arXiv AI

$D^{2}R^{2}$: Discrete Diffusion with Regulation Reinforcement for Single-Cell Perturbation Prediction

arXiv:2608. 15288v1 Announce Type: new Abstract: Predicting single-cell transcriptomic responses to genetic perturbations is central to functional genomics and virtual-cell modeling.

arXiv AI

Aug 10

Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling

arXiv:2608. 06824v1 Announce Type: cross Abstract: A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships.

By Quanquan Li, Yihe Chi, Liuyang Song, Hongbo Zhang, Jingyu Li, Xidong Xi, Conghua Wei, Yijie Sun, Yu Chen, Xin Liu, Qi Hu, Jing Ke, Guitao Cao

diffusion benchmarks

arXiv Machine Learning

Jun 29

PerturbCellRL: Verifier-Guided Reinforcement Learning for Single-Cell Perturbation Prediction

arXiv:2606. 27752v1 Announce Type: new Abstract: Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions.

By Dongxia Wu, Mingyu Li, Yuhui Zhang, Anurendra Kumar, Emma Lundberg, Serena Yeung-Levy, Emily B. Fox

reinforcement-learning benchmarks safety

arXiv AI

Jun 15

CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

arXiv:2606. 13713v1 Announce Type: cross Abstract: Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training.

By Wei Zhang, Xun Jiang, Yuesi Xi, Ming Tang

multimodal benchmarks

arXiv AI

Jun 12

OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction

arXiv:2606. 12838v1 Announce Type: cross Abstract: Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks.

By Danning Jiang, Zheming An, Yalong Zhao, Lipeng Lai

llms rag benchmarks

arXiv Machine Learning

Jun 17

Beyond Independent Genes: Learning Module-Inductive Representations for Single-Cell Gene Perturbation Prediction

arXiv:2602. 04901v2 Announce Type: replace-cross Abstract: Predicting transcriptional responses to genetic perturbations is a central problem in functional genomics.

By Jiafa Ruan, Ruijie Quan, Liyang Xu, Zongxin Yang, Yi Yang

diffusion 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 AI

Jul 23

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

arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.

By Yaodi Luo, Peize He, Bowen Han, Lingbei Mengg

efficiency

arXiv Machine Learning

Jun 5

Plug-and-Play Guidance for Discrete Diffusion Models via Gradient-Informed Logit Correction

arXiv:2606. 06303v1 Announce Type: new Abstract: Controllable generation with discrete diffusion models is often hindered by high computational overhead or the need for retraining.

By Hongkun Dou, Zike Chen, Fengji Li, Hongjue Li, Yue Deng

diffusion fine-tuning benchmarks

arXiv AI

Jul 16

CoDiffGRN: Rethinking Gene Regulatory Network Inference via the BEELINE-KGC Benchmark and Co-evolutionary Discrete Diffusion

arXiv:2607. 13120v1 Announce Type: cross Abstract: Inferring gene regulatory networks (GRNs) from single-cell transcriptomic data is crucial for biological discovery, yet existing approaches suffer from a fundamental misalignment with real-world needs.

By Jiaze Song, Runhao Zhao, Minghao Xu, Bin Cui, Wentao Zhang

diffusion benchmarks

arXiv AI

Jun 2

Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.

By Xinyu Yuan, Xixian Liu, Jianan Zhao, Yashi Zhang, Hongyu Guo, Jian Tang

llms

arXiv AI

1d ago

PertMind: Eliciting Emergent Biological Reasoning in LLM via Reinforcement Learning on Cellular Perturbation Data

arXiv:2608. 16419v1 Announce Type: cross Abstract: Large language models can describe mechanisms, yet scalable post-training still depends on costly, manually curated biological reasoning traces.

By Zhenchao Tang, Xiaogang Xu, Tianxu Lv, Jiahui Guan, Jiale Zhou, Haohuai He, Zhi Song, Hanbo Huang, Jiehui Huang, Jiafei Wu, Zhe Liu

llms reinforcement-learning

arXiv AI

Aug 5

Scaling an Autoregressive Transformer for Single-Cell Generation

arXiv:2608. 02961v1 Announce Type: cross Abstract: We study a self-supervised generation task for single-cell gene expression vectors: given a set of vectors from a cell type, we aim to generate additional gene expression vectors of that cell type.

By Aleksandr Sharipov, Yusif Mukhtarov, Igor Molybog

llms nlp efficiency

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