SciCore-Mol: Augmenting Large Language Models with Pluggable Molecular Cognition Modules

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols and topological molecular or continuous reaction data leads to significant information loss and semantic noise in text-based reasoning. We propose SciCore-Mol, a modular framework that bridges this gap through three deeply integrated pluggable cognitive modules: a topology-aware perception module, a latent diffusion-based molecular generation module, and a reaction-aware reasoning module. Each module is coupled to the LLM backbone through learned representation interfaces, enabling richer information exchange than is possible with text-only tool feedback. Our experiments on diverse chemical tasks demonstrate that SciCore-Mol achieves strong comprehensive performance across molecular understanding, generation, reaction prediction, and general chemistry knowledge, with an 8B-parameter open-source system that is competitive with and in several dimensions surpasses proprietary large models. This work provides a systematic blueprint for equipping LLMs with scientific expertise through decoupled, pluggable, and flexibly orchestrated modules, with direct implications for drug design, chemical synthesis, and broader scientific discovery.

NaviRAG: Towards Active Knowledge Navigation for Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) typically relies on a flat retrieval paradigm that maps queries directly to static, isolated text segments. This approach struggles with more complex tasks that require the conditional retrieval and dynamic synthesis of information across different levels of granularity (e.g., from broad concepts to specific evidence). To bridge this gap, we introduce NaviRAG, a novel framework that shifts from passive segment retrieval to active knowledge navigation. NaviRAG first structures the knowledge documents into a hierarchical form, preserving semantic relationships from coarse-grained topics to fine-grained details. Leveraging this reorganized knowledge records, a large language model (LLM) agent actively navigates the records, iteratively identifying information gaps and retrieving relevant content from the most appropriate granularity level. Extensive experiments on long-document QA benchmarks show that NaviRAG consistently improves both retrieval recall and end-to-end answer performance over conventional RAG baselines. Ablation studies confirm performance gains stem from our method's capacity for multi-granular evidence localization and dynamic retrieval planning. We further discuss efficiency, applicable scenario, and future directions of our method, hoping to make RAG systems more intelligent and autonomous.

Scientific Knowledge-driven Decoding Constraints Improving the Reliability of LLMs

Large language models (LLMs) have shown strong knowledge reserves and task-solving capabilities, but still face the challenge of severe hallucination, hindering their practical application. Though scientific theories and rules can efficiently direct the behaviors of human manipulators, LLMs still do not utilize these highly-condensed knowledge sufficiently through training or prompting. To address this issue, we propose \textbf{SciDC}, an LLM generation method that integrate subject-specific knowledge with strong constraints. By adopting strong LLMs to automatically convert flexible knowledge into multi-layered, standardized rules, we build an extensible framework to effectively constrain the model generation on domain tasks. Experiments on scientific tasks including industrial formulation design, clinical tumor diagnosis and retrosynthesis planning, consistently demonstrate the effectiveness of our method, achieving a 12\% accuracy improvement on average compared with vanilla generation. We further discuss the potential of LLMs in automatically inductively summarizing highly-condensed knowledge, looking ahead to practical solutions for accelerating the overall scientific research process. All the code of this paper can be obtained (https://github.com/Maotian-Ma/SciDC).

ReAlign: Optimizing the Visual Document Retriever with Reasoning-Guided Fine-Grained Alignment

Visual document retrieval aims to retrieve a set of document pages relevant to a query from visually rich collections. Existing methods often employ Vision-Language Models (VLMs) to encode queries and visual pages into a shared embedding space, which is then optimized via contrastive training. However, during visual document representation, localized evidence is usually scattered across complex document layouts, making it difficult for retrieval models to capture crucial cues for effective embedding learning. In this paper, we propose Reasoning-Guided Alignment (ReAlign), a method that enhances visual document retrieval by leveraging the reasoning capability of VLMs to provide fine-grained visual document descriptions as supervision signals for training. Specifically, ReAlign employs a superior VLM to identify query-related regions on a page and then generates a query-aware description grounding the cropped visual regions. The retriever is then trained using these region-focused descriptions to align the semantics between queries and visual documents by encouraging the document ranking distribution induced by the region-focused descriptions to match that induced by the original query. Experiments on diverse visually rich document retrieval benchmarks demonstrate that ReAlign consistently improves visual document retrieval performance on both in-domain and out-of-domain datasets, achieving up to 2% relative improvements. Moreover, the advantages of ReAlign generalize across different VLM backbones by guiding models to better focus their attention on critical visual cues for document representation. All code and datasets are available at https://github.com/NEUIR/ReAlign.

Cheers: Decoupling Patch Details from Semantic Representations Enables Unified Multimodal Comprehension and Generation

A recent cutting-edge topic in multimodal modeling is to unify visual comprehension and generation within a single model. However, the two tasks demand mismatched decoding regimes and visual representations, making it non-trivial to jointly optimize within a shared feature space. In this work, we present Cheers, a unified multimodal model that decouples patch-level details from semantic representations, thereby stabilizing semantics for multimodal understanding and improving fidelity for image generation via gated detail residuals. Cheers includes three key components: (i) a unified vision tokenizer that encodes and compresses image latent states into semantic tokens for efficient LLM conditioning, (ii) an LLM-based Transformer that unifies autoregressive decoding for text generation and diffusion decoding for image generation, and (iii) a cascaded flow matching head that decodes visual semantics first and then injects semantically gated detail residuals from the vision tokenizer to refine high-frequency content. Experiments on popular benchmarks demonstrate that Cheers matches or surpasses advanced UMMs in both visual understanding and generation. Cheers also achieves 4x token compression, enabling more efficient high-resolution image encoding and generation. Notably, Cheers outperforms the Tar-1.5B on the popular benchmarks GenEval and MMBench, while requiring only 20% of the training cost, indicating effective and efficient (i.e., 4x token compression) unified multimodal modeling. We will release all code and data for future research.

Know More, Know Clearer: A Meta-Cognitive Framework for Knowledge Augmentation in Large Language Models

Knowledge augmentation has significantly enhanced the performance of Large Language Models (LLMs) in knowledge-intensive tasks. However, existing methods typically operate on the simplistic premise that model performance equates with internal knowledge, overlooking the knowledge-confidence gaps that lead to overconfident errors or uncertain truths. To bridge this gap, we propose a novel meta-cognitive framework for reliable knowledge augmentation via differentiated intervention and alignment. Our approach leverages internal cognitive signals to partition the knowledge space into mastered, confused, and missing regions, guiding targeted knowledge expansion. Furthermore, we introduce a cognitive consistency mechanism to synchronize subjective certainty with objective accuracy, ensuring calibrated knowledge boundaries. Extensive experiments demonstrate the our framework consistently outperforms strong baselines, validating its rationality in not only enhancing knowledge capabilities but also fostering cognitive behaviors that better distinguish knowns from unknowns.

DrugR: Optimizing Molecular Drugs through LLM-based Explicit Reasoning

Molecule generation and optimization is a fundamental task in chemical domain. The rapid development of intelligent tools, especially large language models (LLMs) with powerful knowledge reserves and interactive capabilities, has provided new paradigms for it. Nevertheless, the intrinsic challenge for LLMs lies in the complex implicit relationship between molecular structure and pharmacological properties and the lack of corresponding labeled data. To bridge this gap, we propose DrugR, an LLM-based method that introduces explicit, step-by-step pharmacological reasoning into the optimization process. Our approach integrates domain-specific continual pretraining, supervised fine-tuning via reverse data engineering, and self-balanced multi-granular reinforcement learning. This framework enables DrugR to effectively improve key ADMET properties while preserving the original molecule's core efficacy. Experimental results demonstrate that DrugR achieves comprehensive enhancement across multiple properties without compromising structural similarity or target binding affinity. Importantly, its explicit reasoning process provides clear, interpretable rationales for each optimization step, yielding actionable design insights and advancing toward automated, knowledge-driven scientific discovery. Our code and model checkpoints are open-sourced to foster future research.

AgentCPM-Report: Interleaving Drafting and Deepening for Open-Ended Deep Research

Generating deep research reports requires large-scale information acquisition and the synthesis of insight-driven analysis, posing a significant challenge for current language models. Most existing approaches follow a plan-then-write paradigm, whose performance heavily depends on the quality of the initial outline. However, constructing a comprehensive outline itself demands strong reasoning ability, causing current deep research systems to rely almost exclusively on closed-source or online large models. This reliance raises practical barriers to deployment and introduces safety and privacy concerns for user-authored data. In this work, we present AgentCPM-Report, a lightweight yet high-performing local solution composed of a framework that mirrors the human writing process and an 8B-parameter deep research agent. Our framework uses a Writing As Reasoning Policy (WARP), which enables models to dynamically revise outlines during report generation. Under this policy, the agent alternates between Evidence-Based Drafting and Reasoning-Driven Deepening, jointly supporting information acquisition, knowledge refinement, and iterative outline evolution. To effectively equip small models with this capability, we introduce a Multi-Stage Agentic Training strategy, consisting of cold-start, atomic skill RL, and holistic pipeline RL. Experiments on DeepResearch Bench, DeepConsult, and DeepResearch Gym demonstrate that AgentCPM-Report outperforms leading closed-source systems, with substantial gains in Insight.

AgentCPM-Explore: Realizing Long-Horizon Deep Exploration for Edge-Scale Agents

While Large Language Model (LLM)-based agents have shown remarkable potential for solving complex tasks, existing systems remain heavily reliant on large-scale models, leaving the capabilities of edge-scale models largely underexplored. In this paper, we present the first systematic study on training agentic models at the 4B-parameter scale. We identify three primary bottlenecks hindering the performance of edge-scale models: catastrophic forgetting during Supervised Fine-Tuning (SFT), sensitivity to reward signal noise during Reinforcement Learning (RL), and reasoning degradation caused by redundant information in long-context scenarios. To address the issues, we propose AgentCPM-Explore, a compact 4B agent model with high knowledge density and strong exploration capability. We introduce a holistic training framework featuring parameter-space model fusion, reward signal denoising, and contextual information refinement. Through deep exploration, AgentCPM-Explore achieves state-of-the-art (SOTA) performance among 4B-class models, matches or surpasses 8B-class SOTA models on four benchmarks, and even outperforms larger-scale models such as Claude-4.5-Sonnet or DeepSeek-v3.2 in five benchmarks. Notably, AgentCPM-Explore achieves 97.09% accuracy on GAIA text-based tasks under pass@64. These results provide compelling evidence that the bottleneck for edge-scale models is not their inherent capability ceiling, but rather their inference stability. Based on our well-established training framework, AgentCPM-Explore effectively unlocks the significant, yet previously underestimated, potential of edge-scale models.

Graph-Anchored Knowledge Indexing for Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) has emerged as a dominant paradigm for mitigating hallucinations in Large Language Models (LLMs) by incorporating external knowledge. Nevertheless, effectively integrating and interpreting key evidence scattered across noisy documents remains a critical challenge for existing RAG systems. In this paper, we propose GraphAnchor, a novel Graph-Anchored Knowledge Indexing approach that reconceptualizes graph structures from static knowledge representations into active, evolving knowledge indices. GraphAnchor incrementally updates a graph during iterative retrieval to anchor salient entities and relations, yielding a structured index that guides the LLM in evaluating knowledge sufficiency and formulating subsequent subqueries. The final answer is generated by jointly leveraging all retrieved documents and the final evolved graph. Experiments on four multi-hop question answering benchmarks demonstrate the effectiveness of GraphAnchor, and reveal that GraphAnchor modulates the LLM's attention to more effectively associate key information distributed in retrieved documents. All code and data are available at https://github.com/NEUIR/GraphAnchor.