In this paper, we discuss the addition of substitutions as a further type of operations to (in particular, context-free) insertion-deletion systems, i.e., in addition to insertions and deletions we allow single letter replacements to occur. We investigate the effect of the addition of substitution rules on the context dependency of such systems, thereby also obtaining new characterizations of and even normal forms for context-sensitive (CS) and recursively enumerable (RE) languages and their phrase-structure grammars. More specifically, we prove that for each RE language, there is a system generating this language that only inserts and deletes strings of length two without considering the context of the insertion or deletion site, but which may change symbols (by a substitution operation) by checking a single symbol to the left of the substitution site. When we allow checking left and right single-letter context in substitutions, even context-free insertions and deletions of single letters suffice to reach computational completeness. When allowing context-free insertions only, checking left and right single-letter context in substitutions gives a new characterization of CS. This clearly shows the power of this new type of rules.
Insertion-deletion systems, or ins-del systems for short, are well established as computational devices and as a research topic within Formal Languages throughout the past nearly 30 years, starting off with the PhD thesis of Lila Kari [11]. In fact, insertion alone has been studied before in [8].
Originating from the field of linguistics [16,20], ins-del systems also take inspiration from the field of molecular biology. Here, the insertion and deletion operation correspond to the mismatched annealing of DNA sequences [21]. When considering ins-del systems, one key question is how context-dependent are they, i.e., how much context information is (in-)sufficient for the operation of such systems to reach computational completeness, i.e., to characterize the class of recursively enumerable languages (RE), and how long are the strings they can insert or delete.
From their very beginning, papers highlighting the potential use of ins-del systems in modelling DNA computing also discussed the replacement of single letters (possibly within some context) by other letters, an operation called substitution in [3,12]. Interestingly, all theoretical studies on grammatical mechanisms involving insertions and deletions omitted including the substitution operation in their studies or have only considered them in a specific context. For instance in [6], substitution rules are only allowed to be applied at the beginning or end of a string. With this paper, we are stepping into this gap by studying more general ins-del systems with substitutions, or ins-del-sub systems for short. In particular we investigate which effect the addition of substitution rules have on the on such systems, that is when is the addition of substitution rules sufficient for ins-del systems to reach computational completeness and how much context-dependence is necessary to achieve this goal.
In this paper, which is an extended version of [28], published at Computability in Europe 2020, we put special emphasis on extending context-free ins-del systems with substitutions. We observe quite diverse effects, depending on whether the substitutions are context-free, one-sided or two-sided. We can also characterize the context-sensitive languages by extending context-free insertion systems with substitutions, which can be seen as a new normal form for monotone Chomsky grammars.
This paper is the first in a series of three papers. The second and third parts appeared as extended abstracts in two conferences [29,30]. Apart from the mentioned characterizations, in particular of the class of recursively enumerable languages, we also see (in this paper) a number of situations where context-free ins-del systems are insufficient to simulate Turing machines, even with substitution rules. There are two potential ways out: either we allow for enhanced context checks (as worked out in [29]) or we allow additional control, say, by designing small (sequential) ‘program fragments’ that prescribe how rules of the ins-del-sub system should be applied (see [30]). As indicated, these are exactly the two research directions that we follow in parts two and three of our study on ins-del-sub systems. Most of the material of these three papers can be also found in [27].
The present paper is structured as follows: In Section 2, we formally introduce the key notions of this paper. We also summarize what has been achieved concerning computational completeness (i.e., characerizations of RE) in terms of ins-del systems in Remark 1. Section 3 constitutes the main part of this work, proving the most important results. More specifically, first we prove that adding context-free substitutions does not change the computational power of ins-del systems, so that the results listed in Remark 1 also apply in such a situation. Then, we consider one-sided substitutions. We prove that for each RE language, there is a system generating this language that only inserts and deletes strings of length two without considering the context of the insertion or deletion site, but may change symbols (by a substitution operation) by checking a single symbol to the left of the substitution site. Notice that with context-free substitutions only, computational completeness cannot be reached. When we allow checking left and right single-letter context in substitutions, even context-free insertions and deletions of single letters suffice to reach computational completeness. When allowing context-free insertions only, checking left and right single-letter context in substitutions gives a new characterization of CS. This also gives the mentioned new normal form for monotone grammars characterizing CS. In the last section, we point to several questions that are left open in the theory of ins-del-sub systems with context-free insertions and deletions and briefly discuss the broader context.
Basic definitions and observations
We assume the reader to be familiar with the basics of formal language theory. In particular, an alphabet is a finite non-empty set, a language is a subset of the free monoid generated by a given alphabet, and λ denotes the neutral element of any free monoid. We denote by ⧢ the binary shuffle operation, which is defined as follows: let , then .
An ins-del system is a 5-tuple , consisting of two alphabets V and T with , a finite language A over V, a set of insertion rules I and a set of deletion rules D. Both sets of rules are formally defined as sets of triples of the form with and . We call elements occurring in T terminal symbols, while referring to elements of as nonterminals. Elements of A are called axioms.
Let , with , be a string. Applying the insertion rule inserts the string between u and v, which results in the string .
The application of a deletion rule results in the removal of an substring a from the context . More formally let be a string. Then, applying results in the string .
We define the relation ⟹ as follows: Let . Then we write if y can be obtained by applying an insertion or deletion rule to x. We also write or to specify whether the applied rule has been an insertion or a deletion rule. Consider or . Then we refer to u as the left context and to v as the right context of /. If , we call such a rule (in analogy to classical Chomsky grammars) context-free. If all rules are context-free then the whole system is called context-free.
Let be an ins-del system. The language generated by is defined by
The size of describes its descriptional complexity and is defined by a tuple , where
By we denote the family of all ins-del systems of size [2,26]. Depending on the context, we also denote the family of languages characterized by ins-del systems of size by . We call a family a family of context-free ins-del systems, while we call a family with or a family of one-sided ins-del systems. According to [2], an ins-del system of size is said to be in normal form if
for any , it holds that , and , and
for any , it holds that , and .
Alhazov et al. [2,26] have shown the following auxiliary result:
For every ins-del system, one can construct an insertion-deletion systemin normal form of the same size with.
We sketch the construction. For an ins-del system , an equivalent insertion-deletion system can be constructed with
The basic idea is to introduce a new symbol $ () to act as a padding symbol to increase the length of the left (respectively, right) contexts of any rule , which does not fit the criteria, to meet the required size. Likewise, the padding symbol $ is also used to increase the length of any string that is inserted (respectively, deleted) by an insertion (respectively, a deletion) rule, to n (respectively, p).
Filling the axioms with the padding symbol $ ensures that rules of or are applicable, as applying any rule of or to any axiom requires to have a minimum size of , in case of an insertion, or , in case of a deletion rule. Clearly is of the same size as . □
In the following sections, we use a modified normal form for ins-del systems of size . Given an arbitrary ins-del system of size , the construction of this modified normal form is as follows:
Letbe an ins-del system of size. Without loss of generality, we assumeand. We constructas follows:
The basic idea of Construction 1 is the same as in the usual normal form constructions (see Theorem 1): the symbol $ is used as a padding symbol to ensure that the left and right contexts of all rules are of the required size. We can show that Construction 1 is equivalent to the usual normal form construction.
Letbe an ins-del system of sizein normal form andbe defined according to Construction
1
. Then,.
The nonterminals X introduced by the axioms of must be deleted at some point of any derivation of , as otherwise the derivation cannot yield a word consisting only of terminal symbols. It is easy to see that for any derivation of leading to a word , there is an equivalent derivation to w, in which the last two rules to be applied are both . It is clear that we can therefore assume that the deletion of both symbols X are the last steps of any derivation of . We remark that there is no insertion rule introducing a nonterminal X. Therefore, all X occurring during the derivation have been introduced via the axiom. Due to our assumption that both nonterminals X of the axiom will not be deleted until the very end, it is easy to see that all insertions and deletions of any derivation of occur between these occurrences of nonterminal X.
We remark that
and hold. Furthermore, iff holds.
Consider the set of deletion rules . Clearly this set of rules is essentially equivalent to a context-free deletions rule of the form as long as $ has arbitrary left and right context. Given our assumption that all occurrences of X are not deleted until the very end, this is always the case.
Therefore, it is easy to see that iff holds. □
Unlike the usual normal form construction, context-free deletions can only occur at the beginning and the end of a sentential form in the case of Construction 1. This fact will prove useful below.
Ins-del systems have been extensively studied regarding the question if they can describe all of the recursively enumerable languages. We summarize these results first by listing the classes of languages known to be equal to RE:
By way of contrast, the following language families are known not to be equal to RE, the first one is even a subset of CF: [26], [18], [13], and [15].
We define substitution rules to be of the form ; ; . Let ; be a string over V. Then applying the substitution rule allows us to substitute a single letter a with another letter b in the context of u and v, resulting in the string . Formally, we define an ins-del-sub system to be a 6-tuple , where V, T, A, I and D are defined as in the case of usual ins-del systems and S is a set of substitution rules. Substitution rules define a relation : Let and be strings over V. We write iff there is a substitution rule . In the context of ins-del-sub systems, we write to denote any of the relations , or . We define the closures and as usual. The language generated by an ins-del-sub system is defined as .
As with usual ins-del system, we measure the complexity of an ins-del-sub system via its size, which is defined as a tuple , where n, m, , p, q and are defined as in the case of usual ins-del systems, while r and limit the maximal length of the left and right context of a substitution rule, respectively, i.e., , . denotes the family of all ins-del-sub systems of size . Note that, as only one letter is replaced by any substitution rule, there is no subscript below . Depending on the context, we also refer to the family of languages generated by ins-del-sub systems of size by . Expanding our previous terminology, we call substitution rules of the form context-free, while substitution rules of the form or with are called one-sided. Substitution rules of the form with are referred to as two-sided.
Let be the reversal (mirror) operator. For a language L and its mirror the following lemma holds.
iff. □
We will now define the term resolve. Let be an ins-del-sub system. We say that a nonterminal X of is resolved if X is either deleted or substituted. The language generated by only contains words consisting of terminal symbols. Therefore, it is easy to see that in any terminal derivation of all occurring nonterminals must be resolved at some point of the derivation otherwise the derivation cannot yield a word consisting only of terminal symbols. We remark that a nonterminal X may be resolved by being substituted with a nonterminal Y, which in turn must be resolved.
As in the case of ins-del systems without substitution rules, we define a normal form for ins-del-sub systems. An ins-del-sub system
of size is said to be in normal form if
for any , it holds that , and ;
for any , it holds that , and ;
for any , it holds that and .
For every ins-del-sub systemof size, one can construct an ins-del-sub systemof the same size in normal form, with.
Let be an ins-del-sub system of size . The basic idea is similar to the normal form construction for ins-del systems in [2,26]. In fact, the sets of insertion and deletion rules of are constructed as in the ins-del system normal form construction. and are defined as follows:
As in Theorem 1, $ is a new symbol, that is, , which is introduced to be the padding symbol. We denote by h the homomorphism from to V defined as follows: and . By induction it can be shown that
where and . While the only-if part follows easily, consider the following for the if part. We can assume that in any derivation of the first i and the last j letters of the axiom are not deleted until the very end of derivation. Hence, insertion rules of the form with , are applicable until the very end. It is clear that due to insertion rules of the form and the deletion rule it is possible to generate an arbitrary number of $ between two letters of any sentential form of .
Let . Let such that the substitution rule is applicable to w. By induction where and . Due to previous considerations it is clear that such that and where with and with . By definition . Hence it is easy to see that our claim holds. □
The following result will be useful in subsequent proofs; compare to Lemma 1.
Letbe a family of languages that is closed under reversal. Then:
iff.
iff. □
Due to the definition of ins-del-sub systems, the following result is clear.
. □
Whether this inclusion is proper, is the question, that will be addressed in the following sections. We will see that while in some cases an arbitrary system of size can be simulated by a system of size , this is not the general case. Furthermore, we will see that families , which are not computationally complete, may reach computational completeness via an extension with substitution rules. Additionally, we will see below that families of ins-del systems which are equally powerful may no longer be after being extended with the same class of substitution rules, i.e., we have , but possibly . The reverse case might occur, as well.
Because the application of an insertion rule corresponds to the application of the monotone rewriting rule and the application of a substitution rule corresponds to the application of the monotone rewriting rule , a monotone grammar can simulate derivations of an insertion-substitution system. (More technically speaking, we have to do the replacements on the level of pseudo-terminals for each terminal a and also add rules , but these are minor details.) Hence, we can conclude:
For any integers,. □
Main results
We will focus on context-free ins-del systems, which are extended with substitution rules. More precisely, we will analyze the computational power of the family of systems .
Extending ins-del systems with context-free substitutions
We are going to analyze substitution rules of the form , which means that letters may be substituted regardless of any context. We will show that extending context-free ins-del systems with context-free substitution rules does not result in a more powerful system. In fact, a context-free ins-del-sub system of size can be simulated by an ins-del system of size .
Let, then there exists an ins-del systemsuch that.
We only sketch the construction of how to build in ins-del system from a given ins-del-sub system with context-free substitution rules in the following. The correctness of the construction follows similarly to the standard proof showing how to eliminate chain rules in context-free grammars, as contained in any introductory textbook on formal languages. Let . It is clear that any letter a, that is to be replaced by a substitution rule , has been introduced by either an insertion rule or as part of an axiom at some point before executing the substitution. As a serves no purpose other than to be replaced (i.e., it is not used as a context), the basic idea is to skip introducing a altogether and introduce b instead. More formally: instead of applying an insertion rule or using an axiom and replacing a via at a later point, we introduce a new insertion rule or a new axiom , respectively, which we apply instead of , or , respectively. This idea can be cast into an algorithm to produce an ins-del system with . As only context-free insertion rules of maximum size are added to , it is clear that holds. □
Considering the question about the generative power of context-free ins-del systems with context-free substitution rules compared to usual context-free ins-del systems, Theorem 5 and Lemma 3 together yield the important fact that ins-del systems and ins-del-sub systems with context-free substitutions are equally powerful:
.
Hence, what has been said about the power of ins-del systems in Remark 1 readily transfers to ins-del-sub systems with context-free substitutions. Although we do not focus on issues of descriptional complexity in this paper, the following examples shows that when considering the size of ins-del systems and ins-del-sub systems with context-free subsitutions, the latter ones could be exponentially more succinct.
Let for . Consider the ins-del-sub system
where , , and . Clearly, the language generated by is as any application of the rule increases the length of the generated word by m and substitution rules do not affect the length. Using the construction introduced in Theorem 5 yields the ins-del system , with . While it is clear that , we remark that this example shows that the construction method of Theorem 5 may yield an ins-del system whose number of rules is exponentially larger than the number of rules of the system with substitutions, as grows exponentially with m.
Extension with one-sided substitution
Now, we will analyze the effect of one-sided substitution rules if used to extend a context-free ins-del system. We will show that using one-sided substitution rules can greatly increase the computational power of context-free insertion and deletion rules. In some cases, we even get computationally completeness results.
We will now construct an ins-del-sub system of size which simulates of size . The idea behind this construction is very simple: instead of applying an insertion rule (inserting a symbol a) with some left context, we first insert some special marker (individual to this rule) in a context-free manner, and in a second step, we substitute this marker by a, watching over the left context inherited from the original insertion rule at this point. Analogously, in the case of a deletion rule that removes a symbol a in some left context, we first replace a by some some symbol that is individual to this deletion rule, observing the context of the simulated deletion rule, and then this specific introduced symbol is deleted without checking any context condition. More formally, the system is constructed in the following manner:
We assume the systemto be in normal form and any rule ofto be labelled in a one-to-one manner, i.e., there is a bijection between a set of labels and the rule set. Let $ be the padding symbol used in the construction of the normal form of. The systemis constructed as follows. For each rule of, we introduce a new nonterminaland defineThe setof insertion rules ofcontains all, where i is the label of an insertion rule of, while the setof deletion rules as containsand all, where i is the label of a deletion rule of. Furthermore, we define the set of substitution rules, with
Each deletion rule of , where i is the label of , corresponds to a deletion rule and a substitution rule of . The basic idea of the construction is to simulate a deletion rule by substituting the letter a with left context u via . The introduced nonterminal is then deleted at some point by the deletion rule . It is clear that a derivation of the form
in which the application of succeeds an application of immediately, is equivalent to the application of a deletion rule . It needs much more care to prove the following converse.
We begin by proving the following statement.
Letbe a deletion rule ofandandbe the corresponding rules of. Consider the derivationof, withandWe refer to the nonterminal, introduced at this point, as, to mark its specific occurrence. Then there is a derivation, leading fromto w, in whichis resolved immediately.
It is clear that the nonterminal must be resolved at some point of the derivation. Given our construction, can only be resolved by the context-free deletion rule . Therefore, any derivation starting out from to produce w is of the form
Because of the construction of , is not the left context of any rule of . For this reason, and follow from the derivation . Hence, there is the derivation
in which is resolved immediately. □
Applying Lemma 4 inductively, it is easy to see that we can assume that all nonterminals , where i is the label of a deletion rule of , are resolved immediately after their introduction. We remark that this means that for any sentential form of a derivation of
holds (without loss of generality). As in the case of deletion rules of , each insertion rule , where j is the label of , corresponds to a context-free insertion rule and a substitution rule of . We now prove that we can assume that a substitution rule is applied immediately after an application of a rule . It is easy to see that applying immediately after achieves the same result as applying .
Letandbe a derivation of, in which at most n insertion rules are used. Then the rules of this derivation can be reordered such that immediately after the application of a rulethe corresponding substitution ruleis applied.
As stated before, we assume that nonterminals , where i is the label of a deletion rule of D, are resolved immediately after being introduced.
We prove our claims by induction on the number n of insertion rules that have been used:
: Consider a derivation of , in which only one insertion rule is used. Let the insertion rule be and the corresponding substitution rule be . Then the derivation is of the form
Consider . As is the only insertion rule ever used in the entire derivation, is achieved with context-free deletion rules and the corresponding substitution rules . As is not the context of any of these rules, we conclude that and hold. Therefore, we also have the derivation
which satisfies our claim.
: Consider a derivation , in which insertion rules are used. Due to our construction, all symbols that are inserted are nonterminals , where j is the label of an insertion rule of , which are eventually substituted via the corresponding rules of the form with . Clearly, there is a nonterminal , which is the first of all inserted nonterminals to be substituted. Let be the substitution rule corresponding to . Then, the derivation is of the form
where for ; with and .
According to Lemma 4, all nonterminals related to deletion rules of are deleted immediately after being introduced. Therefore,
follows. Furthermore, as is the first of all inserted nonterminal to be substituted with a letter in V, all symbols occurring in are either symbols belonging to the initial word α or have substituted symbols of initial word α via sequences of substitution rules in S. Therefore, it is clear that
holds, as and are introduced via context-free insertions and are not used as a context for any rule.
Also observe: Applying all rules of , S and used in the derivation while skipping all rules of yields
Therefore, consider the derivation
in which the substitution rule corresponding to the nonterminal is applied immediately after the introduction of . Due to derivation (1), we can easily see that
holds. Furthermore, it is clear that in the derivation (2) at most n insertion rules are used. Using the induction hypothesis, it follows that in there is a derivation from α to w which satisfies our claim. □
Using Lemma 4 and Lemma 5, it is clear that the following proposition holds.
Let . Consider a derivation of . Then, there is an alternative derivation of , leading from α to w, in which all nonterminals are resolved immediately after being introduced.
Therefore we obtain the following result.
.
”⊆” Let and let be constructed according to Construction 2. Consider an arbitrary derivation of . Then there is a derivation of . Whenever an insertion rule of is applied in the derivation of , we apply the corresponding rule immediately followed by an application of the rule . Whenever a deletion rule is applied, we act in an analogous manner.
”⊇” Consider a derivation of . Without loss of generality, we assume that all nonterminals are resolved by the corresponding rules immediately after being introduced. Replacing all insertion rules and all deletion rules occurring in the derivation of with the corresponding insertion and deletion rules of and removing all rules of yields a derivation of . □
This allows us to state:
.
It is easy to see that a result identical to Theorem 7 can be shown analogously for the mirrors of and . Therefore, we find:
. □
Consider ins-del systems of size extended with one-sided substitution rules; the increase in computational power is quite significant:
.
Both trivial inclusions are proper. For the first inclusion, observe that . Intuitively, it is clear that a system consisting of a single axiom and a single insertion rule yields . On the other hand, if a system of size can generate , where m is arbitrary, then that system must have an insertion rule and thus is included in the generated language as well. For the second inclusion, note that the system of size presented in Example 2 below generates . Verlan [26, Theorem 5.3] has shown that even ins-del systems of size cannot generate the language . □
Consider the following ins-del-sub system: , with , and . The set of insertion rules is defined as , while the set of substitution rules is . The generated language is , as we can easily see that any generated word begins with a letter b and ends with a letter a. Furthermore, any word generated by is not of the form , as the only way to introduce the terminal symbol b (except for the b introduced via the axiom) is by substituting a nonterminal with b. However, this substitution requires a left context a, which means that at some point the letter to the left of any b has been a. There are no insertion rules which can insert an additional b or between a and b. Furthermore, there are no deletion rules at all, which means that no a can be deleted. Therefore, the letter to the left of any b cannot be another b. Using the same argumentation, we can see, that any word generated by is not of the form , either.
As all previous examples of languages not belonging to a specific language class of ins-del(-sub) systems are regular, the question might arise which (known) subregular language classes can be described by certain ins-del(-sub) language families, or if such subregular language classes can be even characterized by them.1
This question was raised by one referee of this paper.
We are not aware of earlier studies in this direction, but we like to add one such result in the following, which possibly inspires further similar results.
The language class can be characterized in the following way.
belongs to if and only if it can be represented as , with and being finite.
First, we have to prove that . As the inclusion ‘⊇’ is trivial, let as consider an ins-del system with . First, observe that describes a finite language . Moreover, defining , one sees that . But now, the only purpose of deletion rules is to delete symbols (in a context-free manner) that have been introduced before (by inserting them in a context-free manner). This explains that these possible deletions are superfluous concerning the generated language, i.e., with , we find that .
What is the language described by a system ? I clearly determines a set of symbols X that can be freely inserted to the finite set of axioms F. As symbols cannot be deleted anymore later, we can assume that without loss of generality. Hence, . Conversely, any language that can be described as , with and being finite, can be described by some system , where allows for context-free insertions of all symbols from X. □
We now analyze the computational power of ins-del-sub systems of size . While the family of ins-del systems of size is known to be a proper subset of , see [25,26], we will show that an extension with substitution rules of the form results in a significant increase in computational power. More precisely, by simulating an ins-del systems of size , we will show that holds.
Letbe an ins-del system of sizein normal form and all insertion rules ofbe labelled in a one-to-one manner. We construct the ins-del-sub systemof size, which simulates, as follows:
The basic idea of Construction 3 is essentially the same as in Construction 2: as context-free insertion rules cannot scan for contexts (by definition), this task is handled by the corresponding substitution rules. Consider an insertion rule of where i is the label of an insertion rule . Then the substitution rules, corresponding to this rule, are and . As in the case of Construction 2, clearly a derivation of the form
in which all introduced nonterminals , are immediately resolved after being inserted, corresponds directly to the application of an insertion rule . In the following paragraphs, we will show that for every derivation of , leading to a terminal string w, there is an alternative derivation leading to w, in which all nonterminals , are immediately resolved after being inserted as described above. We begin with the following lemma:
Let i be the label of an insertion ruleofand. Ifholds, then. Furthermore, with exception of one substitution rule, all rules used in the derivationand the derivationare identical.
Consider the derivation . As must be resolved at some point of this derivation, it is of the form
Clearly, as is not used as a context of any rule according to Construction 3, and follow from . Therefore,
holds. Clearly, the second part of our claim holds as well. □
Informally, Lemma 6 means that not resolving the nonterminal as early as possible does not yield computations which would otherwise be not possible. Thus, we can resolve the nonterminal as early as possible.
Note that the nonterminal cannot be resolved before the corresponding is resolved. Consider the computation , where . Assume that is resolved before its corresponding , then clearly a computation , exists. However, the set of insertion rules only contains rules of the form , where j is the label of an insertion rule in I. Consider for instance the sentential form . By construction it is clear that neither nor can be resolved before is resolved. More generally, it is clear that given a sentential form , where , it holds that the rightmost nonterminal of has to be resolved before any other symbol of . Thus, no computation exists and hence it follows that cannot be resolved before the corresponding .
Furthermore, by Lemma 6, it is clear that resolving immediately after does not affect the computation. Therefore the following lemma holds analogously to Lemma 5.
Let i be the label of an insertion ruleof. Letandbe a derivation of, in which at most n insertion rules are used. Then the rules of this derivation can be reordered such that immediately after the application of a rulethe corresponding substitution rulesandapplied.
As holds according to [18, Theorem 5], we conclude:
. □
This is an interesting result, as the families of ins-del systems of size and of size are known to be equal [26, Theorem 4.7], yet both classes—extended with the same class of substitution rules—differ in their computational power. As and are closed under reversal, the next corollary follows with Lemma 2 and Theorem 4.
and. □
Construction 3 can be generalized in various ways. For instance, an insertion rule , with , and , can be simulated by a context-free insertion rule of the form , together with substitution rules , , …, , . Notice that the context size parameters of the simulated insertion rule determine the context parameters of the simulating substitution rules. We will not follow up on this here, but such generalizations could be useful in other simulations.
Extension with two-sided substitution
After analyzing the effect of context-free and one-sided substitution rules on context-free ins-del systems, we will now proceed to two-sided substitution rules, i.e., substitution rules with left and right context. Somehow surprisingly, this lifts the computational power of even the ‘weakest’ ins-del systems, that is, systems of size , up to the level of RE. Let . We will show that there is a system capable of simulating . The basic idea is that the context checks, necessary for simulating rules with left and right context, are performed by the substitution rules. The system is constructed in the following manner:
Letbe in normal form according to Construction
1
. For each rule of, we have a unique label, say, i, and we introduce a new nonterminal. Definewithwhere X is defined as in Construction
1
. Finally,with
The basic idea is similar to Construction 2. Each deletion rule of , where i is the label of , corresponds to a deletion rule and a substitution rule . We leave the context checks to the substitution rules. The same idea is applied to the insertion rules. With some technical effort, we can prove the following result.
The basic idea is similar to Construction 2. Each deletion rule of , where i is the label of , corresponds to a deletion rule and a substitution rule . We leave the context checks to the substitution rules. More precisely, simulates a deletion rule by substituting a in the context via . The introduced nonterminal is then deleted at some point by the deletion rule .
It is clear that a derivation of the form
in which the application of succeeds an application of immediately, is equivalent to the application of a deletion rule .
The same reasoning applies to insertion rules, where an insertion rule , where i is the label of , corresponds to an insertion rule and a substitution rule . Applying immediately after achieves the same result as applying .
We will show that for every derivation of , leading to a word , there is an alternative derivation, which results in w as well and in which all rules, introducing nonterminals , are immediately followed by the corresponding rules, which resolve . We remark that any sentential form occurring in such a derivation has at most one nonterminal .
Let . Consider a derivation . Then, there is an alternative derivation, leading from α to w, in which all nonterminals are resolved immediately after being introduced.
The claim of Proposition 4 follows by inductively applying Lemma 8 and Lemma 11, as . □
These lemmas and further auxiliary results are described in the following.
Letbe a deletion rule ofandandbe the corresponding rules of. Consider the derivationofwith. We refer to the nonterminal, introduced at this point, as. Then there is an alternative derivation, leading fromto w, in whichis resolved immediately.
Before we prove that there is an equivalent lemma for insertion rules, we show that the following statements holds.
Consider a sentential formof, where i and j are the labels of insertion rules of. There does not exist any wordsuch thatholds.
Let and be the insertion rules corresponding to the labels i and j, respectively. As is in normal form, neither of r, t, f or h is the empty word.
Assuming that there is a , such that , then and must be resolved at some point of the derivation. Given our construction of , can only be resolved by a substitution rule with . Clearly, as the right context of is and all letters that can be inserted between and are nonterminals , where k is the label of an insertion rule, cannot be resolved before is resolved. (Inserting between and would result in the initial situation.)
Resolving in turn requires to have as its left context, as the only rule resolving is . However, the current left context of is the nonterminal , which cannot be resolved before is resolved.
Therefore, neither nor can be resolved. □
No terminal string can be derived from sentential formsorwithand j being the label of an insertion ruleof.
We consider the case . The case is handled analogously. Assuming holds, then clearly has to be resolved at some point of the derivation. The only rule resolving is . However, this rule is not applicable as has no left context and no letters can be inserted to the left of due to Lemma 9. (All insertion rules are of the form , where k is the label of an insertion rule.) □
We now prove that all nonterminals , where j is the label of an insertion rule, can be resolved immediately after being introduced.
Letbe an insertion rule ofandandbe the corresponding rules of. Consider the derivationofwithand.
We refer to the nonterminal, introduced at this point, as. Then there is an alternative derivation, leading fromto w, in whichis resolved immediately.
We begin by analyzing and . Due to Lemma 10, follows. We show that and . In the following, we only prove , as is shown analogously. Due to Lemma 9 and as all insertion rules are of the form , where k is the label of an insertion rule of , it is clear that no letter can be inserted between and .
As all substitution rules require a left and a right context in V and the right context of is , cannot be substituted as long as is not resolved.
Given our construction of , cannot be deleted, as all deleting rules only delete symbols in and X. As
and therefore is resolved via at some point, but can neither be deleted or substituted and no letter can be inserted between and , follows.
We remark that we can assume that holds. If , then this X has been introduced as part of the axiom and follows, as due to Lemma 10, no letter is inserted to the left of the leftmost X of the axiom. Additionally, due to Lemma 10 cannot be deleted. Using the same argument as before, we see that cannot be substituted either and no letter can be inserted between and . Therefore, resolving requires a substitution rule with left context X, which, according to Construction 4, requires an insertion rule of the form of . However, there is no such insertion rule according to Construction 1.
As has to be resolved at some point of the derivation, all derivations leading from to w are of the form
Given our construction, there is no rule which has as either its left or right context.
Therefore, implies both and . Then, the derivation
results in w as well and resolves immediately. □
.
”⊆” Let be in normal form and let be of size and be constructed according to Construction 4. Consider an arbitrary derivation of . Then there is a derivation of . Whenever an insertion rule of is applied in the derivation of , we apply the corresponding rule immediately followed by an application of the rule . Whenever a deletion rule is applied, we act in an analogous manner.
”⊇” Consider a derivation of . Without loss of generality, we assume that all nonterminals are resolved by the corresponding rules immediately after being introduced. Replacing all insertion rules and all deletion rules occurring in the derivation of with the corresponding insertion and deletion rules of and removing all rules of yields a derivation of . □
Thus, we conclude that for any ins-del system of size in normal form according to Construction 4 an equivalent system of size can be constructed. As ins-del system of size are known to be computational complete, we conclude:
. □
We now analyze the power of ins-del-sub systems of size . By definition, it is clear that holds. In the following, we will show that this inclusion is proper. To be more precise, we will show that ins-del-sub systems of size characterize the context-sensitive languages. By Theorem 4, we are left to prove . For every context-sensitive language L, there is a linear bounded automaton (LBA) accepting L. We are going to construct an ins-del-sub system of size to simulate . We refrain from introducing LBA formally, but only mention that □ denotes the blank symbol and that we will use and # as two further symbols denoting the left and right endmarkers, respectively. These will be used, in particular, to describe LBA configurations. Clearly, blanks to the immediate right of $ or to the immediate left of # can be omitted or inserted without changing the configuration.
We first give a brief sketch of the basic idea behind this simulation in the following paragraph. The simulation revolves around strings of the form
where ; , . The concatenation of the first component of each tuple, that is, , is the input word of the linear bounded automaton , while the concatenation of the second component of each tuple, that is, , represents a configuration of running on the input word . If is a transition rule of such that
then this transition is simulated by the ins-del-sub system via the derivation
The idea is thus as follows: first, the ins-del-sub system generates a string
where is clearly the starting configuration of on input . Starting from this string, is simulated via the second components of the tuples. If in this simulation a string
such that is an accepting configuration is generated, i.e., , we substitute all tuples with their respective first component. For instance, a tuple is substituted with . In short, this means that if (the simulation of) running on halts in an accepting configuration, we generate the word . More details follow:
Consider an arbitrary LBAaccepting. Let $ be the left and # be the right endmarker of. Then, the following ins-del-sub systemgenerates the language L by simulating. The set V is defined as, whereStrings of the formwhich encode the input and a configuration ofconsist of symbols in, while the symbols inandare auxiliary symbols. Symbols inare used are used in the initialization phase, that is they are used to generate strings of the formwhereis the starting configuration ofon inputand symbols inare used during the simulation of a transition. We defineandwhere the symbols inandare used to simulate transitions with left and right movement respectively. Furthermore we defineand. If, we add λ to the set of axioms. The set of substitution rules is defined as, where the substitution rules inare used in conjunction withand I during the initialization phase. The set N consists of substitution rules used to simulate a transition ofwith no movement while rules in L and R are used to simulate a transition ofwith left and right movement, respectively. The sets N, L and R are constructed as follows:
ifis a transition rule ofthen N contains the rules,,, where.
ifis a transition rule ofthen L contains the ruleswhereand. Note that applying these rules in this order simulates. Additionally, L containsandandwhich are derivatives of the previous rules and are used in the case of a left-movement next to endmarkers. Furthermore L contains the rulewhich covers the case of a left-movement to the left endmarker and the rulewhich covers the case, i.e. the case of a left-movement from the right endmarker.
ifis a transition rule ofthen R contains the ruleswhereand. Additionally, R containsandandwhich are derivatives of the previous rules and are used in the case of a right-movement next to endmarkers. Furthermore R contains the rulewhich covers the case of a right-movement to the right endmarker and the rulewhich covers the case, i.e. the case of a right-movement from the left endmarker.
The setconsists of substitution rules which substitute symbols inwith their first component. More,, wherecontains rules of the formandcontains rules of the formwith,,.
Before proving the correctness of our construction, let us look into an example, describing a deterministic LBA accepting the language .
Consider the following deterministic LBA .
,
,
δ is given by the following table. R and L indicate head movements. When no target state is given, the processing stops and the input word is not accepted.
The empty columns concerning state and the endmarkers were omitted.
.
We explain the working of the LBA by considering the three smallest words as examples. We omit blanks (□) and the endmarkers at the two ends of the tape and write the state information immediately to the left of the symbol on the tape the head is scanning.
In the following, we describe how the ins-del-sub system our construction yields operates when simulating the LBA described in Example 3. For instance, let simulate a computation of on the input word . To simulate this computation, first generates the string
before starting the actual simulation. To generate this string, our starting point is the axiom . Given our construction, the only rules of that can be applied at this point are the rules in I and . More precisely, using the insertion rules , , and substitution rules , , , , , from , the derivation
is produced. We remark that none of the nonterminals , or can be inserted only to the left of X or to the right of , as otherwise these nonterminal cannot be resolved anymore, because the only rules resolving these nonterminals are the substitution rules , and . Thus, generating a string of the forms , etc. is not possible. Therefore, all insertions occur between X and . Furthermore, note that any of the nonterminals , or must be resolved by the corresponding substitution rule before a new nonterminal in is inserted, as otherwise at least one symbol in cannot be resolved at all, because only the nonterminals in to the immediate right of X can be resolved. Therefore, it follows easily that, after the application of the substitution rule , no further nonterminals can be inserted, as otherwise these nonterminals cannot be resolved anymore. Additionally, we remark that by construction, prior to the application of the substitution rule , none of the substitution rules in can be applied.
Before we describe in the following how the first two transitions of on the input are simulated, we note that the correctness of the set R, i.e., that applying the rules in R only yields correct simulations of transition rules and nothing else, follows from “Révész’s trick” [23]. More precisely, a transition rule of the LBA implies that a derivation
exists for all where and . From the grammar perspective, any derivation of this form can be obtained by a production rule of the form . In [23], it is shown that this production rule is correctly simulated by the sequence of production rules of the form
where W and Z are new symbols, i.e., replacing with this sequence of production rules yields a grammar which is equivalent to the original one. It is easy to see that this sequence of production rules is essentially the same as the sequence
occurring in R. Clearly, the case concerning left movements from rule set L is simply a mirror of this case.
We now describe how the first two transitions of on the input are simulated. Clearly, these transitions (including blank symbols and endmarkers) are
Applying the sequence of rules
from R obtained from the transition rule to yields the derivation
This clearly simulates the first transition. In general it holds by construction that only rules in are applicable to strings of the form
generated by the ins-del-sub system constructed according to Construction 5, where . In our example in particular, note that the substitution rule is the only rule applicable to , aside from insertion rules whose application results in a sentential form from which no terminal string can be derived. Analogously, the sequence
obtained from the transition rule yields the derivation
which clearly simulates . Note that again only rules in are applicable to . In particular, only the rule is applicable to and following the application of this rule only the remaining rule of this sequence can be applied. The remaining transition rules used in the computation of on the input word are simulated analogously. Thus, eventually arrives at
where is the accepting configuration of on input . Applying the rule from and further rules from , we arrive at the derivation
We remark that, by construction, it holds in general that only a rule from is applicable to strings of the form
generated by an ins-del-sub system constructed according to Construction 5 if is an accepting configuration. Clearly, this also holds for our example. After the application of a rule from , only the rules from are applied in a terminal derivation.
We now show that generates the language accepted by in general.
.
By definition it is clear that holds, as any word generated by is accepted by .
We now show . By definition any with is generated by as . Consider a word with . Let with . Clearly there is a derivation of the form
As , the simulation of running on results in a sentential form
such that is an accepting configuration and therefore generates w. □
Working out details proving the correctness of this construction, one can show:
. □
Using a similar approach, one can show a characterization of the recursively enumerable languages.
.
The basic idea is the same as in the simulation of linear bounded automata with the addition of a phase 0 before the first derivation phase, in which the amount of space needed by the Turing machine in addition to the input word is guessed. We give a short description of the workflow and rules used in the phase 0, using the following rules:
Clearly, all symbols must be inserted directly to the left or right of the axiom , otherwise these symbols cannot be resolved.
Phase 0 concludes with the application of the substitution rule after which phase 1 is conducted analogously to the case of linear bounded automata. The basic idea is that after the application of no further nonterminals can be inserted anymore, as they cannot be resolved otherwise. Furthermore, all introduced up to the application of must have been resolved via either or . The idea is that the symbols of the form , where □ is the blank symbol of the Turing machine provide the additional space needed.
In the last phase, we finally delete all symbols of the form where x is some symbol that occurs during the simulation of the Turing machine via a deletion rule of the forms or , . These are the only deletion rules used in the system.
Consider Construction 5. Symbols of the form , , are introduced by substituting symbols which in turn are introduced by context-free insertion rules . It can be shown that if more than one is introduced in phase 0 or if following the application of the introduced in phase 0 is not positioned directly to the right of , no terminal string can be derived. □
As a consequence of Theorem 9, we can formulate the following Penttonen-style normal form theorem for context-sensitive languages.2
Recall that Penttonen [22] proved that for any context-sensitive language, there is a grammar that contains only one-sided rules of the forms , , for nonterminals A, B, C and terminals a.
We believe that this could be useful in particular when dealing with variations of insertion systems. In our experience, it is often more complicated to simulate context-free rules (as opposed to context-sensitive ones), and in the case of the normal form presented in the following theorem, it is obviously only necessary to implement one insertion rule (with one-sided context) instead of presenting a whole simulation of arbitrary context-free rules.
For every context-sensitive language L,, there is a context-sensitive grammar, such that, with rules of the forms
Before we prove Theorem 11 consider the following auxilliary lemma.
Consider an ins-del-sub systemof size. Then there is an ins-del-sub systemof size, such thatand all insertion rules ofare of the form,.
We define . If , we add λ to as well. For each insertion rule of and each we introduce an insertion rule to . Consider an arbitrary derivation of . Then at some point of this derivation a symbol c is inserted such that this c is the leftmost symbol of the sentential form and no further insertions occur left of this c (or any symbol this c is substituted with). The basic idea is that we guess this c in advance and start the derivation of with the corresponding axiom . By induction it is clear that iff where is a string over . As the derivation of is of the form , it is clear that . (If in a derivation of starting with the axiom and leading to no symbol is inserted left of the leftmost symbol of α (or any symbol this symbol is substituted with), then clearly iff .)
Clearly, . Moreover, all insertion rules of are of the form , . □
Consider an ins-del-sub systemof sizesuch that all insertion rules ofare of the form,. Then there is an ins-del-sub systemof the same size such thatconsists of a single axiom of length 1 and all insertion rules ofare of the form,which generates the same language.
Let all axioms of be labelled in a one-to-one manner. is constructed as follows. Let and
For each axiom labelled by i, with , we add the following insertion and substitution rules to and :
If , we simply add the substitution rule to .
For the correctness of our construction, consider the following. Assume that a derivation of begins with the application of . can only be resolved by being substituted with which in turn requires the application of at some point to be resolved. (We remark that by our construction prior to the application no symbol in V can be introduced, as all insertion rules in I are of the form , .) As the application of requires the introduction of the symbol it is clear that all and , , have been introduced at least once before is applied. This means that all insertion rules , , have been applied at least once before the application of . As all are resolved by being substituted by via a rule of the form , we can deduce that every insertion rule is applied exactly once. (Otherwise, some nonterminals cannot be resolved.)
Let L be an arbitrary context-sensitive language. Due to Theorem 9, there is an ins-del-sub system of size which generates L. Then clearly there is an ins-del-sub system of size which generates L with the property specified in Lemma 12. By Lemma 13, let the set of axioms consist of a single symbol X. Based on we construct the context-sensitive grammar as follows: We define . For each insertion rule we add a production rule to P. For each substitution rule we add the production rules and to P. Finally, for each we add a production rule to P. □
Clearly, it is also possible to ‘swap the direction’ in the context-free rules of this normal form, which means that (when interpreted as insertion rules), context information ‘from the other side’ is used.
For every context-sensitive language L,, there is a context-sensitive grammar, such that, with rules of the forms
Allowing erasing productions on top, from Theorem 11 and Corollary 6 we also arrive at new characterizations of the family of recursively enumerable languages. By different methods, we could even prove that either of the two non-context-free forms suffices to achieve RE. Details can be found in the long version of [29]. Therefore, we do not make the phrase structure grammar normal forms for RE explicit in this paper.
Summary, open questions, and general discussions
In this paper, we have introduced substitution as an additional operation and have investigated the effect of the addition of substitution rules on context-free ins-del systems. In particular, we have shown that the addition of substitution rules to ins-del systems yields new characterizations of and . More precisely, we have shown the following equalities: , and . Additionally we have shown . While in the above cases, an extension with (non-context-free) substitution rules leads to an increase in computational power, we have also shown that the addition of context-free substitution rules to context-free ins-del systems does not affect the computational power.
The main open question is if is computationally complete. We conjecture this not to be the case, as with only left context rules, information can only be propagated in one direction. Yet, should equal , this would provide an interesting new normal form. A minor open question is the strictness of the inclusion .
It would be also interesting to know which subregular language classes can be described by certain ins-del(-sub) language families, or if such subregular language classes can be even characterized by them. In more general terminology, this asks about comparing ins-del(-sub) language families that are not computationally complete with the very well-known language classes from the Chomsky hierarchy.
For further results on ins-del systems extended with substitution rules, we refer to [29] and [30] in which the effect of such a type of rules on context-free ins-del systems and matrix ins-del systems, that is ins-del system with matrix control, are investigated, respectively.
Discussing the broader context
Insertion-deletion systems are one model of molecular computing, trying to use elementary operations on (DNA) strings. Admittedly, the basic operations of this study (insertions, deletions, and substitutions) are quite akin to traditional operations on strings; they are even the basic of the definition of edit distance as discussed in [31].
However, there are also other operations motivated by the structure and working of DNA that have been suggested and discussed in the literature. Prominent examples include the Watson-Crick complement and the splicing operation. For a thorough discussion of the biological background, the best source is still probably the original paper of Tom Head [9], both accessible for biologists and for computer scientists. Quite a number of further models have been suggested in (theoretical) biocomputing; for a brief survey, we point to [7], or for a more in-depth presentation, to the already mentioned monograph [21]. Many variations of these models have been shown to be computationally complete, i.e., they are capable of simulating Turing machines and hence, based on the famous Church-Turing thesis, this means that any algorithm can be implemented using these mechanisms.
However, we believe that combining these operations (as we did in the present paper) is an interesting venue also to pave the ground for further applications, going far beyond storage implementations as announced by Microsoft in https://news.microsoft.com/innovation-stories/hello-data-dna-storage/. Further applications range from solving NP-hard problems (as described in [1,10,19]) on more special-purpose machines to building universal computers (we only refer to [5] in the case of splicing systems, catching up on earlier discussions).
Another strand of interest can be deduced from the parsimony principle, also cf. [4]: How small can the resources be that have to be used to build universal computers? If several such resources are available (as length of insertion or deletion strings, or length of contexts in the grammatical mechanisms that we study), we often find trade-off results that are also interesting from the perspective of possibly trading some resources for others. This can be quite important for the sketched applications, also because (due to new technologies) it could happen that resources earlier considered to be cheap later become expensive, or vice versa.
Footnotes
Acknowledgements
We are grateful to the referees of this paper, whose comments helped improve the presentation of this manuscript and also inspired to add several further examples and results.
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