Related papers: MetaCompass: Reference-guided Assembly of Metageno…

We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…

Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…

Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…

Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…

A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…

One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…

To solve a new task from minimal experience, it is essential to effectively reuse knowledge from previous tasks, a problem known as meta-learning. Compositional solutions, where common elements of computation are flexibly recombined into…

We introduce GeNet, a method for shotgun metagenomic classification from raw DNA sequences that exploits the known hierarchical structure between labels for training. We provide a comparison with state-of-the-art methods Kraken and…

There is significant interest in using existing repositories of biological entities, relationships, and models to automate biological model assembly and extension. Current methods aggregate human-curated biological information into…

Genetic Algorithms are a popular set of optimization algorithms often used to aid software testing. However, no work has been done to apply systematic software testing techniques to genetic algorithms because of the stochasticity and the…

This article presents resource-guided synthesis, a technique for synthesizing recursive programs that satisfy both a functional specification and a symbolic resource bound. The technique is type-directed and rests upon a novel type system…

With the advent of the Internet, search engines have begun sprouting like mushrooms after a rainfall. Only in recent years, have developers become more innovative, and came up with guided searching facilities online. The goals of these…

A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it…

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…

In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…

In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…

Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain minimal hyperpaths in B-hypergraphs. This makes it possible to…

Our work aimed at experimentally assessing the benefits of model ensembling within the context of neural methods for passage reranking. Starting from relatively standard neural models, we use a previous technique named Fast Geometric…

This paper presents our proposal for the evolution of the metamodel for the Task Algebra in the Task Flow model for the Discovery Method. The original Task Algebra is based on simple and compound tasks structured using operators such as…

Image-to-image reconstruction problems with free or inexpensive metadata in the form of class labels appear often in biological and medical image domains. Existing text-guided or style-transfer image-to-image approaches do not translate to…