diff --git a/joss.05759/10.21105.joss.05759.crossref.xml b/joss.05759/10.21105.joss.05759.crossref.xml new file mode 100644 index 0000000000..df5a7ba879 --- /dev/null +++ b/joss.05759/10.21105.joss.05759.crossref.xml @@ -0,0 +1,289 @@ + + + + 20231009T171236-138cc0c542a92013199af4288834c9a51805752c + 20231009171236 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 10 + 2023 + + + 8 + + 90 + + + + automata: A Python package for simulating and +manipulating automata + + + + Caleb + Evans + https://orcid.org/0009-0000-8896-6800 + + + Eliot W. + Robson + https://orcid.org/0000-0002-1476-6715 + + + + 10 + 09 + 2023 + + + 5759 + + + 10.21105/joss.05759 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.8419571 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/5759 + + + + 10.21105/joss.05759 + https://joss.theoj.org/papers/10.21105/joss.05759 + + + https://joss.theoj.org/papers/10.21105/joss.05759.pdf + + + + + + Automata, a hybrid system for computational +automata theory + Sutner + Implementation and application of +automata + 10.1007/3-540-44977-9_21 + 978-3-540-44977-5 + 2003 + Sutner, K. (2003). Automata, a hybrid +system for computational automata theory. In J.-M. Champarnaud & D. +Maurel (Eds.), Implementation and application of automata (pp. 221–227). +Springer Berlin Heidelberg. +https://doi.org/10.1007/3-540-44977-9_21 + + + Dk.brics.automaton – finite-state automata +and regular expressions for Java + Møller + 2021 + Møller, A. (2021). Dk.brics.automaton +– finite-state automata and regular expressions for Java. +https://www.brics.dk/automaton/ + + + Testing the equivalence of regular +languages + Almeida + Journal of Automata, Languages and +Combinatorics + 1/2 + 15 + 10.25596/jalc-2010-007 + 2010 + Almeida, M., Moreira, N., & Reis, +R. (2010). Testing the equivalence of regular languages. Journal of +Automata, Languages and Combinatorics, 15(1/2), 7–25. +https://doi.org/10.25596/jalc-2010-007 + + + The minimal deterministic finite-state +automaton for a finite language + Mihov + Finite-state techniques: Automata, +transducers and bimachines + 10.1017/9781108756945.011 + 2019 + Mihov, S., & Schulz, K. U. +(2019). The minimal deterministic finite-state automaton for a finite +language. In Finite-state techniques: Automata, transducers and +bimachines (pp. 253–278). Cambridge University Press. +https://doi.org/10.1017/9781108756945.011 + + + Compilers: Principles, techniques, and tools +(2nd edition) + Aho + 0321486811 + 2006 + Aho, A. V., Lam, M. S., Sethi, R., +& Ullman, J. D. (2006). Compilers: Principles, techniques, and tools +(2nd edition) (pp. 152–155). Addison-Wesley Longman Publishing Co., Inc. +ISBN: 0321486811 + + + An n log n algorithm for minimizing states in +a finite automaton + Hopcroft + Theory of machines and +computations + 10.1016/B978-0-12-417750-5.50022-1 + 978-0-12-417750-5 + 1971 + Hopcroft, J. (1971). An n log n +algorithm for minimizing states in a finite automaton. In Z. Kohavi +& A. Paz (Eds.), Theory of machines and computations (pp. 189–196). +Academic Press. +https://doi.org/10.1016/B978-0-12-417750-5.50022-1 + + + Auto-graded scaffolding exercises for +theoretical computer science + Jeff Erickson + 2023 ASEE annual conference & +exposition + 2023 + Jeff Erickson, E. W. R., Jason Xia, +& Solomon, B. (2023). Auto-graded scaffolding exercises for +theoretical computer science. 2023 ASEE Annual Conference & +Exposition. https://peer.asee.org/42347 + + + Damn cool algorithms: Levenshtein +automata + Johnson + Nick’s Blog + 2010 + Johnson, N. (2010). Damn cool +algorithms: Levenshtein automata. In Nick’s Blog. +http://blog.notdot.net/2010/07/Damn-Cool-Algorithms-Levenshtein-Automata + + + Fast pattern matching in +strings + Knuth + SIAM Journal on Computing + 2 + 6 + 10.1137/0206024 + 1977 + Knuth, D. E., Morris, J. H., Jr., +& Pratt, V. R. (1977). Fast pattern matching in strings. SIAM +Journal on Computing, 6(2), 323–350. +https://doi.org/10.1137/0206024 + + + Introduction to automata theory, languages, +and computation (3rd edition) + Hopcroft + 0321455363 + 2006 + Hopcroft, J. E., Motwani, R., & +Ullman, J. D. (2006). Introduction to automata theory, languages, and +computation (3rd edition). Addison-Wesley Longman Publishing Co., Inc. +ISBN: 0321455363 + + + Introduction to the theory of +computation + Sipser + 978-1-133-18781-3 + 2012 + Sipser, M. (2012). Introduction to +the theory of computation (pp. 45–47). Cengage Learning. +ISBN: 978-1-133-18781-3 + + + Construction of minimal deterministic finite +automata from biological motifs + Marschall + Theoretical Computer Science + 8 + 412 + 10.1016/j.tcs.2010.12.003 + 0304-3975 + 2011 + Marschall, T. (2011). Construction of +minimal deterministic finite automata from biological motifs. +Theoretical Computer Science, 412(8), 922–930. +https://doi.org/10.1016/j.tcs.2010.12.003 + + + Re-describing an algorithm by +Hopcroft + Knuutila + Theoretical Computer Science + 1 + 250 + 10.1016/S0304-3975(99)00150-4 + 0304-3975 + 2001 + Knuutila, T. (2001). Re-describing an +algorithm by Hopcroft. Theoretical Computer Science, 250(1), 333–363. +https://doi.org/10.1016/S0304-3975(99)00150-4 + + + A survey on regular expression matching for +deep packet inspection: Applications, algorithms, and hardware +platforms + Xu + IEEE Communications Surveys & +Tutorials + 4 + 18 + 10.1109/COMST.2016.2566669 + 2016 + Xu, C., Chen, S., Su, J., Yiu, S. M., +& Hui, L. C. K. (2016). A survey on regular expression matching for +deep packet inspection: Applications, algorithms, and hardware +platforms. IEEE Communications Surveys & Tutorials, 18(4), +2991–3029. +https://doi.org/10.1109/COMST.2016.2566669 + + + JFLAP: An interactive formal languages and +automata package + Rodger + 0763738344 + 2006 + Rodger, S. H. (2006). JFLAP: An +interactive formal languages and automata package. Jones; Bartlett +Publishers, Inc. ISBN: 0763738344 + + + + + + diff --git a/joss.05759/10.21105.joss.05759.jats b/joss.05759/10.21105.joss.05759.jats new file mode 100644 index 0000000000..7ef690023f --- /dev/null +++ b/joss.05759/10.21105.joss.05759.jats @@ -0,0 +1,526 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +5759 +10.21105/joss.05759 + +automata: A Python package for simulating and +manipulating automata + + + +https://orcid.org/0009-0000-8896-6800 + +Evans +Caleb + + + + +https://orcid.org/0000-0002-1476-6715 + +Robson +Eliot W. + + +* + + + +Independent Developer, USA + + + + +Department of Computer Science, University of Illinois, +Urbana, IL, USA + + + + +* E-mail: + + +16 +7 +2023 + +8 +90 +5759 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Python +automata + + + + + + Summary +

Automata are abstract machines used to represent models of + computation, and are a central object of study in theoretical computer + science + (J. + E. Hopcroft et al., 2006). Given an input string of characters + over a fixed alphabet, these machines either accept or reject the + string. A language corresponding to an automaton is the set of all + strings it accepts. Three important families of automata in increasing + order of generality are the following:

+ + +

Finite-state automata

+ + +

Pushdown automata

+ + +

Turing machines

+ + +

The automata package facilitates working + with these families by allowing simulation of reading input and + higher-level manipulation of the corresponding languages using + specialized algorithms.

+ + + Statement of need +

Automata are a core component of both computer science education + and research, seeing further theoretical work and applications in a + wide variety of areas such as computational biology + (Marschall, + 2011) and networking + (Xu et al., + 2016). Consequently, the manipulation of automata with software + packages has seen significant attention from researchers in the past. + The similarly named Mathematica package + Automata + (Sutner, + 2003) implements a number of algorithms for use with + finite-state automata, including regular expression conversion and + binary set operations. In Java, the Brics package + (Møller, + 2021) implements similar algorithms, while the JFLAP package + (Rodger, + 2006) places an emphasis on interactivity and simulation of + more general families of automata.

+

automata serves the demand for such a + package in the Python software ecosystem, implementing algorithms and + allowing for simulation of automata in a manner comparable to the + packages described previously. As a popular high-level language, + Python enables significant flexibility and ease of use that directly + benefits many users. The package includes a comprehensive test suite, + support for modern language features (including type annotations), and + has a large number of different automata, meeting the demands of users + across a wide variety of use cases. In particular, the target audience + is both researchers that wish to manipulate automata, and for those in + educational contexts to reinforce understanding about how these models + of computation function.

+ + + The <monospace>automata</monospace> package +

The API of the package is designed to mimic the formal mathematical + description of each automaton using built-in Python data structures + (such as sets and dicts). This is for ease of use by those that are + unfamiliar with these models of computation, while also providing + performance suitable for tasks arising in research. In particular, + algorithms in the package have been written for tackling performance + on large inputs, incorporating optimizations such as only exploring + the reachable set of states in the construction of a new finite-state + automaton. The package also has native display integration with + Jupyter notebooks, enabling easy visualization that allows students to + interact with automata in an exploratory + manner.

+

Of note are some commonly used and technical algorithms implemented + in the package for finite-state automata:

+ + +

An optimized version of the Hopcroft-Karp algorithm to + determine whether two deterministic finite automata (DFA) are + equivalent + (Almeida + et al., 2010).

+ + +

The product construction algorithm for binary set operations + (union, intersection, etc.) on the languages corresponding to two + input DFAs + (Sipser, + 2012).

+ + +

Thompson’s algorithm for converting regular expressions to + equivalent nondeterministic finite automata (NFA) + (Aho + et al., 2006).

+ + +

Hopcroft’s algorithm for DFA minimization + (J. + Hopcroft, 1971; + Knuutila, + 2001).

+ + +

A specialized algorithm for directly constructing a + state-minimal DFA accepting a given finite language + (Mihov + & Schulz, 2019).

+ + +

A specialized algorithm for directly constructing a minimal DFA + recognizing strings containing a given substring + (Knuth + et al., 1977).

+ + +

To the authors’ knowledge, this is the only Python package + implementing all of the automata manipulation algorithms stated + above.

+

automata has already been cited in + publications + (Jeff + Erickson & Solomon, 2023), and has seen use in multiple + large undergraduate courses in introductory theoretical computer + science at the University of Illinois Urbana-Champaign (roughly 2000 + students since Fall 2021). In this instance, the package is being used + both as part of an autograder utility for finite-state automata + created by students, and as an exploratory tool for use by students + directly.

+ + + Example usage + +

A visualization of + target_words_dfa. Transitions on characters + leading to immediate rejections are + omitted.

+ + +

The following example is inspired by the use case described in + Johnson + (2010). + We wish to determine which strings in a given set are within the + target edit distance to a reference string. We will first initialize a + DFA corresponding to a fixed set of target words over the alphabet of + all lowercase ascii characters.

+ from automata.fa.dfa import DFA +from automata.fa.nfa import NFA +import string + +target_words_dfa = DFA.from_finite_language( + input_symbols=set(string.ascii_lowercase), + language={'these', 'are', 'target', 'words', 'them', 'those'}, +) +

A visualization of target_words_dfa, + generated by the package in a Jupyter notebook, is depicted in + [fig:target_words_dfa].

+

Next, we construct an NFA recognizing all strings within a target + edit distance of a fixed reference string, and then immediately + convert this to an equivalent DFA. The package provides builtin + functions to make this construction easy, and we use the same alphabet + as the DFA that was just created.

+ words_within_edit_distance_dfa = DFA.from_nfa( + NFA.edit_distance( + input_symbols=set(string.ascii_lowercase), + reference_str='they', + max_edit_distance=2, + ) +) +

Finally, we take the intersection of the two DFAs we have + constructed and read all of the words in the output DFA into a list. + The library makes this straightforward and idiomatic.

+ found_words_dfa = target_words_dfa & words_within_edit_distance_dfa +found_words = list(found_words_dfa) +

The DFA found_words_dfa accepts strings in + the intersection of the languages of the DFAs given as input, and + found_words is a list containing this language. + Note the power of this technique is that the DFA + words_within_edit_distance_dfa has an infinite + language, meaning we could not do this same computation just using the + builtin sets in Python directly (as they always represent a finite + collection), although the syntax used by + automata is very similar to promote + intuition.

+ + + Acknowledgements +

Thanks (in no particular order) to GitHub users + YtvwlD, + dengl11, + Tagl, + lewiuberg, + CamiloMartinezM, + abhinavsinha‑adrino, + EduardoGoulart1, + and + khoda81 + for their invaluable code contributions to this project.

+ + + + + + + + SutnerKlaus + + Automata, a hybrid system for computational automata theory + Implementation and application of automata + + ChamparnaudJean-Marc + MaurelDenis + + Springer Berlin Heidelberg + Berlin, Heidelberg + 2003 + 978-3-540-44977-5 + https://doi.org/10.1007/3-540-44977-9_21 + 10.1007/3-540-44977-9_21 + 221 + 227 + + + + + + MøllerAnders + + Dk.brics.automaton – finite-state automata and regular expressions for Java + 2021 + https://www.brics.dk/automaton/ + + + + + + AlmeidaMarco + MoreiraNelma + ReisRogério + + Testing the equivalence of regular languages + Journal of Automata, Languages and Combinatorics + 2010 + 15 + 1/2 + https://doi.org/10.25596/jalc-2010-007 + 10.25596/jalc-2010-007 + 7 + 25 + + + + + + MihovStoyan + SchulzKlaus U. + + The minimal deterministic finite-state automaton for a finite language + Finite-state techniques: Automata, transducers and bimachines + Cambridge University Press + 2019 + 10.1017/9781108756945.011 + 253 + 278 + + + + + + AhoAlfred V. + LamMonica S. + SethiRavi + UllmanJeffrey D. + + Compilers: Principles, techniques, and tools (2nd edition) + Addison-Wesley Longman Publishing Co., Inc. + USA + 2006 + 0321486811 + 152 + 155 + + + + + + HopcroftJohn + + An n log n algorithm for minimizing states in a finite automaton + Theory of machines and computations + + KohaviZvi + PazAzaria + + Academic Press + 1971 + 978-0-12-417750-5 + https://www.sciencedirect.com/science/article/pii/B9780124177505500221 + 10.1016/B978-0-12-417750-5.50022-1 + 189 + 196 + + + + + + Jeff EricksonEliot Wong RobsonJason Xia + SolomonBrad + + Auto-graded scaffolding exercises for theoretical computer science + 2023 ASEE annual conference & exposition + ASEE Conferences + Baltimore , Maryland + 2023 + https://peer.asee.org/42347 + + + + + + JohnsonNick + + Damn cool algorithms: Levenshtein automata + Nick’s Blog + 201007 + http://blog.notdot.net/2010/07/Damn-Cool-Algorithms-Levenshtein-Automata + + + + + + KnuthDonald E. + MorrisJames H.Jr. + PrattVaughan R. + + Fast pattern matching in strings + SIAM Journal on Computing + 1977 + 6 + 2 + https://doi.org/10.1137/0206024 + 10.1137/0206024 + 323 + 350 + + + + + + HopcroftJohn E. + MotwaniRajeev + UllmanJeffrey D. + + Introduction to automata theory, languages, and computation (3rd edition) + Addison-Wesley Longman Publishing Co., Inc. + USA + 2006 + 0321455363 + + + + + + SipserM. + + Introduction to the theory of computation + Cengage Learning + 2012 + 978-1-133-18781-3 + 45 + 47 + + + + + + MarschallTobias + + Construction of minimal deterministic finite automata from biological motifs + Theoretical Computer Science + 2011 + 412 + 8 + 0304-3975 + https://www.sciencedirect.com/science/article/pii/S0304397510006948 + 10.1016/j.tcs.2010.12.003 + 922 + 930 + + + + + + KnuutilaTimo + + Re-describing an algorithm by Hopcroft + Theoretical Computer Science + 2001 + 250 + 1 + 0304-3975 + https://www.sciencedirect.com/science/article/pii/S0304397599001504 + 10.1016/S0304-3975(99)00150-4 + 333 + 363 + + + + + + XuChengcheng + ChenShuhui + SuJinshu + YiuS. M. + HuiLucas C. K. + + A survey on regular expression matching for deep packet inspection: Applications, algorithms, and hardware platforms + IEEE Communications Surveys & Tutorials + 2016 + 18 + 4 + 10.1109/COMST.2016.2566669 + 2991 + 3029 + + + + + + RodgerSusan H. + + JFLAP: An interactive formal languages and automata package + Jones; Bartlett Publishers, Inc. + USA + 2006 + 0763738344 + + + + +
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