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Commits on Dec 11, 2012

• Got building again, removed fftw dependency

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Commits on Jun 6, 2012

• Cleaned up README.

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• Added some lagging files in the mercurial -> git transition and cleaned README (again).

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• Cleaned up README for github and purged some old paper drafts that had the wrong formatting (leading Google to erroneously conclude the wrong publication journal).

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Commits on Mar 26, 2012

• Some small changes. Unfortunately after looking at the fraction of the sampled space in c mode, after about 4 or 5 genes we are completely hosed. Need to think of another way.

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Commits on Mar 23, 2012

• Have sampling, but getting weird results when looking at uniqueness.

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Commits on Mar 20, 2012

• Working policy cost and optimal finder. Need to clean things up and begin analyzing results

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• Semi-working control policy finding, only works for networks up to n=3, and it appears to be giving backwards answers. Next I want to look at what the MAP network looks like in the weightedExpansion.

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Commits on Mar 13, 2012

• Added a control parsing function. And a control mode in the main program. Also a ParseControl type. Am now going to look into multimodal option parsing.

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• Fixed small bit indexing bug in Moham mode SSD filtering.

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• Added GRN/SparseLib

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• Updated and fixed the Mohammad mode to handle not specifying all of the inputs. Should be rather more robust now. Also added a perturbation probability that can be used with all sparse matrix simul…

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Commits on Mar 3, 2012

• Working weightedExpansion and getNSamples (should probably change those names) for sampling deterministic networks from the likelihood networks.

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Commits on Mar 2, 2012

• Added dataflow system, now going to remove EM (for build simplicity) and add a likelihood sampler.

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Commits on Feb 6, 2012

• Added test suite and removed paper stuff

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• Ive changed a few things to get into compliance with ghc 7.4.1

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Commits on Sep 19, 2011

• Now mode m of grnsim is outputting a file (moham.dat) with each networks ssd on separate lines. This is much easier on both Mohammad and me.

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Commits on Sep 16, 2011

• Now have a working uncertainty class outputter for Mohammad, the successful approach appears to be filtering the full graph to remove the nodes that dont fall under the input gene values (which by …

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Commits on Sep 15, 2011

• About to begin work on Mohammad collaboration.

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Commits on Jul 27, 2011

• Have a good set of examples to use for the paper in synth2.pw. Make sure and generate the state graph to see what it is doing

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• Now twice as fast (in some benchmarks ;)

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• Now twice as fast (in some benchmarks ;)

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• Okay now I've added EM and Sparse, and am going to start optimizations

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• Apparently working Expectation Maximization code. Now I need to try and optimize it as it is too slow.

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Commits on Jul 19, 2011

• Working parallelism, and a hackish version of splitting the graph into components and performing the density check on each is working.

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Commits on Jul 16, 2011

• A few additions to the README.

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• Now includes a passable README.

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• Added density.hs which enables density estimation with fixed convolution and padding.

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Commits on Jul 13, 2011

• Cleaned up the graphviz printer to use a standard supported library (much cleaner). Now I need to move the rendering code out of GrnSim.hs and clean up the random generations.

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Commits on Jul 9, 2011

• Now working version of the Kmap code.

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• A running version using Kmaps, but it seems to be doing it wrong. Going to check it against the old version.

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• Moved a figure, table, and the algorithm to supp.tex. Also converted the main algorithm to use Karnaugh maps in preparation for fuzzing distribution detection.

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Commits on Jul 8, 2011

• Added a bunch of SWP files, two new haskell codes which will probably both be abandoned, the bioinformatics class stuff, and a few odds and ends. Just turned the paper into Ed in bioinformatics for…

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Commits on Jun 17, 2011

• Final version 8 to send to Ed

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• Almost finished with version 8 to send to Ed. Renamed some figure stuff, simplified the text to use vector matrix multiplication and cleaned up the Karnaugh map text to use subscripts throughout. I…

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