Introduce line source specification
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@ -265,6 +265,39 @@ extensionsHandled = ["tsv", "jsonl"]
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data LineSource m = LineSource (ConduitT () Text m ()) (Text -> ItemTarget) (Text -> Text) SourceSpec Word32
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data LineSourcesSpecification m = LineSourcesSpecification {
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lineSourcesFilter :: Maybe (Text -> Bool),
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lineSourcesInputSource :: LineSource m,
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lineSourcesExpectedSource :: LineSource m,
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lineSourcesOutputSource :: LineSource m }
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dataSourceToLineSourcesSpecification :: DataSource -> LineSourcesSpecification (ResourceT IO)
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dataSourceToLineSourcesSpecification dataSource = LineSourcesSpecification {
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lineSourcesFilter = challengeDataSourceFilter chDataSource,
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lineSourcesInputSource = fileAsLineSource inputSource inOptions,
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lineSourcesExpectedSource = fileAsLineSource expectedSource outOptions,
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lineSourcesOutputSource = fileAsLineSource outSource outOptions}
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where chDataSource = dataSourceChallengeData dataSource
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inputSource = challengeDataSourceInput chDataSource
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expectedSource = challengeDataSourceExpected chDataSource
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outSource = dataSourceOut dataSource
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outOptions = FileProcessingOptions {
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fileProcessingOptionsSelector = mSelector,
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fileProcessingOptionsPreprocess = preprocess,
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fileProcessingOptionsHeader = mOutHeader }
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inOptions = FileProcessingOptions {
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fileProcessingOptionsSelector = mSelector,
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fileProcessingOptionsPreprocess = preprocess,
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fileProcessingOptionsHeader = mInHeader }
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mSelector = challengeDataSourceSelector chDataSource
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preprocess = challengeDataSourcePreprocess chDataSource
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mInHeader = challengeDataSourceInHeader chDataSource
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mOutHeader = challengeDataSourceOutHeader chDataSource
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toWithoutInput lsSpec = WithoutInput expectedSource outSource
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where expectedSource = lineSourcesExpectedSource lsSpec
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outSource = lineSourcesOutputSource lsSpec
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geval :: GEvalSpecification -> IO [(SourceSpec, [MetricOutput])]
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geval gevalSpec = do
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dataSources <- checkAndGetDataSources False gevalSpec
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@ -455,14 +488,24 @@ getDataFormatFromFilePath path =
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dataDecoder fmt mSelector = CC.map (select fmt mSelector)
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gevalCoreOnSingleLines :: Metric -> (Text -> Text) -> (Text -> ItemTarget) -> LineInFile -> (Text -> ItemTarget) -> LineInFile -> (Text -> ItemTarget) -> LineInFile -> IO (MetricOutput)
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gevalCoreOnSingleLines :: Metric
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-> (Text -> Text)
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-> (Text -> ItemTarget)
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-> LineInFile
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-> (Text -> ItemTarget)
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-> LineInFile
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-> (Text -> ItemTarget)
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-> LineInFile -> IO (MetricOutput)
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gevalCoreOnSingleLines metric preprocess inpDecoder inpLine expDecoder expLine outDecoder outLine =
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gevalCoreOnSources metric (singleLineAsLineSource inpLine inpDecoder preprocess)
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(singleLineAsLineSource expLine expDecoder outputPreprocess)
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(singleLineAsLineSource outLine outDecoder outputPreprocess)
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gevalCoreOnSources metric lsSpec
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where outputPreprocess = if isPreprocessable metric
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then preprocess
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else id
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lsSpec = LineSourcesSpecification {
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lineSourcesFilter = Nothing,
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lineSourcesInputSource = singleLineAsLineSource inpLine inpDecoder preprocess,
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lineSourcesExpectedSource = singleLineAsLineSource expLine expDecoder outputPreprocess,
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lineSourcesOutputSource = singleLineAsLineSource outLine outDecoder outputPreprocess }
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singleLineAsLineSource :: LineInFile -> (Text -> ItemTarget) -> (Text -> Text) -> LineSource (ResourceT IO)
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singleLineAsLineSource (LineInFile sourceSpec lineNo line) itemDecoder preprocess =
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@ -492,34 +535,15 @@ gevalCore :: Metric -- ^ evaluation metric
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-> IO (MetricOutput) -- ^ metric value for the output against the expected output
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gevalCore metric mBootstrapResampling dataSource = do
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whenM (isEmptyFileSource outSource) $ throwM $ EmptyOutput
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go metric
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(fileAsLineSource inputSource inOptions)
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(fileAsLineSource expectedSource outOptions)
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(fileAsLineSource outSource outOptions)
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let lsSpec = dataSourceToLineSourcesSpecification dataSource
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go metric lsSpec
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where go = case mBootstrapResampling of
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Nothing -> gevalCoreOnSources
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Just bootstrapResampling -> if handleBootstrap metric
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then gevalBootstrapOnSources bootstrapResampling
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else gevalCoreOnSources
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outOptions = FileProcessingOptions {
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fileProcessingOptionsSelector = mSelector,
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fileProcessingOptionsPreprocess = preprocess,
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fileProcessingOptionsHeader = mOutHeader }
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inOptions = FileProcessingOptions {
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fileProcessingOptionsSelector = mSelector,
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fileProcessingOptionsPreprocess = preprocess,
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fileProcessingOptionsHeader = mInHeader }
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challengeDataSource = dataSourceChallengeData dataSource
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mSelector = challengeDataSourceSelector challengeDataSource
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preprocess = challengeDataSourcePreprocess challengeDataSource
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mInHeader = challengeDataSourceInHeader challengeDataSource
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mOutHeader = challengeDataSourceOutHeader challengeDataSource
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inputSource = challengeDataSourceInput challengeDataSource
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expectedSource = challengeDataSourceExpected challengeDataSource
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outSource = dataSourceOut dataSource
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isEmptyFileSource :: SourceSpec -> IO Bool
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isEmptyFileSource (FilePathSpec filePath) = isEmptyFile filePath
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isEmptyFileSource _ = return False
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@ -531,13 +555,11 @@ data LineInFile = LineInFile SourceSpec Word32 Text
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gevalBootstrapOnSources :: (MonadIO m, MonadThrow m, MonadUnliftIO m) =>
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Int -- ^ number of samples
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-> Metric -- ^ evaluation metric
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-> LineSource (ResourceT m) -- ^ source of the input values
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-> LineSource (ResourceT m) -- ^ source to read the expected output
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-> LineSource (ResourceT m) -- ^ source to read the output
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-> LineSourcesSpecification (ResourceT m)
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-> m (MetricOutput) -- ^ metric values for the output against the expected output
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-- for the time being hardcoded
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gevalBootstrapOnSources numberOfSamples (Mean (MultiLabelFMeasure beta)) inputLineStream expectedLineStream outLineStream = do
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gevalBootstrapOnSources numberOfSamples (Mean (MultiLabelFMeasure beta)) lsSpec = do
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gevalRunPipeline parserSpec (trans step) finalPipeline context
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where parserSpec = (ParserSpecWithoutInput (liftOp expParser) (liftOp outParser))
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context = (WithoutInput expectedLineStream outLineStream)
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@ -550,8 +572,10 @@ gevalBootstrapOnSources numberOfSamples (Mean (MultiLabelFMeasure beta)) inputLi
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$ continueGEvalCalculations SAMSE MSE))
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trans :: ((a, b) -> c) -> ParsedRecord (WithoutInput m a b) -> c
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trans step (ParsedRecordWithoutInput x y) = step (x, y)
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expectedLineStream = lineSourcesExpectedSource lsSpec
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outLineStream = lineSourcesOutputSource lsSpec
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gevalBootstrapOnSources numberOfSamples metric inputLineStream expectedLineStream outLineStream = do
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gevalBootstrapOnSources numberOfSamples metric lsSpec = do
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case toSing $ toHelper metric of
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SomeSing smetric -> gevalRunPipeline parserSpec (trans step) finalPipeline context
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where parserSpec = (ParserSpecWithoutInput (liftOp expParser) (liftOp outParser))
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@ -562,6 +586,8 @@ gevalBootstrapOnSources numberOfSamples metric inputLineStream expectedLineStrea
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finalPipeline = fixer (bootstrapC numberOfSamples $ continueGEvalCalculations smetric metric)
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trans :: ((a, b) -> c) -> ParsedRecord (WithoutInput m a b) -> c
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trans step (ParsedRecordWithoutInput x y) = step (x, y)
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expectedLineStream = lineSourcesExpectedSource lsSpec
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outLineStream = lineSourcesOutputSource lsSpec
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fixer :: ConduitT c Void (ResourceT m) [MetricOutput] -> ConduitT c Void (ResourceT m) MetricOutput
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fixer c = do
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@ -582,26 +608,27 @@ fixer c = do
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-- cases), the work is delegated to @gevalCoreWithoutInput@ function.
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gevalCoreOnSources :: (MonadIO m, MonadThrow m, MonadUnliftIO m) =>
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Metric -- ^ evaluation metric
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-> LineSource (ResourceT m) -- ^ source of the input values
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-> LineSource (ResourceT m) -- ^ source to read the expected output
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-> LineSource (ResourceT m) -- ^ source to read the output
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-> LineSourcesSpecification (ResourceT m)
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-> m (MetricOutput) -- ^ metric values for the output against the expected output
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-- first not-standard metrics
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-- CharMatch is the only metric needing input lines (so far)
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gevalCoreOnSources CharMatch inputLineSource = helper inputLineSource
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gevalCoreOnSources CharMatch = helper
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where
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helper inputLineSource expectedLineSource outputLineSource = do
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helper lsSpec = do
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gevalCoreGeneralized (ParserSpecWithInput justUnpack justUnpack justUnpack) step countAgg (fMeasureOnCounts charMatchBeta) noGraph (WithInput inputLineSource expectedLineSource outputLineSource)
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where inputLineSource = lineSourcesInputSource lsSpec
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expectedLineSource = lineSourcesExpectedSource lsSpec
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outputLineSource = lineSourcesOutputSource lsSpec
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step (ParsedRecordWithInput inp exp out) = getCharMatchCount inp exp out
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justUnpack = liftOp (Right . unpack)
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gevalCoreOnSources (LogLossHashed nbOfBits) _ = helperLogLossHashed nbOfBits id
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gevalCoreOnSources (LikelihoodHashed nbOfBits) _ = helperLogLossHashed nbOfBits logLossToLikehood
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gevalCoreOnSources (LogLossHashed nbOfBits) = helperLogLossHashed nbOfBits id
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gevalCoreOnSources (LikelihoodHashed nbOfBits) = helperLogLossHashed nbOfBits logLossToLikehood
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gevalCoreOnSources (Mean (MultiLabelFMeasure beta)) _
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gevalCoreOnSources (Mean (MultiLabelFMeasure beta))
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= gevalCoreWithoutInputOnItemTargets (Right . intoWords)
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(Right . getWords)
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((fMeasureOnCounts beta) . (getCounts (==)))
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@ -615,7 +642,7 @@ gevalCoreOnSources (Mean (MultiLabelFMeasure beta)) _
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intoWords (RawItemTarget t) = Prelude.map unpack $ Data.Text.words t
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intoWords (PartiallyParsedItemTarget ts) = Prelude.map unpack ts
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gevalCoreOnSources (Mean WER) _
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gevalCoreOnSources (Mean WER)
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= gevalCoreWithoutInputOnItemTargets (Right . intoWords)
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(Right . getWords)
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((uncurry (/.)) . (uncurry werStep))
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@ -629,10 +656,10 @@ gevalCoreOnSources (Mean WER) _
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intoWords (RawItemTarget t) = Prelude.map unpack $ Data.Text.words t
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intoWords (PartiallyParsedItemTarget ts) = Prelude.map unpack ts
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gevalCoreOnSources (Mean _) _ = error $ "Mean/ meta-metric defined only for MultiLabel-F1 and WER for the time being"
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gevalCoreOnSources (Mean _) = error $ "Mean/ meta-metric defined only for MultiLabel-F1 and WER for the time being"
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-- only MultiLabel-F1 handled for JSONs for the time being...
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gevalCoreOnSources (MultiLabelFMeasure beta) _ = gevalCoreWithoutInputOnItemTargets (Right . intoWords)
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gevalCoreOnSources (MultiLabelFMeasure beta) = gevalCoreWithoutInputOnItemTargets (Right . intoWords)
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(Right . getWords)
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(getCounts (==))
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countAgg
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@ -644,13 +671,13 @@ gevalCoreOnSources (MultiLabelFMeasure beta) _ = gevalCoreWithoutInputOnItemTarg
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intoWords (RawItemTarget t) = Prelude.map unpack $ Data.Text.words t
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intoWords (PartiallyParsedItemTarget ts) = Prelude.map unpack ts
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gevalCoreOnSources Pearson _ = gevalCoreByCorrelationMeasure pearson
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gevalCoreOnSources Spearman _ = gevalCoreByCorrelationMeasure spearman
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gevalCoreOnSources Pearson = gevalCoreByCorrelationMeasure pearson
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gevalCoreOnSources Spearman = gevalCoreByCorrelationMeasure spearman
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gevalCoreOnSources (ProbabilisticMultiLabelFMeasure beta) _ = generalizedProbabilisticFMeasure beta
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gevalCoreOnSources (ProbabilisticMultiLabelFMeasure beta) = generalizedProbabilisticFMeasure beta
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SAProbabilisticMultiLabelFMeasure
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gevalCoreOnSources (ProbabilisticSoftFMeasure beta) _ = generalizedProbabilisticFMeasure beta
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gevalCoreOnSources (ProbabilisticSoftFMeasure beta) = generalizedProbabilisticFMeasure beta
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SAProbabilisticSoftFMeasure
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-- and now more typical metrics, which:
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@ -661,18 +688,17 @@ gevalCoreOnSources (ProbabilisticSoftFMeasure beta) _ = generalizedProbabilistic
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-- 5) apply some final funtion on the aggregate
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-- 6) create a graph using the aggregate (applicable only to some metrics)
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gevalCoreOnSources metric _ = gevalCoreOnSourcesStandardWay metric
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gevalCoreOnSources metric = gevalCoreOnSourcesStandardWay metric
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gevalCoreOnSourcesStandardWay :: (MonadIO m, MonadThrow m, MonadUnliftIO m) =>
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Metric -- ^ evaluation metric
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-> LineSource (ResourceT m) -- ^ source to read the expected output
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-> LineSource (ResourceT m) -- ^ source to read the output
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-> LineSourcesSpecification (ResourceT m)
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-> m (MetricOutput) -- ^ metric values for the output against the expected output
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gevalCoreOnSourcesStandardWay metric expectedLineStream outLineStream =
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gevalCoreOnSourcesStandardWay metric lsSpec =
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case toSing $ toHelper metric of
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SomeSing smetric -> gevalRunPipeline parserSpec (trans step) finalPipeline context
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where parserSpec = (ParserSpecWithoutInput (liftOp expParser) (liftOp outParser))
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context = (WithoutInput expectedLineStream outLineStream)
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context = toWithoutInput lsSpec
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step = itemStep smetric
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expParser = expectedParser smetric
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outParser = outputParser smetric
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@ -680,8 +706,8 @@ gevalCoreOnSourcesStandardWay metric expectedLineStream outLineStream =
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trans :: ((a, b) -> c) -> ParsedRecord (WithoutInput m a b) -> c
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trans step (ParsedRecordWithoutInput x y) = step (x, y)
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helperLogLossHashed nbOfBits finalStep expectedLineSource outLineSource =
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gevalCore''' (ParserSpecWithoutInput (liftOp (Right . id)) (liftOp tentativeParser)) (\(lineNo, (t,d)) -> calculateLogLoss nbOfBits lineNo t (parseDistributionWrapper nbOfBits lineNo d)) averageC (finalStep . negate) noGraph (WithoutInput expectedLineSource outLineSource)
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helperLogLossHashed nbOfBits finalStep lsSpec =
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gevalCore''' (ParserSpecWithoutInput (liftOp (Right . id)) (liftOp tentativeParser)) (\(lineNo, (t,d)) -> calculateLogLoss nbOfBits lineNo t (parseDistributionWrapper nbOfBits lineNo d)) averageC (finalStep . negate) noGraph (toWithoutInput lsSpec)
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where -- Unfortunately, we're parsing the distribution twice. We need to
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-- tentatively parse the distribution when the line number is unknown
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-- (so we just set it to 1)
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@ -717,8 +743,7 @@ countFragAgg = CC.foldl countFragFolder (fromInteger 0, fromInteger 0, fromInteg
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gevalCoreByCorrelationMeasure :: (MonadUnliftIO m, MonadThrow m, MonadIO m) =>
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(V.Vector (Double, Double) -> Double) -> -- ^ correlation function
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LineSource (ResourceT m) -> -- ^ source to read the expected output
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LineSource (ResourceT m) -> -- ^ source to read the output
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LineSourcesSpecification (ResourceT m) ->
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m (MetricOutput) -- ^ metric values for the output against the expected output
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gevalCoreByCorrelationMeasure correlationFunction =
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gevalCoreWithoutInput SAPearson correlationC finalStep noGraph
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@ -742,11 +767,10 @@ gevalCoreWithoutInput :: (MonadUnliftIO m, MonadThrow m, MonadIO m)
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-- a "total" value
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-> (d -> Double) -- ^ function to transform the "total" value into the final score
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-> (d -> Maybe GraphSeries)
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-> LineSource (ResourceT m) -- ^ source to read the expected output
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-> LineSource (ResourceT m) -- ^ source to read the output
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-> LineSourcesSpecification (ResourceT m)
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-> m (MetricOutput) -- ^ metric values for the output against the expected output
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gevalCoreWithoutInput smetric aggregator finalStep generateGraph expectedLineStream outLineStream =
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gevalCoreWithoutInputOnItemTargets (liftOp expParser) (liftOp outParser) iStep aggregator finalStep generateGraph expectedLineStream outLineStream
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gevalCoreWithoutInput smetric aggregator finalStep generateGraph lsSpec =
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gevalCoreWithoutInputOnItemTargets (liftOp expParser) (liftOp outParser) iStep aggregator finalStep generateGraph lsSpec
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where expParser = expectedParser smetric
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outParser = outputParser smetric
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iStep = itemStep smetric
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@ -761,11 +785,10 @@ gevalCoreWithoutInputOnItemTargets :: (MonadUnliftIO m, MonadThrow m, MonadIO m)
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-- a "total" value
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-> (d -> Double) -- ^ function to transform the "total" value into the final score
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-> (d -> Maybe GraphSeries)
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-> LineSource (ResourceT m) -- ^ source to read the expected output
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-> LineSource (ResourceT m) -- ^ source to read the output
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-> LineSourcesSpecification (ResourceT m)
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-> m (MetricOutput) -- ^ metric values for the output against the expected output
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gevalCoreWithoutInputOnItemTargets expParser outParser itemStep aggregator finalStep generateGraph expectedLineStream outLineStream =
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gevalCoreGeneralized (ParserSpecWithoutInput expParser outParser) (trans itemStep) aggregator finalStep generateGraph (WithoutInput expectedLineStream outLineStream)
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gevalCoreWithoutInputOnItemTargets expParser outParser itemStep aggregator finalStep generateGraph lsSpec =
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gevalCoreGeneralized (ParserSpecWithoutInput expParser outParser) (trans itemStep) aggregator finalStep generateGraph (toWithoutInput lsSpec)
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where
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trans :: ((a, b) -> c) -> ParsedRecord (WithoutInput m a b) -> c
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trans step (ParsedRecordWithoutInput x y) = step (x, y)
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