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CD8+ "killer" T cells and CD4+ "helper" T cells play a central role in the adaptive immune system by recognizing antigens presented by Major Histocompatibility Complex (pMHC) molecules via T Cell Receptors (TCRs). Modeling binding between T…

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…

It has been verified that only a small fraction of the neoantigens presented by MHC class I molecules on the cell surface can elicit T cells. The limitation can be attributed to the binding specificity of T cell receptor (TCR) to…

The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…

Understanding the binding specificity between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to immunotherapy and vaccine development. However, current predictive models struggle with…

T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is a central component of adaptive immunity, with implications for vaccine design, cancer immunotherapy, and autoimmune disease. While recent advances in machine learning…

The complex nature of tripartite peptide-MHC-TCR interactions is a critical yet underexplored area in immunogenicity prediction. Traditional studies on TCR-antigen binding have not fully addressed the complex dependencies in triad binding.…

Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…

Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex…

T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our…

T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is fundamental to adaptive immunity and central to the development of T cell-based immunotherapies. While transformer-based models have shown promise in predicting TCR-pMHC…

Predicting the sensitivity of cancer cell lines to PLX-4720, a preclinical BRAF inhibitor, requires models capable of capturing the multilayered regulation of oncogenic signaling. Single-omics predictors are often insufficient because drug…

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular…

Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning methods excel at learning antigen binding patterns from known…

We propose AttentionMixer, a unified deep learning framework for multimodal detection of brain edema that combines structural head CT (HCT) with routine clinical metadata. While HCT provides rich spatial information, clinical variables such…

Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…

An accurate binding affinity prediction between T-cell receptors and epitopes contributes decisively to develop successful immunotherapy strategies. Some state-of-the-art computational methods implement deep learning techniques by…

Multimodal learning, integrating histology images and genomics, promises to enhance precision oncology with comprehensive views at microscopic and molecular levels. However, existing methods may not sufficiently model the shared or…

Immune checkpoint therapy is one of the most promising immunotherapeutic methods that are likely able to give rise to durable treatment response for various cancer types. Despite much progress in the past decade, there are still critical…