Simulation computation in grammar-compressed graphs

Like [1], we present an algorithm to compute the simulation of a query pattern in a graph of labeled nodes and unlabeled edges. However, our algorithm works on a compressed graph grammar, instead of on the original graph. The speed-up of our algorithm compared to the algorithm in [1] grows with the size of the graph and with the compression strength

A Survey on Methods and Systems for Graph Compression

We present an informal survey (meant to accompany another paper) on graph compression methods. We focus on lossless methods, briefly list available pproaches, and compare them where possible or give some indicators on their compression ratios. We also mention some relevant results from the field of lossy compression and algorithms specialized for the use on large graphs. --- Note: The comparison is by no means complete. This document is a first draft and will be updated and extended

PLG2: Multiperspective Processes Randomization and Simulation for Online and Offline Settings

Process mining represents an important field in BPM and data mining research. Recently, it has gained importance also for practitioners: more and more companies are creating business process intelligence solutions. The evaluation of process mining algorithms requires, as any other data mining task, the availability of large amount of real-world data. Despite the increasing availability of such datasets, they are affected by many limitations, in primis the absence of a "gold standard" (i.e., the reference model). This paper extends an approach, already available in the literature, for the generation of random processes. Novelties have been introduced throughout the work and, in particular, they involve the complete support for multiperspective models and logs (i.e., the control-flow perspective is enriched with time and data information) and for online settings (i.e., generation of multiperspective event streams and concept drifts). The proposed new framework is able to almost entirely cover the spectrum of possible scenarios that can be observed in the real-world. The proposed approach is implemented as a publicly available Java application, with a set of APIs for the programmatic execution of experiments.Comment: 36 pages, minor update

Tracelets and Tracelet Analysis Of Compositional Rewriting Systems

Taking advantage of a recently discovered associativity property of rule compositions, we extend the classical concurrency theory for rewriting systems over adhesive categories. We introduce the notion of tracelets, which are defined as minimal derivation traces that universally encode sequential compositions of rewriting rules. Tracelets are compositional, capture the causality of equivalence classes of traditional derivation traces, and intrinsically suggest a clean mathematical framework for the definition of various notions of abstractions of traces. We illustrate these features by introducing a first prototype for a framework of tracelet analysis, which as a key application permits to formulate a first-of-its-kind algorithm for the static generation of minimal derivation traces with prescribed terminal events.Comment: In Proceedings ACT 2019, arXiv:2009.0633

Improved ESP-index: a practical self-index for highly repetitive texts

While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing (ESP), an efficient parsing algorithm that guarantees upper bounds of parsing discrepancies between different appearances of the same subtexts in a text. Although ESP-index performs efficient top-down searches of query texts, it has a serious issue on binary searches for finding appearances of variables for a query text, which resulted in slowing down the query searches. We present an improved ESP-index (ESP-index-I) by leveraging the idea behind succinct data structures for large alphabets. While ESP-index-I keeps the same types of efficiencies as ESP-index about the top-down searches, it avoid the binary searches using fast rank/select operations. We experimentally test ESP-index-I on the ability to search query texts and extract subtexts from real world repetitive texts on a large-scale, and we show that ESP-index-I performs better that other possible approaches.Comment: This is the full version of a proceeding accepted to the 11th International Symposium on Experimental Algorithms (SEA2014

Streaming algorithms for language recognition problems

We study the complexity of the following problems in the streaming model. Membership testing for \DLIN We show that every language in \DLIN\ can be recognised by a randomized one-pass $O(\log n)$ space algorithm with inverse polynomial one-sided error, and by a deterministic p-pass $O(n/p)$ space algorithm. We show that these algorithms are optimal. Membership testing for \LL$(k)$ For languages generated by \LL$(k)$ grammars with a bound of $r$ on the number of nonterminals at any stage in the left-most derivation, we show that membership can be tested by a randomized one-pass $O(r\log n)$ space algorithm with inverse polynomial (in $n$) one-sided error. Membership testing for \DCFL We show that randomized algorithms as efficient as the ones described above for \DLIN\ and \LL(k) (which are subclasses of \DCFL) cannot exist for all of \DCFL: there is a language in \VPL\ (a subclass of \DCFL) for which any randomized p-pass algorithm with error bounded by $\epsilon < 1/2$ must use $\Omega(n/p)$ space. Degree sequence problem We study the problem of determining, given a sequence $d_1, d_2,..., d_n$ and a graph $G$, whether the degree sequence of $G$ is precisely $d_1, d_2,..., d_n$. We give a randomized one-pass $O(\log n)$ space algorithm with inverse polynomial one-sided error probability. We show that our algorithms are optimal. Our randomized algorithms are based on the recent work of Magniez et al. \cite{MMN09}; our lower bounds are obtained by considering related communication complexity problems

Evolutionary development of tensegrity structures

Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering

Simulating the DNA String Graph in Succinct Space

Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has advantages over the other depending on the application. Still, the ideal setting would be to have an index of the reads that is easy to build and can be adapted to any type of biological analysis. In this paper, we propose a new data structure we call rBOSS, which gets close to that ideal. Our rBOSS is a de Bruijn graph in practice, but it simulates any length up to k and can compute overlaps of size at least m between the labels of the nodes, with k and m being parameters. If we choose the parameter k equal to the size of the reads, then we can simulate a complete string graph. As most BWT-based structures, rBOSS is unidirectional, but it exploits the property of the DNA reverse complements to simulate bi-directionality with some time-space trade-offs. We implemented a genome assembler on top of rBOSS to demonstrate its usefulness. Our experimental results show that using k = 100, rBOSS can assemble 185 MB of reads in less than 15 minutes and using 110 MB in total. It produces contigs of mean sizes over 10,000, which is twice the size obtained by using a pure de Bruijn graph of fixed length k.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

Data Race Detection on Compressed Traces

We consider the problem of detecting data races in program traces that have been compressed using straight line programs (SLP), which are special context-free grammars that generate exactly one string, namely the trace that they represent. We consider two classical approaches to race detection --- using the happens-before relation and the lockset discipline. We present algorithms for both these methods that run in time that is linear in the size of the compressed, SLP representation. Typical program executions almost always exhibit patterns that lead to significant compression. Thus, our algorithms are expected to result in large speedups when compared with analyzing the uncompressed trace. Our experimental evaluation of these new algorithms on standard benchmarks confirms this observation

On the Use of Quasiorders in Formal Language Theory

In this thesis we use quasiorders on words to offer a new perspective on two well-studied problems from Formal Language Theory: deciding language inclusion and manipulating the finite automata representations of regular languages. First, we present a generic quasiorder-based framework that, when instantiated with different quasiorders, yields different algorithms (some of them new) for deciding language inclusion. We then instantiate this framework to devise an efficient algorithm for searching with regular expressions on grammar-compressed text. Finally, we define a framework of quasiorder-based automata constructions to offer a new perspective on residual automata.Comment: PhD thesi