Show column names in extracted features
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@ -1,7 +1,7 @@
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{-# LANGUAGE OverloadedStrings #-}
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module Data.Conduit.Header
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(processHeader, TabularHeader, readHeaderFile)
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(processHeader, TabularHeader(..), readHeaderFile)
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where
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import Data.Text
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@ -19,6 +19,7 @@ module GEval.FeatureExtractor
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FeatureNamespace(..),
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References(..),
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ReferencesData(..),
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FeatureIndex(..),
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toTextualContent,
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filterExistentialFactors)
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where
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@ -39,6 +40,8 @@ import Data.Attoparsec.Text
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import Data.Attoparsec.Combinator
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import Control.Applicative
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import Data.Conduit.Header
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import qualified Data.HashMap.Strict as H
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import GEval.Annotation
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@ -131,12 +134,19 @@ instance Show AtomicFactor where
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show (TextFactor t) = unpack t
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show (ShapeFactor (WordShape t)) = 'S':'H':'A':'P':'E':':':(unpack t)
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data FeatureNamespace = FeatureNamespace Text | FeatureTabbedNamespace Text Int
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data FeatureIndex = ColumnByNumber Int | ColumnByName Text
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deriving (Eq, Ord)
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instance Show FeatureIndex where
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show (ColumnByNumber ix) = show ix
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show (ColumnByName name) = unpack name
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data FeatureNamespace = FeatureNamespace Text | FeatureTabbedNamespace Text FeatureIndex
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deriving (Eq, Ord)
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instance Show FeatureNamespace where
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show (FeatureNamespace namespace) = unpack namespace
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show (FeatureTabbedNamespace namespace column) = ((unpack namespace) ++ "<" ++ (show column) ++ ">")
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show (FeatureTabbedNamespace namespace columnIndex) = ((unpack namespace) ++ "<" ++ (show columnIndex) ++ ">")
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data References = References (H.HashMap Integer Text)
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@ -205,11 +215,15 @@ extractFactorsFromField mTokenizer bbdo mReferenceData namespace record =
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extractFactors :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> Text -> Text -> [PeggedFactor]
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extractFactors mTokenizer bbdo mReferencesData namespace record = extractFactorsFromField mTokenizer bbdo mReferencesData (FeatureNamespace namespace) record
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extractFactorsFromTabbed :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> Text -> Text -> [PeggedFactor]
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData namespace record =
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extractFactorsFromTabbed :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> Text -> Text -> Maybe TabularHeader -> [PeggedFactor]
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData namespace record mHeader =
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Data.List.concat
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$ Prelude.map (\(n, t) -> extractFactorsFromField mTokenizer bbdo mReferencesData (FeatureTabbedNamespace namespace n) t)
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$ Prelude.zip [1..] (splitOn "\t" record)
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$ Prelude.zip (generateColumnNames mHeader) (splitOn "\t" record)
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generateColumnNames :: Maybe TabularHeader -> [FeatureIndex]
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generateColumnNames Nothing = Data.List.map ColumnByNumber [1..]
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generateColumnNames (Just (TabularHeader fields)) = Data.List.map ColumnByName fields
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addCartesianFactors :: BlackBoxDebuggingOptions -> [LineWithPeggedFactors] -> [LineWithFactors]
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addCartesianFactors bbdo linesWithPeggedFactors = addCartesianFactors' (bbdoCartesian bbdo) linesWithPeggedFactors
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@ -98,9 +98,11 @@ parseReferenceEntry line = (read $ unpack refId, t)
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where [refId, t] = splitOn "\t" line
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runLineByLine :: ResultOrdering -> Maybe String -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runLineByLine ordering featureFilter spec bbdo = runLineByLineGeneralized ordering spec consum
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where consum :: Maybe References -> ConduitT LineRecord Void (ResourceT IO) ()
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consum = (\mReferences -> (runFeatureFilter featureFilter spec bbdo mReferences .| CL.map (encodeUtf8 . formatOutput) .| CC.unlinesAscii .| CC.stdout))
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runLineByLine ordering featureFilter spec bbdo = do
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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runLineByLineGeneralized ordering spec (consum mInHeader)
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where consum :: Maybe TabularHeader -> Maybe References -> ConduitT LineRecord Void (ResourceT IO) ()
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consum = (\mInHeader -> \mReferences -> (runFeatureFilter featureFilter spec bbdo mReferences mInHeader .| CL.map (encodeUtf8 . formatOutput) .| CC.unlinesAscii .| CC.stdout))
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formatOutput (LineRecord inp exp out _ score) = Data.Text.intercalate "\t" [
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formatScore score,
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escapeTabs inp,
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@ -155,15 +157,15 @@ markBadFeatures worstFeaturesMap mTokenizer bbdo field line =
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$ Prelude.map (featureToLineSpan worstFeaturesMap)
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$ extractFactors mTokenizer bbdo Nothing field line
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markBadFeaturesInTabbed :: (M.Map PeggedFactor Double) -> (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Text -> Text -> [LineSpan]
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markBadFeaturesInTabbed worstFeaturesMap mTokenizer bbdo field line =
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markBadFeaturesInTabbed :: (M.Map PeggedFactor Double) -> (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Text -> Text -> Maybe TabularHeader -> [LineSpan]
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markBadFeaturesInTabbed worstFeaturesMap mTokenizer bbdo field line mInHeader =
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catMaybes
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$ Prelude.map (featureToLineSpan worstFeaturesMap)
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$ extractFactorsFromTabbed mTokenizer bbdo Nothing field line
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$ extractFactorsFromTabbed mTokenizer bbdo Nothing field line mInHeader
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doMarking worstFeaturesMap mTokenizer bbdo (LineRecord inpLine expLine outLine _ score) =
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SpanLineRecord (markBadFeaturesInTabbed worstFeaturesMap mTokenizer bbdo "in" inpLine)
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doMarking worstFeaturesMap mTokenizer mInHeader bbdo (LineRecord inpLine expLine outLine _ score) =
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SpanLineRecord (markBadFeaturesInTabbed worstFeaturesMap mTokenizer bbdo "in" inpLine mInHeader)
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(markBadFeatures worstFeaturesMap mTokenizer bbdo "exp" expLine)
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(markBadFeatures worstFeaturesMap mTokenizer bbdo "out" outLine)
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score
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@ -184,16 +186,17 @@ runLineByLineWithWorstFeaturesGeneralized :: ResultOrdering
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-> IO r
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runLineByLineWithWorstFeaturesGeneralized ordering featureFilter spec bbdo consum = do
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hPutStrLn stderr "Looking for worst features..."
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worstFeatures <- runLineByLineGeneralized ordering' spec (\mReferences -> worstFeaturesPipeline False spec bbdo mReferences (CL.take 100))
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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worstFeatures <- runLineByLineGeneralized ordering' spec (\mReferences -> worstFeaturesPipeline False spec bbdo mReferences mInHeader (CL.take 100))
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let worstFeaturesMap = M.fromList
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$ catMaybes
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$ Prelude.map featureToFactor
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$ Prelude.map (\(FeatureWithPValue feature pValue _ _) -> (feature, pValue)) worstFeatures
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runLineByLineGeneralized ordering spec (consum' worstFeaturesMap)
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where consum' worstFeaturesMap = (\mReferences -> (runFeatureFilter featureFilter spec bbdo mReferences
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.| CL.map (doMarking worstFeaturesMap mTokenizer bbdo)
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.| consum))
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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runLineByLineGeneralized ordering spec (consum' worstFeaturesMap mInHeader)
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where consum' worstFeaturesMap mInHeader = (\mReferences -> (runFeatureFilter featureFilter spec bbdo mReferences mInHeader
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.| CL.map (doMarking worstFeaturesMap mTokenizer mInHeader bbdo)
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.| consum))
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ordering' = forceSomeOrdering ordering
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mTokenizer = gesTokenizer spec
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@ -206,18 +209,21 @@ runFeatureFilter :: (Monad m, FeatureSource s) => Maybe String
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-> GEvalSpecification
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-> BlackBoxDebuggingOptions
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-> Maybe References
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-> Maybe TabularHeader
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-> ConduitT s s m ()
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runFeatureFilter Nothing _ _ _ = doNothing
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runFeatureFilter (Just feature) spec bbdo mReferences = CC.map (\l -> (fakeRank, l))
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.| featureExtractor mTokenizer bbdo mReferences
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.| CC.filter (checkFeature feature)
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.| CC.map fst
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runFeatureFilter Nothing _ _ _ _ = doNothing
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runFeatureFilter (Just feature) spec bbdo mReferences mInHeader = CC.map (\l -> (fakeRank, l))
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.| featureExtractor mTokenizer bbdo mReferences mInHeader
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.| CC.filter (checkFeature feature)
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.| CC.map fst
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where mTokenizer = gesTokenizer spec
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fakeRank = 0.0
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checkFeature feature (_, LineWithFactors _ _ fs) = feature `elem` (Prelude.map show fs)
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runWorstFeatures :: ResultOrdering -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runWorstFeatures ordering spec bbdo = runLineByLineGeneralized ordering' spec (\mReferences -> worstFeaturesPipeline False spec bbdo mReferences consumFeatures)
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runWorstFeatures ordering spec bbdo = do
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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runLineByLineGeneralized ordering' spec (\mReferences -> worstFeaturesPipeline False spec bbdo mReferences mInHeader consumFeatures)
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where ordering' = forceSomeOrdering ordering
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consumFeatures = CL.map (encodeUtf8 . formatFeatureWithPValue)
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@ -228,10 +234,11 @@ worstFeaturesPipeline :: Bool
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-> GEvalSpecification
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-> BlackBoxDebuggingOptions
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-> Maybe References
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-> Maybe TabularHeader
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-> ConduitT FeatureWithPValue Void (ResourceT IO) a
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-> ConduitT LineRecord Void (ResourceT IO) a
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worstFeaturesPipeline reversed spec bbdo mReferences consum = rank (lessByMetric reversed $ gesMainMetric spec)
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.| evalStateC 0 (extractFeaturesAndPValues spec bbdo mReferences)
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worstFeaturesPipeline reversed spec bbdo mReferences mInHeader consum = rank (lessByMetric reversed $ gesMainMetric spec)
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.| evalStateC 0 (extractFeaturesAndPValues spec bbdo mReferences mInHeader)
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.| CC.filter (\(FeatureWithPValue _ p _ _) -> not $ isNaN p) -- NaN values would poison sorting
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.| gobbleAndDo (sortBy featureOrder)
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.| filtreCartesian (bbdoCartesian bbdo)
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@ -245,10 +252,10 @@ forceSomeOrdering :: ResultOrdering -> ResultOrdering
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forceSomeOrdering FirstTheBest = FirstTheBest
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forceSomeOrdering _ = FirstTheWorst
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extractFeaturesAndPValues :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, LineRecord) FeatureWithPValue (StateT Integer m) ()
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extractFeaturesAndPValues spec bbdo mReferences =
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extractFeaturesAndPValues :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> Maybe TabularHeader -> ConduitT (Double, LineRecord) FeatureWithPValue (StateT Integer m) ()
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extractFeaturesAndPValues spec bbdo mReferences mInHeader =
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totalCounter
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.| rankedFeatureExtractor spec bbdo mReferences
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.| rankedFeatureExtractor spec bbdo mReferences mInHeader
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.| uScoresCounter (bbdoMinFrequency bbdo)
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@ -268,11 +275,11 @@ formatFeatureWithPValue (FeatureWithPValue f p avg c) =
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(pack $ printf "%0.8f" avg),
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(pack $ printf "%0.20f" p)]
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rankedFeatureExtractor :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, LineRecord) RankedFactor m ()
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rankedFeatureExtractor spec bbdo mReferences = featureExtractor mTokenizer bbdo mReferences
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.| CC.map snd
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.| CC.map unwrapFeatures
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.| CC.concat
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rankedFeatureExtractor :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> Maybe TabularHeader -> ConduitT (Double, LineRecord) RankedFactor m ()
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rankedFeatureExtractor spec bbdo mReferences mInHeader = featureExtractor mTokenizer bbdo mReferences mInHeader
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.| CC.map snd
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.| CC.map unwrapFeatures
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.| CC.concat
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where mTokenizer = gesTokenizer spec
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unwrapFeatures (LineWithFactors rank score fs) = Prelude.map (\f -> RankedFactor f rank score) fs
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@ -288,11 +295,11 @@ instance FeatureSource (LineRecord, LineRecord) where
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getScore (LineRecord _ _ _ _ scoreA, LineRecord _ _ _ _ scoreB) = scoreB - scoreA
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mainLineRecord (_, l) = l
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featureExtractor :: (Monad m, FeatureSource s) => Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, s) (s, LineWithFactors) m ()
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featureExtractor mTokenizer bbdo mReferences = CC.map extract
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featureExtractor :: (Monad m, FeatureSource s) => Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> Maybe TabularHeader -> ConduitT (Double, s) (s, LineWithFactors) m ()
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featureExtractor mTokenizer bbdo mReferences mInHeader = CC.map extract
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.| finalFeatures (bbdoCartesian bbdo) (fromMaybe (bbdoMinFrequency bbdo) (bbdoMinCartesianFrequency bbdo))
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where extract (rank, line) =
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(line, LineWithPeggedFactors rank (getScore line) $ getFeatures mTokenizer bbdo mReferences (mainLineRecord line))
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(line, LineWithPeggedFactors rank (getScore line) $ getFeatures mTokenizer bbdo mReferences (mainLineRecord line) mInHeader)
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finalFeatures :: Monad m => Bool -> Integer -> ConduitT (a, LineWithPeggedFactors) (a, LineWithFactors) m ()
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finalFeatures False _ = CC.map (\(l, p) -> (l, peggedToUnaryLine p))
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@ -324,11 +331,11 @@ filtreCartesian True = CC.concatMapAccum step S.empty
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peggedToUnaryLine :: LineWithPeggedFactors -> LineWithFactors
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peggedToUnaryLine (LineWithPeggedFactors rank score fs) = LineWithFactors rank score (Prelude.map UnaryFactor fs)
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getFeatures :: Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> LineRecord -> [PeggedFactor]
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getFeatures mTokenizer bbdo mReferences (LineRecord inLine expLine outLine _ _) =
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getFeatures :: Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> LineRecord -> Maybe TabularHeader -> [PeggedFactor]
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getFeatures mTokenizer bbdo mReferences (LineRecord inLine expLine outLine _ _) mInHeader =
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Data.List.concat [
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extractFactors mTokenizer bbdo mReferencesData "exp" expLine,
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData "in" inLine,
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData "in" inLine mInHeader,
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extractFactors mTokenizer bbdo mReferencesData "out" outLine]
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where mReferencesData = case mReferences of
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Just references -> Just $ ReferencesData {
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@ -487,13 +494,15 @@ gobbleAndDo fun = do
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CC.yieldMany $ fun l
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runDiff :: ResultOrdering -> Maybe String -> FilePath -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runDiff ordering featureFilter otherOut spec bbdo = runDiffGeneralized ordering otherOut spec consum
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where consum :: Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mReferences -> CL.filter shouldBeShown
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.| runFeatureFilter featureFilter spec bbdo mReferences
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.| CL.map (encodeUtf8 . formatOutput)
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.| CC.unlinesAscii
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.| CC.stdout
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runDiff ordering featureFilter otherOut spec bbdo = do
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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runDiffGeneralized ordering otherOut spec (consum mInHeader)
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where consum :: Maybe TabularHeader -> Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mInHeader -> \mReferences -> CL.filter shouldBeShown
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.| runFeatureFilter featureFilter spec bbdo mReferences mInHeader
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.| CL.map (encodeUtf8 . formatOutput)
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.| CC.unlinesAscii
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.| CC.stdout
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shouldBeShown (LineRecord _ _ outA _ scoreA, LineRecord _ _ outB _ scoreB) =
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outA /= outB && scoreA /= scoreB
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formatOutput (LineRecord inp exp outA _ scoreA, LineRecord _ _ outB _ scoreB) = Data.Text.intercalate "\t" [
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@ -533,15 +542,17 @@ runMultiOutputGeneralized spec consum = do
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mSelector = gesSelector spec
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runMostWorseningFeatures :: ResultOrdering -> FilePath -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runMostWorseningFeatures ordering otherOut spec bbdo = runDiffGeneralized ordering' otherOut spec consum
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runMostWorseningFeatures ordering otherOut spec bbdo = do
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mInHeader <- readHeaderFileWrapper $ getInHeader spec
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runDiffGeneralized ordering' otherOut spec (consum mInHeader)
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where ordering' = forceSomeOrdering ordering
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reversed = case ordering of
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KeepTheOriginalOrder -> False
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FirstTheWorst -> False
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FirstTheBest -> True
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consum :: Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mReferences -> CC.map prepareFakeLineRecord
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.| (worstFeaturesPipeline reversed spec bbdo mReferences consumFeatures)
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consum :: Maybe TabularHeader -> Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mInHeader -> \mReferences -> CC.map prepareFakeLineRecord
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.| (worstFeaturesPipeline reversed spec bbdo mReferences mInHeader consumFeatures)
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prepareFakeLineRecord :: (LineRecord, LineRecord) -> LineRecord
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prepareFakeLineRecord (LineRecord _ _ _ _ scorePrev, LineRecord inp exp out c score) =
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LineRecord inp exp out c (score - scorePrev)
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22
test/Spec.hs
22
test/Spec.hs
@ -654,26 +654,26 @@ main = hspec $ do
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bbdoCartesian = False,
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bbdoMinCartesianFrequency = Nothing,
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bbdoConsiderNumericalFeatures = True }
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(sort $ extractFactorsFromTabbed Nothing bbdo Nothing "in" "I like this\t34.3\ttests") `shouldBe` [
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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(sort $ extractFactorsFromTabbed Nothing bbdo Nothing "in" "I like this\t34.3\ttests" Nothing) `shouldBe` [
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "I"))),
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "like"))),
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "this"))),
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(SimpleExistentialFactor (BigramFactor (TextFactor "I") (TextFactor "like"))),
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(SimpleExistentialFactor (BigramFactor (TextFactor "like") (TextFactor "this"))),
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PeggedFactor (FeatureTabbedNamespace "in" 1)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 1))
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(NumericalFactor Nothing 11),
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PeggedFactor (FeatureTabbedNamespace "in" 2)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 2))
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(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "34.3"))),
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PeggedFactor (FeatureTabbedNamespace "in" 2)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 2))
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(NumericalFactor (Just 34.3) 4),
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PeggedFactor (FeatureTabbedNamespace "in" 3)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 3))
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(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "tests"))),
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PeggedFactor (FeatureTabbedNamespace "in" 3)
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PeggedFactor (FeatureTabbedNamespace "in" (ColumnByNumber 3))
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(NumericalFactor Nothing 5) ]
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describe "Kendall's tau" $ do
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it "tau" $ do
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