Related papers: Extending de Bruijn sequences to larger alphabets
A method for encoding and decoding spectrum shaped binary run-length constrained sequences is described. The binary sequences with predefined range of exponential sums are introduced. On the base of Cover's enumerative scheme, recurrence…
Let k be a positive integer. A sequence s over an n-element alphabet A is called a k-radius sequence if every two symbols from A occur in s at distance of at most k. Let f_k(n) denote the length of a shortest k-radius sequence over A. We…
We study and compare different Graph Neural Network extensions that increase the expressive power of GNNs beyond the Weisfeiler-Leman test. We focus on (i) GNNs based on higher order WL methods, (ii) GNNs that preprocess small substructures…
The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…
Searching for other participants is one of the most important operations in a distributed system. We are interested in topologies in which it is possible to route a packet in a fixed number of hops until it arrives at its destination. Given…
We provide a new algebraic technique to solve the sequential flow problem in polynomial space. The task is to maximise the flow through a graph where edge capacities can be changed over time by choosing a sequence of capacity labelings from…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
We consider the complexities of substitutive sequences over a binary alphabet. By studying various types of special words, we show that, knowing some initial values, its complexity can be completely formulated via a recurrence formula…
De Bruijn graphs are essential for sequencing data analysis and must be efficiently constructed and stored for large-scale population studies. They also need to be dynamic to allow updates such as adding or removing edges and nodes.…
We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced…
We present a finite-order system of recurrence relations for a permanent of circulant matrices containing a band of k any-value diagonals on top of a uniform matrix (for k = 1, 2, and 3) as well as the method for deriving such recurrence…
Motivated by the problem of storing coloured de Bruijn graphs, we show how, if we can already support fast select queries on one string, then we can store a little extra information and support fairly fast select queries on a similar…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
We study the distribution of the number of permutations with a given periodic up-down sequence w.r.t. the last entry, find exponential generating functions and prove asymptotic formulas for this distribution.
Let $\textbf{T}(n,k)$ be the set of strings of length $n$ over the alphabet $\Sigma=\{1,2,\ldots,k\}$. A universal cycle for $\textbf{T}(n,k)$ can be constructed using a greedy algorithm: start with the string $k^n$, and continually append…
A Skolem sequence is a linear arrangement of the multiset, {1, 1, 2, 2, ..., n, n} such that if r in [n] appears in positions i and j, then |i-j| = r. We first translate the problem to a particular set of perfect matchings, then apply the…
We present a family of automata networks that solve the k-parity problem when run in parallel. These solutions are constructed by connecting cliques in a non-cyclical fashion. The size of the local neighbourhood is linear in the size of the…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
Word-representable graphs, which are the same as semi-transitively orientable graphs, generalize several fundamental classes of graphs. In this paper we propose a novel approach to study word-representability of graphs using a technique of…
For any graph $G$ on $n$ vertices and for any {\em symmetric} subgraph $J$ of $K_{n,n}$, we construct an infinite sequence of graphs based on the pair $(G,J)$. The First graph in the sequence is $G$, then at each stage replacing every…