included BNN chapter

_toc.yml

@@ -40,23 +40,27 @@
 - part: Physical Gradients
   chapters:
   - file: physgrad.md
-    sections:
   - file: physgrad-comparison.ipynb
   - file: physgrad-nn.md
   - file: physgrad-discuss.md
 
+- part: PBDL and Uncertainty 
+  chapters:
+  - file: bayesian-intro.md
+  - file: bayesian-code.md
+  
 - part: End Matter
   chapters:
   - file: outlook.md
-  - file: old-phiflow1.md
+ #  - file: old-phiflow1.md
-    sections:
+ #    sections:
-      - file: overview-burgers-forw-v1.ipynb
+ #      - file: overview-burgers-forw-v1.ipynb
-      - file: overview-ns-forw-v1.ipynb
+ #      - file: overview-ns-forw-v1.ipynb
-      - file: physicalloss-code-v2.ipynb
+ #      - file: physicalloss-code-v2.ipynb
-      - file: diffphys-code-gradient-v1.ipynb
+ #      - file: diffphys-code-gradient-v1.ipynb
-      - file: diffphys-code-tf.ipynb
+ #      - file: diffphys-code-tf.ipynb
-      - file: diffphys-code-ns-v1.ipynb
+ #      - file: diffphys-code-ns-v1.ipynb
-      - file: diffphys-code-ns-v2a.ipynb
+ #      - file: diffphys-code-ns-v2a.ipynb
   - file: references.md
   - file: notation.md
   

bayesian-intro.md

@@ -0,0 +1,14 @@
+Introduction to Posterior Inference
+=======================
+
+more complex models -> fit data better , but overfit & dont generalize
+-> posterior (distrib) inference
+
+std NNs do MLE for weights
+"theoretically justifiable" ie correct thing to do -> "posterior inference"
+extremely difficult
+
+useful for uncertainty! esp interesting in phys setting
+
+first example here with airfoils, extension from {doc}`supervised-airfoils`
+

make-pdf.sh

@@ -20,6 +20,14 @@ sed -i '' -e 's/}.jpg}/.jpg}/g' ${JPYFILENAME}
 sed -i '' -e 's/}.jpeg}/.jpeg}/g' ${JPYFILENAME}
 sed -i '' -e 's/sphinxpxdimen]{{/sphinxpxdimen]{/g' ${JPYFILENAME}
 
+# fix chapters
+# sed -i '' -e 's///g' ${JPYFILENAME}
+# sed -i '' -e 's///g' ${JPYFILENAME}
+# sed -i '' -e 's///g' ${JPYFILENAME}
+sed -i '' -e 's/\chapter{/\chaXter{/g' ${JPYFILENAME}
+sed -i '' -e 's/\section{/\chapter{/g' ${JPYFILENAME}
+sed -i '' -e 's/\chaXter{/\subsection{/g' ${JPYFILENAME}
+
 # ugly, -i doesnt work here:
 sed '28i\
 \\usepackage{mathrsfs}  ' ${JPYFILENAME} > tmp-latex