src/Gargantext/Core/Viz/Phylo/Metrics.hs

   1 {-|
   2 Module      : Gargantext.Core.Viz.Phylo.Tools
   3 Description : Phylomemy Tools to build/manage it
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9 -}
  10
  11 {-# LANGUAGE ViewPatterns      #-}
  12
  13 module Gargantext.Core.Viz.Phylo.Metrics
  14   where
  15
  16 import Gargantext.Prelude
  17 import Gargantext.Core.Viz.Phylo
  18 import Gargantext.Core.Viz.Phylo.Tools
  19
  20 import Control.Lens hiding (Level)
  21
  22 import Data.List ((\\), sortOn, concat, nub, take, union, intersect, null, (++), sort)
  23 import Data.Map  (Map, (!), toList, size, insert, unionWith, intersection, intersectionWith, filterWithKey, elems, fromList, findWithDefault, fromListWith)
  24 import Data.Text (Text)
  25
  26 -- import Debug.Trace (trace)
  27
  28 ----------------
  29 -- | Ngrams | --
  30 ----------------
  31
  32
  33 -- | Return the conditional probability of i knowing j
  34 conditional :: Ord a => Map (a,a) Double -> a -> a -> Double
  35 conditional m i j = (findWithDefault 0 (i,j) m)
  36                   / (m ! (j,j))
  37
  38
  39 -- | Return the genericity score of a given ngram
  40 genericity :: Map (Int, Int) Double -> [Int] -> Int -> Double
  41 genericity m l i = ( (sum $ map (\j -> conditional m i j) l)
  42                    - (sum $ map (\j -> conditional m j i) l)) / (fromIntegral $ (length l) + 1)
  43
  44
  45 -- | Return the specificity score of a given ngram
  46 specificity :: Map (Int, Int) Double -> [Int] -> Int -> Double
  47 specificity m l i = ( (sum $ map (\j -> conditional m j i) l)
  48                     - (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1)
  49
  50
  51 -- | Return the inclusion score of a given ngram
  52 inclusion :: Map (Int, Int) Double -> [Int] -> Int -> Double
  53 inclusion m l i = ( (sum $ map (\j -> conditional m j i) l)
  54                   + (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1)
  55
  56
  57 -- | Process some metrics on top of ngrams
  58 getNgramsMeta :: Map (Int, Int) Double -> [Int] -> Map Text [Double]
  59 getNgramsMeta m ngrams = fromList
  60     [ ("genericity" , map (\n -> genericity  m (ngrams \\ [n]) n) ngrams ),
  61       ("specificity", map (\n -> specificity m (ngrams \\ [n]) n) ngrams ),
  62       ("inclusion"  , map (\n -> inclusion   m (ngrams \\ [n]) n) ngrams )]
  63
  64
  65 -- | To get the nth most occurent elems in a coocurency matrix
  66 getNthMostOcc :: Int -> Map (Int,Int) Double -> [Int]
  67 getNthMostOcc nth cooc = (nub . concat)
  68                        $ map (\((idx,idx'),_) -> [idx,idx'])
  69                        $ take nth
  70                        $ reverse
  71                        $ sortOn snd $ toList cooc
  72
  73
  74 -------------------------
  75 -- | Ngrams Dynamics | --
  76 -------------------------
  77
  78 sharedWithParents :: Date -> PhyloBranchId -> Int -> PhyloView -> Bool
  79 sharedWithParents inf bid n pv = elem n
  80                                 $ foldl (\mem pn -> if ((bid == (fromJust $ (pn ^. pn_bid)))
  81                                                       && (inf > (fst $ getNodePeriod pn)))
  82                                                    then nub $ mem ++ (pn ^. pn_idx)
  83                                                    else mem ) []
  84                                 $ (pv ^. pv_nodes)
  85
  86
  87 findDynamics :: Int -> PhyloView -> PhyloNode -> Map Int (Date,Date) -> Double
  88 findDynamics n pv pn m =
  89     let prd = getNodePeriod pn
  90         bid = fromJust $ (pn ^. pn_bid)
  91         end = last' "dynamics" (sort $ map snd $ elems m)
  92     in  if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
  93             -- emergence
  94             then 2
  95         else if ((fst prd) == (fst $ m ! n))
  96             -- recombination
  97             then 0
  98         else if (not $ sharedWithParents (fst prd) bid n pv)
  99             -- decrease
 100             then 1
 101         else 3
 102
 103
 104
 105 processDynamics :: PhyloView -> PhyloView
 106 processDynamics pv = alterPhyloNode (\pn ->
 107             pn & pn_metrics %~ insert "dynamics" (map (\n -> findDynamics n pv pn ngramsDates) $ (pn ^. pn_idx) ) ) pv
 108     where
 109         --------------------------------------
 110         ngramsDates :: Map Int (Date,Date)
 111         ngramsDates = map (\ds -> let ds' = sort ds
 112                                   in  (head' "Dynamics" ds', last' "Dynamics" ds'))
 113                     $ fromListWith (++)
 114                     $ foldl (\mem pn -> mem ++ (map (\n -> (n, [fst $ getNodePeriod pn, snd $ getNodePeriod pn]))
 115                                                  $ (pn ^. pn_idx))) []
 116                     $ (pv ^. pv_nodes)
 117         --------------------------------------
 118
 119
 120
 121 -------------------
 122 -- | Proximity | --
 123 -------------------
 124
 125
 126 -- | Process the inverse sumLog
 127 sumInvLog :: Double -> [Double] -> Double
 128 sumInvLog s l = foldl (\mem x -> mem + (1 / log (s + x))) 0 l
 129
 130
 131 -- | Process the sumLog
 132 sumLog :: Double -> [Double] -> Double
 133 sumLog s l = foldl (\mem x -> mem + log (s + x)) 0 l
 134
 135
 136 -- | To compute a jaccard similarity between two lists
 137 jaccard :: [Int] -> [Int] -> Double
 138 jaccard inter' union' = ((fromIntegral . length) $ inter') / ((fromIntegral . length) $ union')
 139
 140
 141 -- | To get the diagonal of a matrix
 142 toDiago :: Map (Int, Int) Double -> [Double]
 143 toDiago cooc = elems $ filterWithKey (\(x,x') _ -> x == x') cooc
 144
 145
 146 -- | To process WeighedLogJaccard distance between to coocurency matrix
 147 weightedLogJaccard :: Double -> Double -> Map (Int, Int) Double -> Map (Int, Int) Double -> [Int] -> [Int] -> Double
 148 weightedLogJaccard sens nbDocs cooc cooc' ngrams ngrams'
 149   | null gInter      = 0
 150   | gInter == gUnion = 1
 151   | sens == 0        = jaccard gInter gUnion
 152   | sens > 0         = (sumInvLog sens wInter) / (sumInvLog sens wUnion)
 153   | otherwise        = (sumLog sens wInter) / (sumLog sens wUnion)
 154   where
 155     --------------------------------------
 156     gInter :: [Int]
 157     gInter = intersect ngrams ngrams'
 158     --------------------------------------
 159     gUnion :: [Int]
 160     gUnion = union ngrams ngrams'
 161     --------------------------------------
 162     wInter :: [Double]
 163     wInter = toDiago $ map (/nbDocs) $ intersectionWith (+) cooc cooc'
 164     --------------------------------------
 165     wUnion :: [Double]
 166     wUnion = toDiago $ map (/nbDocs) $ unionWith (+) cooc cooc'
 167     --------------------------------------
 168
 169
 170 -- | To process the Hamming distance between two PhyloGroup fields
 171 hamming :: Map (Int, Int) Double -> Map (Int, Int) Double -> Double
 172 hamming f1 f2 = fromIntegral $ max ((size inter) - (size f1)) ((size inter) - (size f2))
 173   where
 174     --------------------------------------
 175     inter :: Map (Int, Int) Double
 176     inter = intersection f1 f2
 177     --------------------------------------