modularity 0.2.0.4 → 0.2.1.0

raw patch · 2 files changed

+25/−3 lines, 2 filesdep ~spectral-clusteringPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: spectral-clustering

API changes (from Hackage documentation)

Files

• modularity.cabal +3/−3
• src/Math/Modularity/Dense.hs +22/−0

@@ -1,9 +1,9 @@ cabal-version: >=1.10 name: modularity-version: 0.2.0.4+version: 0.2.1.0 license: GPL-3 license-file: LICENSE-copyright: 2018 Gregory W. Schwartz+copyright: 2019 Gregory W. Schwartz maintainer: gsch@pennmedicine.upenn.edu author: Gregory W. Schwartz homepage: http://github.com/GregorySchwartz/modularity#readme@@ -31,5 +31,5 @@         eigen ==3.3.4.1,         hmatrix >=0.19.0.0,         sparse-linear-algebra >=0.3.1,-        spectral-clustering >=0.2.1.1,+        spectral-clustering >=0.2.2.0,         vector >=0.12.0.1

@@ -7,11 +7,13 @@  module Math.Modularity.Dense     ( getModularity+    , getBModularity     , Q (..)     ) where  -- Remote import Data.Bool (bool)+import Math.Clustering.Spectral.Dense (B (..), getB) import qualified Data.Vector as V import qualified Data.Vector.Storable as VS import qualified Numeric.LinearAlgebra as H@@ -41,3 +43,23 @@     d = H.vector . fmap H.sumElements . H.toRows $ mat     s = bool (-1) 1 . (== 0) . H.atIndex moduleVec     k = H.atIndex d++-- | Find modularity from a vector of community labels (0 or 1) corresponding to+-- rows in the normalized matrix B. See Shu et al., "Efficient Spectral+-- Neighborhood Blocking for Entity Resolution", 2011.+-- L = sum_i^n sum_j^n A(i,j) - n = 1^TA1 - n = (B^T1)^T(B^T1) - n.+getBModularity :: LabelVector -> B -> Q+getBModularity moduleVec (B b) = Q . sum . fmap inner $ [first, second]+  where+    inner v = (a v v / l) - ((a v (ones n) / l) ** 2)+    first  = H.fromColumns [moduleVec]+    second = H.fromColumns [H.cmap (bool 1 0 . (== 1)) moduleVec]+    l    = a (ones n) (ones n)+    a :: H.Matrix Double -> H.Matrix Double -> Double+    a oneL oneR = ( flip H.atIndex (0, 0)+                  $ (H.tr (partA oneL)) H.<> (partA oneR)+                  )+                - (H.sumElements oneL)+    partA one = (H.tr b) <> one+    n    = H.rows b+    ones x = (x H.>< 1) [1,1..]