Related papers: New algorithmic challenges of adaptive immune repe…
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…
Sequential recommendation (SR) models often capture user preferences based on the historically interacted item IDs, which usually obtain sub-optimal performance when the interaction history is limited. Content-based sequential…
Immune repertoires provide a unique fingerprint reflecting the immune history of individuals, with potential applications in precision medicine. However, the question of how personal that information is and how it can be used to identify…
T-cell receptor (TCR) interactions with antigenic peptides underpin adaptive immunity and are pivotal for personalized immunotherapy and vaccine development. Despite recent progress, computational modeling of TCR-peptide specificity remains…
High-throughput sequencing of T- and B-cell receptors makes it possible to track immune repertoires across time, in different tissues, in acute and chronic diseases and in healthy individuals. However quantitative comparison between…
T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR sequences is of…
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals. However, quantitative comparison between…
The sequential recommendation aims to recommend items, such as products, songs and places, to users based on the sequential patterns of their historical records. Most existing sequential recommender models consider the next item prediction…
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
T cells are a critical component of the adaptive immune system, playing a role in infectious disease, autoimmunity, and cancer. T cell function is mediated by the T cell receptor (TCR) protein, a highly diverse receptor targeting specific…
The recent advancements in Large Language Models (LLMs) have generated considerable interest in their utilization for sequential recommendation tasks. While collaborative signals from similar users are central to recommendation modeling,…
Sequential Recommender Systems (SRSs) have emerged as a highly efficient approach to recommendation systems. By leveraging sequential data, SRSs can identify temporal patterns in user behaviour, significantly improving recommendation…
Designing aligned and robust rewards for open-ended generation remains a key barrier to RL post-training. Rubrics provide structured, interpretable supervision, but scaling rubric construction is difficult: expert rubrics are costly,…
Sequential recommendation systems often struggle to make predictions or take action when dealing with cold-start items that have limited amount of interactions. In this work, we propose SimRec - a new approach to mitigate the cold-start…
Although prevailing supervised and self-supervised learning augmented sequential recommendation (SeRec) models have achieved improved performance with powerful neural network architectures, we argue that they still suffer from two…
Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need.…
A central question in human immunology is how a patient's repertoire of T cells impacts disease. Here, we introduce a method to infer the causal effects of T cell receptor (TCR) sequences on patient outcomes using observational TCR…
Research must be reproducible in order to make an impact on science and to contribute to the body of knowledge in our field. Yet studies have shown that 70% of research from academic labs cannot be reproduced. In software engineering, and…
In response to pathogens, the adaptive immune system generates specific antibodies that bind and neutralize foreign antigens. Understanding the composition of an individual's immune repertoire can provide insights into this process and…
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…