Space-Efficient Parameterized Algorithms on Graphs of Low Shrubdepth

Dynamic programming on various graph decompositions is one of the most fundamental techniques used in parameterized complexity. Unfortunately, even if we consider concepts as simple as path or tree decompositions, such dynamic programming uses space that is exponential in the decomposition’s width, and there are good reasons to believe that this is necessary. However, it has been shown that in graphs of low treedepth it is possible to design algorithms which achieve polynomial space complexity without requiring worse time complexity than their counterparts working on tree decompositions of bounded width. Here, treedepth is a graph parameter that, intuitively speaking, takes into account both the depth and the width of a tree decomposition of the graph, rather than the width alone. Motivated by the above, we consider graphs that admit clique expressions with bounded depth and label count, or equivalently, graphs of low shrubdepth. Here, shrubdepth is a bounded-depth analogue of cliquewidth, in the same way as treedepth is a bounded-depth analogue of treewidth. We show that also in this setting, bounding the depth of the decomposition is a deciding factor for improving the space complexity. More precisely, we prove that on n-vertex graphs equipped with a tree-model (a decomposition notion underlying shrubdepth) of depth d and using k labels, - Independent Set can be solved in time 2^(dk) ⋅ n^(1) using (dk²log n) space; - Max Cut can be solved in time n^(dk) using (dk log n) space; and - Dominating Set can be solved in time 2^(dk) ⋅ n^(1) using n^(1) space via a randomized algorithm. We also establish a lower bound, conditional on a certain assumption about the complexity of Longest Common Subsequence, which shows that at least in the case of Independent Set the exponent of the parametric factor in the time complexity has to grow with d if one wishes to keep the space complexity polynomial

Space-Efficient Parameterized Algorithms on Graphs of Low Shrubdepth

Dynamic programming on various graph decompositions is one of the most fundamental techniques used in parameterized complexity. Unfortunately, even if we consider concepts as simple as path or tree decompositions, such dynamic programming uses space that is exponential in the decomposition's width, and there are good reasons to believe that this is necessary. However, it has been shown that in graphs of low treedepth it is possible to design algorithms which achieve polynomial space complexity without requiring worse time complexity than their counterparts working on tree decompositions of bounded width. Here, treedepth is a graph parameter that, intuitively speaking, takes into account both the depth and the width of a tree decomposition of the graph, rather than the width alone. Motivated by the above, we consider graphs that admit clique expressions with bounded depth and label count, or equivalently, graphs of low shrubdepth (sd). Here, sd is a bounded-depth analogue of cliquewidth, in the same way as td is a bounded-depth analogue of treewidth. We show that also in this setting, bounding the depth of the decomposition is a deciding factor for improving the space complexity. Precisely, we prove that on $n$-vertex graphs equipped with a tree-model (a decomposition notion underlying sd) of depth $d$ and using $k$ labels, we can solve - Independent Set in time $2^{O(dk)}\cdot n^{O(1)}$ using $O(dk^2\log n)$ space; - Max Cut in time $n^{O(dk)}$ using $O(dk\log n)$ space; and - Dominating Set in time $2^{O(dk)}\cdot n^{O(1)}$ using $n^{O(1)}$ space via a randomized algorithm. We also establish a lower bound, conditional on a certain assumption about the complexity of Longest Common Subsequence, which shows that at least in the case of IS the exponent of the parametric factor in the time complexity has to grow with $d$ if one wishes to keep the space complexity polynomial.Comment: Conference version to appear at the European Symposium on Algorithms (ESA 2023

An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design

<p>Abstract</p> <p>Background</p> <p>The "off-target" silencing effect hinders the development of siRNA-based therapeutic and research applications. Existing solutions for finding possible locations of siRNA seats within a large database of genes are either too slow, miss a portion of the targets, or are simply not designed to handle a very large number of queries. We propose a new approach that reduces the computational time as compared to existing techniques.</p> <p>Findings</p> <p>The proposed method employs tree-based storage in a form of a modified truncated suffix tree to sort all possible short string substrings within given set of strings (i.e. transcriptome). Using the new algorithm, we pre-computed a list of the best siRNA locations within each human gene ("siRNA seats"). siRNAs designed to reside within siRNA seats are less likely to hybridize off-target. These siRNA seats could be used as an input for the traditional "set-of-rules" type of siRNA designing software. The list of siRNA seats is available through a publicly available database located at <url>http://web.cos.gmu.edu/~gmanyam/siRNA_db/search.php</url></p> <p>Conclusions</p> <p>In attempt to perform top-down prediction of the human siRNA with minimized off-target hybridization, we developed an efficient algorithm that employs suffix tree based storage of the substrings. Applications of this approach are not limited to optimal siRNA design, but can also be useful for other tasks involving selection of the characteristic strings specific to individual genes. These strings could then be used as siRNA seats, as specific probes for gene expression studies by oligonucleotide-based microarrays, for the design of molecular beacon probes for Real-Time PCR and, generally, any type of PCR primers.</p

28th Annual Symposium on Combinatorial Pattern Matching : CPM 2017, July 4-6, 2017, Warsaw, Poland

Peer reviewe

Aspects of Metric Spaces in Computation

Metric spaces, which generalise the properties of commonly-encountered physical and abstract spaces into a mathematical framework, frequently occur in computer science applications. Three major kinds of questions about metric spaces are considered here: the intrinsic dimensionality of a distribution, the maximum number of distance permutations, and the difficulty of reverse similarity search. Intrinsic dimensionality measures the tendency for points to be equidistant, which is diagnostic of high-dimensional spaces. Distance permutations describe the order in which a set of fixed sites appears while moving away from a chosen point; the number of distinct permutations determines the amount of storage space required by some kinds of indexing data structure. Reverse similarity search problems are constraint satisfaction problems derived from distance-based index structures. Their difficulty reveals details of the structure of the space. Theoretical and experimental results are given for these three questions in a wide range of metric spaces, with commentary on the consequences for computer science applications and additional related results where appropriate

Discovery of Unconventional Patterns for Sequence Analysis: Theory and Algorithms

The biology community is collecting a large amount of raw data, such as the genome sequences of organisms, microarray data, interaction data such as gene-protein interactions, protein-protein interactions, etc. This amount is rapidly increasing and the process of understanding the data is lagging behind the process of acquiring it. An inevitable first step towards making sense of the data is to study their regularities focusing on the non-random structures appearing surprisingly often in the input sequences: patterns. In this thesis we discuss three incarnations of the pattern discovery task, exploring three types of patterns that can model different regularities of the input dataset. While mask patterns have been designed to model short repeated biological sequences, showing a high conservation of their content at some specific positions, permutation patterns have been designed to detect repeated patterns whose parts maintain their physical adjacency but not their ordering in all the pattern occurrences. Transposons, instead, model mobile sequences in the input dataset, which can be discovered by comparing different copies of the same input string, detecting large insertions and deletions in their alignment

Space-Efficient Parameterized Algorithms on Graphs of Low Shrubdepth

Dynamic programming on various graph decompositions is one of the most fundamental techniques used in parameterized complexity. Unfortunately, even if we consider concepts as simple as path or tree decompositions, such dynamic programming uses space that is exponential in the decomposition's width, and there are good reasons to believe that this is necessary. However, it has been shown that in graphs of low treedepth it is possible to design algorithms which achieve polynomial space complexity without requiring worse time complexity than their counterparts working on tree decompositions of bounded width. Here, treedepth is a graph parameter that, intuitively speaking, takes into account both the depth and the width of a tree decomposition of the graph, rather than the width alone. Motivated by the above, we consider graphs that admit clique expressions with bounded depth and label count, or equivalently, graphs of low shrubdepth (sd). Here, sd is a bounded-depth analogue of cliquewidth, in the same way as td is a bounded-depth analogue of treewidth. We show that also in this setting, bounding the depth of the decomposition is a deciding factor for improving the space complexity. Precisely, we prove that on n-vertex graphs equipped with a tree-model (a decomposition notion underlying sd) of depth d and using k labels, we can solve - Independent Set in time 2O(dk)⋅nO(1) using O(dk2logn) space; - Max Cut in time nO(dk) using O(dklogn) space; and - Dominating Set in time 2O(dk)⋅nO(1) using nO(1) space via a randomized algorithm. We also establish a lower bound, conditional on a certain assumption about the complexity of Longest Common Subsequence, which shows that at least in the case of IS the exponent of the parametric factor in the time complexity has to grow with d if one wishes to keep the space complexity polynomial