Computing Runs on a Trie

A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a rooted edge-labeled tree where the endpoints of the path must be a descendant/ancestor of the other. For a trie with n edges, we show that the number of runs is less than n. We also show an O(n sqrt{log n}log log n) time and O(n) space algorithm for counting and finding the shallower endpoint of all runs. We further show an O(n log n) time and O(n) space algorithm for finding both endpoints of all runs. We also discuss how to improve the running time even more

Memoized Symbolic Execution

This paper introduces memoized symbolic execution (Memoise), a novel approach for more efficient application of forward symbolic execution, which is a well-studied technique for systematic exploration of program behaviors based on bounded execution paths. Our key insight is that application of symbolic execution often requires several successive runs of the technique on largely similar underlying problems, e.g., running it once to check a program to find a bug, fixing the bug, and running it again to check the modified program. Memoise introduces a trie-based data structure that stores the key elements of a run of symbolic execution. Maintenance of the trie during successive runs allows re-use of previously computed results of symbolic execution without the need for re-computing them as is traditionally done. Experiments using our prototype embodiment of Memoise show the benefits it holds in various standard scenarios of using symbolic execution, e.g., with iterative deepening of exploration depth, to perform regression analysis, or to enhance coverage

On Counting Triangles through Edge Sampling in Large Dynamic Graphs

Traditional frameworks for dynamic graphs have relied on processing only the stream of edges added into or deleted from an evolving graph, but not any additional related information such as the degrees or neighbor lists of nodes incident to the edges. In this paper, we propose a new edge sampling framework for big-graph analytics in dynamic graphs which enhances the traditional model by enabling the use of additional related information. To demonstrate the advantages of this framework, we present a new sampling algorithm, called Edge Sample and Discard (ESD). It generates an unbiased estimate of the total number of triangles, which can be continuously updated in response to both edge additions and deletions. We provide a comparative analysis of the performance of ESD against two current state-of-the-art algorithms in terms of accuracy and complexity. The results of the experiments performed on real graphs show that, with the help of the neighborhood information of the sampled edges, the accuracy achieved by our algorithm is substantially better. We also characterize the impact of properties of the graph on the performance of our algorithm by testing on several Barabasi-Albert graphs.Comment: A short version of this article appeared in Proceedings of the 2017 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2017

Efficient LZ78 factorization of grammar compressed text

We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string. Given an SLP of size $n$ representing a text $S$ of length $N$, our algorithm computes the LZ78 factorization of $T$ in $O(n\sqrt{N}+m\log N)$ time and $O(n\sqrt{N}+m)$ space, where $m$ is the number of resulting LZ78 factors. We also show how to improve the algorithm so that the $n\sqrt{N}$ term in the time and space complexities becomes either $nL$, where $L$ is the length of the longest LZ78 factor, or $(N - \alpha)$ where $\alpha \geq 0$ is a quantity which depends on the amount of redundancy that the SLP captures with respect to substrings of $S$ of a certain length. Since $m = O(N/\log_\sigma N)$ where $\sigma$ is the alphabet size, the latter is asymptotically at least as fast as a linear time algorithm which runs on the uncompressed string when $\sigma$ is constant, and can be more efficient when the text is compressible, i.e. when $m$ and $n$ are small.Comment: SPIRE 201

Fully-Functional Suffix Trees and Optimal Text Searching in BWT-runs Bounded Space

Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is r, the number of runs in their Burrows-Wheeler Transforms (BWTs). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used O(r) space and was able to efficiently count the number of occurrences of a pattern of length m in the text (in loglogarithmic time per pattern symbol, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of r. In this paper we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the occ occurrences efficiently within O(r) space (in loglogarithmic time each), and reaching optimal time, O(m + occ), within O(r log log w ({\sigma} + n/r)) space, for a text of length n over an alphabet of size {\sigma} on a RAM machine with words of w = {\Omega}(log n) bits. Within that space, our index can also count in optimal time, O(m). Multiplying the space by O(w/ log {\sigma}), we support count and locate in O(dm log({\sigma})/we) and O(dm log({\sigma})/we + occ) time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using O(r log(n/r)) space that replaces the text and extracts any text substring of length ` in almost-optimal time O(log(n/r) + ` log({\sigma})/w). Within that space, we similarly provide direct access to suffix array, inverse suffix array, and longest common prefix array cells, and extend these capabilities to full suffix tree functionality, typically in O(log(n/r)) time per operation.Comment: submitted version; optimal count and locate in smaller space: O(r log log_w(n/r + sigma)

Optimal-Time Text Indexing in BWT-runs Bounded Space

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is $r$, the number of runs in their Burrows-Wheeler Transform (BWT). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used $O(r)$ space and was able to efficiently count the number of occurrences of a pattern of length $m$ in the text (in loglogarithmic time per pattern symbol, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of $r$. Since then, a number of other indexes with space bounded by other measures of repetitiveness --- the number of phrases in the Lempel-Ziv parse, the size of the smallest grammar generating the text, the size of the smallest automaton recognizing the text factors --- have been proposed for efficiently locating, but not directly counting, the occurrences of a pattern. In this paper we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the $occ$ occurrences efficiently within $O(r)$ space (in loglogarithmic time each), and reaching optimal time $O(m+occ)$ within $O(r\log(n/r))$ space, on a RAM machine of $w=\Omega(\log n)$ bits. Within $O(r\log (n/r))$ space, our index can also count in optimal time $O(m)$. Raising the space to $O(r w\log_\sigma(n/r))$, we support count and locate in $O(m\log(\sigma)/w)$ and $O(m\log(\sigma)/w+occ)$ time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using $O(r\log(n/r))$ space that replaces the text and extracts any text substring of length $\ell$ in almost-optimal time $O(\log(n/r)+\ell\log(\sigma)/w)$. (...continues...

Computing Runs on a General Alphabet

We describe a RAM algorithm computing all runs (maximal repetitions) of a given string of length $n$ over a general ordered alphabet in $O(n\log^{\frac{2}3} n)$ time and linear space. Our algorithm outperforms all known solutions working in $\Theta(n\log\sigma)$ time provided $\sigma = n^{\Omega(1)}$, where $\sigma$ is the alphabet size. We conjecture that there exists a linear time RAM algorithm finding all runs.Comment: 4 pages, 2 figure

Enhancing Reuse of Constraint Solutions to Improve Symbolic Execution

Constraint solution reuse is an effective approach to save the time of constraint solving in symbolic execution. Most of the existing reuse approaches are based on syntactic or semantic equivalence of constraints; e.g. the Green framework is able to reuse constraints which have different representations but are semantically equivalent, through canonizing constraints into syntactically equivalent normal forms. However, syntactic/semantic equivalence is not a necessary condition for reuse--some constraints are not syntactically or semantically equivalent, but their solutions still have potential for reuse. Existing approaches are unable to recognize and reuse such constraints. In this paper, we present GreenTrie, an extension to the Green framework, which supports constraint reuse based on the logical implication relations among constraints. GreenTrie provides a component, called L-Trie, which stores constraints and solutions into tries, indexed by an implication partial order graph of constraints. L-Trie is able to carry out logical reduction and logical subset and superset querying for given constraints, to check for reuse of previously solved constraints. We report the results of an experimental assessment of GreenTrie against the original Green framework, which shows that our extension achieves better reuse of constraint solving result and saves significant symbolic execution time.Comment: this paper has been submitted to conference ISSTA 201