src/Gargantext/Viz/Phylo/TemporalMatching.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo.TemporalMatching
   3 Description : Module dedicated to the adaptative temporal matching 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
  12 module Gargantext.Viz.Phylo.TemporalMatching where
  13
  14 import Data.List (concat, splitAt, tail, sortOn, (++), intersect, null, inits, groupBy, scanl, nub, nubBy, union, dropWhile, partition, or, sort, (!!))
  15 import Data.Map  (Map, fromList, elems, restrictKeys, unionWith, findWithDefault, keys, (!), (!?), filterWithKey, singleton, empty, mapKeys, adjust)
  16
  17 import Gargantext.Prelude
  18 import Gargantext.Viz.AdaptativePhylo
  19 import Gargantext.Viz.Phylo.PhyloTools
  20
  21 import Prelude (floor)
  22 import Control.Lens hiding (Level)
  23 import Control.Parallel.Strategies (parList, rdeepseq, using)
  24 import Debug.Trace (trace)
  25
  26 import Text.Printf
  27
  28 import qualified Data.Map as Map
  29 import qualified Data.Set as Set
  30
  31
  32 -------------------
  33 -- | Proximity | --
  34 -------------------
  35
  36
  37 -- | To compute a jaccard similarity between two lists
  38 jaccard :: [Int] -> [Int] -> Double
  39 jaccard inter' union' = ((fromIntegral . length) $ inter') / ((fromIntegral . length) $ union')
  40
  41
  42 -- | Process the inverse sumLog
  43 sumInvLog' :: Double -> Double -> [Double] -> Double
  44 sumInvLog' s nb diago = foldl (\mem occ -> mem + (1 / (log (occ + s) / log (nb + s)))) 0 diago
  45
  46
  47 -- | Process the sumLog
  48 sumLog' :: Double -> Double -> [Double] -> Double
  49 sumLog' s nb diago = foldl (\mem occ -> mem + (log (occ + s) / log (nb + s))) 0 diago
  50
  51
  52 weightedLogJaccard' :: Double -> Double -> Map Int Double -> [Int] -> [Int] -> Double
  53 weightedLogJaccard' sens nbDocs diago ngrams ngrams'
  54   | null ngramsInter           = 0
  55   | ngramsInter == ngramsUnion = 1
  56   | sens == 0    = jaccard ngramsInter ngramsUnion
  57   | sens > 0     = (sumInvLog' sens nbDocs diagoInter) / (sumInvLog' sens nbDocs diagoUnion)
  58   | otherwise    = (sumLog' sens nbDocs diagoInter) / (sumLog' sens nbDocs diagoUnion)
  59   where
  60     --------------------------------------
  61     ngramsInter :: [Int]
  62     ngramsInter = intersect ngrams ngrams'
  63     --------------------------------------
  64     ngramsUnion :: [Int]
  65     ngramsUnion = union ngrams ngrams'
  66     --------------------------------------
  67     diagoInter :: [Double]
  68     diagoInter =  elems $ restrictKeys diago (Set.fromList ngramsInter)
  69     --------------------------------------
  70     diagoUnion :: [Double]
  71     diagoUnion =  elems $ restrictKeys diago (Set.fromList ngramsUnion)
  72     --------------------------------------
  73
  74
  75 -- | To process the proximity between a current group and a pair of targets group
  76 toProximity :: Double -> Map Int Double -> Proximity -> [Int] -> [Int] -> [Int] -> Double
  77 toProximity nbDocs diago proximity egoNgrams targetNgrams targetNgrams' =
  78   case proximity of
  79     WeightedLogJaccard sens ->
  80       let pairNgrams = if targetNgrams == targetNgrams'
  81                           then targetNgrams
  82                           else union targetNgrams targetNgrams'
  83        in weightedLogJaccard' sens nbDocs diago egoNgrams pairNgrams
  84     Hamming -> undefined
  85
  86
  87 ------------------------
  88 -- | Local Matching | --
  89 ------------------------
  90
  91 findLastPeriod :: Filiation -> [PhyloPeriodId] -> PhyloPeriodId
  92 findLastPeriod fil periods = case fil of
  93     ToParents -> head' "findLastPeriod" (sortOn fst periods)
  94     ToChilds  -> last' "findLastPeriod" (sortOn fst periods)
  95
  96
  97 -- | To filter pairs of candidates related to old pointers periods
  98 removeOldPointers :: [Pointer] -> Filiation -> Double -> Proximity -> PhyloPeriodId
  99                   -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
 100                   -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
 101 removeOldPointers oldPointers fil thr prox prd pairs
 102   | null oldPointers = pairs
 103   | null (filterPointers prox thr oldPointers) =
 104     let lastMatchedPrd = findLastPeriod fil (map (fst . fst . fst) oldPointers)
 105      in if lastMatchedPrd == prd
 106         then []
 107         else filter (\((id,_),(id',_)) ->
 108                 case fil of
 109                      ToParents -> (((fst . fst . fst) id ) < (fst lastMatchedPrd))
 110                                || (((fst . fst . fst) id') < (fst lastMatchedPrd))
 111                      ToChilds  -> (((fst . fst . fst) id ) > (fst lastMatchedPrd))
 112                                || (((fst . fst . fst) id') > (fst lastMatchedPrd))) pairs
 113   | otherwise = []
 114
 115
 116 makePairs' :: (PhyloGroupId,[Int]) -> [(PhyloGroupId,[Int])] -> [PhyloPeriodId] -> [Pointer] -> Filiation -> Double -> Proximity
 117            -> Map Date Double -> Map Date Cooc -> [((PhyloGroupId,[Int]),(PhyloGroupId,[Int]))]
 118 makePairs' (egoId, egoNgrams) candidates periods oldPointers fil thr prox docs diagos =
 119     if (null periods)
 120         then []
 121         else removeOldPointers oldPointers fil thr prox lastPrd
 122            {- at least on of the pair candidates should be from the last added period -}
 123            $ filter (\((id,_),(id',_)) -> ((fst . fst) id == lastPrd) || ((fst . fst) id' == lastPrd))
 124            $ listToKeys
 125            $ filter (\(id,ngrams) ->
 126                 let nbDocs = (sum . elems) $ filterDocs docs    ([(fst . fst) egoId, (fst . fst) id])
 127                     diago  = reduceDiagos  $ filterDiago diagos ([(fst . fst) egoId, (fst . fst) id])
 128                  in (toProximity nbDocs diago prox egoNgrams egoNgrams ngrams) >= thr
 129             ) candidates
 130     where
 131       lastPrd :: PhyloPeriodId
 132       lastPrd = findLastPeriod fil periods
 133
 134
 135 filterPointers :: Proximity -> Double -> [Pointer] -> [Pointer]
 136 filterPointers proxi thr pts = filter (\(_,w) -> filterProximity proxi thr w) pts
 137
 138 filterPointers' :: Proximity -> Double -> [(Pointer,[Int])] -> [(Pointer,[Int])]
 139 filterPointers' proxi thr pts = filter (\((_,w),_) -> filterProximity proxi thr w) pts
 140
 141
 142 reduceDiagos :: Map Date Cooc -> Map Int Double
 143 reduceDiagos diagos = mapKeys (\(k,_) -> k)
 144                     $ foldl (\acc diago -> unionWith (+) acc diago) empty (elems diagos)
 145
 146 filterPointersByPeriod :: Filiation -> [(Pointer,[Int])] -> [Pointer]
 147 filterPointersByPeriod fil pts =
 148   let pts' = sortOn (fst . fst . fst . fst) pts
 149       inf  = (fst . fst . fst . fst) $ head' "filterPointersByPeriod" pts'
 150       sup  = (fst . fst . fst . fst) $ last' "filterPointersByPeriod" pts'
 151    in map fst
 152     $ nubBy (\pt pt' -> snd pt == snd pt')
 153     $ filter (\pt -> ((fst . fst . fst . fst) pt == inf) || ((fst . fst . fst . fst) pt == sup))
 154     $ case fil of
 155         ToParents -> reverse pts'
 156         ToChilds  -> pts'
 157
 158 phyloGroupMatching :: [[(PhyloGroupId,[Int])]] -> Filiation -> Proximity -> Map Date Double -> Map Date Cooc
 159                    -> Double -> [Pointer] -> (PhyloGroupId,[Int]) -> [Pointer]
 160 phyloGroupMatching candidates fil proxi docs diagos thr oldPointers (id,ngrams) =
 161         if (null $ filterPointers proxi thr oldPointers)
 162           {- let's find new pointers -}
 163           then if null nextPointers
 164             then []
 165             else filterPointersByPeriod fil
 166                $ head' "phyloGroupMatching"
 167                -- Keep only the best set of pointers grouped by proximity
 168                $ groupBy (\pt pt' -> (snd . fst) pt == (snd . fst) pt')
 169                $ reverse $ sortOn (snd . fst) $ head' "pointers" nextPointers
 170                -- Find the first time frame where at leats one pointer satisfies the proximity threshold
 171           else oldPointers
 172     where
 173         nextPointers :: [[(Pointer,[Int])]]
 174         nextPointers = take 1
 175                  $ dropWhile (null)
 176                  {- for each time frame, process the proximity on relevant pairs of targeted groups -}
 177                  $ scanl (\acc groups ->
 178                             let periods = nub $ map (fst . fst . fst) $ concat groups
 179                                 nbdocs  = sum $ elems $ (filterDocs docs ([(fst . fst) id] ++ periods))
 180                                 diago   = reduceDiagos
 181                                         $ filterDiago diagos ([(fst . fst) id] ++ periods)
 182                                         {- important resize nbdocs et diago dans le make pairs -}
 183                                 pairs = makePairs' (id,ngrams) (concat groups) periods oldPointers fil thr proxi docs diagos
 184                             in acc ++ ( filterPointers' proxi thr
 185                                         $ concat
 186                                         $ map (\(c,c') ->
 187                                             {- process the proximity between the current group and a pair of candidates -}
 188                                             let proximity = toProximity nbdocs diago proxi ngrams (snd c) (snd c')
 189                                             in if ((c == c') || (snd c == snd c'))
 190                                                then [((fst c,proximity),snd c)]
 191                                                else [((fst c,proximity),snd c),((fst c',proximity),snd c')] ) pairs )) []
 192                  $ inits candidates -- groups from [[1900],[1900,1901],[1900,1901,1902],...]
 193
 194
 195 filterDocs :: Map Date Double -> [PhyloPeriodId] -> Map Date Double
 196 filterDocs d pds = restrictKeys d $ periodsToYears pds
 197
 198 filterDiago :: Map Date Cooc -> [PhyloPeriodId] -> Map Date Cooc
 199 filterDiago diago pds = restrictKeys diago $ periodsToYears pds
 200
 201
 202 -----------------------------
 203 -- | Matching Processing | --
 204 -----------------------------
 205
 206
 207 getNextPeriods :: Filiation -> Int -> PhyloPeriodId -> [PhyloPeriodId] -> [PhyloPeriodId]
 208 getNextPeriods fil max' pId pIds =
 209     case fil of
 210         ToChilds  -> take max' $ (tail . snd) $ splitAt (elemIndex' pId pIds) pIds
 211         ToParents -> take max' $ (reverse . fst) $ splitAt (elemIndex' pId pIds) pIds
 212
 213
 214 getCandidates :: PhyloGroup -> [[(PhyloGroupId,[Int])]] -> [[(PhyloGroupId,[Int])]]
 215 getCandidates ego targets =
 216   map (\groups' ->
 217     filter (\g' -> (not . null) $ intersect (ego ^. phylo_groupNgrams) (snd g')
 218   ) groups') targets
 219
 220
 221 matchGroupsToGroups :: Int -> [PhyloPeriodId] -> Proximity -> Double -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 222 matchGroupsToGroups frame periods proximity thr docs coocs groups =
 223   let groups' = groupByField _phylo_groupPeriod groups
 224    in foldl' (\acc prd ->
 225         let -- 1) find the parents/childs matching periods
 226             periodsPar = getNextPeriods ToParents frame prd periods
 227             periodsChi = getNextPeriods ToChilds  frame prd periods
 228             --  2) find the parents/childs matching candidates
 229             candidatesPar = map (\prd' -> map (\g -> (getGroupId g, g ^. phylo_groupNgrams)) $ findWithDefault [] prd' groups') periodsPar
 230             candidatesChi = map (\prd' -> map (\g -> (getGroupId g, g ^. phylo_groupNgrams)) $ findWithDefault [] prd' groups') periodsChi
 231             --  3) find the parents/child number of docs by years
 232             docsPar = filterDocs docs ([prd] ++ periodsPar)
 233             docsChi = filterDocs docs ([prd] ++ periodsChi)
 234             --  4) find the parents/child diago by years
 235             diagoPar = filterDiago (map coocToDiago coocs) ([prd] ++ periodsPar)
 236             diagoChi = filterDiago (map coocToDiago coocs) ([prd] ++ periodsPar)
 237             --  5) match in parallel all the groups (egos) to their possible candidates
 238             egos  = map (\ego ->
 239                       let pointersPar = phyloGroupMatching (getCandidates ego candidatesPar) ToParents proximity docsPar diagoPar
 240                                         thr (getPeriodPointers ToParents ego) (getGroupId ego, ego ^. phylo_groupNgrams)
 241                           pointersChi = phyloGroupMatching (getCandidates ego candidatesChi) ToChilds  proximity docsChi diagoChi
 242                                         thr (getPeriodPointers ToChilds  ego) (getGroupId ego, ego ^. phylo_groupNgrams)
 243                        in addPointers ToChilds  TemporalPointer pointersChi
 244                         $ addPointers ToParents TemporalPointer pointersPar ego)
 245                   $ findWithDefault [] prd groups'
 246             egos' = egos `using` parList rdeepseq
 247          in acc ++ egos'
 248     ) [] periods
 249
 250
 251 -----------------------
 252 -- | Phylo Quality | --
 253 -----------------------
 254
 255
 256 relevantBranches :: Int -> [[PhyloGroup]] -> [[PhyloGroup]]
 257 relevantBranches term branches =
 258     filter (\groups -> (any (\group -> elem term $ group ^. phylo_groupNgrams) groups)) branches
 259
 260 accuracy :: Int -> [PhyloGroup] -> Double
 261 accuracy x bk  = ((fromIntegral $ length $ filter (\g -> elem x $ g ^. phylo_groupNgrams) bk)
 262                /  (fromIntegral $ length bk))
 263
 264 recall :: Int -> [PhyloGroup] -> [[PhyloGroup]] -> Double
 265 recall x bk bx = ((fromIntegral $ length $ filter (\g -> elem x $ g ^. phylo_groupNgrams) bk)
 266                /  (fromIntegral $ length $ filter (\g -> elem x $ g ^. phylo_groupNgrams) $ concat bx))
 267
 268 fScore :: Double -> Int -> [PhyloGroup] -> [[PhyloGroup]] -> Double
 269 fScore beta x bk bx =
 270   let rec = recall x bk bx
 271       acc = accuracy x bk
 272    in ((1 + beta ** 2) * acc * rec)
 273     / (((beta ** 2) * rec + acc))
 274
 275
 276 wk :: [PhyloGroup] -> Double
 277 wk bk = fromIntegral $ length bk
 278
 279
 280 toPhyloQuality' :: Double -> Map Int Double -> [[PhyloGroup]] -> Double
 281 toPhyloQuality' beta freq branches =
 282   if (null branches)
 283     then 0
 284     else sum
 285        $ map (\i ->
 286           let bks = relevantBranches i branches
 287            in (freq ! i) * (sum $ map (\bk -> ((wk bk) / (sum $ map wk bks)) * (fScore beta i bk bks)) bks))
 288        $ keys freq
 289
 290 toRecall :: Map Int Double -> [[PhyloGroup]] -> Double
 291 toRecall freq branches =
 292   if (null branches)
 293     then 0
 294     else sum
 295        $ map (\x ->
 296           let px = freq ! x
 297               bx = relevantBranches x branches
 298               wks = sum $ map wk bx
 299            in (px / pys) * (sum $ map (\bk -> ((wk bk) / wks) * (recall x bk bx)) bx))
 300        $ keys freq
 301   where
 302       pys :: Double
 303       pys = sum (elems freq)
 304
 305
 306 toAccuracy :: Map Int Double -> [[PhyloGroup]] -> Double
 307 toAccuracy freq branches =
 308   if (null branches)
 309     then 0
 310     else sum
 311        $ map (\x ->
 312           let px = freq ! x
 313               bx = relevantBranches x branches
 314               wks = sum $ map wk bx
 315            in (px / pys) * (sum $ map (\bk -> ((wk bk) / wks) * (accuracy x bk)) bx))
 316        $ keys freq
 317   where
 318       pys :: Double
 319       pys = sum (elems freq)
 320
 321
 322 -- | here we do the average of all the local f_scores
 323 toPhyloQuality :: Double -> Map Int Double -> [[PhyloGroup]] -> Double
 324 toPhyloQuality beta freq branches =
 325   if (null branches)
 326     then 0
 327     else sum
 328        $ map (\x ->
 329           let px = freq ! x
 330               bx = relevantBranches x branches
 331               wks = sum $ map wk bx
 332            in (px / pys) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore beta x bk bx)) bx))
 333        $ keys freq
 334   where
 335       pys :: Double
 336       pys = sum (elems freq)
 337
 338
 339 ------------------------------------
 340 -- | Constant Temporal Matching | --
 341 ------------------------------------
 342
 343
 344 groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
 345 groupsToBranches' groups =
 346     -- | run the related component algorithm
 347     let egos = groupBy (\gs gs' -> (fst $ fst $ head' "egos" gs) == (fst $ fst $ head' "egos" gs'))
 348              $ sortOn  (\gs -> fst $ fst $ head' "egos" gs)
 349              $ map (\group -> [getGroupId group]
 350                             ++ (map fst $ group ^. phylo_groupPeriodParents)
 351                             ++ (map fst $ group ^. phylo_groupPeriodChilds) ) $ elems groups
 352         --  first find the related components by inside each ego's period
 353         --  a supprimer
 354         graph' = map relatedComponents egos
 355         --  then run it for the all the periods
 356         graph  = zip [1..]
 357                $ relatedComponents $ concat (graph' `using` parList rdeepseq)
 358     --  update each group's branch id
 359     in map (\(bId,ids) ->
 360         let groups'  = map (\group -> group & phylo_groupBranchId %~ (\(lvl,lst) -> (lvl,lst ++ [bId])))
 361                      $ elems $ restrictKeys groups (Set.fromList ids)
 362          in groups' `using` parList rdeepseq ) graph
 363
 364
 365 reduceFrequency :: Map Int Double -> [[PhyloGroup]] -> Map Int Double
 366 reduceFrequency frequency branches =
 367   restrictKeys frequency (Set.fromList $ (nub . concat) $ map _phylo_groupNgrams $ concat branches)
 368
 369 updateThr :: Double -> [[PhyloGroup]] -> [[PhyloGroup]]
 370 updateThr thr branches = map (\b -> map (\g ->
 371   g & phylo_groupMeta .~ (singleton "seaLevels" (((g ^. phylo_groupMeta) ! "seaLevels") ++ [thr]))) b) branches
 372
 373
 374 --  Sequentially break each branch of a phylo where
 375 -- done = all the allready broken branches
 376 -- ego  = the current branch we want to break
 377 -- rest = the branches we still have to break
 378 breakBranches :: Proximity -> Double -> Map Int Double -> Int -> Double -> Double -> Double
 379               -> Int -> Map Date Double -> Map Date Cooc -> [PhyloPeriodId] -> [([PhyloGroup],Bool)] -> ([PhyloGroup],Bool) -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
 380 breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods done ego rest =
 381   --  1) keep or not the new division of ego
 382   let done' = done ++ (if snd ego
 383                         then
 384                             (if ((null (fst ego')) || (quality > quality'))
 385                                then
 386                                 -- trace ("  ✗ F(β) = " <> show(quality) <> " (vs) " <> show(quality')
 387                                 --         <> "  | "  <> show(length $ fst ego) <> " groups : "
 388                                 --         <> "  |✓ " <> show(length $ fst ego') <> show(map length $ fst ego')
 389                                 --         <> "  |✗ " <> show(length $ snd ego') <> "[" <> show(length $ concat $ snd ego') <> "]")
 390                                   [(fst ego,False)]
 391                                else
 392                                 -- trace ("  ✓ level = " <> printf "%.1f" thr <> "")
 393                                 -- trace ("  ✓ F(β) = " <> show(quality) <> " (vs) " <> show(quality')
 394                                 --         <> "  | "  <> show(length $ fst ego) <> " groups : "
 395                                 --         <> "  |✓ " <> show(length $ fst ego') <> show(map length $ fst ego')
 396                                 --         <> "  |✗ " <> show(length $ snd ego') <> "[" <> show(length $ concat $ snd ego') <> "]")
 397                                   ((map (\e -> (e,True)) (fst ego')) ++ (map (\e -> (e,False)) (snd ego'))))
 398                         else [ego])
 399   in
 400     --  2) if there is no more branches in rest then return else continue
 401     if null rest
 402       then done'
 403       else breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
 404                        done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
 405   where
 406     --------------------------------------
 407     quality :: Double
 408     quality = toPhyloQuality beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
 409     --------------------------------------
 410     ego' :: ([[PhyloGroup]],[[PhyloGroup]])
 411     ego' =
 412       let branches  = groupsToBranches' $ fromList $ map (\g -> (getGroupId g, g))
 413                     $ matchGroupsToGroups frame periods proximity thr docs coocs (fst ego)
 414           branches' = branches `using` parList rdeepseq
 415        in partition (\b -> (length $ nub $ map _phylo_groupPeriod b) >= minBranch)
 416         $ thrToMeta thr
 417         $ depthToMeta (elevation - depth) branches'
 418     --------------------------------------
 419     quality' :: Double
 420     quality' = toPhyloQuality beta frequency
 421                                     ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
 422
 423
 424 seaLevelMatching :: Proximity -> Double -> Int -> Map Int Double -> Double -> Double -> Double -> Double
 425                  -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
 426 seaLevelMatching proximity beta minBranch frequency thr step depth elevation frame periods docs coocs branches =
 427   --  if there is no branch to break or if seaLvl level > 1 then end
 428   if (thr >= 1) || ((not . or) $ map snd branches)
 429     then branches
 430     else
 431       -- break all the possible branches at the current seaLvl level
 432       let quality    = toPhyloQuality beta frequency (map fst branches)
 433           acc        = toAccuracy frequency (map fst branches)
 434           rec        = toRecall frequency (map fst branches)
 435           branches'  = trace ("↑ level = " <> printf "%.3f" thr <> " F(β) = " <> printf "%.5f" quality
 436                                                                 <> " ξ = " <> printf "%.5f" acc
 437                                                                 <> " ρ = " <> printf "%.5f" rec
 438                                                                 <> " branches = " <> show(length branches) <> " ↴")
 439                      $ breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
 440                                      [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
 441           frequency' = reduceFrequency frequency (map fst branches')
 442        in seaLevelMatching proximity beta minBranch frequency' (thr + step) step (depth - 1) elevation frame periods docs coocs branches'
 443
 444
 445 constanteTemporalMatching :: Double -> Double -> Phylo -> Phylo
 446 constanteTemporalMatching start step phylo = updatePhyloGroups 1
 447                          (fromList $ map (\g -> (getGroupId g,g)) $ traceMatchEnd $ concat branches)
 448                          (toPhyloHorizon phylo)
 449   where
 450     --  2) process the temporal matching by elevating seaLvl level
 451     branches :: [[PhyloGroup]]
 452     branches = map fst
 453              $ seaLevelMatching (phyloProximity $ getConfig phylo)
 454                                 (_qua_granularity $ phyloQuality $ getConfig phylo)
 455                                 (_qua_minBranch $ phyloQuality $ getConfig phylo)
 456                                 (phylo ^. phylo_termFreq)
 457                                 start step
 458                                 ((((1 - start) / step) - 1))
 459                                 (((1 - start) / step))
 460                                 (getTimeFrame $ timeUnit $ getConfig phylo)
 461                                 (getPeriodIds phylo)
 462                                 (phylo ^. phylo_timeDocs)
 463                                 (phylo ^. phylo_timeCooc)
 464                                 groups
 465     --  1) for each group process an initial temporal Matching
 466     --  here we suppose that all the groups of level 1 are part of the same big branch
 467     groups :: [([PhyloGroup],Bool)]
 468     groups = map (\b -> (b,(length $ nub $ map _phylo_groupPeriod b) >= (_qua_minBranch $ phyloQuality $ getConfig phylo)))
 469            $ groupsToBranches' $ fromList $ map (\g -> (getGroupId g, g))
 470            $ matchGroupsToGroups (getTimeFrame $ timeUnit $ getConfig phylo)
 471                          (getPeriodIds phylo) (phyloProximity $ getConfig phylo)
 472                          start
 473                          (phylo ^. phylo_timeDocs)
 474                          (phylo ^. phylo_timeCooc)
 475                          (traceTemporalMatching $ getGroupsFromLevel 1 phylo)
 476
 477 -----------------
 478 -- | Horizon | --
 479 -----------------
 480
 481 toPhyloHorizon :: Phylo -> Phylo
 482 toPhyloHorizon phylo =
 483   let t0 = take 1 (getPeriodIds phylo)
 484       groups = getGroupsFromLevelPeriods 1 t0 phylo
 485       sens = getSensibility (phyloProximity $ getConfig phylo)
 486       nbDocs = sum $ elems $ filterDocs (phylo ^. phylo_timeDocs) t0
 487       diago = reduceDiagos $ filterDiago (phylo ^. phylo_timeCooc) t0
 488    in phylo & phylo_horizon .~ (fromList $ map (\(g,g') ->
 489         ((getGroupId g,getGroupId g'),weightedLogJaccard' sens nbDocs diago (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) $ listToCombi' groups)
 490
 491
 492 --------------------------------------
 493 -- | Adaptative Temporal Matching | --
 494 --------------------------------------
 495
 496
 497 thrToMeta :: Double -> [[PhyloGroup]] -> [[PhyloGroup]]
 498 thrToMeta thr branches =
 499   map (\b ->
 500     map (\g -> g & phylo_groupMeta .~ (adjust (\lst -> lst ++ [thr]) "seaLevels" (g ^. phylo_groupMeta))) b) branches
 501
 502 depthToMeta :: Double -> [[PhyloGroup]] -> [[PhyloGroup]]
 503 depthToMeta depth branches =
 504   let break = length branches > 1
 505    in map (\b ->
 506         map (\g ->
 507           if break then g & phylo_groupMeta .~ (adjust (\lst -> lst ++ [depth]) "breaks"(g ^. phylo_groupMeta))
 508                    else g) b) branches
 509
 510 reduceTupleMapByKeys :: Eq a => [a] -> Map (a,a) Double -> Map (a,a) Double
 511 reduceTupleMapByKeys ks m = filterWithKey (\(k,k') _ -> (elem k ks) && (elem k' ks)) m
 512
 513
 514 getInTupleMap :: Ord a => Map (a,a) Double -> a -> a -> Double
 515 getInTupleMap m k k'
 516   | isJust (m !? ( k ,k')) = m ! ( k ,k')
 517   | isJust (m !? ( k',k )) = m ! ( k',k )
 518   | otherwise = 0
 519
 520
 521 toThreshold :: Double -> Map (PhyloGroupId,PhyloGroupId) Double -> Double
 522 toThreshold lvl proxiGroups =
 523   let idx = ((Map.size proxiGroups) `div` (floor lvl)) - 1
 524    in if idx >= 0
 525         then (sort $ elems proxiGroups) !! idx
 526         else 1
 527
 528
 529 -- done = all the allready broken branches
 530 -- ego  = the current branch we want to break
 531 -- rest = the branches we still have to break
 532 adaptativeBreakBranches :: Proximity -> Double -> Double -> Map (PhyloGroupId,PhyloGroupId) Double
 533                -> Double -> Map Int Double -> Int -> Int -> Map Date Double -> Map Date Cooc
 534                -> [PhyloPeriodId] -> [([PhyloGroup],(Bool,[Double]))] -> ([PhyloGroup],(Bool,[Double])) -> [([PhyloGroup],(Bool,[Double]))]
 535                -> [([PhyloGroup],(Bool,[Double]))]
 536 adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods done ego rest =
 537   --  1) keep or not the new division of ego
 538   let done' = done ++ (if (fst . snd) ego
 539                         then (if ((null (fst ego')) || (quality > quality'))
 540                                then
 541                                   [(concat $ thrToMeta thr $ [fst ego],(False, ((snd . snd) ego)))]
 542                                else
 543                                   (  (map (\e -> (e,(True,  ((snd . snd) ego) ++ [thr]))) (fst ego'))
 544                                   ++ (map (\e -> (e,(False, ((snd . snd) ego)))) (snd ego'))))
 545                         else [(concat $ thrToMeta thr $ [fst ego], snd ego)])
 546   in
 547     --  uncomment let .. in for debugging
 548     -- let part1 = partition (snd) done'
 549     --     part2 = partition (snd) rest
 550     --  in trace ( "[✓ " <> show(length $ fst part1) <> "(" <> show(length $ concat $ map (fst) $ fst part1) <> ")|✗ " <> show(length $ snd part1) <> "(" <> show(length $ concat $ map (fst) $ snd part1) <> ")] "
 551     --          <> "[✓ " <> show(length $ fst part2) <> "(" <> show(length $ concat $ map (fst) $ fst part2) <> ")|✗ " <> show(length $ snd part2) <> "(" <> show(length $ concat $ map (fst) $ snd part2) <> ")]"
 552     --            ) $
 553     --  2) if there is no more branches in rest then return else continue
 554     if null rest
 555       then done'
 556       else adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
 557                        done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
 558   where
 559     --------------------------------------
 560     thr :: Double
 561     thr = toThreshold depth $ Map.filter (\v -> v > (last' "breakBranches" $ (snd . snd) ego)) $ reduceTupleMapByKeys (map getGroupId $ fst ego) groupsProxi
 562     --------------------------------------
 563     quality :: Double
 564     quality = toPhyloQuality beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
 565     --------------------------------------
 566     ego' :: ([[PhyloGroup]],[[PhyloGroup]])
 567     ego' =
 568       let branches  = groupsToBranches' $ fromList $ map (\g -> (getGroupId g, g))
 569                     $ matchGroupsToGroups frame periods proxiConf thr docs coocs (fst ego)
 570           branches' = branches `using` parList rdeepseq
 571        in partition (\b -> (length $ nub $ map _phylo_groupPeriod b) > minBranch)
 572         $ thrToMeta thr
 573         $ depthToMeta (elevation - depth) branches'
 574     --------------------------------------
 575     quality' :: Double
 576     quality' = toPhyloQuality beta frequency
 577                                     ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
 578
 579
 580 adaptativeSeaLevelMatching :: Proximity -> Double -> Double -> Map (PhyloGroupId, PhyloGroupId) Double
 581                   -> Double -> Int -> Map Int Double
 582                   -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc
 583                   -> [([PhyloGroup],(Bool,[Double]))] -> [([PhyloGroup],(Bool,[Double]))]
 584 adaptativeSeaLevelMatching proxiConf depth elevation groupsProxi beta minBranch frequency frame periods docs coocs branches =
 585   --  if there is no branch to break or if seaLvl level >= depth then end
 586   if (Map.null groupsProxi) || (depth <= 0) || ((not . or) $ map (fst . snd) branches)
 587     then branches
 588     else
 589       --  break all the possible branches at the current seaLvl level
 590       let branches'  = adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
 591                                       [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
 592           frequency' = reduceFrequency frequency (map fst branches')
 593           groupsProxi' = reduceTupleMapByKeys (map (getGroupId) $ concat $ map (fst) $ filter (fst . snd) branches') groupsProxi
 594           -- thr = toThreshold depth groupsProxi
 595        in trace("\n  " <> foldl (\acc _ -> acc <> "🌊 ") "" [0..(elevation - depth)]
 596                        <> " [✓ " <> show(length $ filter (fst . snd) branches') <> "(" <> show(length $ concat $ map (fst) $ filter (fst . snd) branches')
 597                        <> ")|✗ " <> show(length $ filter (not . fst . snd) branches') <> "(" <> show(length $ concat $ map (fst) $ filter (not . fst . snd) branches') <> ")]"
 598                        <> " thr = ")
 599         $ adaptativeSeaLevelMatching proxiConf (depth - 1) elevation groupsProxi' beta minBranch frequency' frame periods docs coocs branches'
 600
 601
 602 adaptativeTemporalMatching :: Double -> Phylo -> Phylo
 603 adaptativeTemporalMatching elevation phylo = updatePhyloGroups 1
 604                           (fromList $ map (\g -> (getGroupId g,g)) $ traceMatchEnd $ concat branches)
 605                           (toPhyloHorizon phylo)
 606   where
 607     --  2) process the temporal matching by elevating seaLvl level
 608     branches :: [[PhyloGroup]]
 609     branches = map fst
 610              $ adaptativeSeaLevelMatching (phyloProximity $ getConfig phylo)
 611                                  (elevation - 1)
 612                                  elevation
 613                                  (phylo ^. phylo_groupsProxi)
 614                                  (_qua_granularity $ phyloQuality $ getConfig phylo)
 615                                  (_qua_minBranch $ phyloQuality $ getConfig phylo)
 616                                  (phylo ^. phylo_termFreq)
 617                                  (getTimeFrame $ timeUnit $ getConfig phylo)
 618                                  (getPeriodIds phylo)
 619                                  (phylo ^. phylo_timeDocs)
 620                                  (phylo ^. phylo_timeCooc)
 621                                  groups
 622     --  1) for each group process an initial temporal Matching
 623     --  here we suppose that all the groups of level 1 are part of the same big branch
 624     groups :: [([PhyloGroup],(Bool,[Double]))]
 625     groups = map (\b -> (b,((length $ nub $ map _phylo_groupPeriod b) >= (_qua_minBranch $ phyloQuality $ getConfig phylo),[thr])))
 626            $ groupsToBranches' $ fromList $ map (\g -> (getGroupId g, g))
 627            $ matchGroupsToGroups (getTimeFrame $ timeUnit $ getConfig phylo)
 628                          (getPeriodIds phylo) (phyloProximity $ getConfig phylo)
 629                          thr
 630                          (phylo ^. phylo_timeDocs)
 631                          (phylo ^. phylo_timeCooc)
 632                          (traceTemporalMatching $ getGroupsFromLevel 1 phylo)
 633     --------------------------------------
 634     thr :: Double
 635     thr = toThreshold elevation (phylo ^. phylo_groupsProxi)