Related papers: Sneak peek at the tig sequences: useful sequences …
Frequency tagging is a powerful approach to investigate the neural processing of sensory features, and is recently adapted to study the neural correlates of superordinate structures, i.e., chunks, in complex sequences such as speech and…
We study a new type of sequences whose elements are defined in terms of the position, sign and magnitude of another element of the sequence. The name ultra-recursive comes from the fact that these sequences possess terms that are generated…
We discuss an interesting sequence defined recursively; namely, sequence A105774 from the On-Line Encyclopedia of Integer Sequences, and study some of its properties. Our main tools are Fibonacci representation, finite automata, and the…
When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple…
The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. To date, most biosequence transformers have been trained on single-omic data - either…
We look at a family of meta-Fibonacci sequences which arise in studying the number of leaves at the largest level in certain infinite sequences of binary trees, restricted compositions of an integer, and binary compact codes. For this…
The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of…
In this survey, we present a detailed examination of the advancements in Neural Question Generation (NQG), a field leveraging neural network techniques to generate relevant questions from diverse inputs like knowledge bases, texts, and…
The notion of transducer integer sequences is considered through a series of examples. By definition, transducer integer sequences are integer sequences produced, under a suitable interpretation, by finite automata encoding tree morphisms…
These notes are meant to provide a rapid introduction to triangulated categories. We start with the definition of an additive category and end with a glimps of tilting theory. Some exercises are included.
An In Silico model to relate the properties of proteins to the structure, sequence, function and evolutionary history of proteins is shown. The derived ideal sequences for amino acid residues in proteins can then be considered as attractors…
Confidence sequences are collections of confidence regions that simultaneously cover the true parameter for every sample size at a prescribed confidence level. Tightening these sequences is of practical interest and can be achieved by…
This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen…
The superiority of Convolutional Neural Networks (CNNs) largely relies on their architectures that are often manually crafted with extensive human expertise. Unfortunately, such kind of domain knowledge is not necessarily owned by each of…
This work-in-progress research paper explores the effectiveness of tutorials in interdisciplinary learning environments, specifically focusing on bioinformatics. Tutorials are typically designed for a single audience, but our study aims to…
The fields of time series and graphical models emerged and advanced separately. Previous work on the structure learning of continuous and real-valued time series utilizes the time domain, with a focus on either structural autoregressive…
We aim to mine temporal causal sequences that explain observed events (consequents) in time-series traces. Causal explanations of key events in a time-series has applications in design debugging, anomaly detection, planning, root-cause…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
Motivation: The application of PacBio HiFi and ultra-long ONT reads have achieved huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding software,…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…