matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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Maximum WPD for a collection of placement locations #203

Closed cmccoy closed 12 years ago

cmccoy commented 12 years ago

Compute the maximum WPD for a collection of placement locations

Define

Let P = the set of placements on the tree

Let I = the points that form the convex hull of P

Let p_i = the proportion of total mass at point i

Let E = the set of edges connecting I

Let D_e = the subset of I distal to edge e

Let x_e = 1 - 2\sum_{i \in D_e} p_i, for edge e, so |x_e| is one minus the proportion of mass on the side with least mass.

Let l_e = length of edge e

We want to minimize:

z = \sum_e l_e |x_e|

Subject to:

To convert this to a linear program, replace:

subject to xp_e,xn_e >= 0 (see AIIMS linear programming tricks)

The problem becomes:

Minimize:

z = \sum_e l_e (xp_e + xn_e)

Subject to:

matsen commented 12 years ago

This one was my mistake and we have moved onto greener pastures.