Rethinking Scientific Discovery in the Agentic Era

Artificial intelligence has advanced scientific discovery, but most AI4Science systems remain fragmented tools that rely on humans to coordinate problem formulation, literature grounding, model use, simulation, validation, and knowledge reuse. This paper presents \textbf{SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus)}, an agentic scientific operating system that acts as an \textbf{organizational nexus}. Through a Science Agent serving as a \textbf{Meta-Harness}, SCION connects scientific tasks, tools, agents, artifacts, and memory, transforming research into an executable, auditable, and reusable operational process. At its core is the \textbf{Research Execution Plan (REP)}, which compiles high-level scientific intent into staged objectives, dependencies, verification checkpoints, tool requirements, expected artifacts, and fallback conditions. SCION further integrates hierarchical multi-agent execution, profile-driven specialization, selective context construction, governed delegation, and layered epistemic memory to support long-horizon scientific work. We formulate discovery under SCION as \textbf{Target-conditioned Inverse Search} and extend it to hidden-target settings through batch active search under finite experimental budgets. Applications in materials analysis, molecule design, and protein or antibody screening, together with experiments on scientific reading, idea generation, molecule generation, and antibody screening, show that SCION outperforms existing autonomous research-agent baselines, especially in decomposition, verification, refinement, and memory reuse. Overall, SCION shifts AI from isolated tools toward a coordinated operational layer for traceable and reusable scientific innovation.

Rethinking Scientific Discovery in an Agentic Era

Artificial intelligence has advanced scientific discovery, but most AI4Science systems remain fragmented tools that rely on humans to coordinate problem formulation, literature grounding, model use, simulation, validation, and knowledge reuse. This paper presents \textbf{SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus)}, an agentic scientific operating system that acts as an \textbf{organizational nexus}. Through a Science Agent serving as a \textbf{Meta-Harness}, SCION connects scientific tasks, tools, agents, artifacts, and memory, transforming research into an executable, auditable, and reusable operational process. At its core is the \textbf{Research Execution Plan (REP)}, which compiles high-level scientific intent into staged objectives, dependencies, verification checkpoints, tool requirements, expected artifacts, and fallback conditions. SCION further integrates hierarchical multi-agent execution, profile-driven specialization, selective context construction, governed delegation, and layered epistemic memory to support long-horizon scientific work. We formulate discovery under SCION as \textbf{Target-conditioned Inverse Search} and extend it to hidden-target settings through batch active search under finite experimental budgets. Applications in materials analysis, molecule design, and protein or antibody screening, together with experiments on scientific reading, idea generation, molecule generation, and antibody screening, show that SCION outperforms existing autonomous research-agent baselines, especially in decomposition, verification, refinement, and memory reuse. Overall, SCION shifts AI from isolated tools toward a coordinated operational layer for traceable and reusable scientific innovation.

AdaptR1: Reinforcement Learning Based Adaptive Interleaved Thinking in Multi-hop Question Answering

Large Language Models (LLMs) have achieved remarkable performance in complex reasoning tasks through Chain-of-Thought (CoT) prompting. However, this approach often leads to ``over-thinking,'' where models generate unnecessarily long reasoning traces for simple queries and incur avoidable inference cost. While recent work has explored adaptive reasoning, existing methods typically make a single query-level decision about whether to reason. This overlooks the dynamic nature of multi-step tasks, where the need for explicit reasoning varies across intermediate stages. To address this limitation, we introduce AdaptR1, a Reinforcement Learning (RL) based framework for adaptive interleaved thinking in multi-hop Question Answering (QA). Unlike previous approaches that require Supervised Fine-Tuning (SFT) for cold-start initialization, AdaptR1 uses a fully RL-based strategy with a quality-gated efficiency reward to dynamically allocate reasoning budgets at each step. Under the Graph-R1 setting, AdaptR1 reduces average think tokens by 69.71\%, with a 90.35\% reduction on HotpotQA, while maintaining performance comparable to or better than standard baselines. Furthermore, our analysis reveals that overthinking in multi-hop reasoning is not uniformly distributed but occurs predominantly during the initial planning stages, highlighting the effectiveness of step-wise adaptive budget allocation.

AgentLongBench: A Controllable Long Benchmark For Long-Contexts Agents via Environment Rollouts

The evolution of Large Language Models (LLMs) into autonomous agents necessitates the management of extensive, dynamic contexts. Current benchmarks, however, remain largely static, relying on passive retrieval tasks that fail to simulate the complexities of agent-environment interaction, such as non-linear reasoning and iterative feedback. To address this, we introduce \textbf{AgentLongBench}, which evaluates agents through simulated environment rollouts based on Lateral Thinking Puzzles. This framework generates rigorous interaction trajectories across knowledge-intensive and knowledge-free scenarios. Experiments with state-of-the-art models and memory systems (32K to 4M tokens) expose a critical weakness: while adept at static retrieval, agents struggle with the dynamic information synthesis essential for workflows. Our analysis indicates that this degradation is driven by the minimum number of tokens required to resolve a query. This factor explains why the high information density inherent in massive tool responses poses a significantly greater challenge than the memory fragmentation typical of long-turn dialogues.

Multi-hop Reasoning via Early Knowledge Alignment

Retrieval-Augmented Generation (RAG) has emerged as a powerful paradigm for Large Language Models (LLMs) to address knowledge-intensive queries requiring domain-specific or up-to-date information. To handle complex multi-hop questions that are challenging for single-step retrieval, iterative RAG approaches incorporating reinforcement learning have been proposed. However, existing iterative RAG systems typically plan to decompose questions without leveraging information about the available retrieval corpus, leading to inefficient retrieval and reasoning chains that cascade into suboptimal performance. In this paper, we introduce Early Knowledge Alignment (EKA), a simple but effective module that aligns LLMs with retrieval set before planning in iterative RAG systems with contextually relevant retrieved knowledge. Extensive experiments on six standard RAG datasets demonstrate that by establishing a stronger reasoning foundation, EKA significantly improves retrieval precision, reduces cascading errors, and enhances both performance and efficiency. Our analysis from an entropy perspective demonstrate that incorporating early knowledge reduces unnecessary exploration during the reasoning process, enabling the model to focus more effectively on relevant information subsets. Moreover, EKA proves effective as a versatile, training-free inference strategy that scales seamlessly to large models. Generalization tests across diverse datasets and retrieval corpora confirm the robustness of our approach. Overall, EKA advances the state-of-the-art in iterative RAG systems while illuminating the critical interplay between structured reasoning and efficient exploration in reinforcement learning-augmented frameworks. The code is released at \href{https://github.com/yxzwang/EarlyKnowledgeAlignment}{Github}.