A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

InternVL3.5: Advancing Open-Source Multimodal Models in Versatility, Reasoning, and Efficiency

We introduce InternVL 3.5, a new family of open-source multimodal models that significantly advances versatility, reasoning capability, and inference efficiency along the InternVL series. A key innovation is the Cascade Reinforcement Learning (Cascade RL) framework, which enhances reasoning through a two-stage process: offline RL for stable convergence and online RL for refined alignment. This coarse-to-fine training strategy leads to substantial improvements on downstream reasoning tasks, e.g., MMMU and MathVista. To optimize efficiency, we propose a Visual Resolution Router (ViR) that dynamically adjusts the resolution of visual tokens without compromising performance. Coupled with ViR, our Decoupled Vision-Language Deployment (DvD) strategy separates the vision encoder and language model across different GPUs, effectively balancing computational load. These contributions collectively enable InternVL3.5 to achieve up to a +16.0\% gain in overall reasoning performance and a 4.05$\times$ inference speedup compared to its predecessor, i.e., InternVL3. In addition, InternVL3.5 supports novel capabilities such as GUI interaction and embodied agency. Notably, our largest model, i.e., InternVL3.5-241B-A28B, attains state-of-the-art results among open-source MLLMs across general multimodal, reasoning, text, and agentic tasks -- narrowing the performance gap with leading commercial models like GPT-5. All models and code are publicly released.

HiD-VAE: Interpretable Generative Recommendation via Hierarchical and Disentangled Semantic IDs

Recommender systems are indispensable for helping users navigate the immense item catalogs of modern online platforms. Recently, generative recommendation has emerged as a promising paradigm, unifying the conventional retrieve-and-rank pipeline into an end-to-end model capable of dynamic generation. However, existing generative methods are fundamentally constrained by their unsupervised tokenization, which generates semantic IDs suffering from two critical flaws: (1) they are semantically flat and uninterpretable, lacking a coherent hierarchy, and (2) they are prone to representation entanglement (i.e., ``ID collisions''), which harms recommendation accuracy and diversity. To overcome these limitations, we propose HiD-VAE, a novel framework that learns hierarchically disentangled item representations through two core innovations. First, HiD-VAE pioneers a hierarchically-supervised quantization process that aligns discrete codes with multi-level item tags, yielding more uniform and disentangled IDs. Crucially, the trained codebooks can predict hierarchical tags, providing a traceable and interpretable semantic path for each recommendation. Second, to combat representation entanglement, HiD-VAE incorporates a novel uniqueness loss that directly penalizes latent space overlap. This mechanism not only resolves the critical ID collision problem but also promotes recommendation diversity by ensuring a more comprehensive utilization of the item representation space. These high-quality, disentangled IDs provide a powerful foundation for downstream generative models. Extensive experiments on three public benchmarks validate HiD-VAE's superior performance against state-of-the-art methods. The code is available at https://anonymous.4open.science/r/HiD-VAE-84B2.

A Multi-Expert Structural-Semantic Hybrid Framework for Unveiling Historical Patterns in Temporal Knowledge Graphs

Temporal knowledge graph reasoning aims to predict future events with knowledge of existing facts and plays a key role in various downstream tasks. Previous methods focused on either graph structure learning or semantic reasoning, failing to integrate dual reasoning perspectives to handle different prediction scenarios. Moreover, they lack the capability to capture the inherent differences between historical and non-historical events, which limits their generalization across different temporal contexts. To this end, we propose a Multi-Expert Structural-Semantic Hybrid (MESH) framework that employs three kinds of expert modules to integrate both structural and semantic information, guiding the reasoning process for different events. Extensive experiments on three datasets demonstrate the effectiveness of our approach.

Model Merging for Knowledge Editing

Large Language Models (LLMs) require continuous updates to maintain accurate and current knowledge as the world evolves. While existing knowledge editing approaches offer various solutions for knowledge updating, they often struggle with sequential editing scenarios and harm the general capabilities of the model, thereby significantly hampering their practical applicability. This paper proposes a two-stage framework combining robust supervised fine-tuning (R-SFT) with model merging for knowledge editing. Our method first fine-tunes the LLM to internalize new knowledge fully, then merges the fine-tuned model with the original foundation model to preserve newly acquired knowledge and general capabilities. Experimental results demonstrate that our approach significantly outperforms existing methods in sequential editing while better preserving the original performance of the model, all without requiring any architectural changes. Code is available at: https://github.com/Applied-Machine-Learning-Lab/MM4KE.

Training-free LLM Merging for Multi-task Learning

Large Language Models (LLMs) have demonstrated exceptional capabilities across diverse natural language processing (NLP) tasks. The release of open-source LLMs like LLaMA and Qwen has triggered the development of numerous fine-tuned models tailored for various tasks and languages. In this paper, we explore an important question: is it possible to combine these specialized models to create a unified model with multi-task capabilities. We introduces Hierarchical Iterative Merging (Hi-Merging), a training-free method for unifying different specialized LLMs into a single model. Specifically, Hi-Merging employs model-wise and layer-wise pruning and scaling, guided by contribution analysis, to mitigate parameter conflicts. Extensive experiments on multiple-choice and question-answering tasks in both Chinese and English validate Hi-Merging's ability for multi-task learning. The results demonstrate that Hi-Merging consistently outperforms existing merging techniques and surpasses the performance of models fine-tuned on combined datasets in most scenarios. Code is available at: https://github.com/Applied-Machine-Learning-Lab/Hi-Merging.

Elicit and Enhance: Advancing Multimodal Reasoning in Medical Scenarios

Effective clinical decision-making depends on iterative, multimodal reasoning across diverse sources of evidence. The recent emergence of multimodal reasoning models has significantly transformed the landscape of solving complex tasks. Although such models have achieved notable success in mathematics and science, their application to medical domains remains underexplored. In this work, we propose \textit{MedE$^2$}, a two-stage post-training pipeline that elicits and then enhances multimodal reasoning for medical domains. In Stage-I, we fine-tune models using 2,000 text-only data samples containing precisely orchestrated reasoning demonstrations to elicit reasoning behaviors. In Stage-II, we further enhance the model's reasoning capabilities using 1,500 rigorously curated multimodal medical cases, aligning model reasoning outputs with our proposed multimodal medical reasoning preference. Extensive experiments demonstrate the efficacy and reliability of \textit{MedE$^2$} in improving the reasoning performance of medical multimodal models. Notably, models trained with \textit{MedE$^2$} consistently outperform baselines across multiple medical multimodal benchmarks. Additional validation on larger models and under inference-time scaling further confirms the robustness and practical utility of our approach.

MSEarth: A Benchmark for Multimodal Scientific Comprehension of Earth Science

The rapid advancement of multimodal large language models (MLLMs) has unlocked new opportunities to tackle complex scientific challenges. Despite this progress, their application in addressing earth science problems, especially at the graduate level, remains underexplored. A significant barrier is the absence of benchmarks that capture the depth and contextual complexity of geoscientific reasoning. Current benchmarks often rely on synthetic datasets or simplistic figure-caption pairs, which do not adequately reflect the intricate reasoning and domain-specific insights required for real-world scientific applications. To address these gaps, we introduce MSEarth, a multimodal scientific benchmark curated from high-quality, open-access scientific publications. MSEarth encompasses the five major spheres of Earth science: atmosphere, cryosphere, hydrosphere, lithosphere, and biosphere, featuring over 7K figures with refined captions. These captions are crafted from the original figure captions and enriched with discussions and reasoning from the papers, ensuring the benchmark captures the nuanced reasoning and knowledge-intensive content essential for advanced scientific tasks. MSEarth supports a variety of tasks, including scientific figure captioning, multiple choice questions, and open-ended reasoning challenges. By bridging the gap in graduate-level benchmarks, MSEarth provides a scalable and high-fidelity resource to enhance the development and evaluation of MLLMs in scientific reasoning. The benchmark is publicly available to foster further research and innovation in this field. Resources related to this benchmark can be found at https://huggingface.co/MSEarth and https://github.com/xiangyu-mm/MSEarth.

FunReason: Enhancing Large Language Models' Function Calling via Self-Refinement Multiscale Loss and Automated Data Refinement

The integration of large language models (LLMs) with function calling has emerged as a crucial capability for enhancing their practical utility in real-world applications. However, effectively combining reasoning processes with accurate function execution remains a significant challenge. Traditional training approaches often struggle to balance the detailed reasoning steps with the precision of function calls, leading to suboptimal performance. To address these limitations, we introduce FunReason, a novel framework that enhances LLMs' function calling capabilities through an automated data refinement strategy and a Self-Refinement Multiscale Loss (SRML) approach. FunReason leverages LLMs' natural reasoning abilities to generate high-quality training examples, focusing on query parseability, reasoning coherence, and function call precision. The SRML approach dynamically balances the contribution of reasoning processes and function call accuracy during training, addressing the inherent trade-off between these two critical aspects. FunReason achieves performance comparable to GPT-4o while effectively mitigating catastrophic forgetting during fine-tuning. FunReason provides a comprehensive solution for enhancing LLMs' function calling capabilities by introducing a balanced training methodology and a data refinement pipeline. For code and dataset, please refer to our repository at GitHub https://github.com/BingguangHao/FunReason

Measure Domain's Gap: A Similar Domain Selection Principle for Multi-Domain Recommendation

Multi-Domain Recommendation (MDR) achieves the desirable recommendation performance by effectively utilizing the transfer information across different domains. Despite the great success, most existing MDR methods adopt a single structure to transfer complex domain-shared knowledge. However, the beneficial transferring information should vary across different domains. When there is knowledge conflict between domains or a domain is of poor quality, unselectively leveraging information from all domains will lead to a serious Negative Transfer Problem (NTP). Therefore, how to effectively model the complex transfer relationships between domains to avoid NTP is still a direction worth exploring. To address these issues, we propose a simple and dynamic Similar Domain Selection Principle (SDSP) for multi-domain recommendation in this paper. SDSP presents the initial exploration of selecting suitable domain knowledge for each domain to alleviate NTP. Specifically, we propose a novel prototype-based domain distance measure to effectively model the complexity relationship between domains. Thereafter, the proposed SDSP can dynamically find similar domains for each domain based on the supervised signals of the domain metrics and the unsupervised distance measure from the learned domain prototype. We emphasize that SDSP is a lightweight method that can be incorporated with existing MDR methods for better performance while not introducing excessive time overheads. To the best of our knowledge, it is the first solution that can explicitly measure domain-level gaps and dynamically select appropriate domains in the MDR field. Extensive experiments on three datasets demonstrate the effectiveness of our proposed method.