arXiv Machine Learning July 23, 2026 By Rong Fu, Muge Qi, Yang Li, Yabin Jin, Jiekai Wu, Chunlei Meng, Juntao Gao, Li Bao, Qi Zhao, Wei Luo, Youjin Wang, Simon Fong

SwiftRepertoire: Few-Shot Immune-Signature Synthesis via Dynamic Kernel Codes

Read the original on arXiv Machine Learning →

arXiv:2602. 01051v5 Announce Type: replace Abstract: Repertoire-level analysis of T cell receptors offers a biologically grounded signal for disease detection and immune monitoring, yet practical deployment is impeded by label sparsity, cohort heterogeneity, and the computational burden of adapting large encoders to new tasks.

Machine-generated by The Flow from the publisher's headline and feed description — not written or checked by a human. The full article lives at arXiv Machine Learning.

arXiv AI

Jul 23

SubQuad: Near-Quadratic-Free Structure Inference with Distribution-Balanced Objectives in Adaptive Receptor framework

arXiv:2602. 17330v5 Announce Type: replace-cross Abstract: Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority clonotypes.

By Rong Fu, Zijian Zhang, Kun Liu, Jiekai Wu, Xianda Li, Simon Fong

rag efficiency multimodal safety

arXiv Machine Learning

Jul 1

Structure-Regularized Interpretable TCR-Epitope Prediction

arXiv:2606. 30902v1 Announce Type: cross Abstract: T cell receptor (TCR)-epitope binding prediction is essential for understanding adaptive immunity and developing immunotherapies.

By Jiarui Li, Zixiang Yin, Yunbei Zhang, Janet Wang, Samuel J. Landry, Zhengming Ding, Ramgopal R. Mettu

llms rag benchmarks safety

arXiv Machine Learning

Jun 4

EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning

arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.

By Mansoor Ahmed, Huirong Chai, Haoxin Wang, Hemanth Venkateswara, Murray Patterson

efficiency benchmarks

arXiv AI

Jun 4

You Only Train Once: Differentiable Subset Selection for Omics Data

arXiv:2512. 17678v2 Announce Type: replace-cross Abstract: Selecting compact and informative gene subsets from single-cell transcriptomic data is essential for biomarker discovery, improving interpretability, and cost-effective profiling.

By Daphn\'e Chopard, Jorge da Silva Gon\c{c}alves, Irene Cannistraci, Thomas M. Sutter, Julia E. Vogt

efficiency benchmarks safety

arXiv Machine Learning

2d ago

Prototype Guided Post-pretraining for Single-Cell Representation Learning

arXiv:2605.07938v2 Announce Type: replace Abstract: Single-cell representation learning (SCRL) from gene expression data offers a way to uncover the complex regulatory logic underlying cellular funct...

By Sachini Weerasekara, Natasha Darras, Sagar Kamarthi, Colles Price, Jacqueline Isaacs

llms rag fine-tuning

arXiv Machine Learning

4d ago

Estimating the Causal Effects of T Cell Receptors

The paper introduces a method for estimating the causal effects of T cell receptor (TCR) sequences on patient outcomes using observational TCR sequencing and clinical data. It corrects for unobserved confounders by leveraging the pre-selection TCR repertoire generated through V(D)J recombination as a natural experiment, and employs permutation‑invariant neural networks to scale to millions of sequences. The approach is validated on semisynthetic data and applied to COVID‑19 severity, identifying TCRs that are observed in patients, bind SARS‑CoV‑2 antigens in vitro, and positively influence clinical outcomes.

By Eli N. Weinstein, Elizabeth B. Wood, David M. Blei

One email a morning, machine-written

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SubQuad: Near-Quadratic-Free Structure Inference with Distribution-Balanced Objectives in Adaptive Receptor framework

Structure-Regularized Interpretable TCR-Epitope Prediction

EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning

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Prototype Guided Post-pretraining for Single-Cell Representation Learning

Estimating the Causal Effects of T Cell Receptors