diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | flake.lock | 900 | ||||
| -rw-r--r-- | flake.nix | 39 | ||||
| -rw-r--r-- | package.yaml | 20 | ||||
| -rw-r--r-- | ppl.cabal | 31 | ||||
| -rw-r--r-- | src/PPL.hs | 5 | ||||
| -rw-r--r-- | src/PPL/Distr.hs | 100 | ||||
| -rw-r--r-- | src/PPL/Internal.hs | 81 | ||||
| -rw-r--r-- | src/PPL/Sampling.hs | 52 |
9 files changed, 1229 insertions, 0 deletions
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..fcfc4a1 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +result* diff --git a/flake.lock b/flake.lock new file mode 100644 index 0000000..2f052dd --- /dev/null +++ b/flake.lock @@ -0,0 +1,900 @@ +{ + "nodes": { + "HTTP": { + "flake": false, + "locked": { + "lastModified": 1451647621, + "narHash": "sha256-oHIyw3x0iKBexEo49YeUDV1k74ZtyYKGR2gNJXXRxts=", + "owner": "phadej", + "repo": "HTTP", + "rev": "9bc0996d412fef1787449d841277ef663ad9a915", + "type": "github" + }, + "original": { + "owner": "phadej", + "repo": "HTTP", + "type": "github" + } + }, + "blank": { + "locked": { + "lastModified": 1625557891, + "narHash": "sha256-O8/MWsPBGhhyPoPLHZAuoZiiHo9q6FLlEeIDEXuj6T4=", + "owner": "divnix", + "repo": "blank", + "rev": "5a5d2684073d9f563072ed07c871d577a6c614a8", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "blank", + "type": "github" + } + }, + "cabal-32": { + "flake": false, + "locked": { + "lastModified": 1603716527, + "narHash": "sha256-X0TFfdD4KZpwl0Zr6x+PLxUt/VyKQfX7ylXHdmZIL+w=", + "owner": "haskell", + "repo": "cabal", + "rev": "48bf10787e27364730dd37a42b603cee8d6af7ee", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.2", + "repo": "cabal", + "type": "github" + } + }, + "cabal-34": { + "flake": false, + "locked": { + "lastModified": 1640353650, + "narHash": "sha256-N1t6M3/wqj90AEdRkeC8i923gQYUpzSr8b40qVOZ1Rk=", + "owner": "haskell", + "repo": "cabal", + "rev": "942639c18c0cd8ec53e0a6f8d120091af35312cd", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.4", + "repo": "cabal", + "type": "github" + } + }, + "cabal-36": { + "flake": false, + "locked": { + "lastModified": 1641652457, + "narHash": "sha256-BlFPKP4C4HRUJeAbdembX1Rms1LD380q9s0qVDeoAak=", + "owner": "haskell", + "repo": "cabal", + "rev": "f27667f8ec360c475027dcaee0138c937477b070", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.6", + "repo": "cabal", + "type": "github" + } + }, + "cardano-shell": { + "flake": false, + "locked": { + "lastModified": 1608537748, + "narHash": "sha256-PulY1GfiMgKVnBci3ex4ptk2UNYMXqGjJOxcPy2KYT4=", + "owner": "input-output-hk", + "repo": "cardano-shell", + "rev": "9392c75087cb9a3d453998f4230930dea3a95725", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "cardano-shell", + "type": "github" + } + }, + "devshell": { + "inputs": { + "flake-utils": [ + "haskellNix", + "tullia", + "std", + "flake-utils" + ], + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1663445644, + "narHash": "sha256-+xVlcK60x7VY1vRJbNUEAHi17ZuoQxAIH4S4iUFUGBA=", + "owner": "numtide", + "repo": "devshell", + "rev": "e3dc3e21594fe07bdb24bdf1c8657acaa4cb8f66", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "devshell", + "type": "github" + } + }, + "dmerge": { + "inputs": { + "nixlib": [ + "haskellNix", + 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"narHash": "sha256-sIKgO+z7tj4lw3u6oBZxqIhDrzSkvpHtv0Kki+lh9Fg=", + "owner": "angerman", + "repo": "old-ghc-nix", + "rev": "af48a7a7353e418119b6dfe3cd1463a657f342b8", + "type": "github" + }, + "original": { + "owner": "angerman", + "ref": "master", + "repo": "old-ghc-nix", + "type": "github" + } + }, + "root": { + "inputs": { + "flake-utils": "flake-utils", + "haskellNix": "haskellNix", + "nixpkgs": [ + "haskellNix", + "nixpkgs-unstable" + ] + } + }, + "stackage": { + "flake": false, + "locked": { + "lastModified": 1670890221, + "narHash": "sha256-kV7irjUr4Ot3b2MwTcgVKYuEe+legxhGh4ApBeESy1s=", + "owner": "input-output-hk", + "repo": "stackage.nix", + "rev": "56f59c2d4ecdb237348a0774274f38874f81a3ca", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "stackage.nix", + "type": "github" + } + }, + "std": { + "inputs": { + "blank": "blank", + "devshell": "devshell", + "dmerge": "dmerge", + "flake-utils": "flake-utils_4", + "makes": [ + "haskellNix", + "tullia", + "std", + "blank" + ], + "mdbook-kroki-preprocessor": "mdbook-kroki-preprocessor", + "microvm": [ + "haskellNix", + "tullia", + "std", + "blank" + ], + "n2c": "n2c", + "nixago": "nixago", + "nixpkgs": "nixpkgs_4", + "yants": "yants" + }, + "locked": { + "lastModified": 1665513321, + "narHash": "sha256-D6Pacw9yf/HMs84KYuCxHXnNDL7v43gtcka5URagFqE=", + "owner": "divnix", + "repo": "std", + "rev": "94a90eedb9cfc115b12ae8f6622d9904788559e4", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "std", + "type": "github" + } + }, + "tullia": { + "inputs": { + "nix-nomad": "nix-nomad", + "nix2container": "nix2container", + "nixpkgs": [ + "haskellNix", + "nixpkgs" + ], + "std": "std" + }, + "locked": { + "lastModified": 1668711738, + "narHash": "sha256-CBjky16o9pqsGE1bWu6nRlRajgSXMEk+yaFQLibqXcE=", + "owner": "input-output-hk", + "repo": "tullia", + "rev": "ead1f515c251f0e060060ef0e2356a51d3dfe4b0", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "tullia", + "type": "github" + } + }, + "utils": { + "locked": { + "lastModified": 1653893745, + "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "yants": { + "inputs": { + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1660507851, + "narHash": "sha256-BKjq7JnVuUR/xDtcv6Vm9GYGKAblisXrAgybor9hT/s=", + "owner": "divnix", + "repo": "yants", + "rev": "0b895ca02a8fa72bad50b454cb3e7d8a66407c96", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "yants", + "type": "github" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 0000000..76c754c --- /dev/null +++ b/flake.nix @@ -0,0 +1,39 @@ +{ + nixConfig = { + extra-trusted-public-keys = ["hydra.iohk.io:f/Ea+s+dFdN+3Y/G+FDgSq+a5NEWhJGzdjvKNGv0/EQ="]; + extra-substituters = ["https://cache.iog.io"]; + }; + description = "Bayesian phylogentic playground"; + inputs.haskellNix.url = "github:input-output-hk/haskell.nix"; + inputs.nixpkgs.follows = "haskellNix/nixpkgs-unstable"; + inputs.flake-utils.url = "github:numtide/flake-utils"; + outputs = { + self, + nixpkgs, + flake-utils, + haskellNix, + }: + flake-utils.lib.eachSystem ["x86_64-linux"] (system: let + overlays = [ + haskellNix.overlay + (final: prev: { + phylogenies = final.haskell-nix.project' { + src = ./.; + compiler-nix-name = "ghc925"; + shell.tools = { + hlint = {}; + ormolu = {}; + }; + shell.buildInputs = with pkgs; [ + ]; + }; + }) + ]; + pkgs = import nixpkgs { + inherit system overlays; + inherit (haskellNix) config; + }; + flake = pkgs.phylogenies.flake {}; + in + flake // { packages.default = flake.packages."ppl:lib:ppl";}); +} diff --git a/package.yaml b/package.yaml new file mode 100644 index 0000000..7c3a3e8 --- /dev/null +++ b/package.yaml @@ -0,0 +1,20 @@ +name: ppl +version: 0.0.1 +synopsis: Reimplementation of LazyPPL +maintainer: Justin Bedo <cu@cua0.org> +license: MIT + +dependencies: + - base >= 4.9 && < 5 + - transformers + - log-domain + - random + - template-haskell + - containers + +library: + source-dirs: src + exposed-modules: + - PPL + - PPL.Distr + - PPL.Sampling diff --git a/ppl.cabal b/ppl.cabal new file mode 100644 index 0000000..b3b5533 --- /dev/null +++ b/ppl.cabal @@ -0,0 +1,31 @@ +cabal-version: 1.12 + +-- This file has been generated from package.yaml by hpack version 0.34.7. +-- +-- see: https://github.com/sol/hpack + +name: ppl +version: 0.0.1 +synopsis: Reimplementation of LazyPPL +maintainer: Justin Bedo <cu@cua0.org> +license: MIT +build-type: Simple + +library + exposed-modules: + PPL + PPL.Distr + PPL.Sampling + other-modules: + PPL.Internal + Paths_ppl + hs-source-dirs: + src + build-depends: + base >=4.9 && <5 + , containers + , log-domain + , random + , template-haskell + , transformers + default-language: Haskell2010 diff --git a/src/PPL.hs b/src/PPL.hs new file mode 100644 index 0000000..21bb87c --- /dev/null +++ b/src/PPL.hs @@ -0,0 +1,5 @@ +module PPL(module PPL.Internal, module PPL.Sampling, module PPL.Distr) where + +import PPL.Internal +import PPL.Sampling +import PPL.Distr diff --git a/src/PPL/Distr.hs b/src/PPL/Distr.hs new file mode 100644 index 0000000..797379b --- /dev/null +++ b/src/PPL/Distr.hs @@ -0,0 +1,100 @@ +module PPL.Distr where + +import PPL.Internal +import qualified PPL.Internal as I + +-- Acklam's approximation +-- https://web.archive.org/web/20151030215612/http://home.online.no/~pjacklam/notes/invnorm/ +{-# INLINE probit #-} +probit :: Double -> Double +probit p + | p < lower = + let q = sqrt (-2 * log p) + in (((((c1 * q + c2) * q + c3) * q + c4) * q + c5) * q + c6) + / ((((d1 * q + d2) * q + d3) * q + d4) * q + 1) + | p < 1 - lower = + let q = p - 0.5 + r = q * q + in (((((a1 * r + a2) * r + a3) * r + a4) * r + a5) * r + a6) * q + / (((((b1 * r + b2) * r + b3) * r + b4) * r + b5) * r + 1) + | otherwise = -probit (1 - p) + where + a1 = -3.969683028665376e+01 + a2 = 2.209460984245205e+02 + a3 = -2.759285104469687e+02 + a4 = 1.383577518672690e+02 + a5 = -3.066479806614716e+01 + a6 = 2.506628277459239e+00 + + b1 = -5.447609879822406e+01 + b2 = 1.615858368580409e+02 + b3 = -1.556989798598866e+02 + b4 = 6.680131188771972e+01 + b5 = -1.328068155288572e+01 + + c1 = -7.784894002430293e-03 + c2 = -3.223964580411365e-01 + c3 = -2.400758277161838e+00 + c4 = -2.549732539343734e+00 + c5 = 4.374664141464968e+00 + c6 = 2.938163982698783e+00 + + d1 = 7.784695709041462e-03 + d2 = 3.224671290700398e-01 + d3 = 2.445134137142996e+00 + d4 = 3.754408661907416e+00 + + lower = 0.02425 + +iid :: Prob a -> Prob [a] +iid = sequence . repeat + +gauss = probit <$> uniform + +norm m s = (+ m) . (* s) <$> gauss + +-- Marsaglia's fast gamma rejection sampling +gamma a = do + x <- gauss + u <- uniform + if u < 1 - 0.03331 * x ** 4 + then pure $ d * v x + else gamma a + where + d = a - 1 / 3 + v x = (1 + x / sqrt (9 * d)) ** 3 + +beta a b = do + x <- gamma a + y <- gamma b + pure $ x / (x + y) + +bern p = (< p) <$> uniform + +binom n = fmap (length . filter id . take n) . iid . bern + +exponential lambda = negate . (/ lambda) . log <$> uniform + +geom :: Double -> Prob Int +geom p = first 0 <$> iid (bern p) + where + first n (True : _) = n + first n (_ : xs) = first (n + 1) xs + +bounded lower upper = (+ lower) . (* (upper - lower)) <$> uniform + +bounded' lower upper = round <$> bounded (fromIntegral lower) (fromIntegral upper) + +cat :: [Double] -> Prob Int +cat xs = search 0 (tail $ scanl (+) 0 xs) <$> uniform + where + search i [] _ = i + search i (x : xs) r + | x > r = i + | otherwise = search (i + 1) xs r + +dirichletProcess p = go 1 + where + go rest = do + x <- beta 1 p + (x*rest:) <$> go (rest - x*rest) diff --git a/src/PPL/Internal.hs b/src/PPL/Internal.hs new file mode 100644 index 0000000..a729d3d --- /dev/null +++ b/src/PPL/Internal.hs @@ -0,0 +1,81 @@ +{-# LANGUAGE TemplateHaskell #-} +{-# LANGUAGE RankNTypes #-} +{-# LANGUAGE GeneralizedNewtypeDeriving #-} + +module PPL.Internal (uniform, split, Prob(..), Meas, score, scoreLog, sample, +randomTree, samples, mutateTree) where + +import Control.Monad +import Control.Monad.Trans.Class +import Control.Monad.Trans.Writer +import Data.Monoid +import qualified Language.Haskell.TH.Syntax as TH +import Numeric.Log +import System.Random hiding (uniform, split) +import qualified System.Random as R +import Data.Bifunctor +import Control.Monad.IO.Class + +-- Reimplementation of the LazyPPL monads to avoid some dependencies + +data Tree = Tree Double [Tree] + +split :: Tree -> (Tree, Tree) +split (Tree r (t : ts)) = (t, Tree r ts) + +{-# INLINE randomTree #-} +randomTree :: RandomGen g => g -> Tree +randomTree g = let (a, g') = random g in Tree a (randomTrees g') + +{-# INLINE randomTrees #-} +randomTrees :: RandomGe |