chore: import upstream snapshot with attribution

docs/Makefile

@@ -0,0 +1,226 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf generated/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SHAP.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SHAP.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/SHAP"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SHAP"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."

docs/_static/css/style.css

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+.wy-side-nav-search>div.version {
+    color: black;
+}
+@media screen and (min-width: 767px) {
+   .wy-table-responsive table td {
+      white-space: normal;
+   }
+   .wy-table-responsive {
+      overflow: visible;
+   }
+}
+
+.wy-side-nav-search .wy-dropdown>a img.logo,.wy-side-nav-search>a img.logo {
+   max-width: 40%;
+}
+
+.wy-side-nav-search>div.version {
+   color: #d9d9d9;
+}
+
+.wy-nav-top {
+   background: #343131;
+}
+
+.highlight {
+   background: #f7f7f7;
+}
+
+.wy-side-nav-search input[type=text] {
+   border-color: #666666;
+}
+
+a {
+   color: #008bfb;
+}
+
+a:hover {
+   color: #008bfb;
+}
+
+a:visited {
+   color: #008bfb;
+}
+
+html.writer-html4 .rst-content dl:not(.docutils)>dt, html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)>dt {
+   background: #008bfb11;
+   color: #0086f6;
+   border-top: 3px solid #008bfbaa;
+}
+
+.rst-versions .rst-current-version {
+   color: #fcfcfc;
+}
+
+.wy-menu-vertical a {
+   color: #d9d9d9;
+}

docs/_templates/layout.html

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+{# layout.html #}
+{# Import the layout of the theme. #}
+{% extends "!layout.html" %}
+
+{% set css_files = css_files + ['_static/css/style.css'] %}

docs/api.rst

@@ -0,0 +1,154 @@
+.. currentmodule:: shap
+
+API Reference
+=============
+This page contains the API reference for public objects and functions in SHAP.
+There are also :ref:`example notebooks <api_examples>` available that demonstrate how
+to use the API of each object/function.
+
+
+.. _explanation_api:
+
+Explanation
+-----------
+.. autosummary::
+    :toctree: generated/
+
+    shap.Explanation
+    shap.Cohorts
+
+
+.. _explainers_api:
+
+explainers
+----------
+*See also:* :ref:`Explainer API Examples <explainers_examples>`.
+
+.. autosummary::
+    :toctree: generated/
+
+    shap.Explainer
+    shap.TreeExplainer
+    shap.GPUTreeExplainer
+    shap.LinearExplainer
+    shap.PermutationExplainer
+    shap.PartitionExplainer
+    shap.SamplingExplainer
+    shap.AdditiveExplainer
+    shap.DeepExplainer
+    shap.KernelExplainer
+    shap.GradientExplainer
+    shap.ExactExplainer
+    shap.explainers.other.Coefficient
+    shap.explainers.other.Random
+    shap.explainers.other.LimeTabular
+    shap.explainers.other.Maple
+    shap.explainers.other.TreeMaple
+    shap.explainers.other.TreeGain
+
+
+.. _plots_api:
+
+plots
+-----
+*See also:* :ref:`Plot API Examples <plots_examples>`.
+
+.. autosummary::
+    :toctree: generated/
+
+    shap.plots.bar
+    shap.plots.waterfall
+    shap.plots.scatter
+    shap.plots.heatmap
+    shap.plots.force
+    shap.plots.text
+    shap.plots.image
+    shap.plots.partial_dependence
+    shap.plots.decision
+    shap.plots.embedding
+    shap.plots.initjs
+    shap.plots.group_difference
+    shap.plots.image_to_text
+    shap.plots.monitoring
+    shap.plots.beeswarm
+    shap.plots.violin
+
+
+.. _maskers_api:
+
+maskers
+-------
+*See also:* :ref:`Masker API Examples <maskers_examples>`.
+
+.. autosummary::
+    :toctree: generated/
+
+    shap.maskers.Masker
+    shap.maskers.Independent
+    shap.maskers.Partition
+    shap.maskers.Impute
+    shap.maskers.Fixed
+    shap.maskers.Composite
+    shap.maskers.FixedComposite
+    shap.maskers.OutputComposite
+    shap.maskers.Text
+    shap.maskers.Image
+
+
+.. _models_api:
+
+models
+------
+.. autosummary::
+    :toctree: generated/
+
+    shap.models.Model
+    shap.models.TeacherForcing
+    shap.models.TextGeneration
+    shap.models.TopKLM
+    shap.models.TransformersPipeline
+
+
+.. _utils_api:
+
+utils
+-----
+.. autosummary::
+    :toctree: generated/
+
+    shap.utils.hclust
+    shap.utils.hclust_ordering
+    shap.utils.partition_tree
+    shap.utils.partition_tree_shuffle
+    shap.utils.delta_minimization_order
+    shap.utils.approximate_interactions
+    shap.utils.potential_interactions
+    shap.utils.sample
+    shap.utils.shapley_coefficients
+    shap.utils.convert_name
+    shap.utils.OpChain
+    shap.utils.show_progress
+    shap.utils.MaskedModel
+    shap.utils.make_masks
+
+
+.. _datasets_api:
+
+datasets
+--------
+.. autosummary::
+    :toctree: generated/
+
+    shap.datasets.a1a
+    shap.datasets.adult
+    shap.datasets.california
+    shap.datasets.communitiesandcrime
+    shap.datasets.corrgroups60
+    shap.datasets.diabetes
+    shap.datasets.imagenet50
+    shap.datasets.imdb
+    shap.datasets.independentlinear60
+    shap.datasets.iris
+    shap.datasets.linnerud
+    shap.datasets.nhanesi
+    shap.datasets.rank

docs/api_examples.rst

@@ -0,0 +1,71 @@
+.. currentmodule:: shap
+
+.. _api_examples:
+
+API Examples
+----------------
+
+These examples parallel the namespace structure of SHAP. Each object or function in SHAP has a
+corresponding example notebook here that demonstrates its API usage. The source notebooks
+are `available on GitHub <https://github.com/shap/shap/tree/master/notebooks/api_examples>`_.
+
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/api_examples/migrating-to-new-api.ipynb
+
+.. _explainers_examples:
+
+explainers
+==========
+*See also:* :ref:`Explainer API Reference <explainers_api>`.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/api_examples/explainers/*
+
+
+.. _maskers_examples:
+
+maskers
+=======
+*See also:* :ref:`Masker API Reference <maskers_api>`.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/api_examples/maskers/*
+
+
+.. _models_examples:
+
+models
+======
+.. Examples for members of :ref:`shap.models <models_api>`.
+
+Work in progress.
+
+.. TODO: Uncomment this toctree once we have at least one example to share
+    .. toctree::
+        :glob:
+        :maxdepth: 1
+
+        example_notebooks/api_examples/models/*
+
+
+.. _plots_examples:
+
+plots
+=====
+*See also:* :ref:`Plot API Reference <plots_api>`.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/api_examples/plots/*

docs/benchmarks.rst

@@ -0,0 +1,48 @@
+.. currentmodule:: shap
+
+.. benchmarks
+
+Benchmarks
+----------
+
+These benchmark notebooks compare different types of explainers across a variety of metrics.
+They are all generated from Jupyter notebooks
+`available on GitHub <https://github.com/shap/shap/tree/master/notebooks/benchmarks>`_.
+
+Image
+=====
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/benchmarks/image/*
+
+Tabular
+=======
+Benchmarks that compare explainers on tabular datasets.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/benchmarks/tabular/*
+
+Text
+====
+Benchmarks that compare explainers on text datasets.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/benchmarks/text/*
+
+Others
+======
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/benchmarks/others/*

docs/conf.py

@@ -0,0 +1,455 @@
+#!/usr/bin/env python3
+#
+# SHAP documentation build configuration file, created by
+# sphinx-quickstart on Tue May 22 10:44:55 2018.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import shutil
+import sys
+
+import requests
+
+print(os.path.abspath("./shap"))
+sys.path.insert(0, os.path.abspath(".."))
+
+# make copy of notebooks in docs folder, as they must be here for sphinx to
+# pick them up properly.
+NOTEBOOKS_DIR = os.path.abspath("example_notebooks")
+if os.path.exists(NOTEBOOKS_DIR):
+    import warnings
+
+    warnings.warn("example_notebooks directory exists, replacing...")
+    shutil.rmtree(NOTEBOOKS_DIR)
+shutil.copytree(os.path.abspath("../notebooks"), NOTEBOOKS_DIR)
+if os.path.exists(NOTEBOOKS_DIR + "/local_scratch"):
+    shutil.rmtree(NOTEBOOKS_DIR + "/local_scratch")
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
+    "numpydoc",
+    "nbsphinx",  # Allows parsing Jupyter notebooks
+    "myst_parser",  # Allows parsing Markdown, such as CONTRIBUTING.md
+    "sphinx_github_changelog",
+]
+
+# --- Extension options
+# [autodoc]
+autodoc_default_options = {"members": True, "inherited-members": True}
+
+# [autosectionlabel]
+# Make sure the autogenerated targets are unique
+autosectionlabel_prefix_document = True
+
+# [autosummary]
+autosummary_generate = True
+
+# [intersphinx]
+intersphinx_mapping = {
+    # "stdlib": ("https://docs.python.org/3", None),
+    "mpl": (
+        "https://matplotlib.org/stable/",
+        "https://matplotlib.org/stable/objects.inv",
+    ),
+    "scikit-learn": (
+        "https://scikit-learn.org/stable/",
+        "https://scikit-learn.org/stable/objects.inv",
+    ),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+}
+
+# Sphinx defaults to automatically resolve *unresolved* labels using all your Intersphinx mappings.
+# This behavior has unintended side-effects, namely that documentations local references can
+# suddenly resolve to an external location.
+# See also:
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_disabled_reftypes
+intersphinx_disabled_reftypes = ["*"]
+
+# [numpydoc]
+numpydoc_show_class_members = False
+# ---
+
+# Do not create toctree entries for each class/function
+toc_object_entries = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = "SHAP"
+copyright = "2018, Scott Lundberg"
+author = "Scott Lundberg"
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = "latest"
+# The full version, including alpha/beta/rc tags.
+release = "latest"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "example_notebooks/tabular_examples/tree_based_models/tree_shap_paper",
+    "user_studies",
+    "local",
+]
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+# -- Release notes configuration ------------------------------------------
+
+# Make available a URL that points to the latest unreleased changes
+
+
+def get_latest_tag() -> str:
+    """Query GitHub API to get the most recent git tag"""
+    url = "https://api.github.com/repos/shap/shap/releases/latest"
+    response = requests.get(url)
+    response.raise_for_status()
+    return response.json()["tag_name"]
+
+
+_latest_tag = get_latest_tag()
+_url = f"https://github.com/shap/shap/compare/{_latest_tag}...master"
+
+# Make an RST substitution that inserts the correct hyperlink
+rst_epilog = f"""
+.. |unreleasedchanges| replace:: {_latest_tag}...master
+.. _unreleasedchanges: {_url}
+"""
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    #'canonical_url': '',
+    "logo_only": True,
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
+    "style_external_links": False,
+    "style_nav_header_background": "#343131",
+    # Toc options
+    "collapse_navigation": True,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
+}
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = "artwork/shap_logo_white.png"
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = 'SHAP v0.16'
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+html_favicon = "artwork/favicon.ico"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = True
+
+# If false, no index is generated.
+#
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "SHAPdoc"
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, "SHAP.tex", "SHAP Documentation", "Scott Lundberg", "manual"),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, 	itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "shap", "SHAP Documentation", [author], 1)]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "SHAP",
+        "SHAP Documentation",
+        author,
+        "SHAP",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
+
+
+def setup(app):
+    import shap  # noqa: F401
+
+    app.connect("build-finished", build_finished)
+
+
+def build_finished(app, exception):
+    shutil.rmtree(NOTEBOOKS_DIR)

docs/contributing.rst

@@ -0,0 +1,2 @@
+.. include:: ../CONTRIBUTING.md
+   :parser: myst_parser.sphinx_

docs/genomic_examples.rst

@@ -0,0 +1,11 @@
+Genomic examples
+----------------
+
+These examples explain machine learning models applied to genomic data. They are all generated from Jupyter
+notebooks `available on GitHub <https://github.com/shap/shap/tree/master/notebooks/genomic_examples>`_.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/genomic_examples/*

docs/image_examples.rst

@@ -0,0 +1,27 @@
+Image examples
+----------------
+
+These examples explain machine learning models applied to image data. They are all generated from Jupyter
+notebooks `available on GitHub <https://github.com/shap/shap/tree/master/notebooks/image_examples>`_.
+
+
+Image classification
+====================
+Examples using :class:`shap.explainers.Partition` to explain image classifiers.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/image_examples/image_classification/*
+
+
+Image captioning
+================
+Examples using :class:`shap.explainers.Permutation` to produce explanations in a model agnostic manner.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/image_examples/image_captioning/*

docs/index.rst

@@ -0,0 +1,57 @@
+.. SHAP documentation master file, created by
+   sphinx-quickstart on Tue May 22 10:44:55 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to the SHAP documentation
+---------------------------------
+
+.. image:: artwork/shap_header.png
+   :width: 600px
+   :align: center
+
+**SHAP (SHapley Additive exPlanations)** is a game theoretic approach to explain the output of
+any machine learning model. It connects optimal credit allocation with local explanations
+using the classic Shapley values from game theory and their related extensions (see
+`papers <https://github.com/shap/shap#citations>`_ for details and citations).
+
+Install
+=======
+
+SHAP can be installed from either `PyPI <https://pypi.org/project/shap>`_ or
+`conda-forge <https://anaconda.org/conda-forge/shap>`_::
+
+   pip install shap
+   or
+   conda install -c conda-forge shap
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Introduction
+
+   Topical overviews <overviews>
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Examples
+
+   Tabular examples <tabular_examples>
+   Text examples <text_examples>
+   Image examples <image_examples>
+   Genomic examples <genomic_examples>
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Reference
+
+   API reference <api>
+   API examples <api_examples>
+   Benchmarks <benchmarks>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Development
+
+   Release notes <release_notes>
+   Contributing guide <contributing>

docs/make.bat

@@ -0,0 +1,281 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  epub3      to make an epub3
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	echo.  coverage   to run coverage check of the documentation if enabled
+	echo.  dummy      to check syntax errors of document sources
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+REM Check if sphinx-build is available and fallback to Python version if any
+%SPHINXBUILD% 1>NUL 2>NUL
+if errorlevel 9009 goto sphinx_python
+goto sphinx_ok
+
+:sphinx_python
+
+set SPHINXBUILD=python -m sphinx.__init__
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+:sphinx_ok
+
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\SHAP.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\SHAP.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "epub3" (
+	%SPHINXBUILD% -b epub3 %ALLSPHINXOPTS% %BUILDDIR%/epub3
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub3 file is in %BUILDDIR%/epub3.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %~dp0
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "coverage" (
+	%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of coverage in the sources finished, look at the ^
+results in %BUILDDIR%/coverage/python.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+if "%1" == "dummy" (
+	%SPHINXBUILD% -b dummy %ALLSPHINXOPTS% %BUILDDIR%/dummy
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. Dummy builder generates no files.
+	goto end
+)
+
+:end

docs/notebooks/plots/data/crime.py

@@ -0,0 +1,26 @@
+# Create 'crime.pickle'
+
+import pickle
+
+import lightgbm as lgb
+from sklearn.model_selection import train_test_split
+
+import shap
+
+random_state = 1203344
+
+# Load data and train model
+X, y = shap.datasets.communitiesandcrime()
+X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, random_state=random_state)
+model = lgb.LGBMRegressor(random_state=random_state)
+model.fit(X_train, y_train, eval_set=[(X_test, y_test)], verbose=False)
+
+# Calculate and plot SHAP values
+explainer = shap.TreeExplainer(model)
+idx = 13
+shap_values = explainer.shap_values(X_test.iloc[[idx]], y_test[idx])
+
+# Dump to pickle
+o = (explainer.expected_value, shap_values, X_test.iloc[0])
+with open("./crime.pickle", "wb") as fl:
+    pickle.dump(o, fl)

docs/overviews.rst

@@ -0,0 +1,11 @@
+Topical Overviews
+-----------------
+
+These overviews are generated from Jupyter notebooks that are
+`available on GitHub <https://github.com/shap/shap/tree/master/notebooks/overviews>`_
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/overviews/*

docs/references/nature_bme.bib

@@ -0,0 +1,10 @@
+@article{lundberg2018explainable,
+  title={Explainable machine-learning predictions for the prevention of hypoxaemia during surgery},
+  author={Lundberg, Scott M and Nair, Bala and Vavilala, Monica S and Horibe, Mayumi and Eisses, Michael J and Adams, Trevor and Liston, David E and Low, Daniel King-Wai and Newman, Shu-Fang and Kim, Jerry and others},
+  journal={Nature Biomedical Engineering},
+  volume={2},
+  number={10},
+  pages={749},
+  year={2018},
+  publisher={Nature Publishing Group}
+}

docs/references/shap_nips.bib

@@ -0,0 +1,7 @@
+@incollection{NIPS2017_7062,
+title = {A Unified Approach to Interpreting Model Predictions},
+author = {Lundberg, Scott M and Lee, Su-In},
+year = {2017},
+publisher = {Curran Associates, Inc.},
+url = {http://papers.nips.cc/paper/7062-a-unified-approach-to-interpreting-model-predictions.pdf}
+}

docs/references/tree_explainer.bib

@@ -0,0 +1,10 @@
+@article{lundberg2020local2global,
+  title={From local explanations to global understanding with explainable AI for trees},
+  author={Lundberg, Scott M. and Erion, Gabriel and Chen, Hugh and DeGrave, Alex and Prutkin, Jordan M. and Nair, Bala and Katz, Ronit and Himmelfarb, Jonathan and Bansal, Nisha and Lee, Su-In},
+  journal={Nature Machine Intelligence},
+  volume={2},
+  number={1},
+  pages={2522-5839},
+  year={2020},
+  publisher={Nature Publishing Group}
+}

docs/references/treeshap_arxiv.bib

@@ -0,0 +1,6 @@
+@article{lundberg2019explainable,
+  title={Explainable AI for Trees: From Local Explanations to Global Understanding},
+  author={Lundberg, Scott M and Erion, Gabriel and Chen, Hugh and DeGrave, Alex and Prutkin, Jordan M and Nair, Bala and Katz, Ronit and Himmelfarb, Jonathan and Bansal, Nisha and Lee, Su-In},
+  journal={arXiv preprint arXiv:1905.04610},
+  year={2019}
+}

docs/release_notes.rst

@@ -0,0 +1,9 @@
+Release notes
+-------------
+
+To see the latest changes that are due on the next release, see |unreleasedchanges|_.
+
+.. changelog::
+    :changelog-url: https://shap.readthedocs.io/en/latest/release_notes.html
+    :github: https://github.com/shap/shap/releases/
+    :pypi: https://pypi.org/project/shap/

docs/requirements-docs.txt

@@ -0,0 +1,265 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml --group docs --python-version 3.12 -o docs/requirements-docs.txt
+alabaster==1.0.0
+    # via sphinx
+asttokens==3.0.1
+    # via stack-data
+attrs==26.1.0
+    # via
+    #   jsonschema
+    #   referencing
+babel==2.18.0
+    # via sphinx
+beautifulsoup4==4.14.3
+    # via nbconvert
+bleach==6.4.0
+    # via nbconvert
+certifi==2026.2.25
+    # via requests
+charset-normalizer==3.4.6
+    # via requests
+cloudpickle==3.1.2
+    # via shap (pyproject.toml)
+comm==0.2.3
+    # via ipywidgets
+contourpy==1.3.3
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+decorator==5.2.1
+    # via ipython
+defusedxml==0.7.1
+    # via nbconvert
+docutils==0.22.4
+    # via
+    #   myst-parser
+    #   nbsphinx
+    #   sphinx
+    #   sphinx-github-changelog
+    #   sphinx-rtd-theme
+executing==2.2.1
+    # via stack-data
+fastjsonschema==2.21.2
+    # via nbformat
+fonttools==4.62.1
+    # via matplotlib
+idna==3.15
+    # via requests
+imagesize==2.0.0
+    # via sphinx
+ipython==9.12.0
+    # via
+    #   shap (pyproject.toml:docs)
+    #   ipywidgets
+ipython-pygments-lexers==1.1.1
+    # via ipython
+ipywidgets==8.1.8
+    # via shap (pyproject.toml:docs)
+jedi==0.19.2
+    # via ipython
+jinja2==3.1.6
+    # via
+    #   myst-parser
+    #   nbconvert
+    #   nbsphinx
+    #   sphinx
+joblib==1.5.3
+    # via scikit-learn
+jsonschema==4.26.0
+    # via nbformat
+jsonschema-specifications==2025.9.1
+    # via jsonschema
+jupyter-client==8.8.0
+    # via nbclient
+jupyter-core==5.9.1
+    # via
+    #   jupyter-client
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+jupyterlab-pygments==0.3.0
+    # via nbconvert
+jupyterlab-widgets==3.0.16
+    # via ipywidgets
+kiwisolver==1.5.0
+    # via matplotlib
+llvmlite==0.47.0
+    # via
+    #   shap (pyproject.toml)
+    #   numba
+markdown-it-py==4.0.0
+    # via
+    #   mdit-py-plugins
+    #   myst-parser
+markupsafe==3.0.3
+    # via
+    #   jinja2
+    #   nbconvert
+matplotlib==3.10.8
+    # via shap (pyproject.toml:docs)
+matplotlib-inline==0.2.1
+    # via ipython
+mdit-py-plugins==0.5.0
+    # via myst-parser
+mdurl==0.1.2
+    # via markdown-it-py
+mistune==3.2.1
+    # via nbconvert
+myst-parser==5.0.0
+    # via shap (pyproject.toml:docs)
+nbclient==0.10.4
+    # via nbconvert
+nbconvert==7.17.1
+    # via nbsphinx
+nbformat==5.10.4
+    # via
+    #   nbclient
+    #   nbconvert
+    #   nbsphinx
+nbsphinx==0.9.8
+    # via shap (pyproject.toml:docs)
+numba==0.65.0
+    # via shap (pyproject.toml)
+numpy==2.4.4
+    # via
+    #   shap (pyproject.toml)
+    #   contourpy
+    #   matplotlib
+    #   numba
+    #   pandas
+    #   scikit-learn
+    #   scipy
+numpydoc==1.10.0
+    # via shap (pyproject.toml:docs)
+packaging==26.0
+    # via
+    #   shap (pyproject.toml)
+    #   matplotlib
+    #   nbconvert
+    #   sphinx
+pandas==3.0.2
+    # via shap (pyproject.toml)
+pandocfilters==1.5.1
+    # via nbconvert
+parso==0.8.6
+    # via jedi
+pexpect==4.9.0
+    # via ipython
+pillow==12.2.0
+    # via matplotlib
+platformdirs==4.9.4
+    # via jupyter-core
+prompt-toolkit==3.0.52
+    # via ipython
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pygments==2.20.0
+    # via
+    #   ipython
+    #   ipython-pygments-lexers
+    #   nbconvert
+    #   sphinx
+pyparsing==3.3.2
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via
+    #   jupyter-client
+    #   matplotlib
+    #   pandas
+pyyaml==6.0.3
+    # via myst-parser
+pyzmq==27.1.0
+    # via jupyter-client
+referencing==0.37.0
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+requests==2.33.1
+    # via
+    #   shap (pyproject.toml:docs)
+    #   sphinx
+    #   sphinx-github-changelog
+roman-numerals==4.1.0
+    # via sphinx
+rpds-py==0.30.0
+    # via
+    #   jsonschema
+    #   referencing
+scikit-learn==1.8.0
+    # via shap (pyproject.toml)
+scipy==1.17.1
+    # via
+    #   shap (pyproject.toml)
+    #   scikit-learn
+six==1.17.0
+    # via python-dateutil
+slicer==0.0.8
+    # via shap (pyproject.toml)
+snowballstemmer==3.0.1
+    # via sphinx
+soupsieve==2.8.3
+    # via beautifulsoup4
+sphinx==9.1.0
+    # via
+    #   shap (pyproject.toml:docs)
+    #   myst-parser
+    #   nbsphinx
+    #   numpydoc
+    #   sphinx-github-changelog
+    #   sphinx-rtd-theme
+    #   sphinxcontrib-jquery
+sphinx-github-changelog==1.7.2
+    # via shap (pyproject.toml:docs)
+sphinx-rtd-theme==3.1.0
+    # via shap (pyproject.toml:docs)
+sphinxcontrib-applehelp==2.0.0
+    # via sphinx
+sphinxcontrib-devhelp==2.0.0
+    # via sphinx
+sphinxcontrib-htmlhelp==2.1.0
+    # via sphinx
+sphinxcontrib-jquery==4.1
+    # via sphinx-rtd-theme
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==2.0.0
+    # via sphinx
+sphinxcontrib-serializinghtml==2.0.0
+    # via sphinx
+stack-data==0.6.3
+    # via ipython
+threadpoolctl==3.6.0
+    # via scikit-learn
+tinycss2==1.4.0
+    # via bleach
+tornado==6.5.7
+    # via jupyter-client
+tqdm==4.67.3
+    # via shap (pyproject.toml)
+traitlets==5.14.3
+    # via
+    #   ipython
+    #   ipywidgets
+    #   jupyter-client
+    #   jupyter-core
+    #   matplotlib-inline
+    #   nbclient
+    #   nbconvert
+    #   nbformat
+    #   nbsphinx
+typing-extensions==4.15.0
+    # via
+    #   beautifulsoup4
+    #   referencing
+urllib3==2.7.0
+    # via requests
+wcwidth==0.6.0
+    # via prompt-toolkit
+webencodings==0.5.1
+    # via
+    #   bleach
+    #   tinycss2
+widgetsnbextension==4.0.15
+    # via ipywidgets

docs/tabular_examples.rst

@@ -0,0 +1,49 @@
+Tabular examples
+----------------
+
+These examples explain machine learning models applied to tabular data. They are all generated from Jupyter
+notebooks `available on GitHub <https://github.com/shap/shap/tree/master/notebooks/tabular_examples>`_.
+
+
+Tree-based models
+=================
+Examples demonstrating how to explain tree-based machine learning models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/tabular_examples/tree_based_models/*
+
+
+Linear models
+=============
+Examples demonstrating how to explain linear machine learning models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/tabular_examples/linear_models/*
+
+
+Neural networks
+===============
+Examples demonstrating how to explain machine learning models based on neural networks.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/tabular_examples/neural_networks/*
+
+
+Model agnostic
+==============
+Examples demonstrating how to explain arbitrary machine learning pipelines.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/tabular_examples/model_agnostic/*

docs/text_examples.rst

@@ -0,0 +1,81 @@
+Text examples
+-------------
+
+These examples explain machine learning models applied to text data. They are all generated from Jupyter
+notebooks `available on GitHub <https://github.com/shap/shap/tree/master/notebooks/text_examples>`_.
+
+
+Sentiment analysis
+==================
+Examples of how to explain predictions from sentiment analysis models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/sentiment_analysis/*
+
+Translation
+===========
+Examples of how to explain predictions from translation models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/translation/*
+
+
+Text generation
+===============
+Examples of how to explain predictions from text generation models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/text_generation/*
+
+
+Summarization
+=============
+Examples of how to explain predictions from summarization models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/summarization/*
+
+
+Question Answering
+==================
+Examples of how to explain predictions from question answering models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/question_answering/*
+
+
+Language modelling
+==================
+Examples of how to explain predictions from language models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/language_modelling/*
+
+
+Text entailment
+===============
+Examples of how to explain predictions from text entailment models.
+
+.. toctree::
+    :glob:
+    :maxdepth: 1
+
+    example_notebooks/text_examples/text_entailment/*

docs/user_studies/sickness_scores/Approve Hits.ipynb

@@ -0,0 +1,145 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Approve Hits"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import boto3"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "aws_access_key_id = \"AKIAJ7ODKKKLEQNUJYZA\"\n",
+    "aws_secret_access_key = \"XXXXX\"\n",
+    "aws_region = \"us-east-1\"\n",
+    "client = boto3.client('mturk', region_name= \"us-east-1\", aws_access_key_id=aws_access_key_id, aws_secret_access_key=aws_secret_access_key)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'ResponseMetadata': {'RequestId': '5c6b81ce-fc0c-4125-a1c2-bfc4d157bfa9',\n",
+       "  'HTTPStatusCode': 200,\n",
+       "  'HTTPHeaders': {'x-amzn-requestid': '5c6b81ce-fc0c-4125-a1c2-bfc4d157bfa9',\n",
+       "   'content-type': 'application/x-amz-json-1.1',\n",
+       "   'content-length': '2',\n",
+       "   'date': 'Sun, 03 Mar 2019 01:04:12 GMT'},\n",
+       "  'RetryAttempts': 0}}"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "client.approve_assignment(AssignmentId=\"3QFUFYSY9ZFOQSZK8PZXFP84UVOF4N\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'NextToken': 'p1:thjV0Iu9KED6Jtn5ylDyJ+bUn3ooStDrFP8Z1CmhpFWeCbNFBveoYz1nm2qSsQ==',\n",
+       " 'NumResults': 1,\n",
+       " 'Assignments': [{'AssignmentId': '3QFUFYSY9ZFOQSZK8PZXFP84UVOF4N',\n",
+       "   'WorkerId': 'A19H44LQJ0TEXF',\n",
+       "   'HITId': '3R0WOCG21N9NNMH96NQNG98SB7WUDM',\n",
+       "   'AssignmentStatus': 'Approved',\n",
+       "   'AutoApprovalTime': datetime.datetime(2019, 4, 1, 15, 56, 22, tzinfo=tzlocal()),\n",
+       "   'AcceptTime': datetime.datetime(2019, 3, 2, 14, 51, 24, tzinfo=tzlocal()),\n",
+       "   'SubmitTime': datetime.datetime(2019, 3, 2, 14, 56, 22, tzinfo=tzlocal()),\n",
+       "   'ApprovalTime': datetime.datetime(2019, 3, 2, 17, 4, 12, tzinfo=tzlocal()),\n",
+       "   'Answer': '<?xml version=\"1.0\" encoding=\"ASCII\"?><QuestionFormAnswers xmlns=\"http://mechanicalturk.amazonaws.com/AWSMechanicalTurkDataSchemas/2005-10-01/QuestionFormAnswers.xsd\"><Answer><QuestionIdentifier>workerId</QuestionIdentifier><FreeText>A19H44LQJ0TEXF</FreeText></Answer></QuestionFormAnswers>'}],\n",
+       " 'ResponseMetadata': {'RequestId': 'c20c08c1-c74f-4fdb-a170-78a45f8b7369',\n",
+       "  'HTTPStatusCode': 200,\n",
+       "  'HTTPHeaders': {'x-amzn-requestid': 'c20c08c1-c74f-4fdb-a170-78a45f8b7369',\n",
+       "   'content-type': 'application/x-amz-json-1.1',\n",
+       "   'content-length': '687',\n",
+       "   'date': 'Sun, 03 Mar 2019 01:04:29 GMT'},\n",
+       "  'RetryAttempts': 0}}"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "client.list_assignments_for_hit(HITId='3R0WOCG21N9NNMH96NQNG98SB7WUDM', AssignmentStatuses=['Submitted'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def approve_all_submitted_assignments(client):\n",
+    "    for id in [h['HITId'] for h in client.list_hits()['HITs']]:\n",
+    "        lst = client.list_assignments_for_hit(HITId=id, AssignmentStatuses=['Submitted'])\n",
+    "        for aid in [a[\"AssignmentId\"] for a in lst[\"Assignments\"]]:\n",
+    "            client.approve_assignment(AssignmentId=aid)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "approve_all_submitted_assignments(client)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/user_studies/sickness_scores/Debrief.jsx

@@ -0,0 +1,83 @@
+import React from 'react';
+import {Link} from 'react-router';
+import MuiThemeProvider from 'material-ui/styles/MuiThemeProvider';
+import RaisedButton from 'material-ui/RaisedButton';
+import TextField from 'material-ui/TextField';
+
+export default class Debrief extends React.Component {
+  constructor() {
+    super();
+    this.handleChange = this.handleChange.bind(this);
+    this.start_time = new Date();
+    window.psiTurk.recordTrialData({
+      'mark': "debrief_start",
+      'time': this.start_time.valueOf()
+    });
+  }
+
+  finish(answer) {
+    window.psiTurk.recordTrialData({
+      'mark': "debrief_end",
+      'answer': answer,
+      'text': this.text,
+      'time': new Date().valueOf(),
+      'response_time': new Date() - this.start_time
+    });
+
+    psiTurk.saveData({
+      success: function(){
+          psiTurk.completeHIT();
+      },
+      error: this.prompt_resubmit
+    });
+  }
+
+  handleChange(event) {
+    this.text = event.target.value;
+  }
+
+  render() {
+    return (
+      <MuiThemeProvider>
+        <div id="container-instructions">
+
+        	<h1>Debriefing</h1>
+
+        	<hr/>
+
+            <p>Thank you for your participation in our study!  Your anonymous data makes an
+            important contribution to our understanding of human machine interaction. </p>
+
+          <p>If you have any questions about this research, you may contact slund1@cs.washington.edu.</p>
+            <div style={{textAlign: "center"}}>
+            <TextField style={{width: "400px"}}
+                hintText="Comments"
+                multiLine={true}
+                rows={2}
+                rowsMax={8}
+                onChange={this.handleChange}
+              />
+          </div>
+          <br/>
+        	<div className="instructions well">
+
+            <p>I feel that I have been adequately debriefed about the nature
+    					of the study.  The investigator has explained the purposes of the
+    					research to me, and I feel that any questions I have asked were
+    					satisfactorily answered.</p>
+
+        	    <script type="text/javascript">
+        	    //console.log(psiTurk.getInstructionIndicator())
+        	    </script>
+
+        	</div>
+          <div style={{textAlign: "center"}}>
+          <RaisedButton onClick={()=>this.finish("agree")} label="Yes, I agree. Complete this HIT" primary={true} /><br/><br/>
+          <RaisedButton onClick={()=>this.finish("questions")} label="No, please withhold my data. I will contact the experimenter with questions." />
+          </div>
+
+        </div>
+      </MuiThemeProvider>
+    );
+  }
+}

docs/user_studies/sickness_scores/Instructions.jsx

@@ -0,0 +1,53 @@
+import React from 'react';
+import {hashHistory} from 'react-router';
+import RaisedButton from 'material-ui/RaisedButton';
+
+export default class Instructions extends React.Component {
+  constructor() {
+    super();
+    this.next_page = this.next_page.bind(this);
+
+    this.start_time = new Date().getTime();
+    window.psiTurk.recordTrialData({
+      'mark': "instructions_start",
+      'condition': condition,
+      'time': this.start_time.valueOf()
+    });
+  }
+
+  next_page() {
+    window.psiTurk.recordTrialData({
+      'mark': "instructions_stop",
+      'time': new Date().valueOf(),
+      'condition': condition,
+      'response_time': new Date() - this.start_time
+    });
+
+    hashHistory.push("/questions");
+    // if (condition === 0) hashHistory.push("/allocate1");
+    // else if (condition === 1) hashHistory.push("/allocate2");
+  }
+
+  render() {
+    return (
+      <div id="container-instructions">
+      	<h1>Instructions</h1>
+      	<hr/>
+
+      	<div className="instructions well">
+          You will be asked to allocate blame for a person's "sickness score",
+          where 0 is healthy and higher numbers mean more sickness. There are
+          <i> 4 different ways</i> to measure sickness (A, B, C and D). There
+          are also <i>3 different people</i> for each score. This leads to 12
+          total questions. Each question should not take very long to
+          complete, the goal is simply for you to assign blame among a person's
+          symptoms in a way you consider the most intuitive.
+      	</div>
+
+        <div style={{textAlign: "center"}}>
+          <RaisedButton label="Next >" primary={true} onClick={this.next_page} />
+        </div>
+      </div>
+    );
+  }
+}

docs/user_studies/sickness_scores/Main.jsx

@@ -0,0 +1,26 @@
+import React from 'react'
+import {Router, Route, hashHistory} from 'react-router'
+import MuiThemeProvider from 'material-ui/styles/MuiThemeProvider'
+import Instructions from './Instructions'
+import Questions from './Questions'
+import Debrief from './Debrief'
+
+export default class Main extends React.Component {
+  constructor() {
+    super();
+  }
+
+  render() {
+    return (
+      <MuiThemeProvider>
+        <div>
+          <Router history={hashHistory}>
+            <Route path="/" component={Instructions} />
+            <Route path="/questions" component={Questions} />
+            <Route path="/debrief" component={Debrief} />
+          </Router>
+        </div>
+      </MuiThemeProvider>
+    );
+  }
+}

docs/user_studies/sickness_scores/Questions.jsx

@@ -0,0 +1,337 @@
+import React from 'react';
+import {Link, hashHistory} from 'react-router';
+import MuiThemeProvider from 'material-ui/styles/MuiThemeProvider';
+import RaisedButton from 'material-ui/RaisedButton';
+import TextField from 'material-ui/TextField';
+
+export default class QuestionA1 extends React.Component {
+  constructor() {
+    super();
+    this.state = {
+      fever: 0,
+      cough: 0,
+      headache: 0,
+      person: 0,
+      score: 0
+    };
+    this.last_time = new Date().getTime();
+    this.handleChange = this.handleChange.bind(this);
+
+    this.symptoms = [
+      {
+        'fever': true,
+        'cough': true,
+        'headache': true
+      },
+      {
+        'fever': false,
+        'cough': true,
+        'headache': true
+      },
+      {
+        'fever': false,
+        'cough': false,
+        'headache': true
+      }
+    ]
+
+    this.score_names = ["A", "B", "C", "D"];
+    this.score_methods = [
+      { // XOR
+        "true true": 4,
+        "false true": 8,
+        "false false": 0
+      },
+      { // AND
+        "true true": 10,
+        "false true": 2,
+        "false false": 0
+      },
+      { // OR
+        "true true": 10,
+        "false true": 8,
+        "false false": 0
+      },
+      { // SUM
+        "true true": 4,
+        "false true": 2,
+        "false false": 0
+      }
+    ];
+
+
+    window.psiTurk.recordTrialData({
+      'mark': "question"+this.score_names[this.state.score]+this.person+"_start",
+      'time': this.last_time.valueOf()
+    });
+  }
+
+  handleChange(event) {
+    if (event.target.value !== undefined) {
+      var data = {};
+      data[event.target.name] = event.target.value;
+      this.setState(data);
+    }
+  }
+
+  saveAnswers() {
+    if (this.state.person != 2 && parseInt(this.state.fever) + parseInt(this.state.cough) + parseInt(this.state.headache) === 0) {
+      alert("Please consider carefully how to assign blame among the symptoms before submitting.");
+    } else {
+      window.psiTurk.recordTrialData({
+        'mark': "question"+this.score_names[this.state.score]+this.state.person+"_stop",
+        'fever': this.symptoms[this.state.person]['fever'],
+        'cough': this.symptoms[this.state.person]['cough'],
+        'headache': this.symptoms[this.state.person]['headache'],
+        'fever_credit': parseInt(this.state.fever),
+        'cough_credit': parseInt(this.state.cough),
+        'headache_credit': parseInt(this.state.headache),
+        'time': new Date().valueOf(),
+        'condition': condition,
+        'response_time': new Date().getTime() - this.last_time
+      });
+
+      this.state.fever = 0;
+      this.state.cough = 0;
+      this.state.headache = 0;
+
+      if (this.state.person < 2) {
+        this.state.person++;
+      } else if (this.state.score < 3) {
+        this.state.person = 0;
+        this.state.score++;
+      } else {
+        hashHistory.push("/debrief");
+      }
+      this.setState(this.state);
+      this.last_time = new Date().getTime();
+    }
+  }
+
+  render() {
+
+    var fever = this.symptoms[this.state.person]['fever'];
+    var cough = this.symptoms[this.state.person]['cough'];
+
+    var interaction_effect_rule;
+    var interaction_effect_result;
+    if (this.state.score == 0) {
+      interaction_effect_rule = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            If they have a fever <i>OR</i> a cough but not both:
+          </td>
+          <td>
+            +6 points
+          </td>
+        </tr>
+      );
+
+      if ((fever || cough) && !(fever && cough)) {
+        interaction_effect_result = (
+          <tr>
+            <td style={{textAlign: "right", padding: "3px"}}>
+              They have a fever <i>OR</i> a cough but not both:
+            </td>
+            <td>
+              <b>+6 points</b>
+            </td>
+          </tr>
+        );
+      }
+    } else if (this.state.score == 1) {
+      interaction_effect_rule = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            If they have a fever <i>AND</i> a cough:
+          </td>
+          <td>
+            +6 points
+          </td>
+        </tr>
+      );
+
+      if (fever && cough) {
+        interaction_effect_result = (
+          <tr>
+            <td style={{textAlign: "right", padding: "3px"}}>
+              They have a fever <i>AND</i> a cough:
+            </td>
+            <td>
+              <b>+6 points</b>
+            </td>
+          </tr>
+        );
+      }
+    } else if (this.state.score == 2) {
+      interaction_effect_rule = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            If they have a fever <i>OR</i> a cough:
+          </td>
+          <td>
+            +6 points
+          </td>
+        </tr>
+      );
+
+      if (fever || cough) {
+        interaction_effect_result = (
+          <tr>
+            <td style={{textAlign: "right", padding: "3px"}}>
+              They have a fever <i>OR</i> a cough:
+            </td>
+            <td>
+              <b>+6 points</b>
+            </td>
+          </tr>
+        );
+      }
+    }
+
+    var fever_effect_result;
+    if (fever) {
+      fever_effect_result = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            They have a fever:
+          </td>
+          <td>
+            <b>+2 points</b>
+          </td>
+        </tr>
+      );
+    }
+    var cough_effect_result;
+    if (cough) {
+      cough_effect_result = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            They have a cough:
+          </td>
+          <td>
+            <b>+2 points</b>
+          </td>
+        </tr>
+      );
+    }
+
+    if (!fever && !cough) {
+      fever_effect_result = (
+        <tr>
+          <td style={{textAlign: "right", padding: "3px"}}>
+            They have neither a fever nor a cough.
+          </td>
+          <td>
+
+          </td>
+        </tr>
+      );
+    }
+
+    var total_score = this.score_methods[this.state.score][fever + " " + cough];
+
+    return (
+      <MuiThemeProvider>
+        <div id="container-instructions">
+
+        	<h2>Assign blame among symptoms (score {this.score_names[this.state.score]}, person {this.state.person+1})</h2>
+
+        	<hr/>
+
+        	<div className="instructions well">
+
+              <p>"<b>Sickness score {this.score_names[this.state.score]}</b>" is computed in the following manner:</p>
+
+              <div style={{textAlign: "center"}}>
+              <table style={{display: "inline-block", textAlign: "left"}}><tbody>
+                <tr>
+                  <td style={{textAlign: "right", padding: "3px"}}>
+                    If they have a fever:
+                  </td>
+                  <td>
+                    +2 points
+                  </td>
+                </tr>
+                <tr>
+                  <td style={{textAlign: "right", padding: "3px"}}>
+                    If they have a cough:
+                  </td>
+                  <td>
+                    +2 points
+                  </td>
+                </tr>
+                {interaction_effect_rule}
+              </tbody></table>
+              </div>
+              <br/>
+              <b>Person {this.state.person+1}</b> has the following symptoms:<br/>
+              <div style={{textAlign: "center", marginTop: "-20px"}}>
+              <table style={{display: "inline-block", textAlign: "left"}}><tbody>
+                <tr>
+                  <td style={{textAlign: "right", padding: "3px"}}>
+                    Fever:
+                  </td>
+                  <td style={{fontWeight: "bold", color: "#990000"}}>
+                    {this.symptoms[this.state.person]['fever'] ? 'YES' : 'NO'}
+                  </td>
+                </tr>
+                <tr>
+                  <td style={{textAlign: "right", padding: "3px"}}>
+                    Cough:
+                  </td>
+                  <td style={{fontWeight: "bold", color: "#990000"}}>
+                  {this.symptoms[this.state.person]['cough'] ? 'YES' : 'NO'}
+                  </td>
+                </tr>
+                <tr>
+                  <td style={{textAlign: "right", padding: "3px"}}>
+                    Headache:
+                  </td>
+                  <td style={{fontWeight: "bold", color: "#990000"}}>
+                  {this.symptoms[this.state.person]['headache'] ? 'YES' : 'NO'}
+                  </td>
+                </tr>
+              </tbody></table>
+              </div>
+              This leads to a total sickness score {this.score_names[this.state.score]} value of <b>{total_score} points</b> because:<br/>
+              <div style={{textAlign: "center"}}>
+              <table style={{display: "inline-block", textAlign: "left"}}><tbody>
+                {fever_effect_result}
+                {cough_effect_result}
+                {interaction_effect_result}
+              </tbody></table>
+              </div>
+              <br/>
+              Using numbers please assign blame for their sickness score of <b>{total_score} points</b> among the following symptoms{this.state.person == 2 ? ' (zero blame is okay)' : ''}:<br/>
+
+            <br/>
+              <div style={{textAlign: "center"}}>
+              <table style={{display: "inline-block", textAlign: "left"}}><tbody>
+                <tr>
+                  <td style={{textAlign: "center", width: "150px"}}>
+                    <TextField name="fever" value={this.state.fever} onChange={this.handleChange} style={{width: "20px", marginLeft: 3, marginRight: 3}} /> point(s)<br/>
+                    Fever: <b style={{color: "#990000"}}>{this.symptoms[this.state.person]['fever'] ? 'YES' : 'NO'}</b>
+                  </td>
+                  <td style={{textAlign: "center", width: "150px"}}>
+                    <TextField name="cough" value={this.state.cough} onChange={this.handleChange} style={{width: "20px", marginLeft: 3, marginRight: 3}} /> point(s)<br/>
+                    Cough: <b style={{color: "#990000"}}>{this.symptoms[this.state.person]['cough'] ? 'YES' : 'NO'}</b>
+                  </td>
+                  <td style={{textAlign: "center", width: "150px"}}>
+                    <TextField name="headache" value={this.state.headache} onChange={this.handleChange} style={{width: "20px", marginLeft: 3}} /> point(s)<br/>
+                    Headache: <b style={{color: "#990000"}}>{this.symptoms[this.state.person]['headache'] ? 'YES' : 'NO'}</b>
+                  </td>
+                </tr>
+              </tbody></table>
+              </div>
+
+        	</div>
+          <div style={{textAlign: "center"}}>
+          <RaisedButton label={"Submit answer for score " + this.score_names[this.state.score] + ", person " + (this.state.person+1)} primary={true} onClick={()=>this.saveAnswers()} />
+          </div>
+
+        </div>
+      </MuiThemeProvider>
+    );
+  }
+}

docs/user_studies/sickness_scores/README.md

@@ -0,0 +1,41 @@
+# Exclusive OR function experiment based on sickness score
+
+```shell
+npm install
+npm build
+```
+
+Using a python 2 environment
+
+```
+pip install psiturk
+```
+
+Create a `~/.psiturkconfig` with your credentials:
+
+```
+[AWS Access]
+aws_access_key_id = XXXXXXXXXXXXXX
+aws_secret_access_key = XXXXXXXXXXXXXX
+aws_region = us-east-1
+
+[psiTurk Access]
+psiturk_access_key_id = XXXXXXXXXXXXXX
+psiturk_secret_access_id = XXXXXXXXXXXXXX
+```
+
+In `config.txt` replace the host name with the public name of the machine.
+
+In the current directory run PsiTurk
+
+```
+psiturk
+
+> server on
+> debug
+```
+
+Now you can test things and download results with
+```
+> download_datafiles
+```

docs/user_studies/sickness_scores/config.txt

@@ -0,0 +1,45 @@
+[HIT Configuration]
+title = Intuitive credit allocation experiment
+description = Allocate blame for sickness among three symptoms in a simple scenario.
+amt_keywords = explainable, interpretable, machine learning
+lifetime = 24
+us_only = true
+approve_requirement = 95
+contact_email_on_error = slund1@cs.washington.edu
+ad_group = Explainable testing
+psiturk_keywords = shap
+organization_name = University of Washington
+browser_exclude_rule = MSIE, mobile, tablet
+
+[Database Parameters]
+database_url = sqlite:///participants.db
+table_name = turkdemo
+
+[Server Parameters]
+host = 0.0.0.0
+port = 22363
+cutoff_time = 30
+logfile = server.log
+loglevel = 2
+debug = true
+login_username = examplename
+login_pw = examplepassword221s0982927998292900
+threads = auto
+secret_key = 'ksd9f98239s9df8skjkj2j32k09a0-k2lk32kl'
+#certfile = <path_to.crt>
+#keyfile = <path_to.key>
+
+[Task Parameters]
+experiment_code_version = 1.0
+num_conds = 1
+num_counters = 1
+
+[Shell Parameters]
+launch_in_sandbox_mode = true
+
+# If you are not using the psiturk ad server, set `use_psiturk_ad_server` to `false` and point `ad_location` to your proxy server <host> and <port>. Format the ad_location like this:
+#
+#   https://<host>:<port>/ad
+
+use_psiturk_ad_server = true
+ad_location = false

docs/user_studies/sickness_scores/eventdata.csv

@@ -0,0 +1,8 @@
+debugB9EJOF:debug2CU4FC,initialized,0,,1551550976525
+debugB9EJOF:debug2CU4FC,window_resize,0,"[1024, 746]",1551550976525
+debugCVL5VN:debug8MU7CL,initialized,0,,1551555460816
+debugCVL5VN:debug8MU7CL,window_resize,0,"[1024, 746]",1551555460816
+debugCVL5VN:debug8MU7CL,focus,40949,off,1551555501765
+debugCVL5VN:debug8MU7CL,focus,4268,on,1551555506033
+debugCVL5VN:debug8MU7CL,focus,15022,off,1551555521055
+debugCVL5VN:debug8MU7CL,focus,148,on,1551555521203

docs/user_studies/sickness_scores/index.jsx

@@ -0,0 +1,15 @@
+import React from 'react';
+import ReactDom from 'react-dom';
+import injectTapEventPlugin from 'react-tap-event-plugin';
+import Main from './Main';
+
+// Needed for onTouchTap for material-ui
+// http://stackoverflow.com/a/34015469/988941
+injectTapEventPlugin();
+
+// Save some globals for the inline scripts to access
+window.IML = {
+  Main: Main,
+  React: React,
+  ReactDom: ReactDom
+};

docs/user_studies/sickness_scores/package.json

@@ -0,0 +1,30 @@
+{
+  "name": "iml-sickness-score-experiment",
+  "version": "0.1.0",
+  "description": "Measure how people explain a sickness score.",
+  "main": "index.jsx",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "dev": "node_modules/.bin/webpack --content-base build/",
+    "build": "node_modules/.bin/webpack"
+  },
+  "author": "Scott Lundberg",
+  "repository": "https://github.com/interpretable-ml/benchmark/experiments/sickness-score",
+  "license": "MIT",
+  "dependencies": {
+    "d3": "^4",
+    "lodash": "^4",
+    "material-ui": "^0.16",
+    "react": "^15",
+    "react-dom": "^15",
+    "react-router": "^3",
+    "react-tap-event-plugin": "^2"
+  },
+  "devDependencies": {
+    "babel-core": "^6",
+    "babel-loader": "^6",
+    "babel-preset-es2015": "^6",
+    "babel-preset-react": "^6",
+    "webpack": "^2"
+  }
+}

docs/user_studies/sickness_scores/static/css/style.css

@@ -0,0 +1,77 @@
+
+body {
+    padding:0px;
+    margin: 0px;
+    background-color: white;
+    color: black;
+    font-weight: 300;
+    font-size: 13pt;
+}
+
+
+/* text styling */
+strong {
+  font-weight: 600;
+}
+
+.warm {
+  color: steelblue;
+  text-align: justify;
+}
+
+.cool {
+  color: #ccccff;
+}
+
+h1 {
+  margin-top: 0px;
+}
+
+
+/* these are all the same for now, but easy to modify individually */
+#container-not-an-ad, #container-error, #container-exp, #container-consent, #container-instructions, #container-questionnaire {
+    background: white;
+    margin: 30px;
+}
+
+/* ad.html  - the ad that people view first */
+#adlogo {
+    width: 140px;
+    padding: 2px;
+    border: 1px solid #ccc;
+    margin-right: 1em;
+}
+
+/* consent.html - the consent form */
+#consent {
+  margin: 0 auto;
+  margin-top: 0;
+  width: 800px;
+  font-size: 100%;
+}
+
+.legal {
+  text-align: justify;
+  font-size: 11pt;
+  line-height: 1.1em;
+}
+
+#trial {
+  margin: 0 auto;
+  width: 800px;
+  text-align: center;
+}
+
+#query {
+  color: darkgray;
+}
+
+.question {
+  margin-bottom: 30px;
+}
+
+/* errors */
+#error img {
+  padding-right: 10px;
+  padding-top: 15px;
+}