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haskell-gargantext
Commit e454b205 authored by qlobbe's avatar qlobbe
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change beta to lambda [0...1]

parent 3e4bd243
Pipeline #1345 failed with stage
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    src/Gargantext/Core/Viz/AdaptativePhylo.hs
    View file @ e454b205
    ......@@ -147,7 +147,7 @@ defaultConfig =
    , seaElevation = Constante 0.1 0.1
    , findAncestors = True
    , phyloSynchrony = ByProximityThreshold 0.5 10 SiblingBranches MergeAllGroups
    , phyloQuality = Quality 100 1
    , phyloQuality = Quality 0 1
    , timeUnit = Year 3 1 5
    , clique = MaxClique 0
    , exportLabel = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
    ......
    src/Gargantext/Core/Viz/Phylo/PhyloExport.hs
    View file @ e454b205
    ......@@ -673,7 +673,7 @@ tracePhyloAncestors :: [[PhyloGroup]] -> [[PhyloGroup]]
    tracePhyloAncestors groups = trace ( "-- | Found " <> show(length $ concat $ map _phylo_groupAncestors $ concat groups) <> " ancestors") groups
    tracePhyloInfo :: Phylo -> Phylo
    tracePhyloInfo phylo = trace ("\n" <> "##########################" <> "\n\n" <> "-- | Phylo with β = "
    tracePhyloInfo phylo = trace ("\n" <> "##########################" <> "\n\n" <> "-- | Phylo with λ = "
    <> show(_qua_granularity $ phyloQuality $ getConfig phylo) <> " applied to "
    <> show(length $ Vector.toList $ getRoots phylo) <> " foundations"
    ) phylo
    ......
    src/Gargantext/Core/Viz/Phylo/TemporalMatching.hs
    View file @ e454b205
    ......@@ -18,7 +18,7 @@ import Gargantext.Prelude
    import Gargantext.Core.Viz.AdaptativePhylo
    import Gargantext.Core.Viz.Phylo.PhyloTools
    import Prelude (floor)
    import Prelude (floor,tan,pi)
    import Control.Lens hiding (Level)
    import Control.Parallel.Strategies (parList, rdeepseq, using)
    import Debug.Trace (trace)
    ......@@ -272,11 +272,11 @@ recall x bk bx = ((fromIntegral $ length $ filter (\g -> elem x $ g ^. phylo_gro
    / (fromIntegral $ length $ filter (\g -> elem x $ g ^. phylo_groupNgrams) $ concat bx))
    fScore :: Double -> Int -> [(Date,Date)] -> [PhyloGroup] -> [[PhyloGroup]] -> Double
    fScore beta x periods bk bx =
    fScore lambda x periods bk bx =
    let rec = recall x bk bx
    acc = accuracy x periods bk
    in ((1 + beta ** 2) * acc * rec)
    / (((beta ** 2) * rec + acc))
    in ((1 + lambda ** 2) * acc * rec)
    / (((lambda ** 2) * rec + acc))
    wk :: [PhyloGroup] -> Double
    ......@@ -284,14 +284,14 @@ wk bk = fromIntegral $ length bk
    toPhyloQuality' :: Double -> Map Int Double -> [[PhyloGroup]] -> Double
    toPhyloQuality' beta freq branches =
    toPhyloQuality' lambda freq branches =
    if (null branches)
    then 0
    else sum
    $ map (\i ->
    let bks = relevantBranches i branches
    periods = nub $ map _phylo_groupPeriod $ filter (\g -> elem i $ g ^. phylo_groupNgrams) $ concat bks
    in (freq ! i) * (sum $ map (\bk -> ((wk bk) / (sum $ map wk bks)) * (fScore beta i periods bk bks)) bks))
    in (freq ! i) * (sum $ map (\bk -> ((wk bk) / (sum $ map wk bks)) * (fScore lambda i periods bk bks)) bks))
    $ keys freq
    toRecall :: Map Int Double -> [[PhyloGroup]] -> Double
    ......@@ -330,7 +330,7 @@ toAccuracy freq branches =
    -- | here we do the average of all the local f_scores
    toPhyloQuality :: Double -> Double -> Map Int Double -> [[PhyloGroup]] -> Double
    toPhyloQuality fdt beta freq branches =
    toPhyloQuality fdt lambda freq branches =
    if (null branches)
    then 0
    else sum
    ......@@ -341,7 +341,8 @@ toPhyloQuality fdt beta freq branches =
    periods = nub $ map _phylo_groupPeriod $ filter (\g -> elem x $ g ^. phylo_groupNgrams) $ concat bx
    wks = sum $ map wk bx
    -- in (px / pys) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore beta x bk bx)) bx))
    in (1 / fdt) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore beta x periods bk bx)) bx))
    -- in (1 / fdt) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore beta x periods bk bx)) bx))
    in (1 / fdt) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore (tan (lambda * pi / 2)) x periods bk bx)) bx))
    $ keys freq
    -- where
    -- pys :: Double
    ......@@ -390,7 +391,7 @@ updateThr thr branches = map (\b -> map (\g ->
    -- rest = the branches we still have to break
    breakBranches :: Double -> Proximity -> Double -> Map Int Double -> Int -> Double -> Double -> Double
    -> Int -> Map Date Double -> Map Date Cooc -> [PhyloPeriodId] -> [([PhyloGroup],Bool)] -> ([PhyloGroup],Bool) -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
    breakBranches fdt proximity beta frequency minBranch thr depth elevation frame docs coocs periods done ego rest =
    breakBranches fdt proximity lambda frequency minBranch thr depth elevation frame docs coocs periods done ego rest =
    -- 1) keep or not the new division of ego
    let done' = done ++ (if snd ego
    then
    ......@@ -413,12 +414,12 @@ breakBranches fdt proximity beta frequency minBranch thr depth elevation frame d
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else breakBranches fdt proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    else breakBranches fdt proximity lambda frequency minBranch thr depth elevation frame docs coocs periods
    done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
    where
    --------------------------------------
    quality :: Double
    quality = toPhyloQuality fdt beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    quality = toPhyloQuality fdt lambda frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    --------------------------------------
    ego' :: ([[PhyloGroup]],[[PhyloGroup]])
    ego' =
    ......@@ -430,29 +431,29 @@ breakBranches fdt proximity beta frequency minBranch thr depth elevation frame d
    $ depthToMeta (elevation - depth) branches'
    --------------------------------------
    quality' :: Double
    quality' = toPhyloQuality fdt beta frequency
    quality' = toPhyloQuality fdt lambda frequency
    ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
    seaLevelMatching :: Double -> Proximity -> Double -> Int -> Map Int Double -> Double -> Double -> Double -> Double
    -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
    seaLevelMatching fdt proximity beta minBranch frequency thr step depth elevation frame periods docs coocs branches =
    seaLevelMatching fdt proximity lambda minBranch frequency thr step depth elevation frame periods docs coocs branches =
    -- if there is no branch to break or if seaLvl level > 1 then end
    if (thr >= 1) || ((not . or) $ map snd branches)
    then branches
    else
    -- break all the possible branches at the current seaLvl level
    let quality = toPhyloQuality fdt beta frequency (map fst branches)
    let quality = toPhyloQuality fdt lambda frequency (map fst branches)
    acc = toAccuracy frequency (map fst branches)
    rec = toRecall frequency (map fst branches)
    branches' = trace ("↑ level = " <> printf "%.3f" thr <> " F(β) = " <> printf "%.5f" quality
    branches' = trace ("↑ level = " <> printf "%.3f" thr <> " F(λ) = " <> printf "%.5f" quality
    <> " ξ = " <> printf "%.5f" acc
    <> " ρ = " <> printf "%.5f" rec
    <> " branches = " <> show(length branches) <> " ↴")
    $ breakBranches fdt proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    $ breakBranches fdt proximity lambda frequency minBranch thr depth elevation frame docs coocs periods
    [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
    frequency' = reduceFrequency frequency (map fst branches')
    in seaLevelMatching fdt proximity beta minBranch frequency' (thr + step) step (depth - 1) elevation frame periods docs coocs branches'
    in seaLevelMatching fdt proximity lambda minBranch frequency' (thr + step) step (depth - 1) elevation frame periods docs coocs branches'
    constanteTemporalMatching :: Double -> Double -> Phylo -> Phylo
    ......@@ -547,7 +548,7 @@ adaptativeBreakBranches :: Double -> Proximity -> Double -> Double -> Map (Phylo
    -> Double -> Map Int Double -> Int -> Int -> Map Date Double -> Map Date Cooc
    -> [PhyloPeriodId] -> [([PhyloGroup],(Bool,[Double]))] -> ([PhyloGroup],(Bool,[Double])) -> [([PhyloGroup],(Bool,[Double]))]
    -> [([PhyloGroup],(Bool,[Double]))]
    adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods done ego rest =
    adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi lambda frequency minBranch frame docs coocs periods done ego rest =
    -- 1) keep or not the new division of ego
    let done' = done ++ (if (fst . snd) ego
    then (if ((null (fst ego')) || (quality > quality'))
    ......@@ -567,7 +568,7 @@ adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequenc
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    else adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi lambda frequency minBranch frame docs coocs periods
    done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
    where
    --------------------------------------
    ......@@ -575,7 +576,7 @@ adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequenc
    thr = toThreshold depth $ Map.filter (\v -> v > (last' "breakBranches" $ (snd . snd) ego)) $ reduceTupleMapByKeys (map getGroupId $ fst ego) groupsProxi
    --------------------------------------
    quality :: Double
    quality = toPhyloQuality fdt beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    quality = toPhyloQuality fdt lambda frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    --------------------------------------
    ego' :: ([[PhyloGroup]],[[PhyloGroup]])
    ego' =
    ......@@ -587,7 +588,7 @@ adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequenc
    $ depthToMeta (elevation - depth) branches'
    --------------------------------------
    quality' :: Double
    quality' = toPhyloQuality fdt beta frequency
    quality' = toPhyloQuality fdt lambda frequency
    ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
    ......@@ -595,13 +596,13 @@ adaptativeSeaLevelMatching :: Double -> Proximity -> Double -> Double -> Map (Ph
    -> Double -> Int -> Map Int Double
    -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc
    -> [([PhyloGroup],(Bool,[Double]))] -> [([PhyloGroup],(Bool,[Double]))]
    adaptativeSeaLevelMatching fdt proxiConf depth elevation groupsProxi beta minBranch frequency frame periods docs coocs branches =
    adaptativeSeaLevelMatching fdt proxiConf depth elevation groupsProxi lambda minBranch frequency frame periods docs coocs branches =
    -- if there is no branch to break or if seaLvl level >= depth then end
    if (Map.null groupsProxi) || (depth <= 0) || ((not . or) $ map (fst . snd) branches)
    then branches
    else
    -- break all the possible branches at the current seaLvl level
    let branches' = adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    let branches' = adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi lambda frequency minBranch frame docs coocs periods
    [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
    frequency' = reduceFrequency frequency (map fst branches')
    groupsProxi' = reduceTupleMapByKeys (map (getGroupId) $ concat $ map (fst) $ filter (fst . snd) branches') groupsProxi
    ......@@ -610,7 +611,7 @@ adaptativeSeaLevelMatching fdt proxiConf depth elevation groupsProxi beta minBra
    <> " [✓ " <> show(length $ filter (fst . snd) branches') <> "(" <> show(length $ concat $ map (fst) $ filter (fst . snd) branches')
    <> ")|✗ " <> show(length $ filter (not . fst . snd) branches') <> "(" <> show(length $ concat $ map (fst) $ filter (not . fst . snd) branches') <> ")]"
    <> " thr = ")
    $ adaptativeSeaLevelMatching fdt proxiConf (depth - 1) elevation groupsProxi' beta minBranch frequency' frame periods docs coocs branches'
    $ adaptativeSeaLevelMatching fdt proxiConf (depth - 1) elevation groupsProxi' lambda minBranch frequency' frame periods docs coocs branches'
    adaptativeTemporalMatching :: Double -> Phylo -> Phylo
    ......
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