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The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
A determined algorithm is presented for solving the rSUM problem for any natural r with a sub-quadratic assessment of time complexity in some cases. In terms of an amount of memory used the obtained algorithm is the nlog^3(n) order. The…
Consider an ideal $I \subset R = \bC[x_1,...,x_n]$ defining a complex affine variety $X \subset \bC^n$. We describe the components associated to $I$ by means of {\em numerical primary decomposition} (NPD). The method is based on the…
The modular subset sum problem consists of deciding, given a modulus $m$, a multiset $S$ of $n$ integers in $0..m-1$, and a target integer $t$, whether there exists a subset of $S$ with elements summing to $t \mod m $, and to report such a…
The closest string problem is an NP-hard problem, whose task is to find a string that minimizes maximum Hamming distance to a given set of strings. This can be reduced to an integer program (IP). However, to date, there exists no known…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
In database design, Composite Keys are used to uniquely identify records and prevent data duplication. However, they require more memory and storage space than single keys, and can make queries more CPU-intensive. Surrogate Keys are an…
We consider the clustering aggregation problem in which we are given a set of clusterings and want to find an aggregated clustering which minimizes the sum of mismatches to the input clusterings. In the binary case (each clustering is a…
We investigate unification problems related to the Cipher Block Chaining (CBC) mode of encryption. We first model chaining in terms of a simple, convergent, rewrite system over a signature with two disjoint sorts: list and element. By…
We introduce Bayesian Bits, a practical method for joint mixed precision quantization and pruning through gradient based optimization. Bayesian Bits employs a novel decomposition of the quantization operation, which sequentially considers…
The uniqueness of an optimal solution to a combinatorial optimization problem attracts many fields of researchers' attention because it has a wide range of applications, it is related to important classes in computational complexity, and an…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
According to Kolmogorov complexity, every finite binary string is compressible to a shortest code -- its information content -- from which it is effectively recoverable. We investigate the extent to which this holds for infinite binary…
Algorithms to generate various combinatorial structures find tremendous importance in computer science. In this paper, we begin by reviewing an algorithm proposed by Rohl that generates all unique permutations of a list of elements which…
Combinatorial optimization lies at the core of many real-world problems. Especially since the rise of graph neural networks (GNNs), the deep learning community has been developing solvers that derive solutions to NP-hard problems by…
We develop a tensor network technique that can solve universal reversible classical computational problems, formulated as vertex models on a square lattice [Nat. Commun. 8, 15303 (2017)]. By encoding the truth table of each vertex…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
Given positive integers $a_1,..., a_n, t$, the fixed weight subset sum problem is to find a subset of the $a_i$ that sum to $t$, where the subset has a prescribed number of elements. It is this problem that underlies the security of modern…