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cs.AI updates on arXiv.org

Policy Split: Incentivizing Dual-Mode Exploration in LLM Reinforcement with Dual-Mode Entropy Regularization METER: Evaluating Multi-Level Contextual Causal Reasoning in Large Language Models Think Before you Write: QA-Guided Reasoning for Character Descriptions in Books METRO: Towards Strategy Induction from Expert Dialogue Transcripts for Non-collaborative Dialogues Retrieval as Generation: A Unified Framework with Self-Triggered Information Planning Do LLMs Know Tool Irrelevance? Demystifying Structural Alignment Bias in Tool Invocations Enhancing Multimodal Large Language Models for Ancient Chinese Character Evolution Analysis via Glyph-Driven Fine-Tuning Exploring Knowledge Conflicts for Faithful LLM Reasoning: Benchmark and Method CocoaBench: Evaluating Unified Digital Agents in the Wild MathAgent: Adversarial Evolution of Constraint Graphs for Mathematical Reasoning Data Synthesis Efficient Training for Cross-lingual Speech Language Models Shared Emotion Geometry Across Small Language Models: A Cross-Architecture Study of Representation, Behavior, and Methodological Confounds A Systematic Analysis of the Impact of Persona Steering on LLM Capabilities Uncertainty-Aware Web-Conditioned Scientific Fact-Checking When Valid Signals Fail: Regime Boundaries Between LLM Features and RL Trading Policies When Verification Fails: How Compositionally Infeasible Claims Escape Rejection Mem$^2$Evolve: Towards Self-Evolving Agents via Co-Evolutionary Capability Expansion and Experience Distillation AOP-Smart: A RAG-Enhanced Large Language Model Framework for Adverse Outcome Pathway Analysis Advancing Polish Language Modeling through Tokenizer Optimization in the Bielik v3 7B and 11B Series TInR: Exploring Tool-Internalized Reasoning in Large Language Models Do BERT Embeddings Encode Narrative Dimensions? A Token-Level Probing Analysis of Time, Space, Causality, and Character in Fiction Generating Multiple-Choice Knowledge Questions with Interpretable Difficulty Estimation using Knowledge Graphs and Large Language Models Deep-Reporter: Deep Research for Grounded Multimodal Long-Form Generation Too Nice to Tell the Truth: Quantifying Agreeableness-Driven Sycophancy in Role-Playing Language Models Learning and Enforcing Context-Sensitive Control for LLMs Efficient Process Reward Modeling via Contrastive Mutual Information Computational Lesions in Multilingual Language Models Separate Shared and Language-specific Brain Alignment Bridging Linguistic Gaps: Cross-Lingual Mapping in Pre-Training and Dataset for Enhanced Multilingual LLM Performance Early Decisions Matter: Proximity Bias and Initial Trajectory Shaping in Non-Autoregressive Diffusion Language Models LLMs Should Incorporate Explicit Mechanisms for Human Empathy
scBench: Evaluating AI Agents on Single-Cell RNA-seq Anal...
Kenny Workman, Zhen Yang, Harihara Muralidharan, Aidan Abdulali, · 2026-02-09 · via cs.AI updates on arXiv.org

As single-cell RNA sequencing datasets grow in adoption, scale, and complexity, data analysis remains a bottleneck for many research groups. Although frontier AI agents have improved dramatically at software engineering and general data analysis, it remains unclear whether they can extract biological insight from messy, real-world single-cell datasets. We introduce scBench, a benchmark of 394 verifiable problems derived from practical scRNA-seq workflows spanning six sequencing platforms and seven task categories. Each problem provides a snapshot of experimental data immediately prior to an analysis step and a deterministic grader that evaluates recovery of a key biological result. Benchmark data on eight frontier models shows that accuracy ranges from 29-53%, with strong model-task and model-platform interactions. Platform choice affects accuracy as much as model choice, with 40+ percentage point drops on less-documented technologies. scBench complements SpatialBench to cover the two dominant single-cell modalities, serving both as a measurement tool and a diagnostic lens for developing agents that can analyze real scRNA-seq datasets faithfully and reproducibly.