diff --git a/benchmark/Single.hs b/benchmark/Single.hs index 0e55494e..cc8f94f5 100644 --- a/benchmark/Single.hs +++ b/benchmark/Single.hs @@ -1,22 +1,9 @@ {-# LANGUAGE DerivingStrategies #-} {-# LANGUAGE ImportQualifiedPost #-} -import Control.Monad.Bayes.Class (MonadMeasure) -import Control.Monad.Bayes.Inference.MCMC (MCMCConfig (..), Proposal (SingleSiteMH)) -import Control.Monad.Bayes.Inference.RMSMC (rmsmcBasic) -import Control.Monad.Bayes.Inference.SMC - ( SMCConfig (SMCConfig, numParticles, numSteps, resampler), - smc, - ) -import Control.Monad.Bayes.Population import Control.Monad.Bayes.Sampler.Strict -import Control.Monad.Bayes.Traced hiding (model) -import Control.Monad.Bayes.Weighted -import Control.Monad.ST (runST) import Data.Time (diffUTCTime, getCurrentTime) -import HMM qualified -import LDA qualified -import LogReg qualified +import Helper import Options.Applicative ( Applicative (liftA2), ParserInfo, @@ -31,47 +18,6 @@ import Options.Applicative short, ) -data Model = LR Int | HMM Int | LDA (Int, Int) - deriving stock (Show, Read) - -parseModel :: String -> Maybe Model -parseModel s = - case s of - 'L' : 'R' : n -> Just $ LR (read n) - 'H' : 'M' : 'M' : n -> Just $ HMM (read n) - 'L' : 'D' : 'A' : n -> Just $ LDA (5, read n) - _ -> Nothing - -getModel :: MonadMeasure m => Model -> (Int, m String) -getModel model = (size model, program model) - where - size (LR n) = n - size (HMM n) = n - size (LDA (d, w)) = d * w - program (LR n) = show <$> (LogReg.logisticRegression (runST $ sampleSTfixed (LogReg.syntheticData n))) - program (HMM n) = show <$> (HMM.hmm (runST $ sampleSTfixed (HMM.syntheticData n))) - program (LDA (d, w)) = show <$> (LDA.lda (runST $ sampleSTfixed (LDA.syntheticData d w))) - -data Alg = SMC | MH | RMSMC - deriving stock (Read, Show) - -runAlg :: Model -> Alg -> SamplerIO String -runAlg model alg = - case alg of - SMC -> - let n = 100 - (k, m) = getModel model - in show <$> population (smc SMCConfig {numSteps = k, numParticles = n, resampler = resampleSystematic} m) - MH -> - let t = 100 - (_, m) = getModel model - in show <$> unweighted (mh t m) - RMSMC -> - let n = 10 - t = 1 - (k, m) = getModel model - in show <$> population (rmsmcBasic MCMCConfig {numMCMCSteps = t, numBurnIn = 0, proposal = SingleSiteMH} (SMCConfig {numSteps = k, numParticles = n, resampler = resampleSystematic}) m) - infer :: Model -> Alg -> IO () infer model alg = do x <- sampleIOfixed (runAlg model alg) diff --git a/models/Helper.hs b/models/Helper.hs new file mode 100644 index 00000000..151a232d --- /dev/null +++ b/models/Helper.hs @@ -0,0 +1,70 @@ +{-# LANGUAGE DerivingStrategies #-} +{-# LANGUAGE ImportQualifiedPost #-} + +module Helper where + +import Control.Monad.Bayes.Class (MonadMeasure) +import Control.Monad.Bayes.Inference.MCMC (MCMCConfig (..), Proposal (SingleSiteMH)) +import Control.Monad.Bayes.Inference.RMSMC (rmsmcBasic) +import Control.Monad.Bayes.Inference.SMC + ( SMCConfig (SMCConfig, numParticles, numSteps, resampler), + smc, + ) +import Control.Monad.Bayes.Population +import Control.Monad.Bayes.Sampler.Strict +import Control.Monad.Bayes.Traced hiding (model) +import Control.Monad.Bayes.Weighted +import Control.Monad.ST (runST) +import HMM qualified +import LDA qualified +import LogReg qualified + +data Model = LR Int | HMM Int | LDA (Int, Int) + deriving stock (Show, Read) + +parseModel :: String -> Maybe Model +parseModel s = + case s of + 'L' : 'R' : n -> Just $ LR (read n) + 'H' : 'M' : 'M' : n -> Just $ HMM (read n) + 'L' : 'D' : 'A' : n -> Just $ LDA (5, read n) + _ -> Nothing + +serializeModel :: Model -> Maybe String +serializeModel (LR n) = Just $ "LR" ++ show n +serializeModel (HMM n) = Just $ "HMM" ++ show n +serializeModel (LDA (5, n)) = Just $ "LDA" ++ show n +serializeModel (LDA _) = Nothing + +data Alg = SMC | MH | RMSMC + deriving stock (Read, Show, Eq, Ord, Enum, Bounded) + +getModel :: MonadMeasure m => Model -> (Int, m String) +getModel model = (size model, program model) + where + size (LR n) = n + size (HMM n) = n + size (LDA (d, w)) = d * w + program (LR n) = show <$> (LogReg.logisticRegression (runST $ sampleSTfixed (LogReg.syntheticData n))) + program (HMM n) = show <$> (HMM.hmm (runST $ sampleSTfixed (HMM.syntheticData n))) + program (LDA (d, w)) = show <$> (LDA.lda (runST $ sampleSTfixed (LDA.syntheticData d w))) + +runAlg :: Model -> Alg -> SamplerIO String +runAlg model alg = + case alg of + SMC -> + let n = 100 + (k, m) = getModel model + in show <$> population (smc SMCConfig {numSteps = k, numParticles = n, resampler = resampleSystematic} m) + MH -> + let t = 100 + (_, m) = getModel model + in show <$> unweighted (mh t m) + RMSMC -> + let n = 10 + t = 1 + (k, m) = getModel model + in show <$> population (rmsmcBasic MCMCConfig {numMCMCSteps = t, numBurnIn = 0, proposal = SingleSiteMH} (SMCConfig {numSteps = k, numParticles = n, resampler = resampleSystematic}) m) + +runAlgFixed :: Model -> Alg -> IO String +runAlgFixed model alg = sampleIOfixed $ runAlg model alg diff --git a/monad-bayes.cabal b/monad-bayes.cabal index 7934f255..83e49b68 100644 --- a/monad-bayes.cabal +++ b/monad-bayes.cabal @@ -114,6 +114,7 @@ executable example hs-source-dirs: benchmark models other-modules: Dice + Helper HMM LDA LogReg @@ -157,9 +158,13 @@ test-suite monad-bayes-test other-modules: BetaBin ConjugatePriors + Helper HMM + LDA + LogReg Sprinkler TestAdvanced + TestBenchmarks TestDistribution TestEnumerator TestInference diff --git a/test/Spec.hs b/test/Spec.hs index 83d3ac9e..baaa95d1 100644 --- a/test/Spec.hs +++ b/test/Spec.hs @@ -5,6 +5,7 @@ import Test.Hspec (context, describe, hspec, it, shouldBe) import Test.Hspec.QuickCheck (prop) import Test.QuickCheck (ioProperty, property, (==>)) import TestAdvanced qualified +import TestBenchmarks qualified import TestDistribution qualified import TestEnumerator qualified import TestInference qualified @@ -164,3 +165,5 @@ main = hspec do passed6 `shouldBe` True passed7 <- TestAdvanced.passed7 passed7 `shouldBe` True + + TestBenchmarks.test diff --git a/test/TestBenchmarks.hs b/test/TestBenchmarks.hs new file mode 100644 index 00000000..2645d19b --- /dev/null +++ b/test/TestBenchmarks.hs @@ -0,0 +1,33 @@ +module TestBenchmarks where + +import Control.Monad (forM_) +import Data.Maybe (fromJust) +import Helper +import System.IO (readFile') +import System.IO.Error (catchIOError, isDoesNotExistError) +import Test.Hspec + +fixtureToFilename :: Model -> Alg -> String +fixtureToFilename model alg = fromJust (serializeModel model) ++ "-" ++ show alg ++ ".txt" + +models :: [Model] +models = [LR 10, HMM 10, LDA (5, 10)] + +algs :: [Alg] +algs = [minBound .. maxBound] + +test :: SpecWith () +test = describe "Benchmarks" $ forM_ models $ \model -> forM_ algs $ testFixture model + +testFixture :: Model -> Alg -> SpecWith () +testFixture model alg = do + let filename = "test/fixtures/" ++ fixtureToFilename model alg + it ("should agree with the fixture " ++ filename) $ do + fixture <- catchIOError (readFile' filename) $ \e -> + if isDoesNotExistError e + then return "" + else ioError e + sampled <- runAlgFixed model alg + -- Reset in case of fixture update or creation + writeFile filename sampled + fixture `shouldBe` sampled diff --git a/test/fixtures/HMM10-MH.txt b/test/fixtures/HMM10-MH.txt new file mode 100644 index 00000000..c0e713bd --- /dev/null +++ b/test/fixtures/HMM10-MH.txt @@ -0,0 +1 @@ +["[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,2,1,1,1,1,1,1,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,1,1,2,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[1,2,1,1,1,1,1,2,2,0]","[2,2,1,1,1,1,1,2,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,2,1,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[2,1,2,1,1,2,1,1,2,0]","[1,1,2,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,2,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,2,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[1,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]","[0,1,1,1,1,0,1,1,2,0]"] \ No newline at end of file diff --git a/test/fixtures/HMM10-RMSMC.txt b/test/fixtures/HMM10-RMSMC.txt new file mode 100644 index 00000000..279872ed --- /dev/null +++ b/test/fixtures/HMM10-RMSMC.txt @@ -0,0 +1 @@ +[("[2,1,1,1,0,1,1,2,1,1]",2.4438034074800498e-8),("[1,1,1,1,1,2,1,1,1,0]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,1,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,2,0,2,1,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,1,2,1,2,1,2,1,1,2]",2.4438034074800498e-8),("[1,2,1,1,2,2,0,1,1,1]",2.4438034074800498e-8)] \ No newline at end of file diff --git a/test/fixtures/HMM10-SMC.txt b/test/fixtures/HMM10-SMC.txt new file mode 100644 index 00000000..32811d74 --- /dev/null +++ b/test/fixtures/HMM10-SMC.txt @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/test/fixtures/LR10-RMSMC.txt b/test/fixtures/LR10-RMSMC.txt new file mode 100644 index 00000000..37d0537e --- /dev/null +++ b/test/fixtures/LR10-RMSMC.txt @@ -0,0 +1 @@ +[("5.333997036871341e-6",6.253483531321334e-5),("4.7394126422869915e-6",6.253483531321334e-5),("7.798412010176118e-6",6.253483531321334e-5),("3.6537314189667804e-3",6.253483531321334e-5),("2.8719951155583437e-3",6.253483531321334e-5),("8.106430574751586e-3",6.253483531321334e-5),("0.8083297132912659",6.253483531321334e-5),("0.3178833271596258",6.253483531321334e-5),("0.3487591395231385",6.253483531321334e-5),("2.027192522287899e-2",6.253483531321334e-5)] \ No newline at end of file diff --git a/test/fixtures/LR10-SMC.txt b/test/fixtures/LR10-SMC.txt new file mode 100644 index 00000000..f1bdd32e --- /dev/null +++ b/test/fixtures/LR10-SMC.txt @@ -0,0 +1 @@ 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\ No newline at end of file