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.

SurgWound-Bench: A Benchmark for Surgical Wound Diagnosis

Surgical site infection (SSI) is one of the most common and costly healthcare-associated infections and and surgical wound care remains a significant clinical challenge in preventing SSIs and improving patient outcomes. While recent studies have explored the use of deep learning for preliminary surgical wound screening, progress has been hindered by concerns over data privacy and the high costs associated with expert annotation. Currently, no publicly available dataset or benchmark encompasses various types of surgical wounds, resulting in the absence of an open-source Surgical-Wound screening tool. To address this gap: (1) we present SurgWound, the first open-source dataset featuring a diverse array of surgical wound types. It contains 697 surgical wound images annotated by 3 professional surgeons with eight fine-grained clinical attributes. (2) Based on SurgWound, we introduce the first benchmark for surgical wound diagnosis, which includes visual question answering (VQA) and report generation tasks to comprehensively evaluate model performance. (3) Furthermore, we propose a three-stage learning framework, WoundQwen, for surgical wound diagnosis. In the first stage, we employ five independent MLLMs to accurately predict specific surgical wound characteristics. In the second stage, these predictions serve as additional knowledge inputs to two MLLMs responsible for diagnosing outcomes, which assess infection risk and guide subsequent interventions. In the third stage, we train a MLLM that integrates the diagnostic results from the previous two stages to produce a comprehensive report. This three-stage framework can analyze detailed surgical wound characteristics and provide subsequent instructions to patients based on surgical images, paving the way for personalized wound care, timely intervention, and improved patient outcomes.

Majority Bit-Aware Watermarking For Large Language Models

The growing deployment of Large Language Models (LLMs) in real-world applications has raised concerns about their potential misuse in generating harmful or deceptive content. To address this issue, watermarking techniques have emerged as a promising solution by embedding identifiable binary messages into generated text for origin verification and misuse tracing. While recent efforts have explored multi-bit watermarking schemes capable of embedding rich information such as user identifiers, they typically suffer from the fundamental trade-off between text quality and decoding accuracy: to ensure reliable message decoding, they have to restrict the size of preferred token sets during encoding, yet such restrictions reduce the quality of the generated content. In this work, we propose MajorMark, a novel watermarking method that improves this trade-off through majority bit-aware encoding. MajorMark selects preferred token sets based on the majority bit of the message, enabling a larger and more flexible sampling of tokens. In contrast to prior methods that rely on token frequency analysis for decoding, MajorMark employs a clustering-based decoding strategy, which maintains high decoding accuracy even when the preferred token set is large, thus preserving both content quality and decoding accuracy. We further introduce MajorMark$^+$, which partitions the message into multiple blocks to independently encode and deterministically decode each block, thereby further enhancing the quality of watermarked text and improving decoding accuracy. Extensive experiments on state-of-the-art LLMs demonstrate that our methods significantly enhance both decoding accuracy and text generation quality, outperforming prior multi-bit watermarking baselines.

Fed-HeLLo: Efficient Federated Foundation Model Fine-Tuning with Heterogeneous LoRA Allocation

Federated Learning has recently been utilized to collaboratively fine-tune foundation models across multiple clients. Notably, federated low-rank adaptation LoRA-based fine-tuning methods have recently gained attention, which allows clients to fine-tune FMs with a small portion of trainable parameters locally. However, most existing methods do not account for the heterogeneous resources of clients or lack an effective local training strategy to maximize global fine-tuning performance under limited resources. In this work, we propose Fed-HeLLo, a novel federated LoRA-based fine-tuning framework that enables clients to collaboratively fine-tune an FM with different local trainable LoRA layers. To ensure its effectiveness, we develop several heterogeneous LoRA allocation (HLA) strategies that adaptively allocate local trainable LoRA layers based on clients' resource capabilities and the layer importance. Specifically, based on the dynamic layer importance, we design a Fisher Information Matrix score-based HLA that leverages dynamic gradient norm information. To better stabilize the training process, we consider the intrinsic importance of LoRA layers and design a Geometrically-Defined HLA strategy. It shapes the collective distribution of trainable LoRA layers into specific geometric patterns, such as Triangle, Inverted Triangle, Bottleneck, and Uniform. Moreover, we extend GD-HLA into a randomized version, named Randomized Geometrically-Defined HLA, for enhanced model accuracy with randomness. By co-designing the proposed HLA strategies, we incorporate both the dynamic and intrinsic layer importance into the design of our HLA strategy. We evaluate our approach on five datasets under diverse federated LoRA fine-tuning settings, covering three levels of data distribution from IID to extreme Non-IID. Results show that Fed-HeLLo with HLA strategies is both effective and efficient.

DeepTheorem: Advancing LLM Reasoning for Theorem Proving Through Natural Language and Reinforcement Learning

Theorem proving serves as a major testbed for evaluating complex reasoning abilities in large language models (LLMs). However, traditional automated theorem proving (ATP) approaches rely heavily on formal proof systems that poorly align with LLMs' strength derived from informal, natural language knowledge acquired during pre-training. In this work, we propose DeepTheorem, a comprehensive informal theorem-proving framework exploiting natural language to enhance LLM mathematical reasoning. DeepTheorem includes a large-scale benchmark dataset consisting of 121K high-quality IMO-level informal theorems and proofs spanning diverse mathematical domains, rigorously annotated for correctness, difficulty, and topic categories, accompanied by systematically constructed verifiable theorem variants. We devise a novel reinforcement learning strategy (RL-Zero) explicitly tailored to informal theorem proving, leveraging the verified theorem variants to incentivize robust mathematical inference. Additionally, we propose comprehensive outcome and process evaluation metrics examining proof correctness and the quality of reasoning steps. Extensive experimental analyses demonstrate DeepTheorem significantly improves LLM theorem-proving performance compared to existing datasets and supervised fine-tuning protocols, achieving state-of-the-art accuracy and reasoning quality. Our findings highlight DeepTheorem's potential to fundamentally advance automated informal theorem proving and mathematical exploration.

Two Experts Are All You Need for Steering Thinking: Reinforcing Cognitive Effort in MoE Reasoning Models Without Additional Training

Mixture-of-Experts (MoE) architectures within Large Reasoning Models (LRMs) have achieved impressive reasoning capabilities by selectively activating experts to facilitate structured cognitive processes. Despite notable advances, existing reasoning models often suffer from cognitive inefficiencies like overthinking and underthinking. To address these limitations, we introduce a novel inference-time steering methodology called Reinforcing Cognitive Experts (RICE), designed to improve reasoning performance without additional training or complex heuristics. Leveraging normalized Pointwise Mutual Information (nPMI), we systematically identify specialized experts, termed ''cognitive experts'' that orchestrate meta-level reasoning operations characterized by tokens like ''<think>''. Empirical evaluations with leading MoE-based LRMs (DeepSeek-R1 and Qwen3-235B) on rigorous quantitative and scientific reasoning benchmarks demonstrate noticeable and consistent improvements in reasoning accuracy, cognitive efficiency, and cross-domain generalization. Crucially, our lightweight approach substantially outperforms prevalent reasoning-steering techniques, such as prompt design and decoding constraints, while preserving the model's general instruction-following skills. These results highlight reinforcing cognitive experts as a promising, practical, and interpretable direction to enhance cognitive efficiency within advanced reasoning models.

Traceable Black-box Watermarks for Federated Learning

Due to the distributed nature of Federated Learning (FL) systems, each local client has access to the global model, posing a critical risk of model leakage. Existing works have explored injecting watermarks into local models to enable intellectual property protection. However, these methods either focus on non-traceable watermarks or traceable but white-box watermarks. We identify a gap in the literature regarding the formal definition of traceable black-box watermarking and the formulation of the problem of injecting such watermarks into FL systems. In this work, we first formalize the problem of injecting traceable black-box watermarks into FL. Based on the problem, we propose a novel server-side watermarking method, $\mathbf{TraMark}$, which creates a traceable watermarked model for each client, enabling verification of model leakage in black-box settings. To achieve this, $\mathbf{TraMark}$ partitions the model parameter space into two distinct regions: the main task region and the watermarking region. Subsequently, a personalized global model is constructed for each client by aggregating only the main task region while preserving the watermarking region. Each model then learns a unique watermark exclusively within the watermarking region using a distinct watermark dataset before being sent back to the local client. Extensive results across various FL systems demonstrate that $\mathbf{TraMark}$ ensures the traceability of all watermarked models while preserving their main task performance.

Trust, But Verify: A Self-Verification Approach to Reinforcement Learning with Verifiable Rewards

Large Language Models (LLMs) show great promise in complex reasoning, with Reinforcement Learning with Verifiable Rewards (RLVR) being a key enhancement strategy. However, a prevalent issue is ``superficial self-reflection'', where models fail to robustly verify their own outputs. We introduce RISE (Reinforcing Reasoning with Self-Verification), a novel online RL framework designed to tackle this. RISE explicitly and simultaneously trains an LLM to improve both its problem-solving and self-verification abilities within a single, integrated RL process. The core mechanism involves leveraging verifiable rewards from an outcome verifier to provide on-the-fly feedback for both solution generation and self-verification tasks. In each iteration, the model generates solutions, then critiques its own on-policy generated solutions, with both trajectories contributing to the policy update. Extensive experiments on diverse mathematical reasoning benchmarks show that RISE consistently improves model's problem-solving accuracy while concurrently fostering strong self-verification skills. Our analyses highlight the advantages of online verification and the benefits of increased verification compute. Additionally, RISE models exhibit more frequent and accurate self-verification behaviors during reasoning. These advantages reinforce RISE as a flexible and effective path towards developing more robust and self-aware reasoners.

Optimal Client Sampling in Federated Learning with Client-Level Heterogeneous Differential Privacy

Federated Learning with client-level differential privacy (DP) provides a promising framework for collaboratively training models while rigorously protecting clients' privacy. However, classic approaches like DP-FedAvg struggle when clients have heterogeneous privacy requirements, as they must uniformly enforce the strictest privacy level across clients, leading to excessive DP noise and significant model utility degradation. Existing methods to improve the model utility in such heterogeneous privacy settings often assume a trusted server and are largely heuristic, resulting in suboptimal performance and lacking strong theoretical underpinnings. In this work, we address these challenges under a practical attack model where both clients and the server are honest-but-curious. We propose GDPFed, which partitions clients into groups based on their privacy budgets and achieves client-level DP within each group to reduce the privacy budget waste and hence improve the model utility. Based on the privacy and convergence analysis of GDPFed, we find that the magnitude of DP noise depends on both model dimensionality and the per-group client sampling ratios. To further improve the performance of GDPFed, we introduce GDPFed$^+$, which integrates model sparsification to eliminate unnecessary noise and optimizes per-group client sampling ratios to minimize convergence error. Extensive empirical evaluations on multiple benchmark datasets demonstrate the effectiveness of GDPFed$^+$, showing substantial performance gains compared with state-of-the-art methods.

DeepMath-103K: A Large-Scale, Challenging, Decontaminated, and Verifiable Mathematical Dataset for Advancing Reasoning

The capacity for complex mathematical reasoning is a key benchmark for artificial intelligence. While reinforcement learning (RL) applied to LLMs shows promise, progress is significantly hindered by the lack of large-scale training data that is sufficiently challenging, possesses verifiable answer formats suitable for RL, and is free from contamination with evaluation benchmarks. To address these limitations, we introduce DeepMath-103K, a new, large-scale dataset comprising approximately 103K mathematical problems, specifically designed to train advanced reasoning models via RL. DeepMath-103K is curated through a rigorous pipeline involving source analysis, stringent decontamination against numerous benchmarks, and filtering for high difficulty (primarily Levels 5-9), significantly exceeding existing open resources in challenge. Each problem includes a verifiable final answer, enabling rule-based RL, and three distinct R1-generated solutions suitable for diverse training paradigms like supervised fine-tuning or distillation. Spanning a wide range of mathematical topics, DeepMath-103K promotes the development of generalizable reasoning. We demonstrate that models trained on DeepMath-103K achieve significant improvements on challenging mathematical benchmarks, validating its effectiveness. We release DeepMath-103K publicly to facilitate community progress in building more capable AI reasoning systems: https://github.com/zwhe99/DeepMath.