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haskell-gargantext
Commit 32c7fe70 authored by qlobbe's avatar qlobbe
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change the quality function

parent ff268a4d
Pipeline #1189 failed with stage
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    Showing with 34 additions and 29 deletions
    src/Gargantext/Core/Viz/Phylo/TemporalMatching.hs
    View file @ 32c7fe70
    ......@@ -27,6 +27,7 @@ import Text.Printf
    import qualified Data.Map as Map
    import qualified Data.Set as Set
    import qualified Data.Vector as Vector
    -------------------
    ......@@ -320,22 +321,24 @@ toAccuracy freq branches =
    -- | here we do the average of all the local f_scores
    toPhyloQuality :: Double -> Map Int Double -> [[PhyloGroup]] -> Double
    toPhyloQuality beta freq branches =
    toPhyloQuality :: Double -> Double -> Map Int Double -> [[PhyloGroup]] -> Double
    toPhyloQuality fdt beta freq branches =
    if (null branches)
    then 0
    else sum
    $ map (\x ->
    let px = freq ! x
    bx = relevantBranches x branches
    -- let px = freq ! x
    let bx = relevantBranches x branches
    wks = sum $ map wk bx
    in (px / pys) * (sum $ map (\bk -> ((wk bk) / wks) * (fScore beta x bk bx)) 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 bk bx)) bx))
    $ keys freq
    where
    pys :: Double
    pys = sum (elems freq)
    -- where
    -- pys :: Double
    -- pys = sum (elems freq)
    -- 1 / nb de foundation
    -- attention au phenomene d'effritement
    ------------------------------------
    -- | Constant Temporal Matching | --
    ......@@ -376,9 +379,9 @@ updateThr thr branches = map (\b -> map (\g ->
    -- done = all the allready broken branches
    -- ego = the current branch we want to break
    -- rest = the branches we still have to break
    breakBranches :: Proximity -> Double -> Map Int Double -> Int -> Double -> Double -> Double
    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 proximity beta frequency minBranch thr depth elevation frame docs coocs periods done ego rest =
    breakBranches fdt proximity beta 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
    ......@@ -401,12 +404,12 @@ breakBranches proximity beta frequency minBranch thr depth elevation frame docs
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    else breakBranches fdt proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
    where
    --------------------------------------
    quality :: Double
    quality = toPhyloQuality beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    quality = toPhyloQuality fdt beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    --------------------------------------
    ego' :: ([[PhyloGroup]],[[PhyloGroup]])
    ego' =
    ......@@ -418,29 +421,29 @@ breakBranches proximity beta frequency minBranch thr depth elevation frame docs
    $ depthToMeta (elevation - depth) branches'
    --------------------------------------
    quality' :: Double
    quality' = toPhyloQuality beta frequency
    quality' = toPhyloQuality fdt beta frequency
    ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
    seaLevelMatching :: Proximity -> Double -> Int -> Map Int Double -> Double -> Double -> Double -> Double
    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 proximity beta minBranch frequency thr step depth elevation frame periods docs coocs branches =
    seaLevelMatching fdt proximity beta 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 beta frequency (map fst branches)
    let quality = toPhyloQuality fdt beta 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
    <> " ξ = " <> printf "%.5f" acc
    <> " ρ = " <> printf "%.5f" rec
    <> " branches = " <> show(length branches) <> " ↴")
    $ breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    $ breakBranches fdt proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
    frequency' = reduceFrequency frequency (map fst branches')
    in seaLevelMatching proximity beta minBranch frequency' (thr + step) step (depth - 1) elevation frame periods docs coocs branches'
    in seaLevelMatching fdt proximity beta minBranch frequency' (thr + step) step (depth - 1) elevation frame periods docs coocs branches'
    constanteTemporalMatching :: Double -> Double -> Phylo -> Phylo
    ......@@ -451,7 +454,8 @@ constanteTemporalMatching start step phylo = updatePhyloGroups 1
    -- 2) process the temporal matching by elevating seaLvl level
    branches :: [[PhyloGroup]]
    branches = map fst
    $ seaLevelMatching (phyloProximity $ getConfig phylo)
    $ seaLevelMatching (fromIntegral $ Vector.length $ getRoots phylo)
    (phyloProximity $ getConfig phylo)
    (_qua_granularity $ phyloQuality $ getConfig phylo)
    (_qua_minBranch $ phyloQuality $ getConfig phylo)
    (phylo ^. phylo_termFreq)
    ......@@ -530,11 +534,11 @@ toThreshold lvl proxiGroups =
    -- done = all the allready broken branches
    -- ego = the current branch we want to break
    -- rest = the branches we still have to break
    adaptativeBreakBranches :: Proximity -> Double -> Double -> Map (PhyloGroupId,PhyloGroupId) Double
    adaptativeBreakBranches :: Double -> Proximity -> Double -> Double -> Map (PhyloGroupId,PhyloGroupId) Double
    -> 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 proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods done ego rest =
    adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta 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'))
    ......@@ -554,7 +558,7 @@ adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency min
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    else adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    done' (head' "breakBranches" rest) (tail' "breakBranches" rest)
    where
    --------------------------------------
    ......@@ -562,7 +566,7 @@ adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency min
    thr = toThreshold depth $ Map.filter (\v -> v > (last' "breakBranches" $ (snd . snd) ego)) $ reduceTupleMapByKeys (map getGroupId $ fst ego) groupsProxi
    --------------------------------------
    quality :: Double
    quality = toPhyloQuality beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    quality = toPhyloQuality fdt beta frequency ((map fst done) ++ [fst ego] ++ (map fst rest))
    --------------------------------------
    ego' :: ([[PhyloGroup]],[[PhyloGroup]])
    ego' =
    ......@@ -574,21 +578,21 @@ adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency min
    $ depthToMeta (elevation - depth) branches'
    --------------------------------------
    quality' :: Double
    quality' = toPhyloQuality beta frequency
    quality' = toPhyloQuality fdt beta frequency
    ((map fst done) ++ (fst ego') ++ (snd ego') ++ (map fst rest))
    adaptativeSeaLevelMatching :: Proximity -> Double -> Double -> Map (PhyloGroupId, PhyloGroupId) Double
    adaptativeSeaLevelMatching :: Double -> Proximity -> Double -> Double -> Map (PhyloGroupId, PhyloGroupId) Double
    -> Double -> Int -> Map Int Double
    -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc
    -> [([PhyloGroup],(Bool,[Double]))] -> [([PhyloGroup],(Bool,[Double]))]
    adaptativeSeaLevelMatching proxiConf depth elevation groupsProxi beta minBranch frequency frame periods docs coocs branches =
    adaptativeSeaLevelMatching fdt proxiConf depth elevation groupsProxi beta 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 proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    let branches' = adaptativeBreakBranches fdt proxiConf depth elevation groupsProxi beta 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
    ......@@ -597,7 +601,7 @@ adaptativeSeaLevelMatching proxiConf depth elevation groupsProxi beta minBranch
    <> " [✓ " <> 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 proxiConf (depth - 1) elevation groupsProxi' beta minBranch frequency' frame periods docs coocs branches'
    $ adaptativeSeaLevelMatching fdt proxiConf (depth - 1) elevation groupsProxi' beta minBranch frequency' frame periods docs coocs branches'
    adaptativeTemporalMatching :: Double -> Phylo -> Phylo
    ......@@ -608,7 +612,8 @@ adaptativeTemporalMatching elevation phylo = updatePhyloGroups 1
    -- 2) process the temporal matching by elevating seaLvl level
    branches :: [[PhyloGroup]]
    branches = map fst
    $ adaptativeSeaLevelMatching (phyloProximity $ getConfig phylo)
    $ adaptativeSeaLevelMatching (fromIntegral $ Vector.length $ getRoots phylo)
    (phyloProximity $ getConfig phylo)
    (elevation - 1)
    elevation
    (phylo ^. phylo_groupsProxi)
    ......
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