New similarity measure for inter-temporal matching added named WeightedLogSim...

New similarity measure for inter-temporal matching added named WeightedLogSim Adapted from Wang, X., Cheng, Q., Lu, W., 2014. Analyzing evolution of research topics with NEViewer: a new method based on dynamic co-word networks. Scientometrics 101, 1253–1271. https://doi.org/10.1007/s11192-014-1347-y (log added in the formula + pair comparison)

src/Gargantext/Core/Viz/AdaptativePhylo.hs

@@ -72,6 +72,15 @@ data Proximity =
       -- , _wlj_elevation     :: Double
 -}
       }
+    | WeightedLogSim 
+      { _wlj_sensibility   :: Double
+{-
+      -- , _wlj_thresholdInit :: Double
+      -- , _wlj_thresholdStep :: Double
+      -- | max height for sea level in temporal matching
+      -- , _wlj_elevation     :: Double
+-}
+      } 
     | Hamming 
     deriving (Show,Generic,Eq) 
 

src/Gargantext/Core/Viz/Phylo.hs

@@ -261,11 +261,12 @@ data LouvainParams = LouvainParams
 
 -- | Proximity constructors
 data Proximity = WeightedLogJaccard WLJParams
+               | WeightedLogSim WLJParams
                | Hamming HammingParams
                | Filiation
           deriving (Generic, Show, Eq, Read)
 
--- | Parameters for WeightedLogJaccard proximity
+-- | Parameters for WeightedLogJaccard and WeightedLogSim proximity
 data WLJParams = WLJParams
   { _wlj_threshold   :: !Double
   , _wlj_sensibility :: !Double

src/Gargantext/Core/Viz/Phylo/PhyloTools.hs

@@ -295,12 +295,14 @@ filterProximity :: Proximity -> Double -> Double -> Bool
 filterProximity proximity thr local = 
     case proximity of
         WeightedLogJaccard _ -> local >= thr
+        WeightedLogSim _ -> local >= thr
         Hamming -> undefined   
 
 getProximityName :: Proximity -> String
 getProximityName proximity =
     case proximity of
         WeightedLogJaccard _ -> "WLJaccard"
+        WeightedLogSim _ -> "WeightedLogSim"
         Hamming -> "Hamming"            
 
 ---------------
@@ -484,6 +486,7 @@ traceSynchronyStart phylo =
 getSensibility :: Proximity -> Double
 getSensibility proxi = case proxi of 
     WeightedLogJaccard s -> s
+    WeightedLogSim s -> s
     Hamming -> undefined
 
 ----------------

src/Gargantext/Core/Viz/Phylo/TemporalMatching.hs

@@ -73,19 +73,49 @@ weightedLogJaccard' sens nbDocs diago ngrams ngrams'
     diagoUnion =  elems $ restrictKeys diago (Set.fromList ngramsUnion)
     --------------------------------------  
 
+-- | Process the weighted similarity between clusters. Adapted from Wang, X., Cheng, Q., Lu, W., 2014. Analyzing evolution of research topics with NEViewer: a new method based on dynamic co-word networks. Scientometrics 101, 1253–1271. https://doi.org/10.1007/s11192-014-1347-y (log added in the formula + pair comparison)
+-- tests not conclusive 
+weightedLogSim' :: Double -> Double -> Map Int Double -> [Int] -> [Int] -> Double
+weightedLogSim' sens nbDocs diago ego_ngrams target_ngrams
+  | null ngramsInter           = 0
+  | ngramsInter == ngramsUnion = 1
+  | sens == 0    = jaccard ngramsInter ngramsUnion
+  | sens > 0     = (sumInvLog' sens nbDocs diagoInter) / minimum [(sumInvLog' sens nbDocs diagoEgo),(sumInvLog' sens nbDocs diagoTarget)]
+  | otherwise    = (sumLog' sens nbDocs diagoInter) / minimum [(sumLog' sens nbDocs diagoEgo),(sumLog' sens nbDocs diagoTarget)] 
+  where 
+    --------------------------------------
+    ngramsInter :: [Int] 
+    ngramsInter = intersect ego_ngrams target_ngrams  
+    --------------------------------------
+    ngramsUnion :: [Int] 
+    ngramsUnion = union ego_ngrams target_ngrams
+    --------------------------------------
+    diagoInter :: [Double]
+    diagoInter =  elems $ restrictKeys diago (Set.fromList ngramsInter)
+    --------------------------------------  
+    diagoEgo :: [Double]
+    diagoEgo =  elems $ restrictKeys diago (Set.fromList ego_ngrams)
+    --------------------------------------  
+    diagoTarget :: [Double]
+    diagoTarget =  elems $ restrictKeys diago (Set.fromList target_ngrams)
+    --------------------------------------  
 
--- | To process the proximity between a current group and a pair of targets group
 toProximity :: Double -> Map Int Double -> Proximity -> [Int] -> [Int] -> [Int] -> Double
+-- | To process the proximity between a current group and a pair of targets group using the adapted Wang et al. Similarity
 toProximity nbDocs diago proximity egoNgrams targetNgrams targetNgrams' =
   case proximity of 
     WeightedLogJaccard sens -> 
       let pairNgrams = if targetNgrams == targetNgrams'
                           then targetNgrams
                           else union targetNgrams targetNgrams'
-       in weightedLogJaccard' sens nbDocs diago egoNgrams pairNgrams
+       in weightedLogJaccard' sens nbDocs diago egoNgrams pairNgrams       
+    WeightedLogSim sens -> 
+      let pairNgrams = if targetNgrams == targetNgrams'
+                          then targetNgrams
+                          else union targetNgrams targetNgrams'
+       in weightedLogSim' sens nbDocs diago egoNgrams pairNgrams
     Hamming -> undefined
 
-
 ------------------------
 -- | Local Matching | --
 ------------------------

src/Gargantext/Core/Viz/Phylo/Tools.hs

@@ -796,6 +796,7 @@ getPeriodSteps q = q ^. q_periodSteps
 getThreshold :: Proximity -> Double
 getThreshold prox = case prox of 
   WeightedLogJaccard (WLJParams thr _) -> thr
+  WeightedLogSim (WLJParams thr _) -> thr
   Hamming (HammingParams thr)          -> thr
   Filiation                            -> panic "[ERR][Viz.Phylo.Tools.getThreshold] Filiation"
 
@@ -834,6 +835,8 @@ initRelatedComponents (def defaultWeightedLogJaccard -> proxi) = RCParams proxi
 initWeightedLogJaccard :: Maybe Double -> Maybe Double -> WLJParams
 initWeightedLogJaccard (def 0.3 -> thr) (def 20.0 -> sens) = WLJParams thr sens
 
+initWeightedLogSim :: Maybe Double -> Maybe Double -> WLJParams
+initWeightedLogSim (def 0.3 -> thr) (def 20.0 -> sens) = WLJParams thr sens
 
 -- | To initialize a PhyloQueryBuild from given and default parameters
 initPhyloQueryBuild :: Text          -> Text            -> Maybe Int
@@ -896,6 +899,9 @@ defaultHamming = Hamming (initHamming Nothing)
 defaultWeightedLogJaccard :: Proximity
 defaultWeightedLogJaccard = WeightedLogJaccard (initWeightedLogJaccard Nothing Nothing)
 
+defaultWeightedLogSim :: Proximity
+defaultWeightedLogSim = WeightedLogSim (initWeightedLogSim Nothing Nothing)
+
 -- Queries
 type Title = Text
 type Desc  = Text