Related papers: Subsequences With Generalised Gap Constraints: Upp…
We introduce a notion of compatibility between constraint encoding and compositional structure. Phrased in the language of category theory, it is given by a "composable constraint encoding". We show that every composable constraint encoding…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
This paper describes an extension to the constraint satisfaction problem (CSP) called MUSE CSP (MUltiply SEgmented Constraint Satisfaction Problem). This extension is especially useful for those problems which segment into multiple sets of…
Graph structure learning is a well-established problem that aims at optimizing graph structures adaptive to specific graph datasets to help message passing neural networks (i.e., GNNs) to yield effective and robust node embeddings. However,…
In this paper, we study a series of algorithmic problems related to the subsequences occurring in the strings of a given language, under the assumption that this language is succinctly represented by a grammar generating it, or an automaton…
The embedding problem is to decide, given an ordered pair of structures, whether or not there is an injective homomorphism from the first structure to the second. We study this problem using an established perspective in parameterized…
A graph G is c-closed if every two vertices with at least c common neighbors are adjacent to each other. Introduced by Fox, Roughgarden, Seshadhri, Wei and Wein [ICALP 2018, SICOMP 2020], this definition is an abstraction of the triadic…
Constraint Satisfaction Problems are ubiquitous in fields ranging from the physics of solids to artificial intelligence. In many cases, such systems undergo a transition when the ratio of constraints to variables reaches some value…
Sequence modelling approaches for epigenetic profile prediction have recently expanded in terms of sequence length, model size, and profile diversity. However, current models cannot infer on many experimentally feasible tissue and assay…
In 2005, Goddard, Hedetniemi, Hedetniemi and Laskar [Generalized subgraph-restricted matchings in graphs, Discrete Mathematics, 293 (2005) 129 - 138] asked the computational complexity of determining the maximum cardinality of a matching…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…
The mixing set with a knapsack constraint arises as a substructure in mixed-integer programming reformulations of chance-constrained programs with stochastic right-hand-sides over a finite discrete distribution. Recently, Luedtke et al.…
Word embeddings are effective intermediate representations for capturing semantic regularities between words, when learning the representations of text sequences. We propose to view text classification as a label-word joint embedding…
Let $A_q$ be a $q$-letter alphabet and $w$ be a right infinite word on this alphabet. A subword of $w$ is a block of consecutive letters of $w$. The subword complexity function of $w$ assigns to each positive integer $n$ the number $f_w(n)$…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
Graph learning from data represents a canonical problem that has received substantial attention in the literature. However, insufficient work has been done in incorporating prior structural knowledge onto the learning of underlying…
We propose a theoretical framework that generalizes simple and fast algorithms for hierarchical agglomerative clustering to weighted graphs with both attractive and repulsive interactions between the nodes. This framework defines GASP, a…
We propose some new method of constructing configurations, which consists in consecutive inscribing copies of one underlying configuration. A uniform characterization of the obtained class and the one introduced in our paper untitled…
We establish a condition (so called generalized entropic property), equivalent to the fact that for every algebra A from a given variety V, the set of all subalgebras of A is a subuniverse of the complex algebra of A. We investigate the…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…