[Fun] ConfMat

app/Main.hs

+{-# LANGUAGE NoImplicitPrelude   #-}
+
 module Main where
 
 import Graph.Tools

gargantext-graph.cabal

@@ -4,7 +4,7 @@ cabal-version: 1.12
 --
 -- see: https://github.com/sol/hpack
 --
--- hash: 6c4e06602da9033a6525639aa2d86c9093f65dd779b919115c4f39ef319caeba
+-- hash: 94b44a88c27580d41ae4220e3a3c8578c4f72d98ec3ba3638161723463c03df8
 
 name:           gargantext-graph
 version:        0.1.0.0
@@ -41,7 +41,7 @@ library
       Paths_gargantext_graph
   hs-source-dirs:
       src
-  default-extensions: NoImplicitPrelude DataKinds FlexibleInstances OverloadedStrings
+  default-extensions: DataKinds FlexibleInstances OverloadedStrings
   build-depends:
       accelerate
     , accelerate-arithmetic
@@ -68,7 +68,7 @@ executable gargantext-graph-exe
       Paths_gargantext_graph
   hs-source-dirs:
       app
-  default-extensions: NoImplicitPrelude DataKinds FlexibleInstances OverloadedStrings
+  default-extensions: DataKinds FlexibleInstances OverloadedStrings
   ghc-options: -O2 -threaded -rtsopts -with-rtsopts=-N -fprof-auto
   build-depends:
       accelerate
@@ -98,7 +98,7 @@ test-suite gargantext-graph-test
       Paths_gargantext_graph
   hs-source-dirs:
       test
-  default-extensions: NoImplicitPrelude DataKinds FlexibleInstances OverloadedStrings
+  default-extensions: DataKinds FlexibleInstances OverloadedStrings
   ghc-options: -threaded -rtsopts -with-rtsopts=-N
   build-depends:
       accelerate

package.yaml

@@ -39,7 +39,6 @@ dependencies:
 - eigen
 
 default-extensions:
-- NoImplicitPrelude
 - DataKinds
 - FlexibleInstances
 - OverloadedStrings

src/Data/Array/Accelerate/Utils.hs

@@ -27,6 +27,7 @@ Implementation use Accelerate library which enables GPU and CPU computation:
 {-# LANGUAGE TypeOperators       #-}
 {-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE ViewPatterns        #-}
+{-# LANGUAGE NoImplicitPrelude   #-}
 
 module Data.Array.Accelerate.Utils
   where

src/Graph/BAC/Clustering.hs

@@ -10,7 +10,8 @@ Reference: Article POK de QuaC de G
 POK: Parts Overlap Kern
 -}
 
-{-# LANGUAGE FlexibleContexts #-}
+{-# LANGUAGE FlexibleContexts  #-}
+{-# LANGUAGE NoImplicitPrelude #-}
 
 module Graph.BAC.Clustering
   where

src/Graph/BAC/Proxemy.hs

@@ -13,6 +13,8 @@ Références:
 
 -}
 
+{-# LANGUAGE NoImplicitPrelude #-}
+
 module Graph.BAC.Proxemy
   where
 

src/Graph/BAC/ProxemyOptim.hs

@@ -6,10 +6,10 @@ Maintainer  : team@gargantext.org
 Stability   : experimental
 Portability : POSIX
 
-Références:
-- Bruno Gaume, Karine Duvignau, Emmanuel Navarro, Yann Desalle, Hintat Cheung, et al.. Skillex: a graph-based lexical score for measuring the semantic efficiency of used verbs by human subjects describing actions. Revue TAL, Association pour le Traitement Automatique des Langues, 2016, Revue TAL : numéro spécial sur Traitement Automatique des Langues et Sciences Cognitives (55-3), 55 (3), ⟨https://www.atala.org/-Cognitive-Issues-in-Natural-⟩. ⟨hal-01320416⟩
+Confluence for Graph Clustering, B. Gaume and A. Delanoë
 
-- Implémentation Python [Lien]()
+Code written in Haskell by A. Delanoë from Python Specifications by B.
+Gaume.
 
 -}
 
@@ -19,7 +19,9 @@ Références:
              KindSignatures,
              ScopedTypeVariables,
              StandaloneDeriving,
-             TypeOperators #-}
+             TypeOperators       #-}
+{-# LANGUAGE TypeApplications    #-}
+{-# LANGUAGE NoImplicitPrelude   #-}
 
 module Graph.BAC.ProxemyOptim
   where
@@ -34,9 +36,10 @@ import Data.Map (Map)
 import Graph.FGL
 import Protolude hiding (sum, natVal)
 import qualified Eigen.Matrix as DenseMatrix
-import Eigen.SparseMatrix (SparseMatrix, SparseMatrixXd)
-import Eigen.Internal (CTriplet(..), Elem(..), toC, fromC, C(..))
-import Eigen.Matrix (sum)
+import Eigen.SparseMatrix (SparseMatrix, SparseMatrixXd, (!), toMatrix, _unsafeCoeff)
+import Eigen.Internal (CTriplet(..), Elem(..), toC, fromC, C(..), natToInt, Row(..), Col(..))
+import Eigen.Matrix (sum, unsafeCoeff)
+import qualified Eigen.Matrix                      as DMatrix
 import qualified Data.Graph.Inductive              as DGI
 import qualified Data.Graph.Inductive.PatriciaTree as DGIP
 import qualified Data.List                         as List
@@ -78,6 +81,7 @@ tab g = do
 type DenseMatrix      n = DenseMatrix.Matrix n n Double
 type AdjacencyMatrix  n = SparseMatrix n n Double
 type TransitionMatrix n = SparseMatrix n n Double
+type ProxemyMatrix    n = SparseMatrix n n Double
 
 type ConfluenceMatrix n = DenseMatrix n
 type ModularityMatrix n = DenseMatrix n
@@ -124,11 +128,8 @@ transition m = SMatrix.mul m (sumWith (\s -> 1 / s) m)
 
 sumWith :: ( Elem a
            , Elem t
-           , KnownNat n1
-           , KnownNat m1
-           , KnownNat n2
-           , KnownNat m2
-           ) => (t -> a) -> SparseMatrix n2 m2 t -> SparseMatrix n1 m1 a
+           , KnownNat n
+           ) => (t -> a) -> SparseMatrix n n t -> SparseMatrix n n a
 sumWith f m = SMatrix.fromVector
        $ VS.fromList
        $ List.zipWith (\i v -> CTriplet i 1 (toC (f v))) [1..]
@@ -140,17 +141,29 @@ sumWith f m = SMatrix.fromVector
 proxemie :: KnownNat n
          => Length
         -> TransitionMatrix n
-        -> TransitionMatrix n
+        -> ProxemyMatrix n
 proxemie l m = case l < 1 of
   True  -> panic "Length has to be >= 1"
   False -> foldl' (\m' _-> SMatrix.mul m' m) m [1 .. (l :: Int)]
 
 
 ---------------------------------------------------------------
-matconf :: KnownNat n => AdjacencyMatrix n -> TransitionMatrix n -> ConfluenceMatrix n
-matconf a t = undefined {- do
-  let vcount = SMatrix.cols_ a
--}
+matconf :: forall n. KnownNat n => AdjacencyMatrix n -> ProxemyMatrix n -> ConfluenceMatrix n
+matconf a p = symmetry $ toMatrix confmat
+  where
+    vcount  = natToInt @n
+    degs    = sumWith identity a
+    sumdeg  = sum (toMatrix degs)
+    symmetry m = DMatrix.imap (\x y v -> if x < y then v else DMatrix.unsafeCoeff y x m) m
+    confmat    = SMatrix.imap (\x y v -> if x < y
+                              then let
+                                      prox_y_x_length = v
+                                      prox_y_x_infini = (_unsafeCoeff x 1 degs) / sumdeg
+                                 in (prox_y_x_length - prox_y_x_infini)
+                                  / (prox_y_x_length + prox_y_x_infini)
+                              else 0
+                           ) p
+
 
 matmod :: KnownNat n => FiniteGraph n a b -> ModularityMatrix n
 matmod = undefined

src/Graph/BAC/Scores.hs

@@ -12,6 +12,7 @@ POK: Parts Overlap Kern
 
 {-# LANGUAGE TemplateHaskell       #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
+{-# LANGUAGE NoImplicitPrelude #-}
 
 module Graph.BAC.Scores
   where

src/Graph/BAC/Test.hs

@@ -10,6 +10,7 @@ Reference: Article POK de QuaC de G
 POK: Parts Overlap Kern
 -}
 
+{-# LANGUAGE NoImplicitPrelude #-}
 
 module Graph.BAC.Test
   where

src/Graph/BAC/Types.hs

@@ -10,6 +10,7 @@ Portability : POSIX
 
 {-# LANGUAGE TemplateHaskell       #-}
 {-# LANGUAGE MultiParamTypeClasses #-}
+{-# LANGUAGE NoImplicitPrelude #-}
 
 module Graph.BAC.Types
   where

src/Graph/FGL.hs

@@ -12,6 +12,7 @@ Main DGI funs/types to ease portability with IGraph.
 
 {-# LANGUAGE ConstrainedClassMethods #-}
 {-# LANGUAGE ConstraintKinds         #-}
+{-# LANGUAGE NoImplicitPrelude       #-}
 
 module Graph.FGL where
 

src/Graph/IGraph.hs

@@ -13,6 +13,7 @@ Reference:
 
 -}
 
+{-# LANGUAGE NoImplicitPrelude       #-}
 
 module Graph.IGraph where
 

src/Graph/Tools.hs

@@ -11,6 +11,7 @@ Portability : POSIX
 
 {-# LANGUAGE ConstraintKinds #-}
 {-# LANGUAGE InstanceSigs    #-}
+{-# LANGUAGE NoImplicitPrelude       #-}
 
 
 module Graph.Tools where

stack.yaml

@@ -32,7 +32,8 @@ allow-newer: true
 #   - wai
 packages:
 - .
-# Dependency packages to be pulled from upstream that are not in the resolver.
+- '../eigen/'
+  # Dependency packages to be pulled from upstream that are not in the resolver.
 # These entries can reference officially published versions as well as
 # forks / in-progress versions pinned to a git hash. For example:
 #
@@ -44,7 +45,7 @@ extra-deps:
 - git: https://gitlab.iscpif.fr/anoe/accelerate-utility.git
   commit: 83ada76e78ac10d9559af8ed6bd4064ec81308e4
 - accelerate-arithmetic-1.0.0.1@sha256:555639232aa5cad411e89247b27871d09352b987a754230a288c690b6de6d888,2096
-- eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
+# - eigen-3.3.7.0@sha256:7c24a86426b238e02ba0ac2179cc44997518b443a13828ed7a791fe49a6dffa5,82060
 
 
 # Override default flag values for local packages and extra-deps