Constant Multiplicative Sensitivity on the CDAWGs
Abstract
Compact directed acyclic word graphs (CDAWGs) [Blumer et al. 1987] are a fundamental data structure on strings with applications in text pattern searching, data compression, and pattern discovery. Intuitively, the CDAWG of a string is obtained by merging isomorphic subtrees of the suffix tree [Weiner 1973] of the same string , and thus CDAWGs are a compact indexing structure. Indeed, the CDAWG size can be sublinear in for some highly repetitive strings. Of its various applications, the CDAWG allows for computing pattern occurrences, maximal exact matches (MEMs), minimal absent words (MAWs), and minimal unique substrings (MUSs) in optimal time using space. For designing space-efficient data storage, it is crucial that the underlying data structure is robust against data edits and errors. As a mathematical measure for this, the notion of compression sensitivity [Akagi et al. 2023] was introduced as the maximum of the size increase in the compressed data structures after edits operations. In this paper, we investigate the sensitivity of CDAWGs when a single character edit operation is performed at an arbitrary position in the input string . We show that the size of the CDAWG after an edit operation on is asymptotically at most 8 times larger than the original CDAWG before the edit. This upper bound significantly improves on the only known upper bound for the problem.
Keywords and phrases:
string data structures, maximal repeats, data compression, compression sensitivity, CDAWGsFunding:
Rikuya Hamai: JST BOOST Grant Number JPMJBS2406.Copyright and License:
2012 ACM Subject Classification:
Mathematics of computing Combinatorial algorithmsEditors:
Philip Bille and Nicola PrezzaSeries and Publisher:
Leibniz International Proceedings in Informatics, Schloss Dagstuhl β Leibniz-Zentrum fΓΌr Informatik
1 Introduction
Compact directed acyclic word graphs (CDAWGs) [4] are a fundamental data structure on strings with applications in text pattern searching, data compression, and pattern discovery. Intuitively, the CDAWG of a string (denoted ) is a minimal partial DFA that is obtained by merging isomorphic subtrees of the suffix tree [30] of the same string . Let denote the size (i.e. the number of edges) of the CDAWG for the input string. It is known that holds [4] for any strings of length , and can be sublinear in for some highly repetitive strings [27, 2, 25]. CDAWGs can thus be regarded as a compressed text indexing structure, which can be stored in space without explicitly storing the string [3, 14]. A grammar-based string compression of size is also known [3, 7].
Given a pattern of length , the CDAWG of text permits exact pattern matching in optimal time with space, where is the number of occurrences of in . By adapting the suffix-tree based approach (Algorithm 1 in [23]), inexact matches such as exact maximal matches (MEMs) and generalized MEMs (-MEMs and -rare MEMs) can also be computed in optimal time and with space by the CDAWG. Finding (generalized) MEMs has important applications in bioinformatics. CDAWGs are also used as a space-efficient data structure allowing for optimal-time detection of βunusual wordsβ (such as minimal absent words (MAWs) [8], minimal unique substrings (MUSs) [13]), and string net occurrences [12] from the input string with space each [3, 16, 20]. On a more practical side, CDAWGs enjoy applications in natural language processing [29] and in analysis of text generated by language models (LMs) [19].
In this paper, we consider the multiplicative sensitivity of the CDAWG size which is defined by the worst-case value of , where is the input string and is a string obtained by performing a single-character edit operation on . In case where the edit operation to the string is performed at either end of , then the multiplicative sensitivity of CDAWGs is known to be asymptotically at most , and it is tight [15, 9]. However, the general case with an arbitrary single-character-wise edit on was not well understood for CDAWGs. In this paper, we prove that any edit operation at an arbitrary position on the string can increase the size of the CDAWG asymptotically at most 8 times larger than the original. We emphasize that the only known upper bound for the sensitivity of CDAWGs is , which trivially follows since and for any string of length [4, 3]. Our technique for proving the constant sensitivity of CDAWGs is purely combinatorial, which involves new and original ideas that were not present in the special case of left/right-end edits [15, 9].
Compression sensitivity.
Following the earlier work of Lagarde and Perifel [18] and Akagi et al. [1], string compressors and repetitiveness measures can be categorized into three classes:
-
(A)
Stable: Those whose multiplicative sensitivity is ;
-
(B)
Changeable: Those whose multiplicative sensitivity is ;
-
(C)
Catastrophic: Those whose multiplicative sensitivity is with some constant .
To mention a few of them, it is shown in [1] that Class (A) includes the substring complexity [17], the smallest macro scheme [28], the Lempel-Ziv 77 families [31, 28], and the smallest grammar [26, 6]. Our new result implies that the CDAWGs belong to Class (A). Class (B) includes run-length Burrows-Wheeler transform (RLBWT) as shown in [1, 10, 11], and lex-parse [24] as shown by Nakashima et al. [22]. It is shown by Lagarde and Perifel [18] that the Lempel-Ziv 78 [32] belongs to Class (C).
2 Preliminaries
Strings.
Let be an alphabet of size . An element of is called a string. For a string , the length of is denoted by . The empty string, denoted by , is the string of length . For any non-negative integer , let denote the set of strings of length . For any two strings and , let denote the edit distance between and . For any string and a non-negative integer , let .
For string , , , and are called a prefix, substring, and suffix of , respectively. The sets of prefixes, substrings, and suffixes of string are denoted by , , and , respectively. For a string of length , denotes the th character of for , and denotes the substring of that begins at position and ends at position on for .
Maximal substrings and maximal repeats.
A substring of is left-maximal if (1) or (2) there exist two distinct characters such that , and it is right-maximal if (1) or (2) there exist two distinct characters such that . These substrings that occur at least twice in are also called left-maximal repeats and right-maximal repeats in , respectively.
Let and denote the sets of left-maximal and right-maximal substrings in . Let . The elements in are called maximal substrings in , and the elements in are called maximal repeats in . A character is said to be a right-extension of a maximal repeat of if .
For any substring of a string , we define its left-representation and right-representation by and , where are the shortest strings such that is left-maximal in and is right-maximal in , respectively.
CDAWG.
The compact directed acyclic word graph (CDAWG) of a string , denoted , is the minimal DFA that recognizes all substrings of , in which each transition (edge) is labeled by a non-empty substring of . has a unique source that represents the empty string and a unique sink that represents . All the other internal nodes represent the maximal repeats in , namely, the set of the longest strings represented by the nodes of are equal to . See Figure 1 for a concrete example of CDAWGs. The size of for a string of length is the number of edges in , which is equal to the number of right-extensions of maximal repeats in . For each , let denote the number of out-edges of node in . It is clear that . In what follows, we will identify maximal substrings with CDAWG nodes, and right-extensions of maximal repeats with CDAWG edges, respectively.
Sensitivity of CDAWG size and our results.
Using the measure , we define the worst-case multiplicative sensitivity of the CDAWG with an edit operation (insertion, deletion, or substitution) by .
In this paper, we prove the following:
Theorem 1.
For any string of length , holds. For any string of length ending with a unique character , holds.
3 Occurrences of maximal repeats crossing the edited position
To present an upper bound for the sensitivity of CDAWG size, it is essential to consider new occurrences of maximal repeats that contain or touch the edited position . In this section, we introduce several new definitions regarding those new occurrences of maximal repeats.
Definition 2 (Crossing occurrences).
Let be a non-empty substring of that touches or contains the edited position . That is, if the edit operation is insertion and substitution, (1) (touching from left), (2) (containing ), or (3) (touching from right). If the edit operation is deletion, (1) (touching from left), (2) (containing ), or (3) (touching from right). These occurrences of a substring in are said to be crossing occurrences for the edited position . We will call these occurrences simply as crossing occurrences of .
We denote the left most crossing occurrence of as . For , we consider the following substrings and of (see Figure 2 for illustration):
In the case that the edit operation is insertion or substitution, let
In the case that the edit operation is deletion, let
We define the rightmost crossing occurrence , together with and , analogously.
Definition 3.
We categorize strings that have crossing occurrence(s) in the edited string in into the five following types, depending on the properties of :
- Type (i):
-
has only one crossing occurrence of in .
- Type (ii):
-
-
1.
has two or more crossing occurrences of in .
-
2.
If all occurrences of in are crossing occurrences of in , then and .
-
1.
- Type (iii):
-
-
1.
has two or more crossing occurrences of in .
-
2.
If all occurrences of in are crossing occurrences of in , then and .
-
1.
- Type (iv):
-
-
1.
has two or more crossing occurrences of in .
-
2.
If all occurrences of in are crossing occurrences of in , then and .
-
1.
- Type (v):
-
-
1.
has two or more crossing occurrences of in .
-
2.
If all occurrences of in are crossing occurrences of in , then .
-
1.
Figure 3 illustrates the five types of a string when and .
The reason why we only consider and is due to the periodicity for . We remark that when has multiple crossing occurrences which contain or touch the edited position in , then the characters immediately before all crossing occurrences of in except for are the same and the characters immediately after all crossing occurrences of in except for are the same. This is because when has three or more crossing occurrences containing in , then all these crossing occurrences of are periodic (c.f. [5, 21]). Therefore, to examine whether is maximal in or not, we do not need to consider all crossing occurrences of in other than and .
In Definitions 4 and 5 below, we introduce and which are respectively the sets of new maximal repeats and existing maximal repeats in , such that . We then partition each of them into smaller subsets that are suitable for our needs.
Definition 4 (Partition of new maximal repeats).
Let denote the set of new maximal repeats in . We divide into the three following disjoint subsets , , and . Further, we divide into two disjoint subsets and as follows: is the set of strings such that (1) is of Type , and (2) there is no other right-extension of in than the right-extension(s) of the crossing occurrence(s) of , and .
We note that the following properties hold for and by definition:
-
because .
-
because .
-
.
Definition 5.
Let denote the set of existing maximal repeats in . We divide into the two following subsets and .
Namely, (resp. ) is the set of existing nodes of the CDAWG for which the number of out-edges increases (resp. does not increase).
Example 6.
Consider the string
and
the string obtained by deleting the character from highlighted in bold.
The edited position in is designated by a .
For instance,
(also see Figure 4).
Recall that denotes the number of edges in before the edit. In the subsequent sections, we work on the three disjoint subsets , , and of , and show that (Section 4), (Section 5), and (Section 6). All these immediately lead to Theorem 1 that upper bounds the number of edges in after the edit to .
The tighter upper bound for strings ending with is shown in Section 7.
4 Upper bound for total out-degrees of nodes w.r.t.
In this section, we show an upper bound for the total out-degrees of the nodes corresponding to strings in . Recall that implies .
We first describe useful properties of strings .
Lemma 7.
Any occurs in .
Proof.
In the case , since , occurs in .
Let us consider the case that is of Type , , or . Since is not of Type , if all occurrences of in are crossing occurrences of in , then . Therefore, occurs in .
Let us consider the case that is of Type . Due to the definition of , there exists a distinct right-extension of in other than the right-extension(s) of the crossing occurrence(s) of . Therefore, there is a non-crossing occurrence of in , which implies that occurs in (see also Figure 5).
Lemma 8.
For any that is of Type , or , there does not exist such that and , where .
Proof.
If is a prefix of , then clearly there is no satisfying and . In what follows, we consider the case that is not a prefix of .
For a contrary, suppose that for that is of Type , or , there exists such that and , where . See also Figure 6. Let be the character immediately before . Since is of Type , or , every crossing occurrence of in is immediately preceded by . Because , it holds that , or there is a distinct character such that occurs in . This implies that there is a non-crossing occurrence of in , which is as a prefix of or is immediately preceded by in . By Lemma 7, occurs in , and thus that is a suffix of also occurs in . Hence , however, this contradicts that .
Lemma 9.
For any that is of Type or , there do not exist with and satisfying and simultaneously, where .
Proof.
If is a prefix of , then clearly there is no satisfying and . In what follows, we consider the case that is not a prefix of .
For a contrary, suppose that for that is of Type or , there exist with and such that and at the same time, where . Let the character immediately before and the character immediately before be and (), respectively. By Lemma 7, and occur in , and thus that is a suffix of and that is a suffix of both occur in . Therefore, , however, this contradicts that .
4.1 Correspondence between and
For any that is of Type , or , we associate with . For any that is of Type or , if there does not exist such that and with , we associate with , and otherwise we associate with .
By Lemma 8 and Lemma 9, each can be associated to a distinct string with . Note however that may not be maximal in . Thus we introduce a function that bridges each to a distinct maximal substring in .
Definition 10.
For any , let (see Figure 7).
By Lemma 7, occurs in and thus its suffix also occurs in . Hence is well defined.
Lemma 11.
For any , .
Proof.
By Definition 10, . Therefore, it suffices for us to prove . From now on, we consider the four following cases:
Case (a) .
In this case, , therefore that is a suffix of also satisfies . Hence, .
Case (b) and is of Type , or .
Let the character immediately after all crossing occurrences of in be . There exists in or because . Since the character immediately after all crossing occurrences of in is , then there exists or in . Hence, since the character immediately after is . Thus, .
Case (c) and is of Type .
Since is of Type , we associate with . Because is of Type and is a suffix of a , holds. Thus, .
Case (d) and is of Type .
Let the character immediately after be . Since there exists a distinct right-extension of in other than the right-extension(s) of the crossing occurrence(s) of , there exists in . Therefore, . Thus, .
Consequently, we have .
The next lemma states the uniqueness of .
Lemma 12.
For any with , .
Proof.
Suppose that there exist such that and . Let and correspond to and , respectively, where . Let , and assume without loss of generality that due to Lemma 8 and Lemma 9. Then because . Since by Lemma 11, and since is a prefix of (see Figure 8), we have . This contradicts .
4.2 Upper bound w.r.t.
Lemma 13.
.
Proof.
Let , where . Since is a suffix of , . Since there are at most two distinct characters immediately after the crossing occurrences of , . For , we have . Thus . For , we have . Thus . By using Lemma 12 and summing up these, we get .
5 Upper bound for total out-degrees of nodes w.r.t.
In this section, we show an upper bound for the total out-degrees of nodes corresponding to strings that are elements of .
We first present properties of the strings in . In particular, we focus on the strings in , as the strings in are less important and can be handled in a trivial manner.
Lemma 14.
Any occurs in .
Proof.
Since , . Thus occurs in .
Lemma 15.
For any that is of Type , or , there does not exist such that and , where .
Proof.
The case that follows from a symmetrical argument to Lemma 8, in which may belong to or . Let us consider the case that . Suppose that for which is of Type , or , there is such that and , where . If is a suffix of , then there is no such that and . From now on consider the case that is not a suffix of . Let be the character immediately after . Then, since is of Type , or , character immediately follows every crossing occurrence of in . Note that is a prefix of . Due to Lemma 14, occurs in , implying also occurs in . Thus the number of right-extensions of in is no more than the number of right-extensions of in . However, this contradicts .
Lemma 16.
For any that is of Type or , there do not exist with and satisfying and simultaneously, where .
Proof.
If is a suffix of , then clearly there is no satisfying and . In what follows, we consider the case that is not a suffix of .
Suppose that for which is of Type or , there exist with , that satisfy and at the same time, where . Let and () be the character immediately after in and the character immediately after in , respectively. By Lemma 14, and occur in , and hence that is a prefix of and that is a prefix of also occur in . Therefore, . However, if , this contradicts . Also, if , the number of right-extensions of in does not increase from the number of right-extensions of in . However, this contradicts .
5.1 Correspondence between and
For any that is of Type , or , then we associate with both and . For any that is of Type or ,
By Lemmas 15 and 16, each corresponds to a distinct string , where . Below, for each , we define and to which corresponds:
Definition 17.
For each associated to , let . For each associated to , let . See Figure 11. When there is only one crossing occurrence of (i.e. ), only is defined as above and is undefined.
(resp. ) is undefined for any that is not associated to (resp. ).
By Lemma 14 every occurs in , and thus and are well defined when is associated to and , respectively.
Lemma 18.
For any , if is defined, and if is defined.
Proof.
By Definition 17, . Therefore, it suffices for us to prove . For any , . Since is a prefix of , we have . Hence holds.
Lemma 19.
For any with , let be a list of , , , which are defined. Then the elements in differ from each other.
Proof.
By a symmetrical argument to Lemma 12.
5.2 Upper bound w.r.t.
Lemma 20.
.
Proof.
Below, we consider all the four possible cases depending on whether or , and whether .
When and .
-
First, we consider the case that is associated with both and . Since , then . Therefore, the number of characters that are immediately after in is at most one. Moreover, there are at most two distinct characters immediately after the crossing occurrences of . Hence, there are at most three distinct characters immediately after in , namely we have
(1) In addition, since , it holds that . By Inequality 1, we get
-
Second, we consider the case that is associated with only one of or .
-
β
Assume that we associate with . Since , then . Therefore, the number of characters immediately after in is at most one. In this case, we do not associate with , hence, has only one crossing occurrence or there exists such that and where . When has only one crossing occurrence, there are at most one character immediately after the crossing occurrence of . When there exists such that and where , then such occurs in due to Lemma 14. Therefore, although there are at most two distinct characters immediately after the crossing occurrences of , one of them is the character immediately after in as shown in Figure 12. Hence, we have
(2) In addition, since , then holds. By Inequality 2, we get
-
β
Let us assume that we associate with . In the same way as we associate with , we get .
-
β
When and or .
-
Let . Now that is defined, is associated with .
- β
-
β
Second, we consider the case that we only associate with . Since , holds. In the same way as in Inequality 2, we get . Thus, we have .
-
Let . Now that is defined, is associated with . In the same way as in the case for , we get in the case that we associate with both and , and we get in the case that we only associate with .
When and .
Here, we analyze since .
-
First, we consider the case that we associate with both and . There are at most two distinct characters immediately after the crossing occurrences of . Hence,
(3) In addition, since , then holds. By Inequality 3, we get .
-
Second, we consider the case that we associate with only one of or . Here, let us assume that we associate with . In this case, we do not associate with , hence, has only one crossing occurrence or there exists such that and where . When has only one crossing occurrence, there are at most one character immediately after the crossing occurrence of . When there exists such that and where , then such occurs in due to Lemma 14. Therefore, although there are at most two distinct characters immediately after the crossing occurrences of , one of them is the character immediately after in as shown in Figure 12. Hence, we have
(4) In addition, since , then holds. By Inequality 4, we get . In the case that we associate with , in the same way as we associate with , we get .
When and or .
Here, we analyze since .
-
Let . Since is defined, is associated with .
- β
-
β
Second, let us consider the case that we only associate with . Since , holds. In the same way as in Inequality 4, we get . Thus, we have .
-
Let . Since is defined, is associated with . In the same way as in the case for , we get in the case that we associate with both and , and we get in the case that we only associate with .
| When | When | |
|---|---|---|
Wrapping up.
Table 1 summarizes the bounds obtained above. For simplicity, let when is undefined, and let when is undefined. Note that this does not affect our upper bound analysis, since no maximal repeats in are associated to the undefined βs and βs. By Lemma 19, there is at most one string such that or . Thus, by using Lemma 19 and summing up the values in Table 1, we obtain . Also, since the number of out-edges of does not increase, we get . By adding , we get .
6 Upper bound for total out-degrees of nodes w.r.t.
In this section, we show an upper bound for the total out-degrees of nodes corresponding to strings that are elements of . We first describe useful properties of strings .
Definition 21.
For any , let be the string that is obtained by removing and from , namely .
Note that, by the definition of Type , each has two or more crossing occurrences in . Hence always exists (possibly the empty string). See Figures 13 and 14.
Lemma 22.
For any with , .
Proof.
For a contrary, suppose that there exist such that and . Since is of Type , the characters immediately after and are different and let () be these characters, respectively. If , then both and must be prefixes of (see Figures 15 and 16), which contradicts that . The other case where also leads to a contradiction. Hence , which implies . Also, follows in a symmetric manner. These imply , which is a contradiction.
6.1 Correspondence between and
For any , we associate with . For any we define to which corresponds, by using , as follows:
Definition 23.
For any , let (see also Figure 17).
We note that is well defined since is a substring of .
Lemma 24.
For any with , .
Proof.
Suppose that there exist such that and , and without loss of generality that . Then, occurs at least twice in . Therefore, , however, this is a contradiction.
6.2 Upper bound w.r.t.
Lemma 25.
.
Proof.
By the definition of , there is no other right-extension of in than the right-extension(s) of the crossing occurrence(s) of . Thus there are at most two distinct characters immediately after in . Since occurs at least twice in , . Hence, we get . Therefore, we have by Lemma 24.
7 Tighter upper bound for strings ending with $
In this section, we consider any string ending with a unique end-marker , and present a tighter upper bound for the worst-case multiplicative sensitivity of :
Lemma 26.
For any string of length ending with a unique character , holds.
Proof.
We first examine the upper bound in Lemma 13. When ends with a unique character , the argument of Lemma 13 can be adapted as follows. Let , and let be defined in the same way as in Lemma 13. Since every maximal repeat in the CDAWG of any string ending with has at least two outgoing edges, we have . From the same reasoning as in Lemma 13, it follows that , which can be tightened to when .
By Lemma 12, the mapping is injective. Therefore,
By applying similar arguments to the nodes considered in Lemma 20 and Lemma 25, we obtain upper bounds of and , respectively.
Summing up these three bounds gives us
Hence, the total upper bound is , as claimed.
8 Conclusions
This paper proved that the worst-case multiplicative sensitivity of CDAWGs is asymptotically at most 8. Our analysis is built on new combinatorial properties of maximal repeats and their right-extensions, that are incidental to an edit operation on the strings. The only known lower bound for the multiplicative sensitivity of CDAWGs is asymptotically 2 [9]. It is intriguing future work to close the gap between these upper bound and lower bound.
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