arXiv AI

Improving scDiffusion with Sparsity-Biased Classifier-Free Guidance

arXiv:2607. 29043v1 Announce Type: cross Abstract: Single-cell RNA sequencing (scRNA-seq) has become an essential tool in modern cellular biology, and generating accurate synthetic scRNA-seq data is becoming increasingly important.

arXiv Machine Learning

Jun 9

Integrating gene regulatory priors into Transformer attention with scTransformer for interpretable scRNA-seq analysis

arXiv:2606. 09558v1 Announce Type: cross Abstract: Motivation: Transformer-based models are increasingly applied to large-scale single-cell transcriptomics, showing strong performance through self-supervised learning on millions of cells.

By Mikele Milia, Louis Fabrice Tshimanga, Henning Mueller, Manfredo Atzori, Barbara Di Camillo

llms rag safety

arXiv Machine Learning

Aug 4

Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

arXiv:2608. 00985v1 Announce Type: new Abstract: The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values.

By Jiaqi Xiong, Yuntao hu, Yu Zheng, Yifei Shi, Xinyue Guo, Jiaxin Qi

arXiv AI

Jun 16

BRIDGE: Biological Evidence Refinement and Heterogeneous Dynamic Gating for Gene Regulatory Networks

arXiv:2606. 14734v1 Announce Type: cross Abstract: Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs.

By Ziyang Dong, Shanwen Tan, Hengchuang Yin, Wei Liu, Yifan Wang, Siyu Yi, Jiancheng Lv, Wei Ju

benchmarks

arXiv Machine Learning

Jun 2

Prior-Guided Multi-Omic Transformers for Single-Cell Gene Regulatory Network Inference

arXiv:2606. 00685v1 Announce Type: new Abstract: Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease.

By Tianyang Xu, Tianci Liu, Niraj Rayamajhi, Ryan Patrick, Kranthi Varala, Ying Li, Jing Gao

llms multimodal

arXiv Machine Learning

Jul 28

SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing

arXiv:2607. 23821v1 Announce Type: new Abstract: Identifying therapeutic target genes from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in translational biology.

By Shuyu Chen, Chen Zhu, Ye Zhang, Yang Li, Qiqi Xie, Haohan Wang

agents benchmarks safety

arXiv Machine Learning

Jun 9

scCBGM: Interpretable Single-Cell Counterfactual Editing

arXiv:2606. 07760v1 Announce Type: new Abstract: Understanding cellular phenotypes and how they respond to perturbations is critical for disease biology and therapeutic design.

By Alma Andersson, Aya Abdelsalam Ismail, Edward De Brouwer, Doron Haviv, Tommaso Biancalani, Kyunghyun Cho, Gabriele Scalia, A\"icha BenTaieb, Hector Corrada Bravo

diffusion benchmarks

arXiv AI

Jun 9

Single-Cell Cross-Modal Transfer by Adversarial Fine-Tuning of Foundation Models

arXiv:2606. 07676v1 Announce Type: cross Abstract: Spatial transcriptomics (ST) is a powerful tool for exploring biological properties dependent on structure, proximity, and interaction in tissue.

By Joseph Boyd, Matthew Lyon, Martino Mansoldo, Christian Hurry, Finnian Firth

fine-tuning multimodal safety

arXiv AI

Aug 5

Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection

arXiv:2607. 19426v2 Announce Type: replace-cross Abstract: Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training.

By Yaodi Luo, Peize He, Lingbei Meng, Bowen Han, Zheng Lu, Jianqing Zhu, Lian Zhang

rag efficiency benchmarks

arXiv AI

Jun 30

Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction

arXiv:2606. 29949v1 Announce Type: cross Abstract: H&E-stained whole-slide images offer cohort-scale availability and rich spatial context but lack molecular specificity, whereas bulk RNA-seq provides transcriptome-wide resolution at high cost with limited archival availability.

By Dominik Winter, Dominik Vonficht, Lo\"ic Le Bescond, Christian Gebbe, Marco Rosati, Richard J. Chen, Markus Schick, Ross Stewart, Nicolas Brieu

llms fine-tuning multimodal safety

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 AI

Jul 1

Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses

arXiv:2606. 30695v1 Announce Type: cross Abstract: Single-cell drug perturbation models should predict not only transcriptional response magnitude, but also whether a treatment alters the proliferative state of a cell.

By Dingping Zhao, Jie Lin

benchmarks

arXiv Machine Learning

Jun 9

Scaling Laws for Masked-Reconstruction Transformers on Single-Cell Transcriptomics

arXiv:2602. 15253v2 Announce Type: replace Abstract: Neural scaling laws -- power-law relationships between loss, model size, and data -- have been extensively documented for language and vision transformers, yet their existence in single-cell genomics remains largely unexplored.

By Ihor Kendiukhov

llms nlp

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