Related papers: PHORMA: Perfectly Hashable Order Restricted Multid…
Roughly speaking, an $(n,(r,s))$-Cover Free Family (CFF) is a small set of $n$-bit strings such that: "in any $d:=r+s$ indices we see all patterns of weight $r$". CFFs have been of interest for a long time both in discrete mathematics as…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
Performing smart computations in a context of cloud computing and big data is highly appreciated today. Fully homomorphic encryption (FHE) is a smart category of encryption schemes that allows working with the data in its encrypted form. It…
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…
A dictionary (or map) is a key-value store that requires all keys be unique, and a multimap is a key-value store that allows for multiple values to be associated with the same key. We design hashing-based indexing schemes for dictionaries…
An \emph{indeterminate string} $x = x[1..n]$ on an alphabet $\Sigma$ is a sequence of nonempty subsets of $\Sigma$; $x$ is said to be \emph{regular} if every subset is of size one. A proper substring $u$ of regular $x$ is said to be a…
We study countable embedding-universal and homomorphism-universal structures and unify results related to both of these notions. We show that many universal and ultrahomogeneous structures allow a concise description (called here a finite…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
In this paper will be introduced large, probably complete family of complex base systems, which are 'proper' - for each point of the space there is a representation which is unique for all but some zero measure set. The condition defining…
Nonnegative matrix factorization (NMF) has become a prominent technique for the analysis of image databases, text databases and other information retrieval and clustering applications. In this report, we define an exact version of NMF. Then…
Hashing has been widely used for efficient similarity search based on its query and storage efficiency. To obtain better precision, most studies focus on designing different objective functions with different constraints or penalty terms…
Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $\sigma$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
With the growing scale of big data, probabilistic structures receive increasing popularity for efficient approximate storage and query processing. For example, Bloom filters (BF) can achieve satisfactory performance for approximate…
Tries are popular data structures for storing a set of strings, where common prefixes are represented by common root-to-node paths. Over fifty years of usage have produced many variants and implementations to overcome some of their…
The hypergraph container lemma is a powerful tool in probabilistic combinatorics that has found many applications since it was first proved a decade ago. Roughly speaking, it asserts that the family of independent sets of every uniform…
Given a set $S$ of $n$ distinct keys, a function $f$ that bijectively maps the keys of $S$ into the range $\{0,\ldots,n-1\}$ is called a minimal perfect hash function for $S$. Algorithms that find such functions when $n$ is large and retain…
Conventional array designs based on circular fourth-order cumulant typically adopt a single expression form of the fourth-order difference co-array (FODCA), which limits the achievable degrees of freedom (DOFs) and neglects the impact of…
We introduce an algorithm that conjectures the structure of a permutation class in the form of a disjoint cover of "rules"; similar to generalized grid classes. The cover is usually easily verified by a human and translated into an…
We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…