相关论文: ImmSET: Sequence-Based Predictor of TCR-pMHC Speci…

Predicting T-cell receptor (TCR)--peptide-MHC (pMHC) binding is central to vaccine design and T-cell therapy, yet deployed models frequently encounter epitopes unseen during training, causing silent overconfidence and unreliable…

The biophysical interactions between the T cell receptor (TCR) and its ligands determine the specificity of the cellular immune response. However, the immense diversity of receptors and ligands has made it challenging to discover…

The adaptive immune system of vertebrates can detect, respond to, and memorize diverse pathogens from past experience. While the clonal selection of T helper (Th) cells is the simple and established mechanism to better recognize new…

The task of learning to map an input set onto a permuted sequence of its elements is challenging for neural networks. Set-to-sequence problems occur in natural language processing, computer vision and structure prediction, where…

The process of identifying and characterizing B-cell epitopes, which are the portions of antigens recognized by antibodies, is important for our understanding of the immune system, and for many applications including vaccine development,…

The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse (IS). Understanding the biophysical basis for protein patterning by deciphering the…

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent…

Adhesion between a T cell and an antigen presenting cell is achieved by TCR-pMHC and LFA1-ICAM1 protein complexes. These segregate to form a special pattern, known as the immunological synapse (IS), consisting of a central quasi-circular…

Recent advances in immunomics have shown that T-cell receptor (TCR) signatures can accurately predict active or recent infection by leveraging the high specificity of TCR binding to disease antigens. However, the extreme diversity of the…

Predicting the binding free energy between antibodies and antigens is a key challenge in structure-aware biomolecular modeling, with direct implications for antibody design. Most existing methods either rely solely on sequence embeddings or…

An essential feature of the adaptive immune system is the proliferation of antigen-specific lymphocytes during an immune reaction to form a large pool of effector cells. This proliferation must be regulated to ensure an effective response…

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses…

Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…

This paper studies Time Series Extrinsic Regression (TSER): a regression task of which the aim is to learn the relationship between a time series and a continuous scalar variable; a task closely related to time series classification (TSC),…

Our main purpose is to compare classical nonself-centered, two-signal theoretical models of the adaptive immune system with a novel, self-centered, one-signal model developed by our research group. Our model hypothesizes that the immune…

The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…

The ubiquity of time series data creates a strong demand for general-purpose foundation models, yet developing them for classification remains a significant challenge, largely due to the high cost of labeled data. Foundation models capable…

Antibodies play a central role in the immune response by specifically recognizing and neutralizing antigens, and therapeutic antibodies have become major drugs for cancer and autoimmune diseases. However, their discovery still relies on…

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines…

Aligning Large Language Models (LLMs) with human preferences through finetuning is resource-intensive, motivating lightweight alternatives at test time. We address test-time alignment through the lens of sequential decision making, a…