rolog: Prolog queries from R

Matthias Gondan (Department of Psychology, Universität Innsbruck, Austria) and Jan Wielemaker (Vrije Universiteit Amsterdam/SWI-Prolog Solutions b.v.)

2023-01-27

Matthias Gondan
Universität Innsbruck
Department of Psychology
Innrain 9
A-6020 Innsbruck
Matthias.Gondan-Rochon@uibk.ac.at

Abstract

Prolog is a classical logic programming language with many applications in expert systems, computer linguistics and traditional, that is, symbolic artificial intelligence. The main strength of Prolog is its concise representation of facts and rules for the representation of knowledge and grammar, as well as its efficient built-in search engine for closed world domains. R is a statistical programming language for data analysis and statistical modeling which is widely used in academia and industry. Besides the core library, a lot of packages have been developed for all kinds of statistical problems, including statistics-based artificial intelligence tools such as neural networks for machine learning and deep learning. Whereas Prolog is weak in statistical computation, but strong in symbolic manipulation, the converse may be said for the R language. SWI-Prolog is a widely used Prolog system that offers a wide range of extensions for real world applications, and there already exist two Prolog “packs” to invoke R (rserve-client, real) from SWI-Prolog. Given the large user community of R, there may also be a need for a connection in the reverse direction that allows invoking Prolog queries in R computations. The R package rolog connects to the SWI-Prolog system, thus enabling deterministic and non-deterministic queries to the Prolog interpreter. Usage of rolog is illustrated by a few examples.

Keywords

Statistics; Logic Programming; Artificial Intelligence; R; Prolog

1. rolog: Prolog queries from R

The R (R Core Team 2021) programming language and environment is a widely used open source software for statistical data analysis. The basic R is a functional language with lots of support for storage and manipulation of different data types, and a strong emphasis on operations involving vectors and arrays. Moreover, a huge number of packages (e.g., CRAN, https://cran.r-project.org/) have been contributed that cover problems from areas as diverse as bioinformatics, machine learning, specialized statistical methods, web programming and connections to other programming languages.

An interface to Prolog is lacking so far. Based on earlier work by Kowalski, the logic programming language Prolog was invented in the 1970ies by Colmerauer and Roussel (Kowalski 1988), mostly for the purpose of natural language processing. Since then, logic programming has become an important driving force in research on artificial intelligence, natural language processing, program analysis, knowledge representation and theorem proving (Shoham 1994; Lally and Fodor 2011; Carro 2004; Hsiang and Srivas 1987). SWI-Prolog (Wielemaker et al. 2012) is an open-source implementation of Prolog that mainly targets developers of applications, with many users in academia, research and industry. SWI-Prolog includes a large number of libraries for “the real world”, for example, a web server, encryption, interfaces to C/C++ and other programming languages, as well as a development environment and debugger. In addition, pluggable extensions (so-called packs) are available for specific tasks to enhance its capabilities.

Unlike R, Prolog is a declarative programming language consisting of facts and rules that define relations, for example, in a problem space (Newell and Simon 1972). Prolog’s major strength is its built-in query-driven search engine that efficiently deals with complex structured data, with the data not necessarily being numerical. In fact, Prolog only provides a basic collection of arithmetic calculations via a purely functional interface (is/2). More complex calculations such as matrix algebra, statistical models or machine learning need help from other systems, for example, from R.

Angelopoulos et al. (2013) summarize work at the intersection of symbolic knowledge representation and statistical inference, especially in the area of model fits (EM algorithms, MCMC, Sato and Kameya 2013; Angelopoulos and Cussens 2008) and stochastic logic programs (Cussens 2000; Kimmig et al. 2011). One of the major strengths of logic programming is handling constraints; and a number of systems for constraint satisfaction tools have been developed (constraint logic programming on booleans, finite domains, reals, and intervals) for that purpose (e.g., Frühwirth 1998; Triska 2018). Some constraint handlers exist in R (see the CRAN task view for optimization problems), but more of them would be available via a bridge between R and Prolog.

Earlier approaches to connect Prolog and R have been published as SWI-Prolog packs (real, rserve_client, Angelopoulos et al. 2013; Wielemaker 2021b) and as a YAP module (YapR, Azevedo 2011). Whereas real establishes a direct link to an embedded instance of R, rserve-client communicates with a local or remote R service (Urbanek 2021). The former approach emphasizes speed, the latter might be preferred from a security perspective, especially in systems such as SWISH (Wielemaker, Lager, and Riguzzi 2015) that accept only a set of sandboxed commands for Prolog, but do not impose restrictions on R. A common feature of the two packages is that they provide an interface for R calls from Prolog, but not the other way round, that is, querying Prolog from R is not possible, so far.

The present package fills this gap through Prolog queries in R scripts, for example, to perform efficient symbolic computations, searches in complex graphs, parsing natural language and definite clause grammars. In addition, two Prolog predicates are provided that enable Prolog to ring back to the R system for bidirectional communication. Similar to real, tight communication between the two systems is established by linking to a shared library that embeds the current SWI-Prolog runtime. The exchange of data is facilitated by the C++ interfaces of the two languages (Eddelbuettel and Balamuta 2018; Wielemaker 2021a). A less tight connection might be established using the recently developed machine query interface (Zinda 2021) that allows socket-based communication between foreign languages and SWI-Prolog (and, in fact, the MQI documentation includes an example in which R is called).

A bidirectional bridge between R and Prolog might overcome the limitations of both languages, thereby combining the extensive numerical and statistical power of the R system with Prolog’s skills in the representation of knowledge and reasoning. In addition to the useful little tools shown in the examples below, rolog can therefore contribute to progress at the intersection of traditional artificial intelligence and contemporary statistical programming.

The next section presents the interface of rolog in detail. Section 3 presents possible extensions of the package at both ends, in R and Prolog. Section 4 is a list of illustrative examples that offer useful extensions to the R system. Conclusions and further perspectives are summarized in Section 5.

2. Basic syntax

rolog has a rather minimalistic syntax, providing only the basic ingredients to establish communication with the SWI-Prolog runtime. Ways to extend the interface are described in Section 3.

After installation with install.packages("rolog"), the package is loaded in the standard way.

library(rolog)
#> Found R package rswipl: /home/gondan/R/x86_64-pc-linux-gnu-library/4.2/rswipl/swipl/lib/swipl

We can see a short message telling the user which SWI-Prolog was found. The package searches for SWI-Prolog based on the environment variable SWI_HOME_DIR, the registry (Windows only), an executable swipl in the PATH, and if everything fails, R package rswipl (Gondan 2023). The message can be silenced by the usual option quietly=TRUE of the library command.

R interface

Most of the work is done using the three R functions query, submit, and clear. The R program in Listing 1 illustrates a query to Prolog’s member/2 using rolog’s syntax rules.

# member(1, [1, 2.0, a, "b", X, true])
query(call("member", 1L, list(1L, 2.0, quote(a), "b", expression(X), TRUE)))
#> [1] TRUE
#> attr(,"query")
#> [1] "member(1, [1, 2.0, a, b, X, true])"

# returns an empty list, stating that member(1, [1 | _]) is satisfied
submit()
#> list()

# returns a list with constraints, stating that the query is also satisfied 
# if the fifth element of the list, X, is 1
submit()
#> $X
#> [1] 1

# close the query
clear()
Listing 1.
A query to Prolog’s member/2 predicate.

query. The function query(call, options) is used to create a Prolog query (without invoking it yet). The first argument is a regular R call that is created using R’s function call(name, ...). This call represents the Prolog query that will be submitted in the later course. The creation of such predicates and Prolog terms is described below and can become quite contrived (see the examples in Section 4). The second argument, options, may be used for ad hoc modifications of the translation between R and Prolog, see the section below. The function returns TRUE on success. Note that query does not check if a Prolog predicate corresponding to call actually exists (see submit() below). Only a single query can be opened at a given time. If a new query Q is created while another query R is still open, a warning is shown and R is closed.

submit. Once a query has been created, it can be submitted using submit(). If the query fails, the return value is FALSE. If the query succeeds, a list of constraints is returned, with bindings for the variables that satisfy the query. Repeated calls to submit are possible, returning the different solutions of a query (until it eventually fails). The distinction between the different types of return values for success and failure (list vs. FALSE) is facilitated by the R function isFALSE(x).

clear. Closes the query. The name of the function was chosen to avoid name clashes with R’s own built-in function close. The function returns an invisible TRUE, even if there is no open query.

Three more functions consult, once, and findall are provided for convenience.

consult. In most applications, a number of Prolog facts and rules will be loaded into the system. To facilitate this recurrent task, the Prolog directive consult/1 has been mirrored into R, consult(filename), with filename being a string or a vector of strings if multiple files are to be consulted. The function returns TRUE on success; in case of problems, it returns FALSE and an error message is shown.

once and findall. The function once(call, options) is a convenience function that acts as a shortcut for query(call, options), submit(), and clear(). Similarly, findall(call, options) abbreviates the commands query(call, options), repetition of submit() until failure, and clear(), returning a list collecting the return values of the individual submissions.

Creating Prolog terms in R

Table 1 summarizes the rules for the translation from R objects to Prolog. Most rules work in both directions, but a few exceptions exist.

Table 1
Creating Prolog terms from R
R Prolog Note/Alternatives
expression(X) Variable X not necessarily uppercase
as.symbol(abc) Atom abc as.name, quote
TRUE, FALSE, NULL Atoms true, false, null
"abc" String "abc"
3L Integer 3
3 Float 3.0
call("term", 1L, 2L) term(1, 2)
list(1L, 2L, 3L) List [1, 2, 3]
list(a=1, b=2, c=3) List [a-1, b-2, c-3]
c(1, 2, 3, Inf) ##(1.0, 2.0, 3.0, 1.0Inf) vectors of length > 1
c(1L, 2L, 3L) or 1:3 '%%'(1, 2, 3)
c("a", "b", "c") $$("a", "b", "c")
c(TRUE, FALSE, NA) !!(true, false, na)
sin function(x) :- sin(x) primitive function
function(x) sin(x) function(x) :- sin(x) self-written function
matrix(1:4, nrow=2) '%%%'('%%'(1, 3), …) see also ###, $$$, !!!

In R, the basic elements such as integers, floating point numbers, character strings, and logicals are vectorized, and scalar entities are treated like vectors with one element. Conversely, Prolog does not natively support vectors or matrices. The problem is solved in the following way:

In the reverse direction, Prolog terms like ##/N are translated back to R vectors of length N, including the terms ##/0 and ##/1 that map to R vectors of length 0 and 1, respectively. Translation of a polymorphic Prolog term such as ##(a, 1.5) to R will fail, since rolog expects the arguments to be numeric.

If a Prolog object cannot be translated to R (e.g., a cyclic term), an error is raised. If an R object that lacks a suitable representation in Prolog (e.g., S4 class), a warning is printed and the result is unified with na.

To summarize, the rules for translation are not fully symmetrical. A quick check for symmetry of the representation is obtained by a query to =/2 or even r_eval/2 (see also below, subsection Prolog interface):

Q <- call("=", expression(X), c(1, 2, NA, NaN, Inf))
once(Q, options=list(portray=TRUE))
#> $X
#> [1]   1   2  NA NaN Inf
#> 
#> attr(,"query")
#> [1] "X= ##(1.0, 2.0, na, 1.5NaN, 1.0Inf)"

Q <- call("r_eval", c(1, 2, NA, NaN, Inf), expression(X))
once(Q)
#> $X
#> [1]   1   2  NA NaN Inf

The optional argument env to query, once and findall allows to raise the query (and, as a consequence, r_eval/1,2 in a specific environment.

Package options

A few package-specific options have been defined to allow some fine-tuning of the rules for translation between R and Prolog.

The command rolog_options() returns a list with all the options. The options can be globally modified with options() or in the optional argument of query, once, and findall.

options(rolog.intvec="iv")
Q <- call("member", expression(X), list(c(1L, 2L), c(3.5, 4.5)))
query(Q, options=list(realvec="rv"))
#> [1] TRUE
#> attr(,"query")
#> [1] "member(X, [iv(1, 2), rv(3.5, 4.5)])"
submit()
#> $X
#> [1] 1 2
clear()

Prolog interface to R

rolog offers some basic support to call R from Prolog, that is, connecting the two systems in the reverse direction. Two predicates can be used for this purpose, r_eval(Call) and r_eval(Function, Result). The former just invokes R with the command Call (ignoring the result); the latter evaluates Function and unifies the result with Result. Note that proper quoting of R functions is needed at the Prolog end, especially with R functions that start with uppercase letters and/or contain a dot in their name (see Section 4).

Exceptions

Package rolog has limited support for exception handling. If Prolog raises an exception, the error string is forwarded to R using the stop function. The examples below illustrate this by querying an undefined Prolog predicate.

Q <- call("membr", expression(X), list(1, 2, 3))
query(Q)
#> [1] TRUE
#> attr(,"query")
#> [1] "membr(X, [1.0, 2.0, 3.0])"
try(submit())
#> Warning in .submit(): Prolog exception:
#> error(existence_error(procedure,membr/2),context(system:call/1,_7828))
#> Error in eval(expr, envir, enclos) : 
#>   error(existence_error(procedure,membr/2),context(system:call/1,_7828))
clear()

See Section 4 for another example with an error resulting from a malformed query to r_eval/2.

3. Extending the package

R is a functional language, whereas Prolog is declarative. Obviously, there cannot be a perfect one-to-one correspondence between the syntactic components of two programming languages that follow completely different paradigms. Whereas symbols, functions, numbers and character strings are easily mapped between R and Prolog, there are loose ends at both sides. The package is intentionally kept minimalistic, but can easily be extended by convenience functions at both ends, Prolog and R, to facilitate recurrent tasks and/or avoid cumbersome syntax.

In particular, Prolog variables are translated from and to R expressions (not to be confused with R symbols), and R vectors of length greater than 1 are translated to the Prolog terms #/N, %/N, !/N, and $$/N, as mentioned above. These rules are, in principle, arbitrary and can be intercepted at several stages.

The process is illustrated in Figure 1.

G cluster_0 cluster_1 Query Query r2rolog preproc Query->r2rolog Result Result rolog2r postproc Result->rolog2r forth (rolog) r2rolog->forth rolog_pl preproc/2 forth->rolog_pl Prolog Prolog rolog_pl:e->Prolog back (rolog) rolog2r->back pl_rolog postproc/2 back->pl_rolog pl_rolog:e->Prolog
Figure 1
Workflow in rolog

Preprocessing in R

rolog uses a default preprocessing function preproc(query) to map the R operators <= and != to their Prolog counterparts =</2 and \=/2, respectively.

However, we have seen above that raising even simple everyday Prolog queries such as member(X, [1, 2, 3, a, b]) require complicated R expressions like call("member", expression(X), list(1, 2, 3, quote(a), quote(b))). The R function as.rolog(query) is meant to simplify this a bit by translating symbols starting with a dot to Prolog variables, and calls like ""[1, 2, 3, a, b] to lists. In the example below, as.rolog is added to the queue of preprocessing functions.

a <- 5
Q <- quote(member(.X, ""[1, 2, 3, a, (a), 1 <= 2]))
once(Q, options=list(preproc=list(as.rolog, preproc), portray=TRUE))
#> $X
#> [1] 1
#> 
#> attr(,"query")
#> [1] "member(X, [1.0, 2.0, 3.0, a, 5.0, 1.0=<2.0])"

Note that the name of the variable will still be X in the later course, not “dot-X”. As illustrated by the example above, as.rolog treats the argument a as a symbol; to evaluate the respective variable (i.e., “unquote”), it can be put in parentheses.

Preprocessing can be turned off by setting the option preproc to the identity function dontCheck.

Section 3 includes an example for mathematical rendering of R expressions. In that example, a preprocessing function is used to bring function calls with named arguments to a canonical form which is then handled in Prolog. More sophisticated work with quasi-quotations and unquoting expressions is described in “Advanced R” (Wickham 2019).

Postprocessing in R

In most cases, postprocessing will revert the manipulations during preprocessing, and the default function postproc(query) actually translates the Prolog operators =< and \= back to their respective counterparts in R.

Many Prolog programmers are used to operate with atoms, whereas character strings are the preferred representation of symbolic information in R. In the example below, a second hook is put in the queue that converts the result of a query like member(X, [a, b, c]) to strings.

stringify <- function(x)
{
  if(is.symbol(x))
    return(as.character(x))

  if(is.call(x))
    x[-1] <- lapply(x[-1], FUN=stringify)

  if(is.list(x))
    x <- lapply(x, FUN=stringify)

  if(is.function(x))
    body(x) <- stringify(body(x))

  return(x)
}

Q <- quote(member(.X, ""[a, b, c]))
R <- findall(Q, options=list(preproc=list(as.rolog, preproc), 
       postproc=list(stringify, postproc)))
unlist(R)
#>   X   X   X 
#> "a" "b" "c"

In other words, the query is satisfied if X is either “a”, or “b”, or “c”.

Pre- and postprocessing in Prolog

Recent versions of SWI-Prolog support so-called dictionaries of the form Tag{Key1:Value1, Key2:Value2, ...}. The tag is typically an atom (but can be a variable, as well), the keys are unique atom or integers; the values can be anything. Suppose we have a Prolog predicate that does something with dicts, and we would like to query it from R. The simplest solution is a wrapper in Prolog that translates key-value pairs [Key1-Value1, Key2-Value2, ...] back and forth to dicts:

do_something_with_pairs(Pairs0, Pairs1) :-
    dict_pairs(Dict0, my_dict, Pairs0),
    do_something_with_dicts(Dict0, Dict1),
    dict_pairs(Dict1, my_dict, Pairs1).

do_something_with_pairs/2 can then be queried from R using, for example, lists with named elements (see Table 1).

once(call("do_something_with_pairs", list(a=1, b=2), expression(X)))

In the code above, dict_pairs/2 takes the role of both preproc/2 and postproc/2 in Figure 1. It illustrates that complicated syntax on the R side can be much simplified when doing the conversion at the Prolog end. Ways to extend Prolog by add-ons (“packs”) are shown in the next section.

4. Examples and use cases

In this section we present a few usage examples for package rolog in increasing complexity. Although the code snippets are mostly self-explanatory, some familiarity with the Prolog language is helpful.

Hello, world

Prolog’s typical hello world example is a search through a directed acyclic graph (DAG), for example, a family tree like the one given in Listing 2.

parent(pam, bob). parent(bob, ann). parent(bob, pat). parent(pat, jim).

ancestor(X, Z) :-
    parent(X, Z).

ancestor(X, Z) :-
    parent(X, Y),
    ancestor(Y, Z).
Listing 2
A family tree in Prolog (see also family.pl)

Listing 2 is included in the package and is accessed using the function system.file. Within Prolog, the normal workflow is to consult the code with [family] and then to raise queries such as ancestor(X, jim), which returns, one by one, four solutions for the variable X. In R, we obtain the following results:

library(rolog)
consult(system.file(file.path("pl", "family.pl"), package="rolog"))
query(call("ancestor", expression(X), quote(jim)))
#> [1] TRUE
#> attr(,"query")
#> [1] "ancestor(X, jim)"
submit()        # solutions for X
#> $X
#> pat
submit()        # etc.
#> $X
#> pam
clear()         # close the query

As stated above, consult loads the facts and rules of Listing 2 into the Prolog database. query initializes a query, and the subsequent calls to submit return the conditions under which the query succeeds. In this example, the query succeeds if X is either pat, pam, or bob. A query is closed with clear(), or automatically if the query fails. If we are interested in just the first solution, we can use once(Call) as a shortcut to query(Call), then submit(), then clear(). If we want to collect all solutions of a query with a finite set of solutions, we can use findall(Call).

As mentioned in Section 2, a simplified syntax is provided by as.rolog that accepts quoted expressions with dots indicating Prolog variables:

Q <- quote(ancestor(.X, jim))
findall(Q, options=list(preproc=as.rolog))

Backdoor test

A useful application of DAGs is confounder adjustment in causal analysis (Greenland, Pearl, and Robins 1999; Barrett 2021). The Prolog file backdoor.pl is an implementation of Greenland et al.’s criteria for the backdoor test for d-separation in DAGs, with a predicate minimal/3 that searches for minimally sufficient sets of variables for confounder adjustment on the causal path between exposure and outcome. The nodes and arrows refer to Figure 12 in Greenland et al.

consult(system.file(file.path("pl", "backdoor.pl"), package="rolog"))

node <- function(N) invisible(once(call("assert", call("node", N))))
node("a"); node("b"); node("c"); node("f"); node("u")
node("e") # exposure
node("d") # outcome

arrow <- function(X, Y) invisible(once(call("assert", call("arrow", X, Y))))
arrow("a", "d"); arrow("a", "f"); arrow("b", "d"); arrow("b", "f")
arrow("c", "d"); arrow("c", "f"); arrow("e", "d"); arrow("f", "e")
arrow("u", "a"); arrow("u", "b"); arrow("u", "c")

R <- findall(call("minimal", "e", "d", expression(S)))
unlist(R)
#>  S1  S2  S3   S 
#> "a" "b" "c" "f"

The query to minimal/3 returns two minimally sufficient sets of covariates for confounder adjustment (namely, {a, b, c} and {f}).

Definite clause grammars

One of the main driving forces of Prolog development was natural language processing (Dahl 1981). Therefore, the next example is an illustration of sentence parsing using so-called definite clause grammars. As Listing 3 shows, rolog can access modules from SWI’s standard library (e.g., “dcg/basics.pl”).

:- use_module(library(dcg/basics)).

s(s(NP, VP)) --> np(NP, C), blank, vp(VP, C).
np(NP, C) --> pn(NP, C).
np(np(Det, N), C) --> det(Det, C), blank, n(N, C).
np(np(Det, N, PP), C) --> det(Det, C), blank, n(N, C), blank, pp(PP).
vp(vp(V, NP), C) --> v(V, C), blank, np(NP, _).
vp(vp(V, NP, PP), C) --> v(V, C), blank, np(NP, _), blank, pp(PP).
pp(pp(P, NP)) --> p(P), blank, np(NP, _).

det(det(a), sg) --> `a`.
det(det(the), _) --> `the`.
pn(pn(john), sg) --> `john`.
n(n(man), sg) --> `man`.
n(n(men), pl) --> `men`.
n(n(telescope), sg) --> `telescope`.
v(v(sees), sg) --> `sees`.
v(v(see), pl) --> `see`.
p(p(with)) --> `with`.

% Translate R string to code points and invoke phrase/2
sentence(Tree, Sentence) :-
    string_codes(Sentence, Codes),
    phrase(s(Tree), Codes).
Listing 3
Simple grammar and lexicon. sentence/2 preprocesses the R call.

As in the first example, we first consult a little Prolog program with a minimalistic grammar and lexicon (Listing 3, see also pl/telescope.pl), and then raise a query asking for the syntactic structure of “john sees a man with a telescope”. Closer inspection of the two results reveals the two possible meanings, “john sees a man who carries a telescope” versus “john sees a man through a telescope”. Further Prolog examples of natural language processing are found in , including the resolution of anaphoric references and the extraction of semantic meaning.

consult(system.file(file.path("pl", "telescope.pl"), package="rolog"))
Q <- quote(sentence(.Tree, "john sees a man with a telescope"))
unlist(findall(Q, options=list(preproc=as.rolog)))
#> $Tree
#> s(pn(john), vp(v(sees), np(det(a), n(man), pp(p(with), np(det(a), 
#>     n(telescope))))))
#> 
#> $Tree
#> s(pn(john), vp(v(sees), np(det(a), n(man)), pp(p(with), np(det(a), 
#>     n(telescope)))))

Installation of add-ons for Prolog

In description of the previous example, we noted in passing that rolog can access the built-in libraries of SWI-Prolog (e.g., by calls to use_module/1). It is also possible to extend the installation by add-ons, including add-ons that require compilation, if the build tools (essentially, RTools under Windows, and xcode under macOS) are properly configured. This is illustrated below by the demo add-on environ (Wielemaker 2012) that collects the current environment variables.

once(call("pack_install", quote(environ), list(quote(interactive(FALSE)))))
once(quote(use_module(library(environ))))
once(call("environ", expression(X)))

The query then unifies X with a list with Key=Value terms. The purpose of this example is obviously not to mimic the built-in function Sys.getenv() from R, but to illustrate the installation and usage of Prolog extensions from within R. In most situations, the user would install the pack from within Prolog with pack_install(environ)..

Term manipulation

Prolog is homoiconic, that is, code is data. In this example, we make use of Prolog’s ability to match expressions against given patterns and modify these expressions according to a few predefined “buggy rules” (Brown and Burton 1978), inspired by recurrent mistakes in the statistics exams of our students. Consider the \(t\)-statistic for comparing an observed group average to a population mean:

\[ T = \frac{\overline{X} - \mu}{s / \sqrt{N}} \]

Some mistakes may occur in this calculation, for example, omission of the implicit parentheses around the numerator and the denominator when typing the numbers into a calculator, resulting in \(\overline{X} - \frac{\mu}{s} \div \sqrt{N}\), or forgetting the square root around \(N\), or both. Prolog code for the two buggy rules is given in Listing 4.

% Correct steps and mistakes
expert(tratio(X, Mu, S, N), frac(X - Mu, S / sqrt(N))).
buggy(frac(X - Mu, S / SQRTN), X - frac(Mu, S) / SQRTN).
buggy(sqrt(N), N).

% Apply expert and buggy rules, or enter expressions
step(X, Y) :-
    expert(X, Y) ; buggy(X, Y).
step(X, Y) :-
    compound(X),
    mapargs(search, X, Y),
    dif(X, Y).

% Search through problem space
search(X, X).
search(X, Z) :-
    step(X, Y),
    search(Y, Z).
Listing 4
Manipulating terms in Prolog

The little e-learning system shown in Listing 4 produces six response alternatives. The fourth and the sixth result are combinations of the same two buggy rules (parenthesis, then square root, and the other way round). Some additional filters would be needed to eliminate trivial and redundant solutions .

consult(system.file(file.path("pl", "buggy.pl"), package="rolog"))
Q <- quote(search(tratio(x, mu, s, n), .S))
unlist(findall(Q, options=list(preproc=as.rolog)))
#> $S
#> tratio(x, mu, s, n)
#> 
#> $S
#> frac(x - mu, s/sqrt(n))
#> 
#> $S
#> x - frac(mu, s)/sqrt(n)
#> 
#> $S
#> x - frac(mu, s)/n
#> 
#> $S
#> frac(x - mu, s/n)
#> 
#> $S
#> x - frac(mu, s)/n

An important feature of such a term manipulation is that the evaluation of the term can be postponed; for example, there is no need to instantiate the variables x, mu, s, and n with given values before raising a query. This is especially helpful for variables that may represent larger sets of data in later steps.

It should be mentioned that R is homoiconic, too, and the Prolog code above can, in principle, be rewritten in R using non-standard evaluation techniques (Wickham 2019). Prolog’s inbuilt pattern matching algorithm simplifies things a lot, though.

Rendering mathematical expressions

The R extension of the markdown language (Xie, Dervieux, and Riederer 2020) enables reproducible statistical reports with nice typesetting in HTML, Microsoft Word, and Latex. However, so far, R expressions such as pbinom(k, N, p) are typeset as-is; prettier mathematical expressions such as \(P_\mathrm{Bi}(X \le k; N, p)\) require Latex commands like P_\mathrm{Bi}\left(X \le k; N, p\right), which are cumbersome to type in and hard to read even if the expressions are simple. Since recently, manual pages include support for mathematical expressions (Sarkar and Hornik 2022), which already is a big improvement.

Below Prolog’s grammar rules are used for an automatic translation of R calls to MathML. The result can then be used for calculations or it can be rendered on a web page. A limited set of rules for translation from R to MathML is found in pl/mathml.pl of package rolog. A more comprehensive translator is provided by the R package mathml (Gondan 2022). The relevant code snippets are shown in the listings below, along with their output.

library(rolog)
consult(system.file(file.path("pl", "mathml.pl"), package="rolog"))

# R interface to Prolog predicate r2mathml/2
mathml <- function(term)
{
  t <- once(call("r2mathml", term, expression(X)))
  cat(paste(t$X, collapse=""))
}
Listing 4
Generate MathML from R expressions

The first example is easy. At the Prolog end, there is a handler for pbinom/3 that translates the term into a pretty MathML syntax like P_bi(X <= k; N, pi).

term <- quote(pbinom(k, N, p))

# Pretty print
mathml(term)

PBi(Xk;N,p)


# Do some calculations with the same term
k <- 10
N <- 22
p <- 0.4
eval(term)

[1] 0.77195

The next example is interesting because Prolog needs to find out the name of the integration variable for sin. For that purpose, rolog provides a predicate r_eval/2 that calls R from Prolog (i.e., the reverse direction, see also next example). Here, the predicate is used for the R function formalArgs(args(sin)), which returns the name of the function argument of sin, that is, x.

term <- quote(integrate(sin, 0L, 2L*pi))
mathml(term)

02πsin(x)dx

eval(term)

2.221501e-16 with absolute error < 4.4e-14

Note that the Prolog end, the handler for integrate/3 is rather rigid; it accepts only these three arguments in that particular order, and without names, that is, integrate(sin, lower=0L, upper=2L * pi) would not print the desired result.

The extra R function canonical() applies match.call() to non-primitive R calls, basically cleaning up the arguments and bringing them into the correct order. Moreover, an extra handler maps the extractor function $(Fn, "value") to Fn.

canonical <- function(term)
{
  if(is.call(term))
  {
    f <- match.fun(term[[1]])
    if(!is.primitive(f))
      term <- match.call(f, term)
    
    # Recurse into arguments
    term[-1] <- lapply(term[-1], canonical)
  }

  return(term)
}

g <- function(u)
  sin(u)

# Mixture of (partially) named and positional arguments in unusual order
term <- quote(2L * integrate(low=-Inf, up=Inf, g)$value)
mathml(canonical(term))

2-g(u)du


# It is a bit of a mystery that R knows the result of this integral.
eval(term)

[1] 0

Note that both sin nor g in the above terms are R symbols, not R functions. In order to render something like call("integrate", low=-Inf, up=Inf, g), or call("integrate", low=-Inf, up=Inf, sin), with g and sin referring to the respective functions, one would need to determine its name, which is not possible in general.

print(g)
#> function(u)
#>   sin(u)
#> <bytecode: 0x56106ee130e8>

Calling R from Prolog

The basic workflow of the bridge from R to Prolog is to (A) translate an R expression into a Prolog term (i.e., a predicate), (B) query the predicate, and then, (C) translate the result (i.e., the bindings of the variables) back to R (see also Figure 1). The reverse direction is straightforward, we start by translating a Prolog term to an R expression (i.e. Step C), evaluate the R expression, and then translate the result back to a Prolog term (Step A). Package rolog provides two predicates for that purpose, r_eval(Expr) and r_eval(Expr, Res). The former is used to invoke an R expression Expr for its side effects (e.g., initializing a random number generator); it does not return a result. The latter is used to evaluate the R expression and return the result Res. The code snippet in Listing 6 (r_eval.pl) illustrates this behavior.

r_seed(Seed) :-
    r_eval('set.seed'(Seed)).

r_norm(N, L) :-
    r_eval(rnorm(N), L).
Listing 6
Calling R from Prolog using r_eval/1 and r_eval/2. The R call set.seed is quoted because the dot is an operator in Prolog.
consult(system.file(file.path("pl", "r_eval.pl"), package="rolog"))
invisible(once(call("r_seed", 123L)))
once(call("r_norm", 3L, expression(X)))
#> $X
#> [1] -0.5604756 -0.2301775  1.5587083

The example in Listing 6 is a bit trivial, basically illustrating the syntax and the workflow. More serious applications of are shown in the next two sections where r_eval/2 is used to evaluate monotonically behaving R functions and to obtain the names of function arguments in R.

As show below, the default environment of rolog’s r_eval/2 is .GlobalEnv, this can be changed in an optional argument to once(), findall(), and query().

# Set variable in R, read in Prolog
env <- new.env()
with(env, a <- 1)
once(call("r_eval", quote(a), expression(X)), env=env)
#> $X
#> [1] 1

# Set R variable in Prolog, read in R
invisible(once(call("r_eval", call("<-", quote(b), 2))))
cat("b =", b)
#> b = 2

If the R call raises an exception, an error is propagated to Prolog and finally to the rolog package:

try(once(quote(r_eval(rnorm(-1))))) # return "-1 random numbers"
#> Warning in .once(query, options, env): Prolog exception: r_eval(rnorm(-
#> 1.0),"exception occurred")
#> Error in eval(expr, envir, enclos) : 
#>   r_eval(rnorm(- 1.0),"exception occurred")

Interval arithmetic

Let \(\langle\ell, u\rangle\) denote a number between \(\ell\) and \(u\), \(\ell\le u\). It is easily verified that the result of the difference \(\langle\ell_1, u_1\rangle - \langle\ell_2, u_2\rangle\) is somewhere in the interval \(\langle \ell_1 - u_2, u_1 - \ell_2\rangle\), and a number of rules exist for basic arithmetic operations and (piecewise) monotonically behaving functions (Hickey, Ju, and Emden 2001). For ratios, denominators with mixed sign yield two possible intervals, for example, \(\langle 1, 2\rangle / \langle -3, 3\rangle = \langle -\infty, 3\rangle \cup \langle 3, \infty\rangle\), as shown in Figure 4 in Hickey et al.’s article. The number of possible candidates increases if more complicated functions are involved, as unions of intervals themselves appear as arguments (e.g., if \(I_1 \cup I_2\) is added to \(I_3 \cup I_4\), the result is \(I_1 + I_3 \cup I_1 + I_4 \cup I_2 + I_3 \cup I_2 + I_4\)). As a consequence, calculations in interval arithmetic are non-deterministic in nature, and the number of possible results is not foreseeable and cannot, in general, be vectorized as is often done in R. Use cases for interval arithmetic are the limitations of floating-point representations in computer hardware, but intervals can also be used to represent the result of measurements with limited precision, or truncated intermediate results of students doing hand calculations. A few rules for basic interval arithmetic are found in pl/interval.pl; a few examples are shown below. Again, Prolog rings back to R via r_eval/2 to determine the result of dbinom(X, Size, Prob, Log).

consult(system.file(file.path("pl", "interval.pl"), package="rolog"))

Q <- quote(int(`...`(1, 2) / `...`(-3, 3), .Res))
unlist(findall(Q, options=list(preproc=as.rolog)))
#> $Res
#> ...(-Inf, -0.333333333333333)
#> 
#> $Res
#> ...(0.333333333333333, Inf)

D  <- quote(`...`(5.7, 5.8))
mu <- 4
s  <- quote(`...`(3.8, 3.9))
N  <- 24L
tratio <- call("/", call("-", D, mu), call("/", s, call("sqrt", N)))
once(call("int", tratio, expression(Res)))
#> $Res
#> ...(2.13545259627251, 2.32056923000512)

# Binomial density
prob = quote(`...`(0.2, 0.3))
once(call("int", call("dbinom", 4L, 10L, prob, FALSE), expression(Res)))
#> $Res
#> ...(0.088080384, 0.200120949)

The slightly cumbersome syntax for entering an interval \(\langle \ell, u\rangle\) is due to the fact that the ellipsis is a reserved symbol in R and cannot be used as an infix operator. A powerful and comprehensive system for constraint logic programming over intervals is available as a Prolog pack (Workman 2021) and can easily be connected to R using, for example, the present package.

5. Conclusions

R has become the primary language for statistical programming and data science, but is currently lacking support for traditional, symbolic artificial intelligence. There are already two add-ons for SWI-Prolog that allow to run R calculations from Prolog (Angelopoulos et al. 2013; Wielemaker 2021b), but a connection in the other direction was missing, so far. rolog bridges this gap by providing an interface to a SWI-Prolog distribution in an R package. The communication between the two systems is mainly in the form of queries from R to Prolog, but two predicates allow Prolog to ring back and evaluate terms in R. The design of the package is minimalistic, providing three main functions query(), submit(), and clear(), and a very limited set of convenience tools (consult(), once(), and findall()) to facilitate recurrent everyday actions. As both systems are homoiconic in nature, it was easy to establish a one-to-one correspondence between many of the elements of the two languages. Most exceptions (e.g., lack of R support for empty symbols) can be avoided and/or circumvented by wrapper functions at both ends.

Simple ways to extend the package have been described in Section 2; such extensions could, for example, include R objects and structures like those returned by lm(), or S4 classes. In many use cases, this may be realized by transforming the R object to a list with named elements, and rebuild the object on the Prolog end on an as-needed basis. After a query, the process is reversed. If speed is an issue, more of these steps can, in principle, be moved into the package and implemented in Rcpp.

rolog, thus, opens up a wide of applications in logic programming for statisticians and researchers at the intersection of symbolic and connectionist artificial intelligence, where concise knowledge representation is combined with statistical power. Moreover, rolog provides starting points for useful small-scale solutions for everyday issues in data science (term transformations, pretty mathematical output, interval arithmetic, see Section 3).

At its present stage, a major limitation of rolog is its relatively slow speed. For example, translation of R lists or vectors to the respective elements of the Prolog language (also lists, #/N) is done element-wise, in both directions. The translation is optimized by using Rcpp (Eddelbuettel and Balamuta 2018), but there remains an upper bound in the efficiency, because Prolog does not support vectors or matrices. Since Prolog’s primary purpose is not vector or matrix calculation, this limitation may not show up in real-world applications. Another issue, maybe a bit annoying, is the rather cumbersome syntax of the interface, with the need for quoted calls and R expressions for representing Prolog variables. rolog was deliberately chosen to be minimalistic and, so far, only depends on base R. A more concise representation might be obtained by tools from the “Tidyverse” ecosystem, as described in Chapter 19 of Advanced R (Wickham 2019). Finally, at this stage, rolog is unable to deal with cyclic terms (e.g., once(call("=", expression(A), call("f", expression(A)))), i.e., A = f(A) raises an error message).

rolog is available for R Version 4.2 and later, and can easily be installed using the usual install.packages("rolog"). The source code of the package is found at https://github.com/mgondan/rolog/, including installation instructions for Unix, Windows and macOS.

Acknowledgement

Development of the package profited substantially from the Prolog packs rserve_client (Wielemaker 2021b) and real (Angelopoulos et al. 2013).

Note

The results in this paper were obtained using R 2.1.2022 with the rolog 0.9.14 package. R itself and all packages used are available from the Comprehensive R Archive Network (CRAN) at https://CRAN.R-project.org/.

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