Related papers: Efficient Fully-Compressed Sequence Representation…
Let a text $T[1..n]$ be the only string generated by a context-free grammar with $g$ (terminal and nonterminal) symbols, and of size $G$ (measured as the sum of the lengths of the right-hand sides of the rules). Such a grammar, called a…
We study first-order optimization algorithms under the constraint that the descent direction is quantized using a pre-specified budget of $R$-bits per dimension, where $R \in (0 ,\infty)$. We propose computationally efficient optimization…
Unlike in statistical compression, where Shannon's entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures…
We investigate lossy compression (source coding) of data in the form of permutations. This problem has direct applications in the storage of ordinal data or rankings, and in the analysis of sorting algorithms. We analyze the rate-distortion…
We show that if DTIME[2^{O(n)}] is not included in DSPACE[2^{o(n)}], then, for every set B in PSPACE, all strings x in B of length n can be represented by a string compressed(x) of length at most log (|B^{=n}|) + O(log n), such that a…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
High-dimensional sparse data emerge in many critical application domains such as healthcare and cybersecurity. To extract meaningful insights from massive volumes of these multi-dimensional data, scientists employ unsupervised analysis…
We show that the compressed suffix array and the compressed suffix tree of a string $T$ can be built in $O(n)$ deterministic time using $O(n\log\sigma)$ bits of space, where $n$ is the string length and $\sigma$ is the alphabet size.…
The successor and predecessor problem consists of obtaining the closest value in a set of integers, greater/smaller than a given value. This problem has interesting applications, like the intersection of inverted lists. It can be easily…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
The fully-functional succinct tree representation of Navarro and Sadakane (ACM Transactions on Algorithms, 2014) supports a large number of operations in constant time using $2n+o(n)$ bits. However, the full idea is hard to implement. Only…
Electronic Health Records have become popular sources of data for secondary research, but their use is hampered by the amount of effort it takes to overcome the sparsity, irregularity, and noise that they contain. Modern learning…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
Compression also known as entropy coding has a rich and long history. However, a recent explosion of multimedia Internet applications (such as teleconferencing and video streaming for instance) renews an interest in fast compression that…
Maximal clique enumeration is a fundamental graph mining task, but its utility is often limited by computational intractability and highly redundant output. To address these challenges, we introduce \emph{$\rho$-dense aggregators}, a novel…
We revisit the problem of permuting an array of length $n$ according to a given permutation in place, that is, using only a small number of bits of extra storage. Fich, Munro and Poblete [FOCS 1990, SICOMP 1995] obtained an elegant…
Compression algorithms reduce the redundancy in data representation to decrease the storage required for that data. Data compression offers an attractive approach to reducing communication costs by using available bandwidth effectively.…
We introduce a new technique for the efficient management of large sequences of multidimensional data, which takes advantage of regularities that arise in real-world datasets and supports different types of aggregation queries. More…