src/Gargantext/Viz/Phylo/SynchronicClustering.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo.SynchronicClustering
   3 Description : Module dedicated to the adaptative synchronic clustering of a Phylo.
   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 NoImplicitPrelude #-}
  12 {-# LANGUAGE FlexibleContexts  #-}
  13 {-# LANGUAGE OverloadedStrings #-}
  14 {-# LANGUAGE MultiParamTypeClasses #-}
  15
  16 module Gargantext.Viz.Phylo.SynchronicClustering where
  17
  18 import Gargantext.Prelude
  19 import Gargantext.Viz.AdaptativePhylo
  20 import Gargantext.Viz.Phylo.PhyloTools
  21 import Gargantext.Viz.Phylo.TemporalMatching (weightedLogJaccard', filterDiago, reduceDiagos)
  22 import Gargantext.Viz.Phylo.PhyloExport (processDynamics)
  23
  24 import Data.List ((++), null, intersect, nub, concat, sort, sortOn, all, groupBy, group, maximum)
  25 import Data.Map  (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member)
  26 import Data.Text (Text)
  27
  28 import Control.Lens hiding (Level)
  29 import Control.Parallel.Strategies (parList, rdeepseq, using)
  30 -- import Debug.Trace (trace)
  31
  32 import qualified Data.Map as Map
  33 import qualified Data.Set as Set
  34
  35
  36 -------------------------
  37 -- | New Level Maker | --
  38 -------------------------
  39
  40 mergeBranchIds :: [[Int]] -> [Int]
  41 mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq') ids
  42   where
  43     -- | 2) find the most Up Left ids in the hierarchy of similarity
  44     -- mostUpLeft :: [[Int]] -> [[Int]]
  45     -- mostUpLeft ids' =
  46     --      let groupIds = (map (\gIds -> (length $ head' "gIds" gIds, head' "gIds" gIds)) . groupBy (\id id' -> length id == length id') . sortOn length) ids'
  47     --          inf = (fst . minimum) groupIds
  48     --      in map snd $ filter (\gIds -> fst gIds == inf) groupIds
  49     -- | 1) find the most frequent ids
  50     mostFreq' :: [[Int]] -> [[Int]]
  51     mostFreq' ids' =
  52        let groupIds = (map (\gIds -> (length gIds, head' "gIds" gIds)) . group . sort) ids'
  53            sup = (fst . maximum) groupIds
  54         in map snd $ filter (\gIds -> fst gIds == sup) groupIds
  55
  56
  57 mergeMeta :: [Int] -> [PhyloGroup] -> Map Text [Double]
  58 mergeMeta bId groups =
  59   let ego = head' "mergeMeta" $ filter (\g -> (snd (g ^. phylo_groupBranchId)) == bId) groups
  60    in fromList [("breaks",(ego ^. phylo_groupMeta) ! "breaks"),("seaLevels",(ego ^. phylo_groupMeta) ! "seaLevels")]
  61
  62
  63 groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
  64 groupsToBranches' groups =
  65     -- | run the related component algorithm
  66     let egos  = map (\g -> [getGroupId g]
  67                         ++ (map fst $ g ^. phylo_groupPeriodParents)
  68                         ++ (map fst $ g ^. phylo_groupPeriodChilds) ) $ elems groups
  69         graph = relatedComponents egos
  70     -- | update each group's branch id
  71     in map (\ids ->
  72         let groups' = elems $ restrictKeys groups (Set.fromList ids)
  73             bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) groups'
  74          in map (\g -> g & phylo_groupBranchId %~ (\(lvl,_) -> (lvl,bId))) groups') graph
  75
  76
  77 mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup
  78 mergeGroups coocs id mapIds childs =
  79     let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs
  80     in PhyloGroup (fst $ fst id) (snd $ fst id) (snd id)  ""
  81                   (sum $ map _phylo_groupSupport childs)  ngrams
  82                   (ngramsToCooc ngrams coocs)
  83                   ((snd $ fst id),bId)
  84                   (mergeMeta bId childs) [] (map (\g -> (getGroupId g, 1)) childs)
  85                   (updatePointers $ concat $ map _phylo_groupPeriodParents childs)
  86                   (updatePointers $ concat $ map _phylo_groupPeriodChilds  childs)
  87     where
  88         --------------------
  89         bId :: [Int]
  90         bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) childs
  91         --------------------
  92         updatePointers :: [Pointer] -> [Pointer]
  93         updatePointers pointers = map (\(pId,w) -> (mapIds ! pId,w)) pointers
  94
  95
  96 addPhyloLevel :: Level -> Phylo -> Phylo
  97 addPhyloLevel lvl phylo =
  98   over ( phylo_periods .  traverse )
  99        (\phyloPrd -> phyloPrd & phylo_periodLevels
 100                         %~ (insert (phyloPrd ^. phylo_periodPeriod, lvl) (PhyloLevel (phyloPrd ^. phylo_periodPeriod) lvl empty))) phylo
 101
 102
 103 toNextLevel' :: Phylo -> [PhyloGroup] -> Phylo
 104 toNextLevel' phylo groups =
 105     let curLvl = getLastLevel phylo
 106         oldGroups = fromList $ map (\g -> (getGroupId g, getLevelParentId g)) groups
 107         newGroups = concat $ groupsToBranches'
 108                   $ fromList $ map (\g -> (getGroupId g, g))
 109                   $ foldlWithKey (\acc id groups' ->
 110                         -- | 4) create the parent group
 111                         let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
 112                         in  acc ++ [parent]) []
 113                   -- | 3) group the current groups by parentId
 114                   $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
 115
 116         newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
 117     in  traceSynchronyEnd
 118       $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
 119              -- | 6) update each period at curLvl + 1
 120              . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
 121              -- | 7) by adding the parents
 122              (\phyloLvl ->
 123                 if member (phyloLvl ^. phylo_levelPeriod) newPeriods
 124                     then phyloLvl & phylo_levelGroups
 125                             .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
 126                     else phyloLvl)
 127       -- | 2) add the curLvl + 1 phyloLevel to the phylo
 128       $ addPhyloLevel (curLvl + 1)
 129       -- | 1) update the current groups (with level parent pointers) in the phylo
 130       $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo
 131
 132 --------------------
 133 -- | Clustering | --
 134 --------------------
 135
 136 toPairs :: SynchronyStrategy -> [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
 137 toPairs strategy groups = case strategy of
 138   MergeRegularGroups -> pairs
 139                       $ filter (\g -> all (== 3) $ (g ^. phylo_groupMeta) ! "dynamics") groups
 140   MergeAllGroups -> pairs groups
 141   where
 142     pairs :: [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
 143     pairs gs = filter (\(g,g') -> (not . null) $ intersect (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams)) (listToCombi' gs)
 144
 145
 146 toDiamonds :: [PhyloGroup] -> [[PhyloGroup]]
 147 toDiamonds groups = foldl' (\acc groups' ->
 148                         acc ++ ( elems
 149                                $ Map.filter (\v -> length v > 1)
 150                                $ fromListWith (++)
 151                                $ foldl' (\acc' g ->
 152                                     acc' ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodChilds)) [] groups')) []
 153                   $ elems
 154                   $ Map.filter (\v -> length v > 1)
 155                   $ fromListWith (++)
 156                   $ foldl' (\acc g -> acc ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodParents)  ) [] groups
 157
 158
 159 groupsToEdges :: Proximity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)]
 160 groupsToEdges prox sync nbDocs diago groups =
 161     case sync of
 162         ByProximityThreshold  thr sens _ strat ->
 163             filter (\(_,w) -> w >= thr)
 164           $ toEdges sens
 165           $ toPairs strat groups
 166         ByProximityDistribution sens strat ->
 167             let diamonds = sortOn snd
 168                          $ toEdges sens $ concat
 169                          $ map (\gs -> toPairs strat gs) $ toDiamonds groups
 170              in take (div (length diamonds) 2) diamonds
 171     where
 172         toEdges :: Double -> [(PhyloGroup,PhyloGroup)] -> [((PhyloGroup,PhyloGroup),Double)]
 173         toEdges sens edges =
 174             case prox of
 175                 WeightedLogJaccard _ -> map (\(g,g') ->
 176                                                      ((g,g'), weightedLogJaccard' sens nbDocs diago
 177                                                                   (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) edges
 178                 _ -> undefined
 179
 180
 181
 182 toRelatedComponents :: [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)] -> [[PhyloGroup]]
 183 toRelatedComponents nodes edges =
 184   let ref = fromList $ map (\g -> (getGroupId g, g)) nodes
 185       clusters = relatedComponents $ ((map (\((g,g'),_) -> [getGroupId g, getGroupId g']) edges) ++ (map (\g -> [getGroupId g]) nodes))
 186    in map (\cluster -> map (\gId -> ref ! gId) cluster) clusters
 187
 188 toParentId :: PhyloGroup -> PhyloGroupId
 189 toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1), child ^. phylo_groupIndex)
 190
 191
 192 reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 193 reduceGroups prox sync docs diagos branch =
 194     -- | 1) reduce a branch as a set of periods & groups
 195     let periods = fromListWith (++)
 196                  $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
 197     in  (concat . concat . elems)
 198       $ mapWithKey (\prd groups ->
 199             -- | 2) for each period, transform the groups as a proximity graph filtered by a threshold
 200             let diago = reduceDiagos $ filterDiago diagos [prd]
 201                 edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
 202              in map (\comp ->
 203                     -- | 4) add to each groups their futur level parent group
 204                     let parentId = toParentId (head' "parentId" comp)
 205                     in  map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
 206                 -- |3) reduce the graph a a set of related components
 207               $ toRelatedComponents groups edges) periods
 208
 209
 210 adjustClustering :: Synchrony -> [[PhyloGroup]] -> [[PhyloGroup]]
 211 adjustClustering sync branches = case sync of
 212   ByProximityThreshold _ _ scope _ -> case scope of
 213       SingleBranch -> branches
 214       SiblingBranches -> groupBy (\g g' -> (last' "adjustClustering" $ (g  ^. phylo_groupMeta) ! "breaks")
 215                                         == (last' "adjustClustering" $ (g' ^. phylo_groupMeta) ! "breaks"))
 216                        $ sortOn _phylo_groupBranchId $ concat branches
 217       AllBranches -> [concat branches]
 218   ByProximityDistribution _ _ -> branches
 219
 220
 221
 222 synchronicClustering :: Phylo -> Phylo
 223 synchronicClustering phylo =
 224     let prox = phyloProximity $ getConfig phylo
 225         sync = phyloSynchrony $ getConfig phylo
 226         docs = phylo ^. phylo_timeDocs
 227         diagos = map coocToDiago $ phylo ^. phylo_timeCooc
 228         newBranches  = map (\branch -> reduceGroups prox sync docs diagos branch)
 229                      $ map processDynamics
 230                      $ adjustClustering sync
 231                      $ phyloToLastBranches
 232                      $ traceSynchronyStart phylo
 233         newBranches' = newBranches `using` parList rdeepseq
 234      in toNextLevel' phylo $ concat newBranches'
 235
 236
 237 ----------------
 238 -- | probes | --
 239 ----------------
 240
 241 -- synchronicDistance :: Phylo -> Level -> String
 242 -- synchronicDistance phylo lvl =
 243 --     foldl' (\acc branch ->
 244 --              acc <> (foldl' (\acc' period ->
 245 --                               acc' <> let prox  = phyloProximity $ getConfig phylo
 246 --                                           sync  = phyloSynchrony $ getConfig phylo
 247 --                                           docs  = _phylo_timeDocs phylo
 248 --                                           prd   = _phylo_groupPeriod $ head' "distance" period
 249 --                                           edges = groupsToEdges prox 0.1 (_bpt_sensibility sync)
 250 --                                                   ((sum . elems) $ restrictKeys docs $ periodsToYears [_phylo_groupPeriod $ head' "distance" period]) period
 251 --                                       in foldl' (\mem (_,w) ->
 252 --                                           mem <> show (prd)
 253 --                                               <> "\t"
 254 --                                               <> show (w)
 255 --                                               <> "\n"
 256 --                                         ) "" edges
 257 --                      ) ""  $ elems $ groupByField _phylo_groupPeriod branch)
 258 --     ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo