File	Date	Author	Commit
Random123	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
Makefile	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
README	2015-07-02	George Slota	[2edfe5] added in outer-loop parallelism
colorcount.hpp	2015-07-02	George Slota	[2edfe5] added in outer-loop parallelism
dynamic_table_path.hpp	2015-06-26	George Slota	[c0cb1c] minor bug fixes and optimizations, added in max...
fastpath.cpp	2015-07-02	George Slota	[2edfe5] added in outer-loop parallelism
fastpath.h	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
graph.hpp	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
max_heap.hpp	2015-06-26	George Slota	[c0cb1c] minor bug fixes and optimizations, added in max...
mint-human.graph	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
parse_mint.cpp	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit
util.hpp	2014-09-29	gslota	[03a9c6] FastPath Version 1.0 initial commit

Read Me

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Finding pathways using the FASCIA subgraph counting framework

26 May 2015 -- v1.1
Optimizations and bug fixes, added in max heap and outer-loop parallelism

29 September 2014 -- v1.0
Initial version

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To compile: 
  1. If needed, edit Makefile and change default compiler options (g++)
  2. $ make


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To run: ./path -g [graphfile] -l [path_length] [options]
options =
  -i [iterations]  number of iterations to run
  -n [num paths]   number of paths to find
  -o               use outer-loop parallelism
  -v               verbose output
  -t               report timing
  -h               print this


################################################################################
Graphfile format: 
  -Use mint-human.graph for reference
  -Initial line gives 'number of vertices' and 'number of undirected edges'
  -Each subsequent line represents an edge as: 
    (vertex 1) (label 1) (vertex 2) (label 2) (Weight [0.0-1.0])
  -Vertex ids should be zero indexed, max id = ('number of vertices' - 1)
  -There should be a total of ('number of undirected edges' + 1) lines in graphfile
  -Multi-edges and self-loops will be ignored during calculation


graphfile:
100 1000
0 Q9BV28 1 Q8WVB3 0.15
0 Q9BV28 2 P51159 0.25
0 Q9BV28 3 Q16643 0.05
1 Q8WVB3 2 P51159 0.15
2 P51159 3 Q16643 0.10
...
...


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Examples:

1. Find best length 6 path on mint-human graph, run 100 iterations
  ./path -g mint-human.graph -l 6 -i 100

2. Find 10 best length 4 paths on mint-human graph, run 10 iterations, verbose output
  ./path -g mint-human.graph -l 4 -i 10 -n 10 -v

3. Report execution time for finding best length 10 path mint-human after 100 iterations
  ./path -g mint-human.graph -l 7 -i 100 -t


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Questions, bugs, comments, etc:

Please direct all comments and questions to:
  George Slota <gslota@psu.edu>