Related papers: IGoR: a tool for high-throughput immune repertoire…
International Classification of Diseases (ICD) is a globally recognized coding system that records diagnostic events during each patient encounter, providing a standardized data foundation for various clinical tasks. However, the irregular…
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts…
Understanding the structure of the human T-cell receptor repertoire is a crucial precondition to understand the ability of the immune system to recognize and respond to antigens. T-cells are often compared via the complementarity…
Recent breakthroughs in single-cell technology have ushered in unparalleled opportunities to decode the molecular intricacy of intricate biological systems, especially those linked to diseases unique to humans. However, these progressions…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Motivation: Microarray results accumulated in public repositories are widely re-used in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment and…
Retrieval-Augmented Generation (RAG) is increasingly employed in generative AI-driven scientific workflows to integrate rapidly evolving scientific knowledge bases, yet its reliability is frequently compromised by non-determinism in their…
Historically, Recurrent neural networks (RNNs) and its variants such as LSTM and GRU and more recently Transformers have been the standard go-to components when processing sequential data with neural networks. One notable issue is the…
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,…
Retrieval-augmented generation (RAG) equips large language models (LLMs) with reliable knowledge memory. To strengthen cross-text associations, recent research integrates graphs and hypergraphs into RAG to capture pairwise and multi-entity…
Accurate molecular sequence analysis is a key task in the field of bioinformatics. To apply molecular sequence classification algorithms, we first need to generate the appropriate representations of the sequences. Traditional numeric…
Subclasses of lymphocytes carry different functional roles to work together to produce an immune response and lasting immunity. Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains…
The repertoire of lymphocyte receptors in the adaptive immune system protects organisms from diverse pathogens. A well-adapted repertoire should be tuned to the pathogenic environment to reduce the cost of infections. We develop a general…
Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their specific recognition of antigens plays a crucial role in the…
Interpretation of electrocardiography (ECG) signals is required for diagnosing cardiac arrhythmia. Recently, machine learning techniques have been applied for automated computer-aided diagnosis. Machine learning tasks can be divided into…
Sequential dense retrieval models utilize advanced sequence learning techniques to compute item and user representations, which are then used to rank relevant items for a user through inner product computation between the user and all item…
Existing clustering methods for functional data often prioritize partitioning accuracy over interpretability, making it challenging to extract meaningful insights when the data-generating process follows a specific underlying structure and…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus.…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…