arXiv AI

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.

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

Hugging Face Trending Papers

Jun 15

How Post-Training Shapes Biological Reasoning Models

Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins. These models are built through post-training, yet how each stage shapes reasoning and generalization remains poorly understood.

llms reinforcement-learning fine-tuning multimodal

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 Machine Learning

Jun 16

How Post-Training Shapes Biological Reasoning Models

arXiv:2606. 16517v1 Announce Type: new Abstract: Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins.

By Lukas Fesser, Hanlin Zhang, Michelle M. Li, Eric Wang, Bryan Perozzi, Shekoofeh Azizi, Sham M. Kakade, Marinka Zitnik

llms reinforcement-learning fine-tuning multimodal

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

Jul 14

Nested-ReFT: Efficient Reinforcement Learning for Large Language Model Fine-Tuning via Off-Policy Rollouts

arXiv:2508. 10123v3 Announce Type: replace-cross Abstract: Advanced reasoning in LLMs on challenging domains like mathematical reasoning can be tackled using verifiable rewards based reinforced fine-tuning (ReFT).

By Maxime Heuillet, Yufei Cui, Boxing Chen, Audrey Durand, Prasanna Parthasarathi

llms reinforcement-learning fine-tuning benchmarks safety

arXiv Machine Learning

Jun 9

Attention Illuminates LLM Reasoning: The Preplan-and-Anchor Rhythm Enables Fine-Grained Policy Optimization

arXiv:2510. 13554v2 Announce Type: replace-cross Abstract: The reasoning pattern of Large language models (LLMs) remains opaque, and reinforcement learning (RL) typically applies uniform credit across an entire generation, blurring the distinction between pivotal and routine steps.

By Yang Li, Zhichen Dong, Yuhan Sun, Weixun Wang, Shaopan Xiong, Yijia Luo, Jiashun Liu, Han Lu, Jiamang Wang, Wenbo Su, Bo Zheng, Junchi Yan

llms reinforcement-learning

arXiv AI

Jun 9

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.

By Jake Fawkes, Liam Hodgson, Jason Hartford

llms reinforcement-learning

arXiv AI

Jun 16

STRIDE: Strategic Trajectory Reasoning via Discriminative Estimation for Verifiable Reinforcement Learning

arXiv:2606. 15866v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has become an effective post-training paradigm for improving the reasoning abilities of large language models.

By Qinjian Zhao, Zhihao Dou, Dinggen Zhang, Xiangyu Li, Chaoda Song, Zhongwei Wan, Xinpeng Li, Yanyan Zhang, Kaijie Chen, Qingtao Pan, Chengcheng Feng, Zhiqiang Gao, Xiaoyu Xia

llms agents reinforcement-learning

arXiv AI

Jul 2

Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization

arXiv:2607. 00531v1 Announce Type: cross Abstract: Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge.

By Xuefeng Liu, Mingxuan Cao, Qinan Huang, Thomas Brettin, Rick Stevens, Le Cong

llms reinforcement-learning fine-tuning

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 AI

Jul 17

Reachability-Aware Pretraining for Efficient Target-Oriented Path Exploration in Temporal Knowledge Graph Reasoning

arXiv:2607. 14886v1 Announce Type: new Abstract: Temporal Knowledge Graph (TKG) reasoning under the extrapolation setting focuses on forecasting future time-stamped events (facts) from historical data in a temporal knowledge graph.

By Chien-Liang Liu, Tsao-Lun Chen

agents reinforcement-learning fine-tuning safety

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