On generative models of T-cell receptor sequences

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 key importance for immunology and medical applications. Here,...

Full description

Saved in:

Bibliographic Details
Published in:	arXiv.org
Main Authors:	Isacchini, Giulio, Sethna, Zachary, Elhanati, Yuval, Nourmohammad, Armita, Walczak, Aleksandra M, Mora, Thierry
Format:	Paper
Language:	English
Published:	Ithaca Cornell University Library, arXiv.org 13.03.2020
Subjects:	Coders Lymphocytes T cell receptors
ISSN:	2331-8422
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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 key importance for immunology and medical applications. Here, we compare two inference methods trained on high-throughput sequencing data: a knowledge-guided approach, which accounts for the details of sequence generation, supplemented by a physics-inspired model of selection; and a knowledge-free Variational Auto-Encoder based on deep artificial neural networks. We show that the knowledge-guided model outperforms the deep network approach at predicting TCR probabilities, while being more interpretable, at a lower computational cost.
Bibliography:	SourceType-Working Papers-1 ObjectType-Working Paper/Pre-Print-1 content type line 50
ISSN:	2331-8422
DOI:	10.48550/arxiv.1911.12279