pdfa nan weights

pdfa nan weights

--- examples/src/worksheets/pdfa.clj
+++ examples/src/worksheets/pdfa.clj
@@ -7,6 +7,7 @@
 ;; @@
 (ns pdfa
   (:require anglican.infcomp.csis
+            anglican.importance
             anglican.smc
             anglican.infcomp.core
             [anglican.infcomp.network :refer :all]
@@ -19,7 +20,7 @@
 (anglican.infcomp.core/reset-infcomp-addressing-scheme!)
 ;; @@
 ;; =>
-;;; {"type":"html","content":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--27417$fn--27418]","value":"#function[anglican.infcomp.core/reset-infcomp-addressing-scheme!$fn--27417$fn--27418]"}
+;;; {"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]"}
 ;; <=

 ;; **
@@ -43,7 +44,11 @@
                 nextstate (transition currentstate (first obs))]
             (recur (rest obs)
                    (conj state nextstate)))
-          {:statesequence state})))))
+          {:K K
+           :alphabet alphabet
+           :transition transition
+           :emissiondist emissiondist}
+          )))))
 ;; @@
 ;; =>
 ;;; {"type":"html","content":"#'pdfa/pdfa","value":"#'pdfa/pdfa"}
@@ -54,11 +59,11 @@
 ;; **

 ;; @@
-(def alphabet [0 1 2 3 4])
+(def alphabet "ABCDE")
 (sample-observes-from-prior pdfa [(repeat 10 nil) alphabet])
 ;; @@
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+;;; {"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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 ;; <=

 ;; @@
@@ -94,7 +99,7 @@
 test-observations
 ;; @@
 ;; =>
-;;; {"type":"list-like","open":"(","close":")","separator":" ","items":[{"type":"html","content":"0","value":"0"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"},{"type":"html","content":"1","value":"1"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"1","value":"1"},{"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 1 1 0 1 0 0 0 0)"}
+;;; {"type":"list-like","open":"(","close":")","separator":" ","items":[{"type":"html","content":"4","value":"4"},{"type":"html","content":"3","value":"3"},{"type":"html","content":"1","value":"1"},{"type":"html","content":"3","value":"3"},{"type":"html","content":"3","value":"3"},{"type":"html","content":"4","value":"4"},{"type":"html","content":"3","value":"3"},{"type":"html","content":"0","value":"0"},{"type":"html","content":"3","value":"3"},{"type":"html","content":"2","value":"2"}],"value":"(4 3 1 3 3 4 3 0 3 2)"}
 ;; <=

 ;; **
@@ -108,22 +113,36 @@
 ;; **

 ;; @@
-(def num-particles 1000)
+(def num-particles 10)
 (def csis-states (take num-particles (infer :csis pdfa [test-observations alphabet])))
-(repeatedly 1 #(sample* (categorical (vec (empirical-distribution (collect-results csis-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/csis-states","value":"#'pdfa/csis-states"}
 ;; <=

 ;; @@
-(def num-particles 1000)
-(def is-states (take num-particles (infer :importance pdfa [test-observations alphabet])))
-(repeatedly 1 #(sample* (categorical (vec (empirical-distribution (collect-results is-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])))
+
+;; @@
+;; =>
+;;; {"type":"html","content":"#'pdfa/is-states","value":"#'pdfa/is-states"}
+;; <=
+
+;; @@
+(sample* (categorical (vec (empirical-distribution (collect-results is-states)))))
+;; @@

 ;; @@
 (def num-particles 1000)


+diagnostic messages

+diagnostic messages

--- src/babel/generate.cljc
+++ src/babel/generate.cljc
@@ -76,9 +76,15 @@
                                         (let [result (unify a b)]
                                           (when (and (not (= :fail a)) (not (= :fail b)))
                                             (if (= :fail result)
-                                              (log/debug (str "unify(" ((:morph-ps model) a) "," ((:morph-ps model) b) ") => fail@"
-                                                              (fail-path a b)))
-                                              (log/debug (str "unify(" ((:morph-ps model) a) "," ((:morph-ps model) b) ") => "
+                                              ;; warn because fails are expensive and should be filtered out before hitting this.
+                                              (do
+                                                (log/warn (str "failed to unify("))
+                                                (log/warn (str "  a: " ((:morph-ps model) a) ","))
+                                                (log/warn (str "  b: " ((:morph-ps model) b)))
+                                                (log/warn (str "  ser a: (def a (dag_unify.core/deserialize '(" (string/join "" (:dag_unify.core/serialized a)) ")))"))
+                                                (log/warn (str "  ser b: (def b (dag_unify.core/deserialize '(" (string/join "" (:dag_unify.core/serialized b)) ")))"))
+                                                (log/warn (str ") => fail@" (fail-path a b))))
+                                              (log/debug (str "unify(" ((:morph-ps model) a) " , " ((:morph-ps model) b) ") => "
                                                               ((:morph-ps model) result)))))
                                           result))
                                       (cons bolt


filter out :fails

filter out :fails

--- src/babel/generate.cljc
+++ src/babel/generate.cljc
@@ -153,11 +153,12 @@
     (->
      (clojure.core/take
       take
-      (flatten
-       (mapfn #(do
-                 (log/debug (str "top-level add-bolt-at: " ((:morph-ps language-model) %)))
-                 (add-bolt-at % % [] % language-model depth max-depth truncate-children take))
-              (lightning-bolts language-model spec 0 max-total-depth))))
+      (filter #(not (= :fail %))
+              (flatten
+               (mapfn #(do
+                         (log/debug (str "top-level add-bolt-at: " ((:morph-ps language-model) %)))
+                         (add-bolt-at % % [] % language-model depth max-depth truncate-children take))
+                      (lightning-bolts language-model spec 0 max-total-depth)))))
      ((fn [seq]
         (if (= take 1)
           (first seq)