This release contains two important changes.
- Added command line option --edge-penalty. PathLinker will divide the weight of every edge by the value of this parameter before computing highly scoring paths. The effect of this parameter is to divide the score of a path by the value of this parameter raised to the number of edges in the path. The larger this parameter, the more PathLinker will favour paths with fewer edges. Note: To obtain the same results as with PathLinker 1.0, pass a large value for this parameter, e.g., the sum of the weights in the input network.
- Path scores reported are now in terms of the original weigths, i.e., the score of a path is the product of the weights of the edges in it. In PathLinker 1.0, we reported the sum of the negative of the logarithms of the edge weights.