_config.yml

# Book settings
title: Combined Learning from Data materials
copyright : "2026"  # Copyright year to be placed in the footer
author: Christian Forssén, Dick Furnstahl, and Daniel Phillips
email: christian.forssen@chalmers.se
logo: ./logo/logo-copilot.png
description: >- # this means to ignore newlines
  This book is a merged and enhanced version of lecture notes by Christian Forssén for courses
  at taught at Chalmers University of Technology and Gothenburg University and lecture notes 
  by Dick Furnstahl and Daniel Phillips for courses taught at Ohio State University and Ohio
  University, respectively.
only_build_toc_files: true

#######################################################################################
# Execution exclude list in JB 1.x (still build the pages, just don't run them)
# Translated all options from the previous execute block to the mystnb block to
# avoid conflicts
# EDIT: redundant since a sphinx config block was added which has priority
# EDIT: mystnb:
# EDIT:   execution_mode: force        # (old: execute_notebooks)
# EDIT:   execution_timeout: 100       # (old: timeout)
# EDIT:   execution_in_temp: false     # (old: run_in_temp)
# EDIT:   execution_allow_errors: false # (old: allow_errors)
# EDIT:   execution_show_tb: false     # similar to old stderr behavior
# EDIT:   output_stderr: show          # (old: stderr_output) One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe'
# EDIT:   execution_cache+path: ""     # (old: cache)
# EDIT: 
# EDIT:   execution_excludepatterns:
# EDIT:     - "exercise-jupyter-notebooks-and-python.ipynb"
# EDIT:     - "**/demo-cnn.ipynb"
# EDIT:     - "**/demo-ball-drop-experiment.ipynb"
# EDIT:     - "**/demo-making-a-simple-widget-based-ui.ipynb"
# EDIT:     - "**/*ptemcee*.ipynb"
# EDIT:     - "**/demo-*cnn*.ipynb"
# EDIT:     - "**/demo-gaussian-processes.ipynb"
# EDIT:     - "**/demo-comparing-samplers-for-a-simple-problem.ipynb"
# EDIT:     - "**/demo-multimodal-distributions-with-two-samplers.ipynb"
# EDIT:     - "**/demo-pymc-introduction.ipynb"
# EDIT:     - "**/demo-variational-inference-and-bnn.ipynb"
# EDIT:     - "**/exercise-logreg-and-neural-networks.ipynb"
# EDIT:     - "**/mini-project_IIIa_bayesian_optimization.ipynb"
# EDIT:     - "**/mini-project_IIIb_Bayesian_neural_networks_from_demo.ipynb"

#######################################################################################
# LaTeX-specific settings
latex:
  latex_engine: xelatex             # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex'
  latex_documents:
    targetname: book.tex

bibtex_bibfiles: 
  - content/References/references.bib

bibtex_reference_style:  
  - author_year

#######################################################################################
# Information about where the book exists on the web
repository:
  url                       : https://github.com/cforssen/LFD_development_v2.0  # The URL to your book's repository
  path_to_book              : "./"  # A path to your book's folder, relative to the repository root.
  branch                    : main  # Which branch of the repository should be used when creating links

#######################################################################################
# HTML-specific settings
# Add GitHub buttons to your book
# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
html:
  use_multitoc_numbering    : true   # true means chapters are labeled consecutively through the book
  favicon                   : ""  # A path to a favicon image
  use_edit_page_button      : false  # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
  use_repository_button     : true  # Whether to add a link to your repository button
  use_issues_button         : true  # Whether to add an "open an issue" button
  extra_navbar              : Powered by <a href="https://jupyterbook.org">Jupyter Book</a>  # Will be displayed underneath the left navbar.
  extra_footer              : ""  # Will be displayed underneath the footer.
  analytics.google_analytics_id: "" # A GA id that can be used to track book views.
# google_analytics_id       : ""  # A GA id that can be used to track book views.
  comments:
    hypothesis              : false
#  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
#  baseurl                   : ""  # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/    
  extra_css:
    - https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css

#######################################################################################
# Customize LaTeX via Sphinx
# see also https://www.sphinx-doc.org/en/master/latex.html

# old settings...
#sphinx:
#  config:
#    bibtex_reference_style: label
#    bibtex_default_style: 'alpha'  
#    # By default MathJax version 2 is currently used. If you are using a lot of math, you may want to try using version 3, which claims to improve load speeds by 60 - 80%:  
#    #mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML
#    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
#    #myst_override_mathjax: true
 


# from tif385   
sphinx:
  config:
    nb_execution_mode: "auto"
    nb_execution_timeout: 100
    nb_execution_in_temp: false
    nb_execution_allow_errors: false
    nb_execution_show_tb: false
    nb_output_stderr: "show"
    nb_execution_cache_path: ""
    nb_execution_excludepatterns:
      - "**/demo-ball-drop-experiment.ipynb"
      - "**/demo-making-a-simple-widget-based-ui.ipynb"
      - "exercise-jupyter-notebooks-and-python.ipynb"
      - "**/demo-cnn.ipynb"
      - "**/demo-ball-drop-experiment.ipynb"
      - "**/demo-making-a-simple-widget-based-ui.ipynb"
      - "**/*ptemcee*.ipynb"
      - "**/demo-*cnn*.ipynb"
      - "**/demo-gaussian-processes.ipynb"
      - "**/demo-comparing-samplers-for-a-simple-problem.ipynb"
      - "**/demo-multimodal-distributions-with-two-samplers.ipynb"
      - "**/demo-pymc-introduction.ipynb"
      - "**/demo-variational-inference-and-bnn.ipynb"
      - "**/exercise-logreg-and-neural-networks.ipynb"
      - "**/mini-project_IIIa_bayesian_optimization.ipynb"
      - "**/mini-project_IIIb_Bayesian_neural_networks_from_demo.ipynb"
    source_encoding: utf-8-sig
    html_css_files:
      - coloredpages.css
      - custom.css
    html_js_files:
      - custom.js    
    nb_mime_priority_overrides:
      - ["html", "application/vnd.holoviews_load.v0+json", null]
      - ["html", "application/vnd.holoviews_exec.v0+json", null]
    mathjax3_config:
      loader: {
        load: ['[tex]/textmacros']
      }
      chtml: {
        mtextInheritFont: True,
      }
      tex:
        #tags: ams
        #packages: ['base', 'ams']
        packages: {'[+]': ['textmacros']}
        macros:
          "data": "\\mathcal{D}"
          "pars": "\\boldsymbol{\\theta}"
          "para": "\\theta"
          "optpars": "\\pars^*"
          "optpara": "\\para^*"
          "prob": "\\mathbb{P}"
          "cprob": ["\\prob\\left( #1 \\, \\left\\vert \\, #2 \\right. \\right)",2]
          "cprobsub": ["\\prob_{#1}\\left( #2 \\, \\left\\vert \\, #3 \\right. \\right)",3]
          "pdf": ["p \\left( #1 \\, \\left\\vert \\, #2 \\right. \\right)",2]
          "pdfsub": ["p_{#1} \\left( #2 \\, \\left\\vert \\, #3 \\right. \\right)",3]
          "p": ["p \\left( #1 \\right)",1]
          "psub": ["p_{#1} \\left( #2 \\right)",2]
          "futuredata": "\\mathcal{F}"
          "expect": ["\\mathbb{E} \\left[ #1 \\right]",1]
          "var": ["\\text{Var} \\left( #1 \\right)",1]
          "std": ["\\text{Std} \\left( #1 \\right)",1]
          "cov": ["\\text{Cov} \\left( #1, #2 \\right)",2]
          "dmat": "\\boldsymbol{X}"
          "models": ["\\boldsymbol{M}\\left( #1 \\, ; \\, #2 \\right)",2]
          "model": ["M\\left( #1 \\, ; \\, #2 \\right)",2]
          "modeloutputs": "\\boldsymbol{M}"
          "modeloutput": "M"
          "MLmodel": ["\\boldsymbol{\\hat{y}}\\left( #1 \\right)",1]
          "MLoutputs": "\\boldsymbol{\\hat{y}}"
          "MLoutput": "\\hat{y}"
          "outputs": "\\boldsymbol{y}"
          "inputs": "\\boldsymbol{x}"
          "targets": "\\boldsymbol{t}"
          "weights": "\\boldsymbol{w}"
          "testoutputs": "\\boldsymbol{y}^\\odot"
          "testinputs": "\\boldsymbol{x}^\\odot"
          "output": "y"
          "inputt": "x"
          "target": "t"
          "weight": "w"
          "testoutput": "y^\\odot"
          "MLtestoutput": "\\hat{y}^\\odot"
          "testinput": "x^\\odot"
          "trainingdata": "\\mathcal{T}"
          "LaTeX": "\\text{LaTeX}"
          "residual": "\\epsilon"
          "residuals": "\\boldsymbol{\\epsilon}"
          "zeros": "\\boldsymbol{0}"
          "covres": "\\boldsymbol{\\Sigma_{\\epsilon}}"
          "covpars": "\\boldsymbol{\\Sigma_{\\pars}}"
          "tildecovpars": "\\boldsymbol{\\widetilde{\\Sigma}_{\\pars}}"
          "sigmas": "\\boldsymbol{\\sigma}"
          "sigmai": "\\sigma_i"
          "sigmares": "\\sigma_{\\epsilon}"
          "cbar": "\\bar c"
          "Lra": "\\Longrightarrow"
          "yth": "y_{\\rm th}"
          "yexp": "y_{\\rm exp}"
          "ym": "y_{\\rm m}"
          "thetavec": "\\boldsymbol{\\theta}"
          "parsLR": "\\boldsymbol{\\beta}"
          "paraLR": "\\beta"
          "covparsLR": "\\boldsymbol{\\Sigma_{\\parsLR}}"
          "optparsLR": "\\parsLR^*"
          "optparaLR": "\\paraLR^*"
          "tildecovparsLR": "\\boldsymbol{\\widetilde{\\Sigma}_{\\parsLR}}"
          "alphavec": "\\boldsymbol{\\alpha}"
          "muvec": "\\boldsymbol{\\mu}"
          "phivec": "\\boldsymbol{\\phi}"
          "betavec": "\\boldsymbol{\\beta}"
          "sigmavec": "\\boldsymbol{\\sigma}"
          "Sigmavec": "\\boldsymbol{\\Sigma}"
          "thetavechat": "\\widehat\\thetavec"
          "avec": "\\boldsymbol{a}"
          "Bvec": "\\boldsymbol{B}"
          "fvec": "\\boldsymbol{f}"
          "mvec": "\\boldsymbol{m}"
          "qvec": "\\boldsymbol{q}"
          "rvec": "\\boldsymbol{r}"
          "uvec": "\\boldsymbol{u}"
          "vvec": "\\boldsymbol{v}"
          "wvec": "\\boldsymbol{w}"
          "xvec": "\\boldsymbol{x}"
          "yvec": "\\boldsymbol{y}"
          "wt": "\\widetilde"
          "nb": "n_b"
          "mel": ["\\langle #1 | #2 | #3 \\rangle",3]
          "qoi": "\\mathbf{Q}"
          "ytrue": "y_{\\rm true}"
    # tex macros have to be repeated as latex_elements below. BE CAREFUL.
    # Had to make renewcommand for some of these. Might be DANGEROUS.
    # From \residuals is for the BLR chapter. BE CAREFUL
    latex_elements:
        preamble: |
          \newcommand{\data}{\mathcal{D}}
          \newcommand{\pars}{\boldsymbol{\theta}}
          \newcommand{\para}{\theta}
          \newcommand{\optpars}{\pars^*}
          \newcommand{\optpara}{\para^*}
          \newcommand{\prob}{\mathbb{P}}
          \newcommand{\cprob}[2]{\prob\left( #1 \, \left\vert \, #2 \right. \right)}
          \newcommand{\cprobsub}[3]{\prob_{#1}\left( #2 \, \left\vert \, #3 \right. \right)}
          \newcommand{\pdf}[2]{p \left( #1 \, \left\vert \, #2 \right. \right)}
          \newcommand{\pdfsub}[3]{p_{#1} \left( #2 \, \left\vert \, #3 \right. \right)}
          \newcommand{\p}[1]{p \left( #1 \right)}
          \newcommand{\psub}[2]{p_{#1} \left( #2 \right)}
          \newcommand{\futuredata}{\mathcal{F}}
          \newcommand{\expect}[1]{\mathbb{E} \left[ #1 \right]}
          \newcommand{\var}[1]{\text{Var} \left( #1 \right)}
          \newcommand{\std}[1]{\text{Std} \left( #1 \right)}
          \newcommand{\cov}[2]{\text{Cov} \left( #1, #2 \right)}
          \newcommand{\dmat}{\boldsymbol{X}}
          \renewcommand{\models}[2]{\boldsymbol{M}\left( #1 \, ; \, #2 \right)}
          \newcommand{\model}[2]{M\left( #1 \, ; \, #2 \right)}
          \newcommand{\modeloutputs}{\boldsymbol{M}}
          \newcommand{\modeloutput}{M}
          \newcommand{\MLmodel}[1]{\boldsymbol{\hat{y}}\left( #1 \right)}
          \newcommand{\MLoutputs}{\boldsymbol{\hat{y}}}
          \newcommand{\MLoutput}{\hat{y}}
          \newcommand{\outputs}{\boldsymbol{y}}
          \newcommand{\inputs}{\boldsymbol{x}}
          \newcommand{\targets}{\boldsymbol{t}}
          \newcommand{\weights}{\boldsymbol{w}}
          \newcommand{\testoutputs}{\boldsymbol{y}^\odot}
          \newcommand{\testinputs}{\boldsymbol{x}^\odot}
          \renewcommand{\output}{y}
          \newcommand{\inputt}{x}
          \newcommand{\target}{t}
          \newcommand{\weight}{w}
          \newcommand{\testoutput}{y^\odot}
          \newcommand{\MLtestoutput}{\hat{y}^\odot}
          \newcommand{\testinput}{x^\odot}
          \newcommand{\trainingdata}{\mathcal{T}}
          \renewcommand{\LaTeX}{\text{LaTeX}}
          \newcommand{\residual}{\epsilon}
          \newcommand{\residuals}{\boldsymbol{\epsilon}}
          \newcommand{\zeros}{\boldsymbol{0}}
          \newcommand{\covres}{\boldsymbol{\Sigma_{\epsilon}}}
          \newcommand{\covpars}{\boldsymbol{\Sigma_{\pars}}}
          \newcommand{\tildecovpars}{\boldsymbol{\widetilde{\Sigma}_{\pars}}}
          \newcommand{\sigmas}{\boldsymbol{\sigma}}
          \newcommand{\sigmai}{\sigma_i}
          \newcommand{\sigmares}{\sigma_{\epsilon}} 
          \newcommand{\cbar}{\bar c}
          \newcommand{\Lra}{\Longrightarrow}
          \newcommand{\yth}{y_{\rm th}}
          \newcommand{\yexp}{y_{\rm exp}}
          \newcommand{\ym}{y_{\rm m}}
          \newcommand{\thetavec}{\pars}
          \newcommand{\parsLR}{\boldsymbol{\beta}}
          \newcommand{\paraLR}{\beta}
          \newcommand{\covparsLR}{\boldsymbol{\Sigma_{\parsLR}}}
          \newcommand{\optparsLR}{\parsLR^*}
          \newcommand{\optparaLR}{\paraLR^*}
          \newcommand{\tildecovparsLR}{\boldsymbol{\widetilde{\Sigma}_{\parsLR}}}
          \newcommand{\alphavec}{\boldsymbol{\alpha}}
          \newcommand{\muvec}{\boldsymbol{\mu}}
          \newcommand{\phivec}{\boldsymbol{\phi}}
          \newcommand{\betavec}{\boldsymbol{\beta}}
          \newcommand{\sigmavec}{\boldsymbol{\sigma}}
          \newcommand{\Sigmavec}{\boldsymbol{\Sigma}}
          \newcommand{\thetavec}{\boldsymbol{\theta}}
          \newcommand{\thetavechat}{\widehat\thetavec}
          \newcommand{\avec}{\boldsymbol{a}}
          \newcommand{\Bvec}{\boldsymbol{B}}
          \newcommand{\fvec}{\boldsymbol{f}}
          \newcommand{\mvec}{\boldsymbol{m}}
          \newcommand{\qvec}{\boldsymbol{q}}
          \newcommand{\rvec}{\boldsymbol{r}}
          \newcommand{\uvec}{\boldsymbol{u}}
          \newcommand{\vvec}{\boldsymbol{v}}
          \newcommand{\wvec}{\boldsymbol{w}}
          \newcommand{\xvec}{\boldsymbol{x}}
          \newcommand{\yvec}{\boldsymbol{y}}
          \newcommand{\wt}{\widetilde}
          \newcommand{\nb}{n_b}
          \newcommand{\mel}[3]{\langle #1 | #2 | #3 \rangle}
          \newcommand{\qoi}{\mathbf{Q}}
          \newcommand{\ytrue}{y_{\rm true}}
          
          

          
          

          
          

          
          

          

          

          

          
    nb_custom_formats:
      .Rmd:
        - jupytext.reads
        - fmt: Rmd
  extra_extensions:
    - sphinx_proof
    - sphinx_exercise
    # see https://sphinx-proof.readthedocs.io/en/latest/index.html
    # see https://ebp-sphinx-exercise.readthedocs.io/en/latest/index.html
    #- sphinx_inline_tabs
    # https://jupyterbook.org/advanced/pdf.html#pdf-latex

    # https://jupyterbook.org/advanced/pdf.html#pdf-latex
    #CF removed. Tope level is chapter.
    #latex_toplevel_sectioning: 'part'
    
#######################################################################################
# Parse and render settings
parse:
  myst_url_schemes          : [mailto, http, https]  # URI schemes that will be recognised as external URLs in Markdown links (kept from CFs config)
  myst_substitutions:
    sub_extra: "This section contains extra material that is not included in the TIF285 course."  
    #sub_extra_admonition: ""
    sub_extra_tif385_admonition: ""
    sub_extra_admonition: |
        ::::{admonition} extra material
        :class: danger
        {{ sub_extra  }}
        ::::
    sub_duplicate_admonition: |
        ::::{admonition} duplicate material
        :class: danger
        This section contains duplicated material (to be removed).
        ::::
    sub_Statistics_notation: |
        | Quantity | General notation |
        | :------ | :------: |
        | Conditional probability | $\cprob{A}{B}$ |
        | Covariance | $\cov{X}{Y}$ |
        | Distribution function | $P(x)$ |
        | Empty set | $\emptyset$ |
        | Event | $A$ |
        | Expectation value | $\expect{X}$ |
        | Likelihood function | $\mathcal{L}(\para)$
        | Model parameters | $\para$
        | Probability density function | $\p{x}$ |
        | Probability mass function | $\p{x}$ |
        | Probability measure | $\prob$ |
        | Random variable | $X$ |
        | Sample space | $S$ |
        | Standard deviation | $\std{X}$ |
        | Variance | $\var{X}$ |
    sub_OverviewModeling_notation: |
        | Quantity | General notation |
        | :------ | :------: |
        | Dataset | $\data$ |
        | Dependent or response variables (output) | $\outputs{}$ |
        | Independent or predictor variables (input) | $\inputs{}$ |
        | Model | $\model{\pars}{\inputs}$ |
        | Model parameters | $\pars$ |
        | Parameter optimum | $\optpars$ |
    sub_StochasticProcesses_notation: |
        | English | General notation |
        | :------ | :------: |
        | Acceptance probability | $A$ |
        | Limiting distribution | |
        | Markov chain | |
        | Proposal distribution | $S$ |
        | Random walk | |
        | Reversibility | |
        | Stationary distribution (or equilibrium distribution) | |
        | Stochastic process | |
        | Transition density| $T$ | 
    sub_MachineLearning_notation: |
        | Quantity | General notation |
        | :------ | :------: |
        | Activation | $z$ |
        | Activation function | $f(z)$ |
        | Bias (term) | ${b}$ or $\weight_0$ |
        | Cost function | $C(\MLoutputs, \outputs)$ or alternatively $C(\pars)$ |
        | Cross validation | CV |
        | Error function | $E(\MLoutputs, \outputs)$ |
        | False negative | FN |
        | False positive | FP |
        | Features | $\inputs$ |
        | Machine learning model | $\MLmodel{\inputs}$ |
        | Targets | $\targets$ or $\outputs$|
        | Test input | $\testinputs$|
        | Test output | $\testoutputs$|
        | Training data | $\trainingdata = \left\{ (\inputs_i, \outputs_i) \right\}_{i=1}^{N_\mathrm{train}}$ or $\data_\mathrm{train}$ |
        | True negative | TN |
        | True positive | TP |
        | Validation data | $\data_\mathrm{val}$ |
        | Weights | $\weights$ |

  myst_enable_extensions:  # default extensions to enable in the myst parser. The original config had only ["dollarmath", "amsmath","html_image"]. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html
    - amsmath
    - attrs_block
    - attrs_inline
    - colon_fence
    - deflist
    - dollarmath
    - html_admonition  # removed     - html
    - html_image
    - linkify
    - replacements
    - smartquotes
    - substitution
    - tasklist  # This enables checkboxes


#######################################################################################
# Launch button settings
launch_buttons:
#  #colab_url                 : "https://colab.research.google.com"
#  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
  binderhub_url             : https://mybinder.org  # The URL of the BinderHub (e.g., https://mybinder.org)
#  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)