Related papers: Sneak peek at the tig sequences: useful sequences …
In this expository article we collect the integer sequences that count several different types of matrices over finite fields and provide references to the Online Encyclopedia of Integer Sequences (OEIS). Section 1 contains the sequences,…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
Infinite sequences are of tremendous theoretical and practical importance, and in the Information Age sequences of 0s and 1s are of particular interest. Over the past century, the field of symbolic dynamics has developed to study sequences…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
We first show how the cohomology of some Bernstein-Gelfand-Gelfand (BGG) sequences that are important for the numerical analysis of partial differential equations, can be obtained through the construction of a long exact sequence connecting…
Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works…
We consider the problem of analyzing social network data sets in which the edges of the network have timestamps, and we wish to analyze the subgraphs formed from edges in contiguous subintervals of these timestamps. We provide data…
Event sequences often emerge in data mining. Modeling these sequences presents two main challenges: methodological and computational. Methodologically, event sequences are non-uniform and sparse, making traditional models unsuitable.…
Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly…
Directed acyclic graphs (DAGs) are a class of graphs commonly used in practice, with examples that include electronic circuits, Bayesian networks, and neural architectures. While many effective encoders exist for DAGs, it remains…
A program is a finite piece of data that produces a (possibly infinite) sequence of primitive instructions. From scratch we develop a linear notation for sequential, imperative programs, using a familiar class of primitive instructions and…
Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research. This discipline represents the convergence of genomics, biotechnology and…
We introduce hypergeometric-type sequences. They are linear combinations of interlaced hypergeometric sequences (of arbitrary interlacements). We prove that they form a subring of the ring of holonomic sequences. An interesting family of…
Graph neural networks (GNNs) have recently grown in popularity in the field of artificial intelligence (AI) due to their unique ability to ingest relatively unstructured data types as input data. Although some elements of the GNN…
Cyclic codes over finite fields are widely implemented in data storage systems, communication systems, and consumer electronics, as they have very efficient encoding and decoding algorithms. They are also important in theory, as they are…
Scaffolding is an important subproblem in "de novo" genome assembly in which mate pair data are used to construct a linear sequence of contigs separated by gaps. Here we present SLIQ, a set of simple linear inequalities derived from the…
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
This paper describes an application, called Medici, designed to produce synthetic data for social network graphs, which can be used for analysis, hypothesis testing and application development by researchers and practitioners in the field.…
Building interactive data interfaces is hard because the design of an interface depends on the data processing needs for the underlying analysis task, yet we do not have a good representation for analysis tasks. To fill this gap, this paper…
In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several…