arXiv AI

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.

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 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

5d ago

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 Machine Learning

Jun 9

Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction

arXiv:2606. 08147v1 Announce Type: cross Abstract: DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels.

By Yi Duan, Zhao Yang, Jiwei Zhu, Ying Ba, Chuan Cao, Bing Su

llms reinforcement-learning benchmarks safety

arXiv Machine Learning

Aug 7

BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells

arXiv:2608. 05928v1 Announce Type: new Abstract: Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes.

By Yuhao Wang, Zelin Zang, Yuxuan Liu, Zhen Lei, Stan Z. Li

rag fine-tuning efficiency

arXiv Machine Learning

Jun 9

Graph-GRPO: Training Graph Flow Models with Reinforcement Learning

arXiv:2603. 10395v2 Announce Type: replace Abstract: Graph generation is a fundamental task with broad applications, such as drug discovery.

By Baoheng Zhu, Deyu Bo, Delvin Ce Zhang, Xiao Wang

diffusion reinforcement-learning benchmarks

arXiv AI

Jul 7

rePIRL: Learn PRM with Inverse RL for LLM Reasoning

arXiv:2602. 07832v3 Announce Type: replace-cross Abstract: Process rewards have been widely used in deep reinforcement learning to improve training efficiency, reduce variance, and prevent reward hacking.

By Xian Wu, Kaijie Zhu, Ying Zhang, Lun Wang, Wenbo Guo

llms reinforcement-learning benchmarks

arXiv Machine Learning

Jun 5

SUPERNOVA: Eliciting General Reasoning in LLMs with Reinforcement Learning on Natural Instructions

arXiv:2604. 08477v2 Announce Type: replace-cross Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has substantially improved reasoning in formal domains such as mathematics and code, but extending these gains beyond STEM remains challenging.

By Ashima Suvarna, Kendrick Phan, Mehrab Beikzadeh, Hritik Bansal, Saadia Gabriel

llms reinforcement-learning benchmarks

arXiv Machine Learning

Jul 8

Canopy: A Heterograph Foundation Model for Metabolic Engineering

arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.

By Jake Bowden, Laurence Legon, Satnam Surae

llms rag multimodal

Hugging Face Trending Papers

Jul 6

Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics.

rag diffusion benchmarks

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