dafsa 1.0
Library for computing Deterministic Acyclic Finite State Automata (DAFSA)
License: MIT
Keywords: dafsa,dawg,finite state automata,deterministic acyclic finite state automaton,directed acyclic word graph

DAFSA
=====

DAFSA is a library for computing `Deterministic Acyclic Finite State
Automata <https://en.wikipedia.org/wiki/Deterministic_acyclic_finite_state_automaton>`__
(also known as “directed acyclic word graphs”, or DAWG). DAFSA are data
structures derived from `tries <https://en.wikipedia.org/wiki/Trie>`__
that allow to represent a set of sequences (typically character strings
or *n*-grams) in the form of a directed acyclic graph with a single
source vertex (the ``start`` symbol of all sequences) and at least one
sink edge (``final`` symbols, each pointed to by one or more sequences).
In the current implementation, a trait of each node expresses whether it
can be used a sink.

The primary difference between DAFSA and tries is that the latter
eliminates suffix and infix redundancy, as in the example of Figure 1
(from the linked Wikipedia article) storing the set of strings
``"tap"``, ``"taps"``, ``"top"``, and ``"tops"``. Even though DAFSAs
cannot be used to store precise frequency information, given that
multiple paths might reach the same terminal node, they still allow to
estimate the sampling frequency; being acyclic, they can also reject any
sequence not included in the training. Fuzzy extensions will allow to
estimate the sampling probability of unobserved sequences.

.. figure:: https://raw.githubusercontent.com/tresoldi/dafsa/master/figures/trie-vs-dafsa.png
   :alt: Trie vs. DAFSA

   Trie vs. DAFSA

This data structure is a special case of a finite state recognizer that
acts as a deterministic finite state automaton, as it recognizes all and
only the sequences it was built upon. Frequently used in computer
science for the space-efficient storage of sets of sequences without
common compression techniques, such as dictionary or entropy types, or
without probabilistic data structures, such as Bloom filters, the
automata generated by this library are intended for linguistic
exploration, and extend published models by allowing to approximate
probability of random observation by carrying information on the weight
of each graph edge.

Installation and usage
----------------------

The library can be installed as any standard Python library with
``pip``, and used as demonstrated in the following snippet:

In any standard Python environment, ``dafsa`` can be installed with:

.. code:: bash

   $ pip install dafsa

A ``conda`` package is also available, and can be installed (from the
``tresoldi`` channel) with:

.. code:: bash

   $ conda install -c tresoldi dafsa

Detailed instructions on how to use the library can be found in the
`official
documentation <https://dafsa.readthedocs.io/en/latest/quickstart.html>`__.
For most purposes, it is enough to pass a list of sequences to the
``DAFSA`` object:

.. code:: python

   >>> from dafsa import DAFSA
   >>> print(DAFSA(["dib", "tip", "tips", "top"]))
   DAFSA with 8 nodes and 9 edges (4 inserted sequences)
     +-- #0: 0(#1/4:<d>/1|#4/4:<t>/3) [('t', 4), ('d', 1)]
     +-- #1: n(#2/1:<i>/1) [('i', 2)]
     +-- #2: n(#3/1:<b>/1) [('b', 3)]
     +-- #3: F() []
     +-- #4: n(#5/3:<i>/2|#8/3:<o>/1) [('i', 5), ('o', 8)]
     +-- #5: n(#6/2:<p>/2) [('p', 6)]
     +-- #6: F(#3/2:
/1) [('s', 3)]
     +-- #8: n(#3/1:<p>/1) [('p', 3)]

Full documentation is available `at
ReadTheDocs.io <https://dafsa.readthedocs.io>`__.

Showcase
--------

-  Basic example:

.. figure:: https://raw.githubusercontent.com/tresoldi/dafsa/master/figures/example.png
   :alt: First example

   First example

-  Output can be textual, GML, DOT, or (via dot and third-party
   software) PNG, PDF, ASCII-art and Unicode-art:

.. figure:: https://raw.githubusercontent.com/tresoldi/dafsa/master/figures/dna.png
   :alt: DNA example

   DNA example

::

                                      G                                A
                                  +---------------------+          +----------+
                                  |                     v          |          v
         #====#  C   +---+  G   +---+  C   +---+  G   +---+  A   +---+  T   +---+  A   #===#
     +-- H 0  H ---> | 5 | ---> | 6 | ---> | 7 | ---> | 8 | ---> | 9 | ---> | 3 | ---> H 4 H
     |   #====#      +---+      +---+      +---+      +---+      +---+      +---+      #===#
     |     |    A                                                             ^
     | G   +-----------+                                                      |
     |                 v                                                      |
     |   +----+  G   +---+  A   +---+  T                                      |
     +-> | 20 | ---> | 1 | ---> | 2 | ----------------------------------------+
         +----+      +---+      +---+

::

                                      G                                A
                                  ┌─────────────────────┐          ┌──────────┐
                                  │                     ▼          │          ▼
         ╔════╗  C   ┌───┐  G   ┌───┐  C   ┌───┐  G   ┌───┐  A   ┌───┐  T   ┌───┐  A   ╔═══╗
     ┌── ║ 0  ║ ───▶ │ 5 │ ───▶ │ 6 │ ───▶ │ 7 │ ───▶ │ 8 │ ───▶ │ 9 │ ───▶ │ 3 │ ───▶ ║ 4 ║
     │   ╚════╝      └───┘      └───┘      └───┘      └───┘      └───┘      └───┘      ╚═══╝
     │     │    A                                                             ▲
     │ G   └───────────┐                                                      │
     │                 ▼                                                      │
     │   ┌────┐  G   ┌───┐  A   ┌───┐  T                                      │
     └─▶ │ 20 │ ───▶ │ 1 │ ───▶ │ 2 │ ────────────────────────────────────────┘
         └────┘      └───┘      └───┘

-  With or without single-path joining:

.. figure:: https://raw.githubusercontent.com/tresoldi/dafsa/master/figures/phonemes.png
   :alt: Phoneme example

   Phoneme example

.. figure:: https://raw.githubusercontent.com/tresoldi/dafsa/master/figures/reduced_phonemes.png
   :alt: Reduced Phoneme example

   Reduced Phoneme example

Changelog
---------

Version 0.6:

-  Documentation improvements following JOSS review
-  Fixed bug where node finality was not considered in minimization

Version 0.5.1:

-  Minor changes in preparation for submission (including tagged
   release)

Version 0.5:

-  Improvements in speed, particularly in the ``__eq__()`` method of
   ``DAFSANode`` and the ``_minimize()`` method of ``DAFSA``. The
   computation of a DAFSA for the contents of ``/usr/share/dict/words``
   in the test machine (99,171 sequences) is now performed in under 8
   minutes.
-  Added code from Daciuk’s packages in an extra directory, along with
   notes on license

Version 0.4:

-  Full documentation for existing code
-  Added GML, PDF, and SVG export
-  Allow to access all options from command-line

Version 0.3:

-  Allow to join transitions in single sub-paths
-  Allows to export a DAFSA as a ``networkx`` graph
-  Preliminary documentation at
   `ReadTheDocs <https://dafsa.readthedocs.io>`__

Version 0.2.1:

-  Added support for segmented data

Version 0.2:

-  Added support for weighted edges and nodes
-  Added DOT export and Graphviz generation
-  Refined minimization method, which can be skipped if desired
   (resulting in a standard trie)
-  Added examples in the resources, also used for test data

Version 0.1:

-  First public release.

Roadmap
-------

After 1.0:

-  Preliminary generation of minimal regular expressions matching the
   contents of a DAFSA
-  Consider adding support for empty transitions (or depend on the user
   aligning those)
-  Work on options for nicer graphviz output (colors, widths, etc.)

Community guidelines
--------------------

While the author can be contacted directly for support, it is
recommended that third parties use GitHub standard features, such as
issues and pull requests, to contribute, report problems, or seek
support.

Contributing guidelines, including a code of conduct, can be found in
the CONTRIBUTING.md file.

Author and citation
-------------------

The library is developed by Tiago Tresoldi (tresoldi@shh.mpg.de).

The author has received funding from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation
programme (grant agreement No. \ `ERC Grant
#715618 <https://cordis.europa.eu/project/rcn/206320/factsheet/en>`__,
`Computer-Assisted Language Comparison <https://digling.org/calc/>`__.

If you use ``dafsa``, please cite it as:

   Tresoldi, Tiago (2020). DAFSA, a a library for computing
   Deterministic Acyclic Finite State Automata. Version 1.0. Jena.
   Available at: https://github.com/tresoldi/dafsa

In BibTeX:

.. code:: bibtex

   @misc{Tresoldi2020dafsa,
     author = {Tresoldi, Tiago},
     title = {DAFSA, a a library for computing Deterministic Acyclic Finite State Automata. Version 1.0.},
     howpublished = {\url{https://github.com/tresoldi/dafsa}},
     address = {Jena},
     year = {2020},
   }

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