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Commit 406ae431 authored by qlobbe's avatar qlobbe
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optimisation for temporal matching

parent b0826576
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Showing with 193 additions and 136 deletions
src/Gargantext/Viz/AdaptativePhylo.hs
View file @ 406ae431
......@@ -88,7 +88,13 @@ data ContextualUnit =
Fis
{ _fis_support :: Int
, _fis_size :: Int }
deriving (Show,Generic,Eq)
deriving (Show,Generic,Eq)
data Quality =
Quality { _qua_relevance :: Double
, _qua_minBranch :: Int }
deriving (Show,Generic,Eq)
data Config =
......@@ -100,6 +106,7 @@ data Config =
, phyloLevel :: Int
, phyloProximity :: Proximity
, phyloSynchrony :: Synchrony
, phyloQuality :: Quality
, timeUnit :: TimeUnit
, contextualUnit :: ContextualUnit
, exportLabel :: [PhyloLabel]
......@@ -118,8 +125,9 @@ defaultConfig =
, phyloLevel = 1
, phyloProximity = WeightedLogJaccard 10 0 0.1
, phyloSynchrony = ByProximityDistribution 0
, phyloQuality = Quality 1 1
, timeUnit = Year 3 1 5
, contextualUnit = Fis 2 4
, contextualUnit = Fis 1 4
, exportLabel = [BranchLabel MostInclusive 2, GroupLabel MostEmergentInclusive 2]
, exportSort = ByHierarchy
, exportFilter = [ByBranchSize 2]
......@@ -147,6 +155,8 @@ instance FromJSON Filter
instance ToJSON Filter
instance FromJSON Synchrony
instance ToJSON Synchrony
instance FromJSON Quality
instance ToJSON Quality
-- | Software parameters
......@@ -362,6 +372,7 @@ data PhyloExport =
makeLenses ''Config
makeLenses ''Proximity
makeLenses ''Quality
makeLenses ''ContextualUnit
makeLenses ''PhyloLabel
makeLenses ''TimeUnit
......
src/Gargantext/Viz/Phylo/Example.hs
View file @ 406ae431
......@@ -83,7 +83,7 @@ queryViewEx = "level=3"
phyloQueryView :: PhyloQueryView
phyloQueryView = PhyloQueryView 2 Merge False 2 [BranchAge,BranchBirth,BranchGroups] [] [BranchPeakInc,GroupLabelIncDyn] (Just (ByBranchBirth,Asc)) Json Flat True
phyloQueryView = PhyloQueryView 1 Merge False 1 [BranchAge,BranchBirth,BranchGroups] [] [BranchPeakInc,GroupLabelIncDyn] (Just (ByBranchBirth,Asc)) Json Flat True
--------------------------------------------------
......@@ -110,7 +110,7 @@ queryEx = "title=Cesar et Cleôpatre"
phyloQueryBuild :: PhyloQueryBuild
phyloQueryBuild = PhyloQueryBuild "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
3 1 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.5 20) 5 0.8 0.5 4 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.3 0)
3 1 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.9 10) 5 0.8 0.5 4 1 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.3 0)
......
src/Gargantext/Viz/Phylo/PhyloExport.hs
View file @ 406ae431
......@@ -156,6 +156,8 @@ mergePointers groups =
exportToDot :: Phylo -> PhyloExport -> DotGraph DotId
exportToDot phylo export =
trace ("\n-- | Convert " <> show(length $ export ^. export_branches) <> " branches and "
<> show(length $ export ^. export_groups) <> " groups to a dot file\n") $
digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do
-- | 1) init the dot graph
......@@ -238,10 +240,12 @@ filterByBranchSize thr export =
& export_groups %~ (filter (\g -> not $ elem (g ^. phylo_groupBranchId) (map _branch_id $ snd branches')))
processFilters :: [Filter] -> PhyloExport -> PhyloExport
processFilters filters export =
processFilters :: [Filter] -> Quality -> PhyloExport -> PhyloExport
processFilters filters qua export =
foldl (\export' f -> case f of
ByBranchSize thr -> filterByBranchSize thr export'
ByBranchSize thr -> if (thr < (fromIntegral $ qua ^. qua_minBranch))
then filterByBranchSize (fromIntegral $ qua ^. qua_minBranch) export'
else filterByBranchSize thr export'
) export filters
--------------
......@@ -439,7 +443,7 @@ processDynamics groups =
toPhyloExport :: Phylo -> DotGraph DotId
toPhyloExport phylo = exportToDot phylo
$ processFilters (exportFilter $ getConfig phylo)
$ processFilters (exportFilter $ getConfig phylo) (phyloQuality $ getConfig phylo)
$ processSort (exportSort $ getConfig phylo)
$ processLabels (exportLabel $ getConfig phylo) (getRoots phylo)
$ processMetrics export
......
src/Gargantext/Viz/Phylo/TemporalMatching.hs
View file @ 406ae431
......@@ -15,14 +15,14 @@ Portability : POSIX
module Gargantext.Viz.Phylo.TemporalMatching where
import Data.List (concat, splitAt, tail, sortOn, (++), intersect, null, inits, groupBy, scanl, nub, union, elemIndex, (!!), dropWhile, partition)
import Data.Map (Map, fromList, elems, restrictKeys, unionWith, intersectionWith, findWithDefault, filterWithKey)
import Data.List (concat, splitAt, tail, sortOn, (++), intersect, null, inits, groupBy, scanl, nub, union, elemIndex, (!!), dropWhile)
import Data.Map (Map, fromList, elems, restrictKeys, unionWith, intersectionWith, findWithDefault, filterWithKey, keys, (!))
import Gargantext.Prelude
import Gargantext.Viz.AdaptativePhylo
import Gargantext.Viz.Phylo.PhyloTools
import Prelude (logBase)
-- import Prelude (logBase)
import Control.Lens hiding (Level)
import Control.Parallel.Strategies (parList, rdeepseq, using)
-- import Debug.Trace (trace)
......@@ -98,90 +98,84 @@ toProximity docs proximity ego target target' =
-- | Local Matching | --
------------------------
toLastPeriod :: Filiation -> [PhyloPeriodId] -> PhyloPeriodId
toLastPeriod fil periods = case fil of
ToParents -> head' "toLastPeriod" (sortOn fst periods)
ToChilds -> last' "toLastPeriod" (sortOn fst periods)
toLazyPairs :: [Pointer] -> Filiation -> Double -> Proximity -> PhyloPeriodId -> [(PhyloGroup,PhyloGroup)] -> [(PhyloGroup,PhyloGroup)]
toLazyPairs pointers fil thr prox prd pairs =
if null pointers then pairs
else let rest = filterPointers prox thr pointers
in if null rest
then let prd' = toLastPeriod fil (map (fst . fst . fst) pointers)
in if prd' == prd
then []
else filter (\(g,g') ->
case fil of
ToParents -> ((fst $ g ^. phylo_groupPeriod) < (fst prd'))
|| ((fst $ g' ^. phylo_groupPeriod) < (fst prd'))
ToChilds -> ((fst $ g ^. phylo_groupPeriod) > (fst prd'))
|| ((fst $ g' ^. phylo_groupPeriod) > (fst prd'))) pairs
else []
-- | Find pairs of valuable candidates to be matched
makePairs :: [PhyloGroup] -> [PhyloPeriodId] -> [PhyloPeriodId] -> [(PhyloGroup,PhyloGroup)]
makePairs candidates periods periods' = case null periods of
True -> []
-- | at least on of the pair candidates should be from the last added period
False -> filter (\(cdt,cdt') ->
((inLastPeriod cdt periods) || (inLastPeriod cdt' periods))
&& (not $ inOldPeriods cdt periods')
&& (not $ inOldPeriods cdt' periods'))
$ listToKeys candidates
makePairs' :: PhyloGroup -> [PhyloGroup] -> [PhyloPeriodId] -> [Pointer] -> Filiation -> Double -> Proximity -> Map Date Double -> [(PhyloGroup,PhyloGroup)]
makePairs' ego candidates periods pointers fil thr prox docs =
case null periods of
True -> []
False -> toLazyPairs pointers fil thr prox lastPrd
-- | at least on of the pair candidates should be from the last added period
$ filter (\(g,g') -> ((g ^. phylo_groupPeriod) == lastPrd)
|| ((g' ^. phylo_groupPeriod) == lastPrd))
$ listToKeys
$ filter (\g -> (g ^. phylo_groupPeriod == lastPrd)
|| ((toProximity docs prox ego ego g) >= thr)) candidates
where
inLastPeriod :: PhyloGroup -> [PhyloPeriodId] -> Bool
inLastPeriod g prds = (g ^. phylo_groupPeriod) == (last' "makePairs" prds)
--------------------------------------
inOldPeriods :: PhyloGroup -> [PhyloPeriodId] -> Bool
inOldPeriods g prds = elem (g ^. phylo_groupPeriod) prds
lastPrd :: PhyloPeriodId
lastPrd = toLastPeriod fil periods
keepOldOnes :: Filiation -> Proximity -> Double -> PhyloGroup -> Bool
keepOldOnes fil proxi thr ego = any (\(_,w) -> filterProximity proxi thr w)
$ getPeriodPointers fil ego
filterPointers :: Proximity -> Double -> [Pointer] -> [Pointer]
filterPointers proxi thr pts = filter (\(_,w) -> filterProximity proxi thr w) pts
findLastPeriod :: Filiation -> [Pointer] -> PhyloPeriodId
findLastPeriod fil pts = case fil of
ToParents -> head' "findLastPeriod" $ sortOn fst $ map (fst . fst . fst) pts
ToChilds -> head' "findLastPeriod" $ reverse $ sortOn fst $ map (fst . fst . fst) pts
phyloGroupMatching :: [[PhyloGroup]] -> Filiation -> Proximity -> Map Date Double -> Double -> PhyloGroup -> PhyloGroup
phyloGroupMatching candidates fil proxi docs thr ego =
if keepOldOnes fil proxi thr ego
-- | keep some of the old pointers
then addPointers ego fil TemporalPointer
$ filterPointers proxi thr
$ getPeriodPointers fil ego
else case null pointers of
case null nextPointers of
-- | let's find new pointers
True -> addPointers ego fil TemporalPointer []
True -> if null $ filterPointers proxi thr $ getPeriodPointers fil ego
then addPointers ego fil TemporalPointer []
-- | or keep the old ones
else addPointers ego fil TemporalPointer
$ filterPointers proxi thr $ getPeriodPointers fil ego
False -> addPointers ego fil TemporalPointer
$ head' "phyloGroupMatching"
-- | Keep only the best set of pointers grouped by proximity
$ groupBy (\pt pt' -> snd pt == snd pt')
$ reverse $ sortOn snd $ head' "pointers" pointers
$ reverse $ sortOn snd $ head' "pointers"
$ nextPointers
-- | Find the first time frame where at leats one pointer satisfies the proximity threshold
where
--------------------------------------
oldPeriods :: [PhyloPeriodId] -> [PhyloPeriodId]
oldPeriods periods =
if (null $ getPeriodPointers fil ego)
then []
else
let period = findLastPeriod fil $ getPeriodPointers fil ego
in fst $ partition (\prd -> case fil of
ToChilds -> prd <= period
ToParents -> prd >= period ) periods
--------------------------------------
pointers :: [[Pointer]]
pointers = take 1
nextPointers :: [[Pointer]]
nextPointers = take 1
$ dropWhile (null)
-- | for each time frame, process the proximity on relevant pairs of targeted groups
$ scanl (\acc groups ->
let periods = nub
$ concat $ map (\gs -> if null gs
then []
else [_phylo_groupPeriod $ head' "pointers" gs]) groups
periods' = oldPeriods periods
pairs = makePairs (concat groups) periods periods'
in acc ++ ( filterPointers proxi thr
$ concat
$ map (\(c,c') ->
-- | process the proximity between the current group and a pair of candidates
let proximity = toProximity (filterDocs docs ([ego ^. phylo_groupPeriod] ++ periods)) proxi ego c c'
in if (c == c')
then [(getGroupId c,proximity)]
else [(getGroupId c,proximity),(getGroupId c',proximity)] ) pairs)
) []
-- | groups from [[1900],[1900,1901],[1900,1901,1902],...]
$ inits candidates
let periods = nub $ map _phylo_groupPeriod $ concat groups
docs' = (filterDocs docs ([ego ^. phylo_groupPeriod] ++ periods))
pairs = makePairs' ego (concat groups) periods (getPeriodPointers fil ego) fil thr proxi docs
in acc ++ ( filterPointers proxi thr
$ concat
$ map (\(c,c') ->
-- | process the proximity between the current group and a pair of candidates
let proximity = toProximity docs' proxi ego c c'
in if (c == c')
then [(getGroupId c,proximity)]
else [(getGroupId c,proximity),(getGroupId c',proximity)] ) pairs )) []
$ inits candidates -- | groups from [[1900],[1900,1901],[1900,1901,1902],...]
filterDocs :: Map Date Double -> [PhyloPeriodId] -> Map Date Double
......@@ -215,18 +209,22 @@ getCandidates fil ego targets =
phyloBranchMatching :: Int -> [PhyloPeriodId] -> Proximity -> Double -> Map Date Double -> [PhyloGroup] -> [PhyloGroup]
phyloBranchMatching frame periods proximity thr docs branch = traceBranchMatching proximity thr
$ matchByPeriods ToParents
$ groupByField _phylo_groupPeriod
$ matchByPeriods ToChilds
-- $ matchByPeriods ToParents
-- $ groupByField _phylo_groupPeriod
$ matchByPeriods
$ groupByField _phylo_groupPeriod branch
where
--------------------------------------
matchByPeriods :: Filiation -> Map PhyloPeriodId [PhyloGroup] -> [PhyloGroup]
matchByPeriods fil branch' = foldl' (\acc prd ->
let periods' = getNextPeriods fil frame prd periods
candidates = map (\prd' -> findWithDefault [] prd' branch') periods'
docs' = filterDocs docs ([prd] ++ periods')
egos = map (\g -> phyloGroupMatching (getCandidates fil g candidates) fil proximity docs' thr g)
matchByPeriods :: Map PhyloPeriodId [PhyloGroup] -> [PhyloGroup]
matchByPeriods branch' = foldl' (\acc prd ->
let periodsPar = getNextPeriods ToParents frame prd periods
periodsChi = getNextPeriods ToChilds frame prd periods
candidatesPar = map (\prd' -> findWithDefault [] prd' branch') periodsPar
candidatesChi = map (\prd' -> findWithDefault [] prd' branch') periodsChi
docsPar = filterDocs docs ([prd] ++ periodsPar)
docsChi = filterDocs docs ([prd] ++ periodsChi)
egos = map (\ego -> phyloGroupMatching (getCandidates ToParents ego candidatesPar) ToParents proximity docsPar thr
$ phyloGroupMatching (getCandidates ToChilds ego candidatesChi) ToChilds proximity docsChi thr ego)
$ findWithDefault [] prd branch'
egos' = egos `using` parList rdeepseq
in acc ++ egos' ) [] periods
......@@ -237,48 +235,78 @@ phyloBranchMatching frame periods proximity thr docs branch = traceBranchMatchin
-----------------------
termFreq :: Int -> [[PhyloGroup]] -> Double
termFreq term branches = (sum $ map (\g -> findWithDefault 0 (term,term) (g ^. phylo_groupCooc)) $ concat branches)
/ (sum $ map (\g -> getTrace $ g ^. phylo_groupCooc) $ concat branches)
entropy :: [[PhyloGroup]] -> Double
entropy branches =
let terms = ngramsInBranches branches
in sum $ map (\term -> (1 / log (termFreq term branches))
/ (sum $ map (\branch -> 1 / log (termFreq term [branch])) branches)
* (sum $ map (\branch ->
let q = branchObs term (length $ concat branches) branch
in if (q == 0)
then 0
else - q * logBase 2 q ) branches) ) terms
where
-- | Probability to observe a branch given a random term of the phylo
branchObs :: Int -> Int -> [PhyloGroup] -> Double
branchObs term total branch = (fromIntegral $ length $ filter (\g -> elem term $ g ^. phylo_groupNgrams) branch)
/ (fromIntegral total)
homogeneity :: [[PhyloGroup]] -> Double
homogeneity branches =
let nbGroups = length $ concat branches
in sum
$ map (\branch -> (if (length branch == nbGroups)
then 1
else (1 / log (branchCov branch nbGroups))
/ (sum $ map (\branch' -> 1 / log (branchCov branch' nbGroups)) branches))
* (sum $ map (\term -> (termFreq term branches)
/ (sum $ map (\term' -> termFreq term' branches) $ ngramsInBranches [branch])
* (fromIntegral $ sum $ ngramsInBranches [filter (\g -> elem term $ g ^. phylo_groupNgrams) branch])
/ (fromIntegral $ sum $ ngramsInBranches [branch])
) $ ngramsInBranches [branch]) ) branches
count :: Eq a => a -> [a] -> Int
count x = length . filter (== x)
termFreq' :: Int -> [PhyloGroup] -> Double
termFreq' term groups =
let ngrams = concat $ map _phylo_groupNgrams groups
in (fromIntegral $ count term ngrams)
/ (fromIntegral $ length ngrams)
relevantBranches :: Int -> Int -> [[PhyloGroup]] -> [[PhyloGroup]]
relevantBranches term thr branches =
filter (\groups -> (length groups >= thr)
&& (any (\group -> elem term $ group ^. phylo_groupNgrams) groups)) branches
branchCov' :: [PhyloGroup] -> [[PhyloGroup]] -> Double
branchCov' branch branches =
(fromIntegral $ length branch) / (fromIntegral $ length $ concat branches)
toRecall :: Double -> Int -> Int -> [[PhyloGroup]] -> Double
toRecall freq term thr branches =
-- | given a random term in a phylo
freq
-- | for each relevant branches
* (sum $ map (\branch ->
-- | given its local coverage
((branchCov' branch branches') / (sum $ map (\b -> branchCov' b branches') branches'))
-- | compute the local recall
* ( (fromIntegral $ length $ filter (\group -> elem term $ group ^. phylo_groupNgrams) branch)
/ (fromIntegral $ length $ filter (\group -> elem term $ group ^. phylo_groupNgrams) $ concat branches'))) branches')
where
branches' :: [[PhyloGroup]]
branches' = relevantBranches term thr branches
toAccuracy :: Double -> Int -> Int -> [[PhyloGroup]] -> Double
toAccuracy freq term thr branches =
-- | given a random term in a phylo
freq
-- | for each relevant branches
* (sum $ map (\branch ->
-- | given its local coverage
((branchCov' branch branches') / (sum $ map (\b -> branchCov' b branches') branches'))
-- | compute the local accuracy
* ( (fromIntegral $ length $ filter (\group -> elem term $ group ^. phylo_groupNgrams) branch)
/ (fromIntegral $ length branch))) branches')
where
branchCov :: [PhyloGroup] -> Int -> Double
branchCov branch total = (fromIntegral $ length branch) / (fromIntegral total)
branches' :: [[PhyloGroup]]
branches' = relevantBranches term thr branches
toPhyloQuality' :: Quality -> Map Int Double -> [[PhyloGroup]] -> Double
toPhyloQuality' quality frequency branches =
if (foldl' (\acc b -> acc && (length b < (quality ^. qua_minBranch))) True branches)
-- | the local phylo is composed of small branches
then 0
else
let relevance = quality ^. qua_relevance
-- | compute the F score for a given relevance
in ((1 + relevance ** 2) * accuracy * recall)
/ (((relevance ** 2) * accuracy + recall))
where
terms :: [Int]
terms = keys frequency
-- | for each term compute the global accuracy
accuracy :: Double
accuracy = sum $ map (\term -> toAccuracy (frequency ! term) term (quality ^. qua_minBranch) branches) terms
-- | for each term compute the global recall
recall :: Double
recall = sum $ map (\term -> toRecall (frequency ! term) term (quality ^. qua_minBranch) branches) terms
toPhyloQuality :: [[PhyloGroup]] -> Double
toPhyloQuality branches = sqrt (homogeneity branches / entropy branches)
-----------------------------
......@@ -289,37 +317,44 @@ toPhyloQuality branches = sqrt (homogeneity branches / entropy branches)
groupsToBranches :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
groupsToBranches groups =
-- | run the related component algorithm
let graph = zip [1..]
$ relatedComponents
$ map (\group -> [getGroupId group]
let egos = groupBy (\gs gs' -> (fst $ fst $ head' "egos" gs) == (fst $ fst $ head' "egos" gs'))
$ sortOn (\gs -> fst $ fst $ head' "egos" gs)
$ map (\group -> [getGroupId group]
++ (map fst $ group ^. phylo_groupPeriodParents)
++ (map fst $ group ^. phylo_groupPeriodChilds) ) $ elems groups
-- | first find the related components by inside each ego's period
graph' = map relatedComponents egos
-- | then run it for the all the periods
graph = zip [1..]
$ relatedComponents $ concat (graph' `using` parList rdeepseq)
-- | update each group's branch id
in map (\(bId,ids) ->
map (\group -> group & phylo_groupBranchId %~ (\(lvl,lst) -> (lvl,lst ++ [bId])))
$ elems $ restrictKeys groups (Set.fromList ids)) graph
let groups' = map (\group -> group & phylo_groupBranchId %~ (\(lvl,lst) -> (lvl,lst ++ [bId])))
$ elems $ restrictKeys groups (Set.fromList ids)
in groups' `using` parList rdeepseq ) graph
recursiveMatching :: Proximity -> Double -> Int -> [PhyloPeriodId] -> Map Date Double -> Double -> [[PhyloGroup]] -> [PhyloGroup]
recursiveMatching proximity thr frame periods docs quality branches =
recursiveMatching :: Proximity -> Quality -> Map Int Double -> Double -> Int -> [PhyloPeriodId] -> Map Date Double -> Double -> [[PhyloGroup]] -> [PhyloGroup]
recursiveMatching proximity qua freq thr frame periods docs quality branches =
if (length branches == (length $ concat branches))
then concat branches
else if thr > 1
else if thr >= 1
then concat branches
else
-- trace (show(quality) <> " (vs) sum of " <> show(nextQualities))
case quality <= (sum nextQualities) of
-- | success : the new threshold improves the quality score, let's go deeper (traceMatchSuccess thr quality (sum nextQualities))
True -> concat
$ map (\branches' ->
let idx = fromJust $ elemIndex branches' nextBranches
in recursiveMatching proximity (thr + (getThresholdStep proximity)) frame periods docs (nextQualities !! idx) branches')
let idx = fromJust $ elemIndex branches' nextBranches
in recursiveMatching proximity qua freq (thr + (getThresholdStep proximity)) frame periods docs (nextQualities !! idx) branches')
$ nextBranches
-- | failure : last step was a local maximum of quality, let's validate it (traceMatchFailure thr quality (sum nextQualities))
False -> concat branches
where
-- | 2) for each of the possible next branches process the phyloQuality score
nextQualities :: [Double]
nextQualities = map toPhyloQuality nextBranches
nextQualities = map (\nextBranch -> toPhyloQuality' qua freq nextBranch) nextBranches
-- | 1) for each local branch process a temporal matching then find the resulting branches
nextBranches :: [[[PhyloGroup]]]
nextBranches =
......@@ -338,7 +373,9 @@ temporalMatching phylo = updatePhyloGroups 1 branches' phylo
branches' = fromList
$ map (\g -> (getGroupId g, g))
$ traceMatchEnd
$ recursiveMatching (phyloProximity $ getConfig phylo)
$ recursiveMatching (phyloProximity $ getConfig phylo)
(phyloQuality $ getConfig phylo)
frequency
( (getThresholdInit $ phyloProximity $ getConfig phylo)
+ (getThresholdStep $ phyloProximity $ getConfig phylo))
(getTimeFrame $ timeUnit $ getConfig phylo)
......@@ -346,7 +383,12 @@ temporalMatching phylo = updatePhyloGroups 1 branches' phylo
(phylo ^. phylo_timeDocs) quality branches
-- | 3) process the quality score
quality :: Double
quality = toPhyloQuality branches
quality = toPhyloQuality' (phyloQuality $ getConfig phylo) frequency branches
-- | 3) process the constants of the quality score
frequency :: Map Int Double
frequency =
let terms = ngramsInBranches branches
in fromList $ map (\t -> (t, ((termFreq' t $ concat branches) / (sum $ map (\t' -> termFreq' t' $ concat branches) terms)))) terms
-- | 2) group into branches
branches :: [[PhyloGroup]]
branches = groupsToBranches $ fromList $ map (\group -> (getGroupId group, group)) groups'
......
src/Gargantext/Viz/Phylo/Tools.hs
View file @ 406ae431
......@@ -815,7 +815,7 @@ getProximity cluster = case cluster of
-- | To initialize all the Cluster / Proximity with their default parameters
initFis :: Maybe Bool -> Maybe Support -> Maybe Int -> FisParams
initFis (def True -> kmf) (def 2 -> min') (def 4 -> thr) = FisParams kmf min' thr
initFis (def True -> kmf) (def 0 -> min') (def 0 -> thr) = FisParams kmf min' thr
initHamming :: Maybe Double -> HammingParams
initHamming (def 0.01 -> sens) = HammingParams sens
......
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