arXiv AI June 9, 2026 By Jake Fawkes, Liam Hodgson, Jason Hartford

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors

arXiv:2606. 08816v1 Announce Type: cross Abstract: Predicting the effect of an unseen gene knockout perturbation on transcriptomic gene expression remains a highly challenging problem for virtual cell models.

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 AI.

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

Aug 18

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 Machine Learning

Jul 22

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects

arXiv:2607. 18777v1 Announce Type: new Abstract: Evaluating machine learning in scientific domains requires separating correct predictions from correct reasons under realistic distribution shifts.

By Dongkwan Kim, Yiming Gao, Yining Yang, Yang Shen

llms benchmarks

arXiv AI

Aug 14

EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

arXiv:2608. 12906v1 Announce Type: cross Abstract: RNA-Protein Interactions (RPIs) are critical for regulating cellular functions.

By Danyu Li, Ling Zhou, Rubing Huang, Xian Zhong, Bin Zou, Kui Jiang

efficiency 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

Sep 17

Procedural Pretraining for Molecular Property Prediction

The paper proposes a three‑stage training pipeline that begins with procedural pretraining on abstract, procedurally generated data, followed by molecular pretraining on SMILES, and finally downstream fine‑tuning for molecular property prediction. Experiments show that procedural pretraining improves downstream performance—e.g., a 4.8% error reduction on Lipophilicity—especially when labeled data are scarce, and that the benefit peaks at an intermediate procedural training budget. Analysis indicates that transferable knowledge resides mainly in attention layers, while feed‑forward layers may over‑specialize.

By Moritz Friedemann, Zachary Shinnick, Philip Torr, Bruno Andreis

fine-tuning

One email a morning, machine-written

Related stories

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

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

PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects

EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

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

Procedural Pretraining for Molecular Property Prediction