tests/Phylomemy/TemporalMatchingSpec.hs

   1 {-# LANGUAGE OverloadedLists #-}
   2 {-# LANGUAGE OverloadedStrings #-}
   3 {-# LANGUAGE ParallelListComp #-}
   4 {-# OPTIONS_GHC -Wno-orphans #-}
   5
   6 module Phylomemy.TemporalMatchingSpec where
   7
   8 import Control.Monad (Monad (..), foldM, foldM_, forM_, void)
   9 import Data.Function (($), (&), (.))
  10 import Data.Functor (Functor (..), (<$>), (<&>))
  11 import Data.GenValidity
  12 import Data.GenValidity.Map ()
  13 import Data.GenValidity.Sequence ()
  14 import Data.GenValidity.Set ()
  15 import Data.GenValidity.Text ()
  16 import Data.GenValidity.Time ()
  17 import Data.Int (Int)
  18 import Data.List qualified as List
  19 import Data.Map.Strict qualified as Map
  20 import Data.Maybe (Maybe (..), fromJust)
  21 import Data.Ord (Ord)
  22 import Data.Sequence qualified as Seq
  23 import Data.Set qualified as Set
  24 import Data.Text.Short (ShortText)
  25 import Data.Text.Short qualified as ShortText
  26 import Data.Time (UTCTime)
  27 import Data.Tree qualified as Tree
  28 import Data.Validity.Map ()
  29 import Data.Validity.Set ()
  30 import Data.Validity.Text ()
  31 import Debug.Pretty.Simple (pTraceShow, pTraceShowId)
  32 import GHC.IsList (toList)
  33 import Logic
  34 import Numeric (showFFloat)
  35 import Numeric.Natural (Natural)
  36 import System.FilePath ((<.>))
  37 import Test.Syd
  38 import Test.Syd.Validity
  39 import Text.Show (Show (..))
  40 import Prelude (Double, Integral (..), Num (..), Rational, fromRational)
  41
  42 import Phylomemy
  43 import Phylomemy.IndexationSpec (Pos (..), Rang)
  44
  45 import Utils
  46
  47 rangeToDocs0 :: Pos :-> Seq.Seq (Document Pos)
  48 rangeToDocs0 =
  49   Map.fromList
  50     [ ( Pos rangeIndex
  51       , Seq.fromList
  52           [ Document
  53             { documentPosition = Pos (2 * rangeIndex + 3 * docIndex)
  54             , documentRoots = Map.fromList [(r, ()) | r <- roots]
  55             }
  56           | roots <- docs
  57           | docIndex <- [1 ..]
  58           ]
  59       )
  60     | docs <-
  61         [ [["a", "b", "c"], ["a", "d", "e"], ["e", "f", "g"]]
  62         , [["a", "b"], ["d", "f"], ["a", "d"]]
  63         , [["f"], ["d", "f"], ["f", "g", "a"]]
  64         , [["b", "c", "e"], ["a", "d", "e"], ["a", "b", "c"]]
  65         , [["d", "f", "g"], ["b", "f"], ["a", "c", "d"], ["a", "f"]]
  66         , [["c", "d", "g"], ["b", "c", "g"], ["a", "b", "c"], ["e", "g"]]
  67         ]
  68     | rangeIndex <- [1 ..]
  69     ]
  70
  71 {-
  72 rangeToDocs0 :: Pos :-> Seq.Seq (Document Pos)
  73 rangeToDocs0 =
  74   Map.fromListWith
  75     (<>)
  76     [ (Pos (pos - (pos `rem` 2)), Seq.singleton doc)
  77     | doc <- docs0 & toList
  78     , let Pos pos = documentPosition doc
  79     ]
  80 -}
  81
  82 spec :: Spec
  83 spec = do
  84   {-
  85   describe "splitMaximalSpanningTree" do
  86     let mst0 :: MaximalSpanningTree Int Int =
  87           Tree.Node MSTNode{mstNodeRangeCluster=(2,1), mstNodeSimilarity=proba1}
  88             [ Tree.Node MSTNode{mstNodeRangeCluster=(1,1), mstNodeSimilarity=proba0} []
  89             , Tree.Node MSTNode{mstNodeRangeCluster=(1,2), mstNodeSimilarity=assertProbability 0.2} []
  90             , Tree.Node MSTNode{mstNodeRangeCluster=(1,3), mstNodeSimilarity=assertProbability 0.3}
  91               [ Tree.Node MSTNode{mstNodeRangeCluster=(2,3), mstNodeSimilarity=assertProbability 0.3} []
  92               , Tree.Node MSTNode{mstNodeRangeCluster=(2,4), mstNodeSimilarity=proba0}
  93                  [ Tree.Node MSTNode{mstNodeRangeCluster=(1,4), mstNodeSimilarity=assertProbability 0.2}
  94                    [ Tree.Node MSTNode{mstNodeRangeCluster=(2,2), mstNodeSimilarity=assertProbability 0.3} []
  95                    , Tree.Node MSTNode{mstNodeRangeCluster=(2,5), mstNodeSimilarity=assertProbability 0.3} []
  96                    ]
  97                  ]
  98               ]
  99             ]
 100     goldenBuilder ("mst=0" <.> "split=0") $
 101       dotMaximalSpanningTrees [mst0]
 102     goldenBuilder ("mst=0" <.> "split=1") $
 103       dotMaximalSpanningTrees $
 104         splitMaximalSpanningTree mst0
 105     goldenBuilder ("mst=0" <.> "split=2") $
 106       dotMaximalSpanningTrees $
 107         mst0
 108           & splitMaximalSpanningTree
 109           >>= splitMaximalSpanningTree
 110     goldenBuilder ("mst=0" <.> "split=3") $
 111       dotMaximalSpanningTrees $
 112         mst0
 113           & splitMaximalSpanningTree
 114           >>= splitMaximalSpanningTree
 115           >>= splitMaximalSpanningTree
 116   -}
 117   letName rangeToDocs0 $ \rangeToDocs ->
 118     letName ["a", "b", "c", "d", "e", "f", "g"] $ \roots ->
 119       forM_ ([1 .. 1] :: [Int]) \minSupp ->
 120         forM_ ([2 .. 2] :: [Int]) \minSize -> do
 121           let clusters = clusterize roots (assertStrictlyPositive minSupp) (assertStrictlyPositive minSize) rangeToDocs
 122           -- let allSimils = allSimilarities similarityJaccard (clusters <&> unName)
 123           let msf = maximalSpanningForest similarityJaccard (clusters <&> unName)
 124           describe "dotMaximalSpanningTrees" do
 125             forM_ ([0, 0.3, 1] :: [Rational]) \lambda -> do
 126               letName (predictionMeasureF (assertProbability lambda)) \predMeasure -> do
 127                 goldenBuilder ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize <.> "lambda=" <> showFFloat (Just 2) (fromRational @Double lambda) "") $
 128                   dotMaximalSpanningForest $
 129                     msfSplit predMeasure roots msf
 130
 131 -- describe "dotMaximalSpanningTrees" do
 132 --  ([Map.keysSet similToMST | similToMST <- msf & Map.elems] & Set.unions & toList)
 133 --    & (`foldM_` msf) \acc simil -> do
 134 --      let similS = showFFloat Nothing (fromRational @Double (runProbability simil)) ""
 135 --      let acc' = acc & (`Map.foldrWithKey` Map.empty) \_simil mst ->
 136 --                          Map.unionWith (Map.unionWith (Map.unionWith (Seq.><))) $
 137 --                          splitMaximalSpanningTree mst
 138 --      goldenBuilder ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize <.> "simil=" <> similS) $
 139 --        dotMaximalSpanningTrees acc
 140 --      return acc'
 141 -- describe "splitMaximalSpanningTrees" do
 142 --  forM_ ([0] :: [Rational]) \lambda -> do
 143 --    letName (predictionMeasureF (assertProbability lambda)) \predMeasure -> do
 144 --      goldenBuilder ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize <.> "lambda=" <> showFFloat (Just 2) (fromRational @Double lambda) "") $
 145 --        dotMaximalSpanningTrees $
 146 --          splitMaximalSpanningTrees predMeasure roots msf
 147 -- describe "dotSimilarities" do
 148 -- forM_ ([0] :: [Rational]) \lambda -> do
 149 -- --letName (predictionMeasureF (assertProbability lambda)) \predMeasure -> do
 150 -- goldenBuilder ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize <.> "lambda=" <> showFFloat (Just 2) (fromRational @Double lambda) "") $
 151 -- dotSimilarities
 152 -- --(splitMaximalSpanningTrees predMeasure roots msf)
 153 -- msf
 154 -- allSimils
 155 -- describe "similarities" do
 156 --   goldenShow ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize) weights
 157 -- describe "phylomemyDOT" do
 158 --   forM_ weights \minWeight ->
 159 --     goldenBuilder ("docs=docs0" <.> "minSupp=" <> show minSupp <.> "minSize=" <> show minSize <.> "minWeight=" <> show minWeight) $
 160 --       phylomemyDOT $
 161 --         phylomemyRaise minWeight phy