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Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…
Semantic segmentation consists in classifying each pixel of an image by assigning it to a specific label chosen from a set of all the available ones. During the last few years, a lot of attention shifted to this kind of task. Many computer…
This paper presents COGENT3 (or Collective Growth and Entropy-modulated Triads System), a novel approach for emergent cognition integrating pattern formation networks with group influence dynamics. Contrasting with traditional strategies…
Cancer is a number of related yet highly heterogeneous diseases. Correct identification of cancer subtypes is critical for clinical decisions. The advance in sequencing technologies has made it possible to study cancer based on abundant…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large metagenomic…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Biomedical image segmentation is a very important part in disease diagnosis. The term "colonic polyps" refers to polypoid lesions that occur on the surface of the colonic mucosa within the intestinal lumen. In clinical practice, early…
We present an automated method of identifying communities of functionally related genes from the biomedical literature. These communities encapsulate human gene and protein interactions and identify groups of genes that are complementary in…
In this paper we propose a Deep Autoencoder MIxture Clustering (DAMIC) algorithm based on a mixture of deep autoencoders where each cluster is represented by an autoencoder. A clustering network transforms the data into another space and…
The in vitro clonogenic assay is a technique to study the ability of a cell to form a colony in a culture dish. By optical imaging, dishes with stained colonies can be scanned and assessed digitally. Identification, segmentation and…
Humans exhibit remarkable compositional reasoning by integrating knowledge from various sources. For example, if someone learns ( B = f(A) ) from one source and ( C = g(B) ) from another, they can deduce ( C=g(B)=g(f(A)) ) even without…
Aggregating different pieces of similar information is necessary to generate concise and easy to understand reports in technical domains. This paper presents a general algorithm that combines similar messages in order to generate one or…
Humans possess an inherent ability to chunk sequences into their constituent parts. In fact, this ability is thought to bootstrap language skills and learning of image patterns which might be a key to a more animal-like type of…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
Metagenomic binning is an essential task in analyzing metagenomic sequence datasets. To analyze structure or function of microbial communities from environmental samples, metagenomic sequence fragments are assigned to their taxonomic…
Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings leverage pretrained language models to encode terms, and…
Retrieval-Augmented Generation (RAG) systems lose retrieval accuracy when similar documents coexist in the vector database, causing unnecessary information, hallucinations, and factual errors. To alleviate this issue, we propose CHOP, a…