init

7 files changed, 1080 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/bin/cluster.hs b/bin/cluster.hs
new file mode 100644
index 0000000..70e22c7
--- /dev/null
+++ b/bin/cluster.hs
@@ -0,0 +1,88 @@
+{-# LANGUAGE ViewPatterns #-}
+
+module Main where
+
+import Data.Fixed (mod')
+import Data.Foldable (toList)
+import Data.List
+import qualified Data.Map as M
+import qualified Data.Vector.Unboxed as V
+import Numeric.Log hiding (sum)
+import PPL
+import System.Random (mkStdGen, setStdGen)
+
+cumsum = scanl1 (+)
+
+first f xs = snd . head . filter (f . fst) $ zip xs [0 ..]
+
+stirling n = n * log n - n
+
+pois lambda (fromIntegral -> k) = lambda' ** k' * Exp (negate lambda) / Exp (stirling k)
+  where
+    lambda' = Exp $ log lambda
+    k' = Exp $ log k
+
+-- (infinite) binary trees
+data Tree a = Empty | Tree a (Tree a) (Tree a)
+  deriving (Show)
+
+instance Foldable Tree where
+  foldMap f t = bftrav [t]
+    where
+      bftrav [] = mempty
+      bftrav (Empty : ts) = bftrav ts
+      bftrav ((Tree a l r) : ts) = f a <> bftrav (ts <> [l, r])
+
+-- Infinite trees from infinite lists
+-- NB: it's harder to partition a list so that it folds back to
+-- equivalence. It doesn't really matter here since we're only
+-- unfolding random uniforms anyway.
+treeFromList (x : xs) = Tree x (treeFromList lpart) (treeFromList rpart)
+  where
+    (lpart, rpart) = unzip $ partition xs
+    partition (a : b : xs) = (a, b) : partition xs
+
+-- Constrain trees so leaves sum to node value
+normTree :: Tree Double -> Tree Double
+normTree (Tree x l r) = go $ Tree x l r
+  where
+    go (Tree x (Tree u l r) (Tree v l' r')) =
+      let s = x / (u + v)
+       in Tree x (go $ Tree (s * u) l r) (go $ Tree (s * v) l' r')
+
+drawTreeProbs = toList . normTree . treeFromList <$> iid uniform
+
+model xs = do
+  (clmuAcinar, clmuDuctal, params, clusters) <- sample $ do
+    -- Sample hyperparameters
+    a <- bounded 1 10
+
+    -- CRP style
+    dir <- cumsum <$> dirichletProcess a
+    rs <- iid uniform
+    clmuAcinar <- drawTreeProbs
+    clmuDuctal <- drawTreeProbs
+    let clusters = map (\r -> first (>= r) dir) rs
+        params = map (\i -> zip clmuAcinar clmuDuctal !! i) clusters
+    pure (clmuAcinar, clmuDuctal, params, clusters)
+  mapM_ scoreLog $ zipWith likelihood params (V.toList xs)
+  let cls = take (V.length xs) clusters
+      k = maximum cls + 1
+  pure (take k clmuAcinar, take k clmuDuctal, cls)
+  where
+    likelihood (ap, dp) (ac, ad, dc, dd) =
+      max (pois (fromIntegral ad * ap) ac) (pois (fromIntegral ad * ap / 2) ac)
+        * max (pois (fromIntegral dd * dp) dc) (pois (fromIntegral dd * dp / 2) dc)
+
+main = do
+  setStdGen $ mkStdGen 42
+  (hdr : lines) <- lines <$> readFile "/nix/store/9xkb2apajv9sy37akz24x3jj6kw5hn7h-bionix-dump-counts"
+  let parsed = V.fromList $ map ((\[_, ac, ad, dc, dd] -> (dbl ac, dbl ad, dbl dc, dbl dd)) . words) lines
+      dbl = round . read :: String -> Int
+  ((a, d, cl), _) <- foldl1' (\a c -> if mml a < mml c then a else c) . take 100000 <$> mh 0.3 (model parsed)
+  writeFile "/data/props" . unlines $ zipWith (\a b -> show a <> "," <> show b) a d
+  writeFile "/data/clusters" . unlines $ map show cl
+  where
+    mml ((a, d, cl), lik) = sum (map (log . (+ 1)) a) + sum (map (log . (+ 1)) d) + sum (map (log . (+ 1)) tab) - sum (map stirling tab) - ln lik
+      where
+        tab = M.elems $ M.fromListWith (+) [(c, 1) | c <- cl]
diff --git a/cabal.project b/cabal.project
new file mode 100644
index 0000000..265b3e2
--- /dev/null
+++ b/cabal.project
@@ -0,0 +1,7 @@
+packages: *.cabal
+
+source-repository-package
+  type: git
+  location: https://vk3.wtf/cgit/ppl.git
+  tag: b906da9afa6802bf8104dfabe26b67a6c673af91
+  --sha256: 14gqgs4akf74q5wh3spn72fnggb28dgmmh52vi9a5kx7dc23pxj2
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",
+          "tullia",
+          "std",
+          "nixpkgs"
+        ],
+        "yants": [
+          "haskellNix",
+          "tullia",
+          "std",
+          "yants"
+        ]
+      },
+      "locked": {
+        "lastModified": 1659548052,
+        "narHash": "sha256-fzI2gp1skGA8mQo/FBFrUAtY0GQkAIAaV/V127TJPyY=",
+        "owner": "divnix",
+        "repo": "data-merge",
+        "rev": "d160d18ce7b1a45b88344aa3f13ed1163954b497",
+        "type": "github"
+      },
+      "original": {
+        "owner": "divnix",
+        "repo": "data-merge",
+        "type": "github"
+      }
+    },
+    "flake-compat": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1635892615,
+        "narHash": "sha256-harGbMZr4hzat2BWBU+Y5OYXlu+fVz7E4WeQzHi5o8A=",
+        "owner": "input-output-hk",
+        "repo": "flake-compat",
+        "rev": "eca47d3377946315596da653862d341ee5341318",
+        "type": "github"
+      },
+      "original": {
+        "owner": "input-output-hk",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-compat_2": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1650374568,
+        "narHash": "sha256-Z+s0J8/r907g149rllvwhb4pKi8Wam5ij0st8PwAh+E=",
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "b4a34015c698c7793d592d66adbab377907a2be8",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1667395993,
+        "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "locked": {
+        "lastModified": 1644229661,
+        "narHash": "sha256-1YdnJAsNy69bpcjuoKdOYQX0YxZBiCYZo4Twxerqv7k=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "3cecb5b042f7f209c56ffd8371b2711a290ec797",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_3": {
+      "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"
+      }
+    },
+    "flake-utils_4": {
+      "locked": {
+        "lastModified": 1659877975,
+        "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_5": {
+      "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"
+      }
+    },
+    "ghc-8.6.5-iohk": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1600920045,
+        "narHash": "sha256-DO6kxJz248djebZLpSzTGD6s8WRpNI9BTwUeOf5RwY8=",
+        "owner": "input-output-hk",
+        "repo": "ghc",
+        "rev": "95713a6ecce4551240da7c96b6176f980af75cae",
+        "type": "github"
+      },
+      "original": {
+        "owner": "input-output-hk",
+        "ref": "release/8.6.5-iohk",
+        "repo": "ghc",
+        "type": "github"
+      }
+    },
+    "gomod2nix": {
+      "inputs": {
+        "nixpkgs": "nixpkgs_2",
+        "utils": "utils"
+      },
+      "locked": {
+        "lastModified": 1655245309,
+        "narHash": "sha256-d/YPoQ/vFn1+GTmSdvbSBSTOai61FONxB4+Lt6w/IVI=",
+        "owner": "tweag",
+        "repo": "gomod2nix",
+        "rev": "40d32f82fc60d66402eb0972e6e368aeab3faf58",
+        "type": "github"
+      },
+      "original": {
+        "owner": "tweag",
+        "repo": "gomod2nix",
+        "type": "github"
+      }
+    },
+    "hackage": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1671063994,
+        "narHash": "sha256-4YZ6+JUSFPBlK0zNErqBY8GLvBVbS8q1ldNcBwqSuME=",
+        "owner": "input-output-hk",
+        "repo": "hackage.nix",
+        "rev": "f42f80c9eda52453b6042aee6f614302d076b852",
+        "type": "github"
+      },
+      "original": {
+        "owner": "input-output-hk",
+        "repo": "hackage.nix",
+        "type": "github"
+      }
+    },
+    "haskellNix": {
+      "inputs": {
+        "HTTP": "HTTP",
+        "cabal-32": "cabal-32",
+        "cabal-34": "cabal-34",
+        "cabal-36": "cabal-36",
+        "cardano-shell": "cardano-shell",
+        "flake-compat": "flake-compat",
+        "flake-utils": "flake-utils_2",
+        "ghc-8.6.5-iohk": "ghc-8.6.5-iohk",
+        "hackage": "hackage",
+        "hpc-coveralls": "hpc-coveralls",
+        "hydra": "hydra",
+        "iserv-proxy": "iserv-proxy",
+        "nixpkgs": [
+          "haskellNix",
+          "nixpkgs-unstable"
+        ],
+        "nixpkgs-2003": "nixpkgs-2003",
+        "nixpkgs-2105": "nixpkgs-2105",
+        "nixpkgs-2111": "nixpkgs-2111",
+        "nixpkgs-2205": "nixpkgs-2205",
+        "nixpkgs-2211": "nixpkgs-2211",
+        "nixpkgs-unstable": "nixpkgs-unstable",
+        "old-ghc-nix": "old-ghc-nix",
+        "stackage": "stackage",
+        "tullia": "tullia"
+      },
+      "locked": {
+        "lastModified": 1671065520,
+        "narHash": "sha256-Mbcbyx0DKTdzNWmDj17nzfaazL7qg/cNAzJFKZ1i92E=",
+        "owner": "input-output-hk",
+        "repo": "haskell.nix",
+        "rev": "af2c47f5909c5c74c28124f8793539736680d606",
+        "type": "github"
+      },
+      "original": {
+        "owner": "input-output-hk",
+        "repo": "haskell.nix",
+        "type": "github"
+      }
+    },
+    "hpc-coveralls": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1607498076,
+        "narHash": "sha256-8uqsEtivphgZWYeUo5RDUhp6bO9j2vaaProQxHBltQk=",
+        "owner": "sevanspowell",
+        "repo": "hpc-coveralls",
+        "rev": "14df0f7d229f4cd2e79f8eabb1a740097fdfa430",
+        "type": "github"
+      },
+      "original": {
+        "owner": "sevanspowell",
+        "repo": "hpc-coveralls",
+        "type": "github"
+      }
+    },
+    "hydra": {
+      "inputs": {
+        "nix": "nix",
+        "nixpkgs": [
+          "haskellNix",
+          "hydra",
+          "nix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1646878427,
+        "narHash": "sha256-KtbrofMtN8GlM7D+n90kixr7QpSlVmdN+vK5CA/aRzc=",
+        "owner": "NixOS",
+        "repo": "hydra",
+        "rev": "28b682b85b7efc5cf7974065792a1f22203a5927",
+        "type": "github"
+      },
+      "original": {
+        "id": "hydra",
+        "type": "indirect"
+      }
+    },
+    "iserv-proxy": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1639165170,
+        "narHash": "sha256-QsWL/sBDL5GM8IXd/dE/ORiL4RvteEN+aok23tXgAoc=",
+        "rev": "6e95df7be6dd29680f983db07a057fc2f34f81f6",
+        "revCount": 7,
+        "type": "git",
+        "url": "https://gitlab.haskell.org/ghc/iserv-proxy.git"
+      },
+      "original": {
+        "rev": "6e95df7be6dd29680f983db07a057fc2f34f81f6",
+        "type": "git",
+        "url": "https://gitlab.haskell.org/ghc/iserv-proxy.git"
+      }
+    },
+    "lowdown-src": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1633514407,
+        "narHash": "sha256-Dw32tiMjdK9t3ETl5fzGrutQTzh2rufgZV4A/BbxuD4=",
+        "owner": "kristapsdz",
+        "repo": "lowdown",
+        "rev": "d2c2b44ff6c27b936ec27358a2653caaef8f73b8",
+        "type": "github"
+      },
+      "original": {
+        "owner": "kristapsdz",
+        "repo": "lowdown",
+        "type": "github"
+      }
+    },
+    "mdbook-kroki-preprocessor": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1661755005,
+        "narHash": "sha256-1TJuUzfyMycWlOQH67LR63/ll2GDZz25I3JfScy/Jnw=",
+        "owner": "JoelCourtney",
+        "repo": "mdbook-kroki-preprocessor",
+        "rev": "93adb5716d035829efed27f65f2f0833a7d3e76f",
+        "type": "github"
+      },
+      "original": {
+        "owner": "JoelCourtney",
+        "repo": "mdbook-kroki-preprocessor",
+        "type": "github"
+      }
+    },
+    "n2c": {
+      "inputs": {
+        "flake-utils": "flake-utils_5",
+        "nixpkgs": [
+          "haskellNix",
+          "tullia",
+          "std",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1665039323,
+        "narHash": "sha256-SAh3ZjFGsaCI8FRzXQyp56qcGdAqgKEfJWPCQ0Sr7tQ=",
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "rev": "b008fe329ffb59b67bf9e7b08ede6ee792f2741a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "type": "github"
+      }
+    },
+    "nix": {
+      "inputs": {
+        "lowdown-src": "lowdown-src",
+        "nixpkgs": "nixpkgs",
+        "nixpkgs-regression": "nixpkgs-regression"
+      },
+      "locked": {
+        "lastModified": 1643066034,
+        "narHash": "sha256-xEPeMcNJVOeZtoN+d+aRwolpW8mFSEQx76HTRdlhPhg=",
+        "owner": "NixOS",
+        "repo": "nix",
+        "rev": "a1cd7e58606a41fcf62bf8637804cf8306f17f62",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "2.6.0",
+        "repo": "nix",
+        "type": "github"
+      }
+    },
+    "nix-nomad": {
+      "inputs": {
+        "flake-compat": "flake-compat_2",
+        "flake-utils": [
+          "haskellNix",
+          "tullia",
+          "nix2container",
+          "flake-utils"
+        ],
+        "gomod2nix": "gomod2nix",
+        "nixpkgs": [
+          "haskellNix",
+          "tullia",
+          "nixpkgs"
+        ],
+        "nixpkgs-lib": [
+          "haskellNix",
+          "tullia",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1658277770,
+        "narHash": "sha256-T/PgG3wUn8Z2rnzfxf2VqlR1CBjInPE0l1yVzXxPnt0=",
+        "owner": "tristanpemble",
+        "repo": "nix-nomad",
+        "rev": "054adcbdd0a836ae1c20951b67ed549131fd2d70",
+        "type": "github"
+      },
+      "original": {
+        "owner": "tristanpemble",
+        "repo": "nix-nomad",
+        "type": "github"
+      }
+    },
+    "nix2container": {
+      "inputs": {
+        "flake-utils": "flake-utils_3",
+        "nixpkgs": "nixpkgs_3"
+      },
+      "locked": {
+        "lastModified": 1658567952,
+        "narHash": "sha256-XZ4ETYAMU7XcpEeAFP3NOl9yDXNuZAen/aIJ84G+VgA=",
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "rev": "60bb43d405991c1378baf15a40b5811a53e32ffa",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "type": "github"
+      }
+    },
+    "nixago": {
+      "inputs": {
+        "flake-utils": [
+          "haskellNix",
+          "tullia",
+          "std",
+          "flake-utils"
+        ],
+        "nixago-exts": [
+          "haskellNix",
+          "tullia",
+          "std",
+          "blank"
+        ],
+        "nixpkgs": [
+          "haskellNix",
+          "tullia",
+          "std",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1661824785,
+        "narHash": "sha256-/PnwdWoO/JugJZHtDUioQp3uRiWeXHUdgvoyNbXesz8=",
+        "owner": "nix-community",
+        "repo": "nixago",
+        "rev": "8c1f9e5f1578d4b2ea989f618588d62a335083c3",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nixago",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1632864508,
+        "narHash": "sha256-d127FIvGR41XbVRDPVvozUPQ/uRHbHwvfyKHwEt5xFM=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "82891b5e2c2359d7e58d08849e4c89511ab94234",
+        "type": "github"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "ref": "nixos-21.05-small",
+        "type": "indirect"
+      }
+    },
+    "nixpkgs-2003": {
+      "locked": {
+        "lastModified": 1620055814,
+        "narHash": "sha256-8LEHoYSJiL901bTMVatq+rf8y7QtWuZhwwpKE2fyaRY=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "1db42b7fe3878f3f5f7a4f2dc210772fd080e205",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-20.03-darwin",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-2105": {
+      "locked": {
+        "lastModified": 1659914493,
+        "narHash": "sha256-lkA5X3VNMKirvA+SUzvEhfA7XquWLci+CGi505YFAIs=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "022caabb5f2265ad4006c1fa5b1ebe69fb0c3faf",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-21.05-darwin",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-2111": {
+      "locked": {
+        "lastModified": 1659446231,
+        "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-21.11-darwin",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-2205": {
+      "locked": {
+        "lastModified": 1663981975,
+        "narHash": "sha256-TKaxWAVJR+a5JJauKZqibmaM5e/Pi5tBDx9s8fl/kSE=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "309faedb8338d3ae8ad8f1043b3ccf48c9cc2970",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-22.05-darwin",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-2211": {
+      "locked": {
+        "lastModified": 1669997163,
+        "narHash": "sha256-vhjC0kZMFoN6jzK0GR+tBzKi5KgBXgehadfidW8+Va4=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "6f87491a54d8d64d30af6663cb3bf5d2ee7db958",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-22.11-darwin",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-regression": {
+      "locked": {
+        "lastModified": 1643052045,
+        "narHash": "sha256-uGJ0VXIhWKGXxkeNnq4TvV3CIOkUJ3PAoLZ3HMzNVMw=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "215d4d0fd80ca5163643b03a33fde804a29cc1e2",
+        "type": "github"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "rev": "215d4d0fd80ca5163643b03a33fde804a29cc1e2",
+        "type": "indirect"
+      }
+    },
+    "nixpkgs-unstable": {
+      "locked": {
+        "lastModified": 1663905476,
+        "narHash": "sha256-0CSwRKaYravh9v6qSlBpM0gNg0UhKT2lL7Yn6Zbx7UM=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "e14f9fb57315f0d4abde222364f19f88c77d2b79",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1653581809,
+        "narHash": "sha256-Uvka0V5MTGbeOfWte25+tfRL3moECDh1VwokWSZUdoY=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "83658b28fe638a170a19b8933aa008b30640fbd1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_3": {
+      "locked": {
+        "lastModified": 1654807842,
+        "narHash": "sha256-ADymZpr6LuTEBXcy6RtFHcUZdjKTBRTMYwu19WOx17E=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "fc909087cc3386955f21b4665731dbdaceefb1d8",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_4": {
+      "locked": {
+        "lastModified": 1665087388,
+        "narHash": "sha256-FZFPuW9NWHJteATOf79rZfwfRn5fE0wi9kRzvGfDHPA=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "95fda953f6db2e9496d2682c4fc7b82f959878f7",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "old-ghc-nix": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1631092763,
+        "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..90d4b35
--- /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."phylogenies:exe:phylogenies";});
+}
diff --git a/package.yaml b/package.yaml
new file mode 100644
index 0000000..4d96c25
--- /dev/null
+++ b/package.yaml
@@ -0,0 +1,17 @@
+name: phylogenies
+version: 0.0.1
+synopsis: phylogeny playground
+maintainer: Justin Bedo <cu@cua0.org>
+license: MIT
+
+executable:
+  main: cluster.hs
+  source-dirs: bin
+  ghc-options: [-rtsopts]
+  dependencies:
+    - base >= 4.9 && < 5
+    - ppl
+    - containers
+    - log-domain
+    - vector
+    - random
diff --git a/phylogenies.cabal b/phylogenies.cabal
new file mode 100644
index 0000000..15db8d9
--- /dev/null
+++ b/phylogenies.cabal
@@ -0,0 +1,28 @@
+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:           phylogenies
+version:        0.0.1
+synopsis:       phylogeny playground
+maintainer:     Justin Bedo <cu@cua0.org>
+license:        MIT
+build-type:     Simple
+
+executable phylogenies
+  main-is: cluster.hs
+  other-modules:
+      Paths_phylogenies
+  hs-source-dirs:
+      bin
+  ghc-options: -rtsopts
+  build-depends:
+      base >=4.9 && <5
+    , containers
+    , log-domain
+    , ppl
+    , random
+    , vector
+  default-language: Haskell2010