Related papers: Predicting T-Cell Receptor Specificity

We study the prediction of T-cell response for specific given peptides, which could, among other applications, be a crucial step towards the development of personalized cancer vaccines. It is a challenging task due to limited, heterogeneous…

Random Forest (RF) is a widely used ensemble learning technique known for its robust classification performance across diverse domains. However, it often relies on hundreds of trees and all input features, leading to high inference cost and…

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…

Objectives To develop and validate a deep learning-based diagnostic model incorporating uncertainty estimation so as to facilitate radiologists in the preoperative differentiation of the pathological subtypes of renal cell carcinoma (RCC)…

Anomaly detection underpins critical applications from network security and intrusion detection to fraud prevention, where recognizing aberrant patterns rapidly is indispensable. Progress in this area is routinely impeded by two obstacles:…

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…

Accurate survival prediction is crucial for development of precision cancer medicine, creating the need for new sources of prognostic information. Recently, there has been significant interest in exploiting routinely collected clinical and…

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…

Transcriptional profiling on microarrays to obtain gene expressions has been used to facilitate cancer diagnosis. We propose a deep generative machine learning architecture (called DeepCancer) that learn features from unlabeled microarray…

Adapting machine learning algorithms to better handle the presence of clusters or batch effects within training datasets is important across a wide variety of biological applications. This article considers the effect of ensembling Random…

Quantifying prediction uncertainty when applying object detection models to new, unlabeled datasets is critical in applied machine learning. This study introduces an approach to estimate the performance of deep learning-based object…

Random Fourier features (RFFs) provide a promising way for kernel learning in a spectral case. Current RFFs-based kernel learning methods usually work in a two-stage way. In the first-stage process, learning the optimal feature map is often…

Random Forest (Breiman, 2001) is a successful and widely used regression and classification algorithm. Part of its appeal and reason for its versatility is its (implicit) construction of a kernel-type weighting function on training data,…

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…

Click-Through Rate (CTR) prediction models are integral to a myriad of industrial settings, such as personalized search advertising. Current methods typically involve feature extraction from users' historical behavior sequences combined…

Decision Trees and Random Forests are among the most widely used machine learning models, and often achieve state-of-the-art performance in tabular, domain-agnostic datasets. Nonetheless, being primarily discriminative models they lack…

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…

Precise prognostic stratification of colorectal cancer (CRC) remains a major clinical challenge due to its high heterogeneity. The conventional TNM staging system is inadequate for personalized medicine. We aimed to develop and validate a…

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 incidence rate for skin cancer has been steadily increasing throughout the world, leading to it being a serious issue. Diagnosis at an early stage has the potential to drastically reduce the harm caused by the disease, however, the…