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Commit e2d3bfad authored by Davis King's avatar Davis King
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Moved all the graph tools onto their own page.

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docs/docs/algorithms.xml
View file @ e2d3bfad
......@@ -60,26 +60,6 @@
<item>distance_to_rect_edge</item>
</sub>
</item>
<item nolink="true">
<name>Graph Utilities</name>
<sub>
<item>graph_contains_directed_cycle</item>
<item>graph_has_symmetric_edges</item>
<item>graph_contains_undirected_cycle</item>
<item>create_moral_graph</item>
<item>triangulate_graph_and_find_cliques</item>
<item>graph_contains_length_one_cycle</item>
<item>find_connected_nodes</item>
<item>graph_is_connected</item>
<item>is_clique</item>
<item>is_maximal_clique</item>
<item>copy_graph_structure</item>
<item>copy_graph</item>
<item>edge</item>
<item>is_join_tree</item>
<item>create_join_tree</item>
</sub>
</item>
<item>hsort_array</item>
<item>isort_array</item>
<item>put_in_range</item>
......@@ -630,75 +610,6 @@
</component>
<!-- ************************************************************************* -->
<component>
<name>edge</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> or
<a href="containers.html#directed_graph">directed_graph</a> object and a
pair of indices. It returns a reference to the edge object between the two nodes
with the given indices.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>is_join_tree</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes two <a href="containers.html#graph">graph</a> objects and
checks if the second of the two graphs is a valid join tree (aka tree decomposition)
of the first graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>create_join_tree</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> object and
creates a join tree for that graph. Or in other words, this function finds a
tree decomposition of the given graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>graph_contains_directed_cycle</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function checks a <a href="containers.html#directed_graph">directed_graph</a> for directed cycles.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>graph_has_symmetric_edges</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function checks if a <a href="containers.html#directed_graph">directed_graph</a>
has a pair of nodes with just one edge between them. If so then it
does not have symmetric edges.
</description>
</component>
<!-- ************************************************************************* -->
<component>
......@@ -751,141 +662,6 @@
</component>
<!-- ************************************************************************* -->
<component>
<name>triangulate_graph_and_find_cliques</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> and
turns it into a chordal graph. It also returns a
<a href="containers.html#set">set</a> that contains
all the cliques present in the chordal graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>create_moral_graph</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#directed_graph">directed_graph</a>
and returns the moralized version of the graph in the form of a
<a href="containers.html#graph">graph</a> object.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>graph_contains_length_one_cycle</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a>
or <a href="containers.html#directed_graph">directed_graph</a> object and
returns true if and only if the graph contains a node that has an edge that
links back to itself.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>find_connected_nodes</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a node from a <a href="containers.html#graph">graph</a>
or <a href="containers.html#directed_graph">directed_graph</a> object and a
<a href="containers.html#set">set</a> of unsigned longs. It finds all the
nodes in the given graph that are connected to the given node by an
undirected path and returns them in the set (also note that the
original query node is also returned in this set).
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>graph_is_connected</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> or
<a href="containers.html#directed_graph">directed_graph</a> object and
determines if the graph is connected. That is, it returns true if and only if
there is an undirected path between any two nodes in the given graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>is_clique</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> and a
<a href="containers.html#set">set</a> of node index values and checks
if the specified set of nodes is a clique in the graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>copy_graph</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> or
<a href="containers.html#directed_graph">directed_graph</a> and
makes a copy of it.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>copy_graph_structure</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> or
<a href="containers.html#directed_graph">directed_graph</a> and copies
its structure to another graph or directed_graph object. The only
restriction is that you can't copy the structure of a graph into a
directed_graph. The three other possible combinations are allowed
however.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>is_maximal_clique</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function takes a <a href="containers.html#graph">graph</a> and a
<a href="containers.html#set">set</a> of node index values and checks
if the specified set of nodes is a maximal clique in the graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
......@@ -1162,18 +938,6 @@
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>graph_contains_undirected_cycle</name>
<file>dlib/graph_utils.h</file>
<spec_file link="true">dlib/graph_utils/graph_utils_abstract.h</spec_file>
<description>
This function checks a <a href="containers.html#directed_graph">directed_graph</a> for undirected cycles.
</description>
</component>
<!-- ************************************************************************* -->
</components>
......
docs/docs/graph_tools.xml 0 → 100644
View file @ e2d3bfad
This diff is collapsed.
docs/docs/main_menu.xml
View file @ e2d3bfad
......@@ -10,6 +10,11 @@
<link>algorithms.html</link>
<chm_sub>algorithms.xml</chm_sub>
</item>
<item>
<name>Graph Tools</name>
<link>graph_tools.html</link>
<chm_sub>graph_tools.xml</chm_sub>
</item>
<item>
<name>Optimization</name>
<link>optimization.html</link>
......
docs/docs/ml.xml
View file @ e2d3bfad
......@@ -140,27 +140,6 @@ Davis E. King. <a href="http://www.jmlr.org/papers/volume10/king09a/king09a.pdf"
<name>Semi-Supervised</name>
<item>linear_manifold_regularizer</item>
<item>discriminant_pca</item>
<item nolink="true">
<name>manifold_regularization_tools</name>
<sub>
<item>sample_pair</item>
<item>ordered_sample_pair</item>
<item>find_percent_shortest_edges_randomly</item>
<item>find_k_nearest_neighbors</item>
<item>find_approximate_k_nearest_neighbors</item>
<item>remove_short_edges</item>
<item>remove_duplicate_edges</item>
<item>remove_long_edges</item>
<item>remove_percent_longest_edges</item>
<item>remove_percent_shortest_edges</item>
<item>squared_euclidean_distance</item>
<item>use_weights_of_one</item>
<item>use_gaussian_weights</item>
<item>is_ordered_by_index</item>
<item>find_neighbor_ranges</item>
<item>convert_unordered_to_ordered</item>
</sub>
</item>
</section>
<section>
<name>Feature Selection</name>
......@@ -277,234 +256,6 @@ Davis E. King. <a href="http://www.jmlr.org/papers/volume10/king09a/king09a.pdf"
<components>
<!-- ************************************************************************* -->
<component>
<name>use_gaussian_weights</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/function_objects_abstract.h</spec_file>
<description>
This is a simple function object that takes a single argument
which should be an object similar to <a href="#sample_pair">sample_pair</a>.
</description>
<examples>
<example>linear_manifold_regularizer_ex.cpp.html</example>
</examples>
</component>
<!-- ************************************************************************* -->
<component>
<name>use_weights_of_one</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/function_objects_abstract.h</spec_file>
<description>
This is a simple function object that takes a single argument
and always returns 1
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>squared_euclidean_distance</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/function_objects_abstract.h</spec_file>
<description>
This is a simple function object that computes squared euclidean distance
between two <a href="containers.html#matrix">matrix</a> objects.
</description>
<examples>
<example>linear_manifold_regularizer_ex.cpp.html</example>
</examples>
</component>
<!-- ************************************************************************* -->
<component>
<name>find_k_nearest_neighbors</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a function which finds all the k nearest neighbors of a set of points and outputs
the result as a vector of <a href="#sample_pair">sample_pair</a> objects. It takes O(n^2) where
n is the number of data samples. A faster approximate version is provided by
<a href="#find_approximate_k_nearest_neighbors">find_approximate_k_nearest_neighbors</a>.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>remove_short_edges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a simple function for removing edges with a small distance value from
a vector of <a href="#sample_pair">sample_pair</a> or <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>is_ordered_by_index</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This function checks if a vector of <a href="#sample_pair">sample_pair</a> or
<a href="#ordered_sample_pair">ordered_sample_pair</a> objects is in sorted
order according to their index values.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>convert_unordered_to_ordered</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This function takes a graph, defined by a vector of
<a href="#sample_pair">sample_pair</a> objects and converts it into the equivalent
graph defined by a vector of <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>find_neighbor_ranges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This function takes a graph, defined by a vector of
<a href="#ordered_sample_pair">ordered_sample_pair</a> objects, and finds the
ranges that contain the edges for each node in the graph. The output therefore
lets you easily locate the neighbors of any node in the graph.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>remove_duplicate_edges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a simple function for removing duplicate edges (i.e. edges that compare equal
according to ==) from
a vector of <a href="#sample_pair">sample_pair</a> or <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>remove_percent_shortest_edges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a simple function for removing edges with a small distance value from
a vector of <a href="#sample_pair">sample_pair</a> or <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>remove_long_edges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a simple function for removing edges with a large distance value from
a vector of <a href="#sample_pair">sample_pair</a> or <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>remove_percent_longest_edges</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This is a simple function for removing edges with a large distance value from
a vector of <a href="#sample_pair">sample_pair</a> or <a href="#ordered_sample_pair">ordered_sample_pair</a> objects.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>find_approximate_k_nearest_neighbors</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This function is a simple approximate form of <a href="#find_k_nearest_neighbors">find_k_nearest_neighbors</a>.
Instead of checking all possible edges it randomly samples a large number of them and then performs
exact k-nearest-neighbors on that randomly selected subset.
</description>
</component>
<!-- ************************************************************************* -->
<component>
<name>find_percent_shortest_edges_randomly</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/graph_creation_abstract.h</spec_file>
<description>
This function is a simple approximate form of <a href="#find_k_nearest_neighbors">find_k_nearest_neighbors</a>.
Instead of checking all possible edges it randomly samples a large number of them and
then returns the best ones.
</description>
<examples>
<example>linear_manifold_regularizer_ex.cpp.html</example>
</examples>
</component>
<!-- ************************************************************************* -->
<component>
<name>sample_pair</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/sample_pair_abstract.h</spec_file>
<description>
This object is intended to represent an edge in an undirected graph
which has data samples at its vertices. Therefore, it is the undirected version
of <a href="#ordered_sample_pair">ordered_sample_pair</a>.
</description>
<examples>
<example>linear_manifold_regularizer_ex.cpp.html</example>
</examples>
</component>
<!-- ************************************************************************* -->
<component>
<name>ordered_sample_pair</name>
<file>dlib/manifold_regularization.h</file>
<spec_file link="true">dlib/manifold_regularization/ordered_sample_pair_abstract.h</spec_file>
<description>
This object is intended to represent an edge in a directed graph
which has data samples at its vertices. Therefore, it is the directed version
of <a href="#sample_pair">sample_pair</a>.
</description>
</component>
<!-- ************************************************************************* -->
<component>
......@@ -923,7 +674,7 @@ Davis E. King. <a href="http://www.jmlr.org/papers/volume10/king09a/king09a.pdf"
However, it would be nice to be able to benefit from unlabeled data.
The idea of manifold regularization is to extract useful information from
unlabeled data by first defining which data samples are "close" to each other
(perhaps by using their 3 <a href="#find_k_nearest_neighbors">nearest neighbors</a>)
(perhaps by using their 3 <a href="graph_tools.html#find_k_nearest_neighbors">nearest neighbors</a>)
and then adding a term to
the above function that penalizes any decision rule which produces
different outputs on data samples which we have designated as being close.
......
docs/docs/term_index.xml
View file @ e2d3bfad
......@@ -141,9 +141,9 @@
<term link="algorithms.html#disjoint_subsets" name="union-find"/>
<term file="algorithms.html" name="rectangle"/>
<term file="algorithms.html" name="border_enumerator"/>
<term file="algorithms.html" name="edge"/>
<term file="algorithms.html" name="is_join_tree"/>
<term file="algorithms.html" name="create_join_tree"/>
<term file="graph_tools.html" name="edge"/>
<term file="graph_tools.html" name="is_join_tree"/>
<term file="graph_tools.html" name="create_join_tree"/>
<term file="algorithms.html" name="set_intersection_size"/>
<term file="algorithms.html" name="set_intersection"/>
<term file="algorithms.html" name="set_union"/>
......@@ -157,19 +157,19 @@
<term file="algorithms.html" name="qsort_array"/>
<term file="algorithms.html" name="rand"/>
<term link="algorithms.html#rand" name="Mersenne Twister"/>
<term file="algorithms.html" name="graph_contains_undirected_cycle"/>
<term file="algorithms.html" name="graph_has_symmetric_edges"/>
<term file="algorithms.html" name="graph_contains_directed_cycle"/>
<term file="algorithms.html" name="copy_graph_structure"/>
<term file="algorithms.html" name="copy_graph"/>
<term file="algorithms.html" name="create_moral_graph"/>
<term file="algorithms.html" name="triangulate_graph_and_find_cliques"/>
<term file="algorithms.html" name="graph_contains_length_one_cycle"/>
<term file="algorithms.html" name="find_connected_nodes"/>
<term file="algorithms.html" name="graph_is_connected"/>
<term file="algorithms.html" name="is_clique"/>
<term file="algorithms.html" name="is_maximal_clique"/>
<term file="graph_tools.html" name="graph_contains_undirected_cycle"/>
<term file="graph_tools.html" name="graph_has_symmetric_edges"/>
<term file="graph_tools.html" name="graph_contains_directed_cycle"/>
<term file="graph_tools.html" name="copy_graph_structure"/>
<term file="graph_tools.html" name="copy_graph"/>
<term file="graph_tools.html" name="create_moral_graph"/>
<term file="graph_tools.html" name="triangulate_graph_and_find_cliques"/>
<term file="graph_tools.html" name="graph_contains_length_one_cycle"/>
<term file="graph_tools.html" name="find_connected_nodes"/>
<term file="graph_tools.html" name="graph_is_connected"/>
<term file="graph_tools.html" name="is_clique"/>
<term file="graph_tools.html" name="is_maximal_clique"/>
<term file="algorithms.html" name="square_root"/>
<term file="algorithms.html" name="vector"/>
<term file="algorithms.html" name="point"/>
......@@ -218,22 +218,22 @@
<term file="ml.html" name="svm_pegasos"/>
<term file="ml.html" name="empirical_kernel_map"/>
<term file="ml.html" name="sample_pair"/>
<term file="ml.html" name="ordered_sample_pair"/>
<term file="graph_tools.html" name="sample_pair"/>
<term file="graph_tools.html" name="ordered_sample_pair"/>
<term file="dlib/manifold_regularization/sample_pair_abstract.h.html" name="order_by_index"/>
<term file="dlib/manifold_regularization/sample_pair_abstract.h.html" name="order_by_distance"/>
<term file="dlib/manifold_regularization/sample_pair_abstract.h.html" name="order_by_distance_and_index"/>
<term file="ml.html" name="find_percent_shortest_edges_randomly"/>
<term file="ml.html" name="find_k_nearest_neighbors"/>
<term file="ml.html" name="remove_short_edges"/>
<term file="ml.html" name="remove_duplicate_edges"/>
<term file="ml.html" name="is_ordered_by_index"/>
<term file="ml.html" name="convert_unordered_to_ordered"/>
<term file="ml.html" name="find_neighbor_ranges"/>
<term file="ml.html" name="remove_long_edges"/>
<term file="ml.html" name="remove_percent_longest_edges"/>
<term file="ml.html" name="remove_percent_shortest_edges"/>
<term file="ml.html" name="find_approximate_k_nearest_neighbors"/>
<term file="graph_tools.html" name="find_percent_shortest_edges_randomly"/>
<term file="graph_tools.html" name="find_k_nearest_neighbors"/>
<term file="graph_tools.html" name="remove_short_edges"/>
<term file="graph_tools.html" name="remove_duplicate_edges"/>
<term file="graph_tools.html" name="is_ordered_by_index"/>
<term file="graph_tools.html" name="convert_unordered_to_ordered"/>
<term file="graph_tools.html" name="find_neighbor_ranges"/>
<term file="graph_tools.html" name="remove_long_edges"/>
<term file="graph_tools.html" name="remove_percent_longest_edges"/>
<term file="graph_tools.html" name="remove_percent_shortest_edges"/>
<term file="graph_tools.html" name="find_approximate_k_nearest_neighbors"/>
<term file="dlib/manifold_regularization/graph_creation_abstract.h.html" name="contains_duplicate_pairs"/>
<term name="max_index_plus_one">
<term link="dlib/manifold_regularization/graph_creation_abstract.h.html#max_index_plus_one" name="for graphs"/>
......@@ -245,9 +245,9 @@
<term file="dlib/svm/sparse_vector_abstract.h.html" name="assign"/>
<term file="ml.html" name="linear_manifold_regularizer"/>
<term file="ml.html" name="squared_euclidean_distance"/>
<term file="ml.html" name="use_weights_of_one"/>
<term file="ml.html" name="use_gaussian_weights"/>
<term file="graph_tools.html" name="squared_euclidean_distance"/>
<term file="graph_tools.html" name="use_weights_of_one"/>
<term file="graph_tools.html" name="use_gaussian_weights"/>
<term file="dlib/svm/empirical_kernel_map_abstract.h.html" name="empirical_kernel_map_error"/>
<term file="dlib/svm/empirical_kernel_map_abstract.h.html" name="convert_to_decision_function"/>
......
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