) "An introduction to the bootstrap", Chapters 6-7
  • Y. Benjamini, Y. Hochberg and P.B. Stark, "Confidence Intervals with more Power to determine the Sign: Two Ends constrain the Means", Journal of the American Statistical Association, 93 (1998) 309–317