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.

Turing Machine Evaluation for Large Language Model

With the rapid development and widespread application of Large Language Models (LLMs), rigorous evaluation has become particularly crucial. This research adopts a novel perspective, focusing on evaluating the core computational reasoning ability of LLMs, defined as the capacity of model to accurately understand rules, and execute logically computing operations. This capability assesses the reliability of LLMs as precise executors, and is critical to advanced tasks such as complex code generation and multi-step problem-solving. We propose an evaluation framework based on Universal Turing Machine (UTM) simulation. This framework requires LLMs to strictly follow instructions and track dynamic states, such as tape content and read/write head position, during multi-step computations. To enable standardized evaluation, we developed TMBench, a benchmark for systematically studying the computational reasoning capabilities of LLMs. TMBench provides several key advantages, including knowledge-agnostic evaluation, adjustable difficulty, foundational coverage through Turing machine encoding, and unlimited capacity for instance generation, ensuring scalability as models continue to evolve. We find that model performance on TMBench correlates strongly with performance on other recognized reasoning benchmarks (Pearson correlation coefficient is 0.73), clearly demonstrating that computational reasoning is a significant dimension for measuring the deep capabilities of LLMs. Code and data are available at https://github.com/HaitaoWuTJU/Turing-Machine-Bench.

Right Question is Already Half the Answer: Fully Unsupervised LLM Reasoning Incentivization

While large language models (LLMs) have demonstrated exceptional capabilities in challenging tasks such as mathematical reasoning, existing methods to enhance reasoning ability predominantly rely on supervised fine-tuning (SFT) followed by reinforcement learning (RL) on reasoning-specific data after pre-training. However, these approaches critically depend on external supervisions--such as human labelled reasoning traces, verified golden answers, or pre-trained reward models--which limits scalability and practical applicability. In this work, we propose Entropy Minimized Policy Optimization (EMPO), which makes an early attempt at fully unsupervised LLM reasoning incentivization. EMPO does not require any supervised information for incentivizing reasoning capabilities (i.e., neither verifiable reasoning traces, problems with golden answers, nor additional pre-trained reward models). By continuously minimizing the predictive entropy of LLMs on unlabeled user queries in a latent semantic space, EMPO enables purely self-supervised evolution of reasoning capabilities with strong flexibility and practicality. Our experiments demonstrate competitive performance of EMPO on both mathematical reasoning and free-form commonsense reasoning tasks. Specifically, without any supervised signals, EMPO boosts the accuracy of Qwen2.5-Math-7B Base from 30.7\% to 48.1\% on mathematical benchmarks and improves truthfulness accuracy of Qwen2.5-7B Instruct from 87.16\% to 97.25\% on TruthfulQA.

Bridging the Vision-Brain Gap with an Uncertainty-Aware Blur Prior

Can our brain signals faithfully reflect the original visual stimuli, even including high-frequency details? Although human perceptual and cognitive capacities enable us to process and remember visual information, these abilities are constrained by several factors, such as limited attentional resources and the finite capacity of visual memory. When visual stimuli are processed by human visual system into brain signals, some information is inevitably lost, leading to a discrepancy known as the \textbf{System GAP}. Additionally, perceptual and cognitive dynamics, along with technical noise in signal acquisition, degrade the fidelity of brain signals relative to the visual stimuli, known as the \textbf{Random GAP}. When encoded brain representations are directly aligned with the corresponding pretrained image features, the System GAP and Random GAP between paired data challenge the model, requiring it to bridge these gaps. However, in the context of limited paired data, these gaps are difficult for the model to learn, leading to overfitting and poor generalization to new data. To address these GAPs, we propose a simple yet effective approach called the \textbf{Uncertainty-aware Blur Prior (UBP)}. It estimates the uncertainty within the paired data, reflecting the mismatch between brain signals and visual stimuli. Based on this uncertainty, UBP dynamically blurs the high-frequency details of the original images, reducing the impact of the mismatch and improving alignment. Our method achieves a top-1 accuracy of \textbf{50.9\%} and a top-5 accuracy of \textbf{79.7\%} on the zero-shot brain-to-image retrieval task, surpassing previous state-of-the-art methods by margins of \textbf{13.7\%} and \textbf{9.8\%}, respectively. Code is available at \href{https://github.com/HaitaoWuTJU/Uncertainty-aware-Blur-Prior}{GitHub}.

Semantic Object-level Modeling for Robust Visual Camera Relocalization

Visual relocalization is crucial for autonomous visual localization and navigation of mobile robotics. Due to the improvement of CNN-based object detection algorithm, the robustness of visual relocalization is greatly enhanced especially in viewpoints where classical methods fail. However, ellipsoids (quadrics) generated by axis-aligned object detection may limit the accuracy of the object-level representation and degenerate the performance of visual relocalization system. In this paper, we propose a novel method of automatic object-level voxel modeling for accurate ellipsoidal representations of objects. As for visual relocalization, we design a better pose optimization strategy for camera pose recovery, to fully utilize the projection characteristics of 2D fitted ellipses and the 3D accurate ellipsoids. All of these modules are entirely intergrated into visual SLAM system. Experimental results show that our semantic object-level mapping and object-based visual relocalization methods significantly enhance the performance of visual relocalization in terms of robustness to new viewpoints.

Provable Dynamic Fusion for Low-Quality Multimodal Data

The inherent challenge of multimodal fusion is to precisely capture the cross-modal correlation and flexibly conduct cross-modal interaction. To fully release the value of each modality and mitigate the influence of low-quality multimodal data, dynamic multimodal fusion emerges as a promising learning paradigm. Despite its widespread use, theoretical justifications in this field are still notably lacking. Can we design a provably robust multimodal fusion method? This paper provides theoretical understandings to answer this question under a most popular multimodal fusion framework from the generalization perspective. We proceed to reveal that several uncertainty estimation solutions are naturally available to achieve robust multimodal fusion. Then a novel multimodal fusion framework termed Quality-aware Multimodal Fusion (QMF) is proposed, which can improve the performance in terms of classification accuracy and model robustness. Extensive experimental results on multiple benchmarks can support our findings.