Update PDFA

Update PDFA

--- examples/src/worksheets/pdfa.clj
+++ examples/src/worksheets/pdfa.clj
@@ -13,14 +13,90 @@
             [anglican.infcomp.network :refer :all]
             [anglican.inference :refer [infer]]
             [anglican.stat :refer [empirical-distribution collect-predicts collect-by collect-results]]
-            [helpers.gmm :refer [normalize]])
+            [helpers.gmm :refer [normalize]]
+            [rhizome.viz]
+            [clojure.string])
   (:use [anglican emit runtime]
         [gorilla-plot core]))

 (anglican.infcomp.core/reset-infcomp-addressing-scheme!)
 ;; @@
 ;; =>
-;;; {"type":"html","content":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26285$fn--26286]","value":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26285$fn--26286]"}
+;;; {"type":"html","content":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26362$fn--26363]","value":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--26362$fn--26363]"}
+;; <=
+
+;; **
+;;; ## PDFA object
+;; **
+
+;; @@
+(defm new-pdfa [alphabet K transition emissiondist]
+  (let [alphabet (map str (seq alphabet))
+
+        states (range K)
+
+        edges (into {} (map (fn [state]
+                              [state (into {} (map #(vector % (transition state %))
+                                                   alphabet))])
+                            states))
+
+        probs (into {} (map (fn [state]
+                              [state (into {} (map (fn [[symbol prob]]
+                                                     [(str symbol) prob])
+                                                   (:categories (emissiondist state))))])
+                            states))]
+    {:edges edges
+     :probs probs}))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/new-pdfa","value":"#'pdfa/new-pdfa"}
+;; <=
+
+;; @@
+(defn pdfa-states [pdfa]
+  (keys (:edges pdfa)))
+
+(defn pdfa-edges [pdfa]
+  (let [t (:edges pdfa)]
+    (into {} (map (fn [state]
+                    [state (vec (set (vals (get t state))))])
+                  (keys t)))))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/pdfa-edges","value":"#'pdfa/pdfa-edges"}
+;; <=
+
+;; @@
+(defn pdfa-node->descriptor [pdfa]
+   (fn [node]
+     {:label (str node)}))
+
+(defn pdfa-edge->descriptor [pdfa]
+  (fn [state nextstate]
+    (let [edges (get-in pdfa [:edges state])
+          probs (get-in pdfa [:probs state])
+
+          emissions (filter #(= nextstate (get edges %))
+                            (keys edges))
+          probs (into {}
+                      (map #(vector % (get probs %))
+                           emissions))]
+      {:label (clojure.string/join "|" (map #(format "%.3f%s"(get probs %) %)
+                                            emissions))})))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/pdfa-edge->descriptor","value":"#'pdfa/pdfa-edge->descriptor"}
+;; <=
+
+;; @@
+(defn view-pdfa [pdfa]
+  (rhizome.viz/view-graph (pdfa-states pdfa)
+                          (pdfa-edges pdfa)
+                          :node->descriptor (pdfa-node->descriptor pdfa)
+                          :edge->descriptor (pdfa-edge->descriptor pdfa)))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/view-pdfa","value":"#'pdfa/view-pdfa"}
 ;; <=

 ;; **
@@ -28,14 +104,17 @@
 ;; **

 ;; @@
+; Pfau, D., Bartlett, N., & Wood, F. (2011). Probabilistic Deterministic Infinite Automata. In Advances in Neural Information Processing Systems (pp. 1930–1938)
 (with-primitive-procedures [normalize]
   (defquery pdfa [observedsequence alphabet]
     (let [K (sample (uniform-discrete 1 5))
-          nextstatedist (discrete (repeat K 1))
           emissionprior (fn [] (normalize (repeatedly (count alphabet) (fn [] (sample (uniform-continuous 0 1))))))
-          transition (mem (fn [state symbol] (sample nextstatedist)))
-          emissiondist (mem (fn [state] (categorical (zipmap alphabet (emissionprior)))))
-          N (count observedsequence)]
+          emissiondist (mem (fn [state] (categorical (zipmap alphabet (emissionprior))))) ; \pi
+
+          transitiondist (discrete (repeat K 1))
+          transition (mem (fn [state symbol] (sample transitiondist))) ; \delta
+          ]
+
       (loop [obs observedsequence
              state [0]]
         (if (not (empty? obs))
@@ -44,11 +123,7 @@
                 nextstate (transition currentstate (first obs))]
             (recur (rest obs)
                    (conj state nextstate)))
-          {:K K
-           :alphabet alphabet
-           :transition transition
-           :emissiondist emissiondist}
-          )))))
+          (new-pdfa alphabet K transition emissiondist))))))
 ;; @@
 ;; =>
 ;;; {"type":"html","content":"#'pdfa/pdfa","value":"#'pdfa/pdfa"}
@@ -59,27 +134,89 @@
 ;; **

 ;; @@
-(def alphabet "ABCDE")
+(def alphabet "ab")
+(def alphabet-len (count alphabet))
+(defn one-hot [len hot]
+  (assoc (vec (replicate len 0)) hot 1))
+(defn encode-char [s]
+  (let [i (.indexOf alphabet s)]
+    (one-hot alphabet-len i)))
+(defn encode-string [s]
+  (vec (map #(encode-char (str %)) s)))
+
+(encode-string "abaabab")
+;(sample-observes-from-prior pdfa [(repeat 200 nil) alphabet])
+;; @@
+;; =>
+;;; {"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"}],"value":"[0 1]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"}],"value":"[0 1]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"}],"value":"[0 1]"}],"value":"[[1 0] [0 1] [1 0] [1 0] [0 1] [1 0] [0 1]]"}
+;; <=
+
+;; @@
+(defn combine-observes-fn [observes]
+  (encode-string (apply str (map (comp #(nth alphabet %) :value) observes))))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/combine-observes-fn","value":"#'pdfa/combine-observes-fn"}
+;; <=
+
+;; @@
 (sample-observes-from-prior pdfa [(repeat 10 nil) alphabet])
 ;; @@
 ;; =>
-;;; {"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"list-like","open":"{","close":"}","separator":", ","items":[{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":time-index","value":":time-index"},{"type":"html","content":"0","value":"0"}],"value":"[:time-index 0]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":observe-address","value":":observe-address"},{"type":"html","content":"O11","value":"O11"}],"value":"[:observe-address O11]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":observe-instance","value":":observe-instance"},{"type":"html","content":"0","value":"0"}],"value":"[:observe-instance 0]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":value","value":":value"},{"type":"html","content":"2","value":"2"}],"value":"[:value 2]"}],"value":"{:time-index 0, :observe-address 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:observe-address O11, :observe-instance 0, :value 2} {:time-index 1, :observe-address O11, :observe-instance 1, :value 2} {:time-index 2, :observe-address O11, :observe-instance 2, :value 0} {:time-index 3, :observe-address O11, :observe-instance 3, :value 0} {:time-index 4, :observe-address O11, :observe-instance 4, :value 1} {:time-index 5, :observe-address O11, :observe-instance 5, :value 1} {:time-index 6, :observe-address O11, :observe-instance 6, :value 2} {:time-index 7, :observe-address O11, :observe-instance 7, :value 3} {:time-index 8, :observe-address O11, :observe-instance 8, :value 0} {:time-index 9, :observe-address O11, :observe-instance 9, :value 4}]"}
-;; <=
-
-;; @@
-(defn combine-observes-fn [observes]
-  (map :value observes))
-;; @@
-;; =>
-;;; {"type":"html","content":"#'pdfa/combine-observes-fn","value":"#'pdfa/combine-observes-fn"}
-;; <=
-
-;; @@
-(def torch-connection (start-torch-connection pdfa [(repeat 10 nil) alphabet] combine-observes-fn))
+;;; {"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"list-like","open":"{","close":"}","separator":", ","items":[{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":time-index","value":":time-index"},{"type":"html","content":"0","value":"0"}],"value":"[:time-index 0]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":observe-address","value":":observe-address"},{"type":"html","content":"O44","value":"O44"}],"value":"[:observe-address O44]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":observe-instance","value":":observe-instance"},{"type":"html","content":"0","value":"0"}],"value":"[:observe-instance 0]"},{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":value","value":":value"},{"type":"html","content":"1","value":"1"}],"value":"[:value 1]"}],"value":"{:time-index 0, :observe-address 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+;; <=
+
+;; @@
+(combine-observes-fn (sample-observes-from-prior pdfa [(repeat 10 nil) alphabet]))
+;; @@
+;; =>
+;;; {"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"}],"value":"[0 1]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"}],"value":"[1 0]"}],"value":"[[1 0] [1 0] [1 0] [1 0] [1 0] [1 0] [1 0] [0 1] [1 0] [1 0]]"}
+;; <=
+
+;; **
+;;; Initialize Torch connection:
+;; **
+
+;; @@
+(def torch-connection (start-torch-connection pdfa [(repeat 100 nil) alphabet] combine-observes-fn :tcp-endpoint "tcp://*:5555"))
 ;; @@
 ;; =>
 ;;; {"type":"html","content":"#'pdfa/torch-connection","value":"#'pdfa/torch-connection"}
 ;; <=
+
+;; **
+;;; Now, run
+;;;
+;;; `python -m infcomp.compile --obsEmb lstm --oneHotDim 512 --visdom`
+;;;
+;;; until you are happy with the loss value. Use Ctrl + C to stop training.
+;;;
+;;;
+;;; Alternatively, you can run it with the `--maxTraces` flag to stop after a set number of traces, such as:
+;;;
+;;; `python -m infcomp.compile --obsEmb lstm --oneHotDim 512 --maxTraces 2000`
+;;;
+;;;
+;;; If you want to use GPU, you can use the `--cuda` flag:
+;;;
+;;; `python -m infcomp.compile --obsEmb lstm --oneHotDim 512 --cuda`
+;;;
+;;;
+;;; More flags/options are available with:
+;;;
+;;; `python -m infcomp.compile --help`
+;; **
+
+;; **
+;;; The compilation process saves time-stamped compilation artifacts with names like `compile-artifact-20170427-135221` in the current folder (the target folder can be changed with the `--folder` flag). There are also corresponding log files like `compile-log-20170427-135221'.
+;;;
+;;; One can get information about the latest saved artifact by using:
+;;; `python -m infcomp.artifact_info`
+;;;
+;;; This command also has some flags you can learn about with `python -m infcomp.artifact_info --help`.
+;;;
+;;; Before moving on to inference, you should stop the torch connection for compilation:
+;; **

 ;; @@
 ;; Stop the Torch connection
@@ -95,11 +232,36 @@

 ;; @@
 (def test-observations
-  (combine-observes-fn (sample-observes-from-prior pdfa [(repeat 10 nil) alphabet])))
+  (combine-observes-fn (sample-observes-from-prior pdfa [(repeat 100 nil) alphabet])))
+
+
+(defn indices [pred coll]
+   (keep-indexed #(when (pred %2) %1) coll))
+
+(defn first-index [pred coll]
+  (first (indices pred coll)))
+
+(first-index #(= % 1) [0 0 1])
+
+(def test-observations-str
+  (apply str (mapv #(nth alphabet (first-index (fn [x] (= x 1)) %)) test-observations)))
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/test-observations-str","value":"#'pdfa/test-observations-str"}
+;; <=
+
+;; @@
 test-observations
 ;; @@
 ;; =>
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+;; <=
+
+;; @@
+test-observations-str
+;; @@
+;; =>
+;;; {"type":"html","content":""babbbbbababaabbbbbaaababbbaaaababbbbaababbbabbbbaabbbbababababbbbbbbaabaabaaaabababaabbbaababbbbbbaa"","value":"\"babbbbbababaabbbbbaaababbbaaaababbbbaababbbabbbbaabbbbababababbbbbbbaabaabaaaabababaabbbaababbbbbbaa\""}
 ;; <=

 ;; **
@@ -114,45 +276,55 @@

 ;; @@
 (def num-particles 10)
-(def csis-states (take num-particles (infer :csis pdfa [test-observations alphabet])))
+(def csis-states (take num-particles (infer :csis pdfa [test-observations-str alphabet] :observe-embedder-input test-observations)))
 ;; @@
 ;; =>
 ;;; {"type":"html","content":"#'pdfa/csis-states","value":"#'pdfa/csis-states"}
 ;; <=

 ;; @@
+(first csis-states)
+;; @@
+
+;; @@
 (categorical (vec (empirical-distribution (collect-results csis-states))))
 ;; @@
 ;; =>
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 ;; <=

 ;; @@
 (sample* (categorical (vec (empirical-distribution (collect-results csis-states)))))
 ;; @@
-
-;; @@
-(def num-particles 10)
-(def is-states (take num-particles (infer :importance pdfa [test-observations alphabet])))
-
+;; =>
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0.24321730463346974, \"B\" 0.21659609737770497, \"C\" 0.3729257738520613, \"D\" 0.02486516371407356, \"E\" 0.1423956604226905}}"}],"value":"[:probs {0 {\"A\" 0.046419407761521495, \"B\" 0.35747293528036234, \"C\" 0.21934892557883817, \"D\" 0.06834856657755085, \"E\" 0.30841016480172717}, 1 {\"A\" 0.2520505866763071, \"B\" 0.2700908845756072, \"C\" 0.271053943116372, \"D\" 0.1528563048031675, \"E\" 0.053948280828546094}, 2 {\"A\" 0.24321730463346974, \"B\" 0.21659609737770497, \"C\" 0.3729257738520613, \"D\" 0.02486516371407356, \"E\" 0.1423956604226905}}]"}],"value":"{:edges {0 {\"A\" 2, \"B\" 0, \"C\" 2, \"D\" 1, \"E\" 2}, 1 {\"A\" 0, \"B\" 1, \"C\" 1, \"D\" 1, \"E\" 2}, 2 {\"A\" 0, \"B\" 0, \"C\" 0, \"D\" 0, \"E\" 2}}, :probs {0 {\"A\" 0.046419407761521495, \"B\" 0.35747293528036234, \"C\" 0.21934892557883817, \"D\" 0.06834856657755085, \"E\" 0.30841016480172717}, 1 {\"A\" 0.2520505866763071, \"B\" 0.2700908845756072, \"C\" 0.271053943116372, \"D\" 0.1528563048031675, \"E\" 0.053948280828546094}, 2 {\"A\" 0.24321730463346974, \"B\" 0.21659609737770497, \"C\" 0.3729257738520613, \"D\" 0.02486516371407356, \"E\" 0.1423956604226905}}}"}
+;; <=
+
+;; @@
+(def num-particles 1000)
+(def test-obs "bbbbbbbbabbabbaaabbaaabbabbaaaaaabbaaabbabbaaabbbbbbabbaaabbbbbbbbbbabbbbbbbbbbabbaabbabbbbabbbbaaaaaaaaabbabbabbaaaabbabbaaaaabbaabbabbbbabbbbbbaabbabbabbbbabbabbbbbbaaabbabbbbaaabbbbaaabbbbbbabbaaaa")
+(def is-states (take num-particles (infer :importance pdfa [test-obs alphabet])))
 ;; @@
 ;; =>
 ;;; {"type":"html","content":"#'pdfa/is-states","value":"#'pdfa/is-states"}
 ;; <=

 ;; @@
-(sample* (categorical (vec (empirical-distribution (collect-results is-states)))))
-;; @@
+(view-pdfa (sample* (categorical (vec (empirical-distribution (collect-results is-states))))))
+;; @@
+;; =>
+;;; {"type":"html","content":"nil","value":"nil"}
+;; <=

 ;; @@
 (def num-particles 1000)
-(def smc-states (take num-particles (infer :smc pdfa [test-observations alphabet] :number-of-particles 1000)))
+(def smc-states (take num-particles (infer :smc pdfa [test-observations-str alphabet] :number-of-particles 1000)))
 (repeatedly 1 #(sample* (categorical (vec (empirical-distribution (collect-results smc-states))))))
 ;; @@
 ;; =>
-;;; {"type":"list-like","open":"(","close":")","separator":" ","items":[{"type":"list-like","open":"{","close":"}","separator":", ","items":[{"type":"list-like","open":"","close":"","separator":" ","items":[{"type":"html","content":":statesequence","value":":statesequence"},{"type":"list-like","open":"[","close":"]","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"}],"value":"[0 0 0 0 0 0 0 0 0 0 0]"}],"value":"[:statesequence [0 0 0 0 0 0 0 0 0 0 0]]"}],"value":"{:statesequence [0 0 0 0 0 0 0 0 0 0 0]}"}],"value":"({:statesequence [0 0 0 0 0 0 0 0 0 0 0]})"}
-;; <=
-
-;; @@
-
-;; @@
+;;; {"type":"html","content":"#'pdfa/num-particles","value":"#'pdfa/num-particles"}
+;; <=
+
+;; @@
+
+;; @@