116 lines
5.2 KiB
Org Mode
116 lines
5.2 KiB
Org Mode
* dds: A Home-made Toolkit for Discrete Dynamical Systems in Racket
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This is a toolkit for playing with various discrete dynamical systems
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in [[https://racket-lang.org/][Racket]]. A discrete dynamical system is a system which evolves from
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a discrete state to some other discrete states (many or one). The
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systems are discrete in the sense that we can identify successive
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states with no other states in between. Equivalently, the phase state
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of the system is discrete (and is often called the state graph).
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These constraints imply the possibility of associating discrete,
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possibly branching timelines to any evolution of the system.
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*DISCLAIMER:* I develop this toolkit as a support for my research on
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discrete dynamical systems. The primary objective for this framework
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is to fit my approach to these systems. Essentially, this framework
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should fit to the "shape of my mind", which is not necessarily the
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same as yours.
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Currently, the toolkit includes the following files:
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- [[file:generic.rkt][generic.rkt]]: The generic interface for a discrete dynamical
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system, with functions for constructing state graphs.
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- [[file:utils.rkt][utils.rkt]]: Misc utility functions.
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- [[file:networks.rkt][networks.rkt]]: Implements network-based models, which generalise
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Boolean networks, threshold Boolean automata networks, multivalued
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networks, etc.
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- [[file:rs.rkt][rs.rkt]]: Implements reaction systems, a variant of set rewriting.
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The toolkit is designed with Emacs [[https://orgmode.org/][Org-mode]] interoperability in mind.
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The file [[file:example/example.org][example/example.org]] explains the features available for
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interaction with Org-mode.
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** Roadmap
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Here is my current roadmap for this toolkit, in order. The first
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element is what I am currently working on. The degree of certainty
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that I work on the subsequent items decreases with their position
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in the list.
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*** TODO Write new functions for building the interaction graphs
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1. =variables-interact?=
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2. =get-interaction-sign=
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3. =build-interaction-graph=
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I currently have two different kinds of function for building
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interaction graphs: the syntactic interaction graphs and the
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interaction graphs as typically defined in the papers. These two
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kinds of graphs are not exactly the same. I have already started
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marking the split by renaming the original =build-interaction-graph= to =build-syntactic-interaction-graph=.
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The other functions are somewhat badly structured, somewhat badly
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written, and potentially somewhat wrong.
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*** TODO Add variable domains to the network
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I currently define a network as a mapping from variables to
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functions, but in fact I very often need the /domains/ of the
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variables for very many operations.
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I started this transformation a couple of days ago, and decided
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against it, because I thought that some networks may have
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unbounded domains. That's right, but stays hypothetical, while
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right now I need domains with my networks all the time.
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*** TODO Review =build-interaction-graph=
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Check that the definition of this function really follows the
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definition of the interaction graph. Pay attention to the
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existential vs. universal quantifiers.
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*** TODO Start writing the docs properly with Scribble
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Convert some of the comments to Scribble, in particular
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module-level comments introducing the modules and each of
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the sections.
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Set up the infrastructure for extracting the in-source comments
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using [[https://docs.racket-lang.org/scribble/srcdoc.html][this]].
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*** TODO Think about /not/ using generics for the dynamics
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Typed Racket can now type classes, and I can implement the idea
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from the module =generics= as a class. However, I got this advice
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on Racket Users group:
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#+BEGIN_QUOTE
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If you don't need to support arbitrary user implementations, you
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can avoid generics and classes altogether and use structs whose
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fields contain functions.
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#+END_QUOTE
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I will need to think about simpler implementations of the
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interface to dynamics, which should also be simpler to type.
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*** TODO Convert =dds= to Typed Racket
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This will necessarily lead to updates in the comments, which
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should be rewritten with Scribble.
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I will do the conversion in the directory =typed/=, by
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incrementally translating existing modules, definition
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by definition.
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The order I will convert the modules:
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1. =utils=
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2. =functions=
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3. the module defining the interface to dynamics (currently =generics=)
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4. =networks=
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5. =rs=
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*** TODO Split =networks= into general networks and threshold Boolean networks
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*** TODO Submit =update-graph= to =stchang=
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*** TODO Implement the BN \to RS conversion
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*** TODO Implement the minimisation of TBF/SBF
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*** TODO Contribute to Racket
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- Make sequence-filter allow multivalued sequences, provided the
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arity of the predicate is consistent with the arity of
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the sequence.
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- Add a sequence->hash function that accepts a multivalued
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sequence of keys and values (exactly like what in-hash produces)
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and copies them into a hash table.
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*** TODO Test network inference with [[https://docs.racket-lang.org/racklog/index.html][Racklog]]
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