Greedy Newton: Newton's Method with Exact Line Search

A defining characteristic of Newton's method is local superlinear convergence within a neighbourhood of a strict local minimum. However, outside this neighborhood Newton's method can converge slowly or even diverge. A common approach to dealing with non-convergence is using a step size that is set by an Armijo backtracking line search. With suitable initialization the line-search preserves local superlinear convergence, but may give sub-optimal progress when not near a solution. In this work we consider Newton's method under an exact line search, which we call "greedy Newton" (GN). We show that this leads to an improved global convergence rate, while retaining a local superlinear convergence rate. We empirically show that GN may work better than backtracking Newton by allowing significantly larger step sizes

Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays

BACKGROUND: Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation. RESULTS: A method and SPR Opt (SNP and PCR-RFLP Optimization) software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed) are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes. CONCLUSION: This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As more sequence data becomes available for multiple strains and isolates of a species, automated, computational approaches such as those described here will be essential to make sense of large amounts of information, and to guide and optimize efforts in the laboratory. The software and source code for SPR Opt is publicly available and free for non-profit use at

Measurement of surface physical properties and radiation balance for KUREX-91 study

Biophysical properties and radiation balance components were measured at the Streletskaya Steppe Reserve of the Russian Republic in July 1991. Steppe vegetation parameters characterized include leaf area index (LAI), leaf angle distribution, mean tilt angle, canopy height, leaf spectral properties, leaf water potential, fraction of absorbed photosynthetically active radiation (APAR), and incoming and outgoing shortwave and longwave radiation. Research results, biophysical parameters, radiation balance estimates, and sun-view geometry effects on estimating APAR are discussed. Incoming and outgoing radiation streams are estimated using bidirectional spectral reflectances and bidirectional thermal emittances. Good agreement between measured and modeled estimates of the radiation balance were obtained

Calibration of field reference panel and radiometers used in FIFE 1989

Remote sensing of the earth's surface features involves the measurement of reflected solar radiation and the interpretation of the data in biophysical terms. Reflected radiation is a function of the surface properties and incident solar irradiance. The amount of radiation reflected from a surface is compared to the amount of solar radiation received at the surface as a means of comparing information from different times of day as well as for different days of the year. Thus, it is imperative to calibrate the instruments used to measure the incoming and reflected radiation