[ADMIN] Adding linear Algebra utils for Accelerate

package.yaml

@@ -108,6 +108,7 @@ library:
   - SHA
   - Unique
   - accelerate
+  - accelerate-arithmetic
   - aeson
   - aeson-lens
   - aeson-pretty

src/Gargantext/Core/Methods/Distances/Accelerate/Distributional.hs

 {-|
 Module      : Gargantext.Core.Methods.Distances.Accelerate.Distributional
-Description : 
+Description :
 Copyright   : (c) CNRS, 2017-Present
 License     : AGPL + CECILL v3
 Maintainer  : team@gargantext.org
 Stability   : experimental
 Portability : POSIX
 
-This module aims at implementig distances of terms context by context is
-the same referential of corpus.
 
-Implementation use Accelerate library which enables GPU and CPU computation
-See Gargantext.Core.Methods.Graph.Accelerate)
+* Distributional Distance metric
+__Definition :__ Distributional metric is a relative metric which depends on the
+selected list, it represents structural equivalence of mutual information.
+
+__Objective :__ We want to compute with matrices processing the similarity between term $i$ and term $j$ :
+ distr(i,j)=$\frac{\Sigma_{k \neq i,j} min(\frac{n_{ik}^2}{n_{ii}n_{kk}},\frac{n_{jk}^2}{n_{jj}n_{kk}})}{\Sigma_{k \neq i}\frac{n_{ik}^2}{ n_{ii}n_{kk}}}$
+
+where $n_{ij}$ is the cooccurrence between term $i$ and term $j$
+
+* For a vector V=[$x_1$ ... $x_n$], we note $|V|_1=\Sigma_ix_i$
+* operator : .* and ./ cell by cell multiplication and division of the matrix
+* operator * is the matrix multiplication
+* Matrice M=[$n_{ij}$]$_{i,j}$
+* opérateur : Diag(M)=[$n_{ii}$]$_i$ (vecteur)
+* Id= identity matrix
+* O=[1]$_{i,j}$ (matrice one)
+* D(M)=Id .* M
+* O * D(M) =[$n_{jj}$]$_{i,j}$
+* D(M) * O =[$n_{ii}$]$_{i,j}$
+* $V_i=[0~0~0~1~0~0~0]'$ en i
+* MI=(M ./ O * D(M)) .* (M / D(M) * O )
+* distr(i,j)=$\frac{|min(V'_i * (MI-D(MI)),V'_j * (MI-D(MI)))|_1}{|V'_i.(MI-D(MI))|_1}$
+
+[Specifications written by David Chavalarias on Garg v4 shared NodeWrite, team Pyremiel 2020]
 
 -}
 
@@ -30,15 +50,31 @@ import Data.Array.Accelerate.Interpreter (run)
 import Gargantext.Core.Methods.Matrix.Accelerate.Utils
 import qualified Gargantext.Prelude as P
 
-
--- * Metrics of proximity
 -----------------------------------------------------------------------
--- ** Distributional Distance
+-- * Distributional Distance
+distributional' :: Elt a => Matrix a -> Matrix a
+distributional' _m' = undefined
+{-
+ where
+    m = use m'
+    n = dim m'
+-}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
--- | Distributional Distance metric
---
--- Distributional metric is a relative metric which depends on the
--- selected list, it represents structural equivalence of mutual information.
 --
 -- The distributional metric P(c) of @i@ and @j@ terms is: \[
 -- S_{MI} = \frac {\sum_{k \neq i,j ; MI_{ik} >0}^{} \min(MI_{ik},
@@ -59,6 +95,7 @@ import qualified Gargantext.Prelude as P
 -- Total cooccurrences of terms given a map list of size @m@
 --            \[N_{m} = \sum_{i,i \neq i}^{m} \sum_{j, j \neq j}^{m} S_{ij}\]
 --
+
 distributional :: Matrix Int -> Matrix Double
 distributional m = -- run {- $ matMiniMax -}
                    run  $ diagNull n

src/Gargantext/Core/Methods/Matrix/Accelerate/Utils.hs

@@ -296,7 +296,7 @@ cross' :: Matrix Double -> Matrix Double
 cross' mat = run $ cross n mat'
   where
     mat' = use mat
-    n = dim mat
+    n    = dim mat
 
 
 {-

stack.yaml

@@ -7,6 +7,8 @@ packages:
 #- 'deps/patches-map'
 #- 'deps/servant-job'
 #- 'deps/clustering-louvain'
+#- 'deps/accelerate'
+#- 'deps/accelerate-utility'
 
 docker:
   enable: false
@@ -20,6 +22,7 @@ nix:
   shell-file: build-shell.nix
 
 allow-newer: true
+
 extra-deps:
 - git: https://github.com/delanoe/data-time-segment.git
   commit: 10a416b9f6c443866b36479c3441ebb3bcdeb7ef
@@ -62,9 +65,18 @@ extra-deps:
 - git: https://github.com/kaizhang/haskell-igraph.git
   commit: 34553acc4ebdcae7065311dcefb426e0fd58c5a0
 
+  # Accelerate Linear Algebra and specific instances
+  # (UndecidableInstances for newer GHC version)
+- git: https://gitlab.iscpif.fr/anoe/accelerate.git
+  commit: f5c0e0071ec7b6532f9a9cd3eb33d14f340fbcc9
+- git: https://gitlab.iscpif.fr/anoe/accelerate-utility.git
+  commit: 83ada76e78ac10d9559af8ed6bd4064ec81308e4
+- accelerate-arithmetic-1.0.0.1@sha256:555639232aa5cad411e89247b27871d09352b987a754230a288c690b6de6d888,2096
+
 - KMP-0.2.0.0@sha256:6dfbac03ef00ebd9347234732cb86a40f62ab5a80c0cc6bedb8eb51766f7df28,2562
 - Unique-0.4.7.7@sha256:2269d3528271e25d34542e7c24a4e541e27ec33460e1ea00845da95b82eec6fa,2777
-- accelerate-1.2.0.1@sha256:bb1928efe602545df4043692916ed427c959110cbd678d03c3f9c3be25d1ae88,20112
+
+
 - duckling-0.1.6.1@sha256:dab60953f405b45fe93e1e745f8cc83e5166e1788b1f4999cc06382e131153d8,47147
 - fclabels-2.0.4@sha256:efcc20c6c903d0a59e36eb1cb547a7bbbbba93b6e20b84b06e919c350891beb2,4492
 - full-text-search-0.2.1.4@sha256:81f6df3327e5b604f99b15e78635e5d6ca996e504c21d268a6d751d7d131aa36,6032