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6.6 publication packages Britian’s Royal Society is the first group of academics to gather regularly and discuss what we now call science. A key feature of their gatherings was the presentation of experiments. Experimental evidence and demonstration were critical aspects of this group. It is disturbing how common the lack of experimental demonstration has become. Papers have experimental results, but public demonstration of these results is rare. Some scientists release their experimental codes, others do not. This situation is unacceptable. Computational results are some of the easiest to publicly demonstrate and share. Within this thesis, the majority of the experiments work with roughly 200 lines of code. This code is part of the thesis, incorporated into the text, and publicly released. Furthermore, the experimental scripts for the thesis are also publicly available. Anyone with access to similar computational resources and a bit of patience has the capability of reproducing our results. Furthermore, a similar public disclosure holds for the publications sup- porting this thesis. We now describe the three publication packages. rapr Computing the Random Alpha PageRank vectors involves merely a few lines of Matlab codes, as program 5, program 6, and program 7 show. In the RAPr24 package, we provide these codes along with all of 2 4 Available online: http://stanford. edu/~dgleich/publications/2008/ the experimental routines. These routines reproduce all the figures in rapr. chapter 4 and even include other experiments that are not incorporated into the text. Within these codes, we also provide the C++ routines to compute the RAPr statistics using libbvg. innout We decided to pun on the name of the popular California burger chain “In-n-out” with the name of the package corresponding to the inner-outer iteration.25 Just like the RAPrpackage, the innout package contains all the Matlab codes, C and C++ programs, and experimental drivers to reproduce the figures in chapter 5. thesis A forthcoming package includes all the codes generated for extra figures in this thesis.26 Some of these programs use the RAPr and innout packages to derive new results. One example is the list of pages in Wikipedia with largest derivative from table 3.3. Another example is the derivative code itself.27 We hope that releases like these become standard in the future. reproducible research Thereissomecauseforhope.JonClaerbout at Stanford has long advocated reproducible research for scientific computa- tions [Schwab et al., 2000]. Others have adopted his philosophy [Buckheit and Donoho, 1995; Donoho et al., 2009]. Indeed, an entire issue of the Com- puting in Science and Engineering journal was recently devoted to this topic [Fomel and Claerbout, 2009]. The software packages of this thesis fit the general motivation of reproducible research, although some of the specifics differ. 25 Available online: http://stanford. edu/~dgleich/publications/2009/ innout. 26 Available online: http://stanford. edu/~dgleich/publications/2009/ thesis. 27 While there was never a prior deriva- tive package, our derivative routine was released in an older Matlab PageRank package. 6.6 ⋅ publication packages 141PDF Image | ALGORITHMS FOR PAGERANK SENSITIVITY DISSERTATION
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