Large Language Models (LLMs) have demonstrated improved generation performance by incorporating externally retrieved knowledge, a process known as retrieval-augmented generation (RAG). Despite the potential of this approach, existing studies evaluate RAG effectiveness by 1) assessing retrieval and generation components jointly, which obscures retrieval's distinct contribution, or 2) examining retrievers using traditional metrics such as NDCG, which creates a gap in understanding retrieval's true utility in the overall generation process. To address the above limitations, in this work, we introduce an automatic evaluation method that measures retrieval quality through the lens of information gain within the RAG framework. Specifically, we propose Semantic Perplexity (SePer), a metric that captures the LLM's internal belief about the correctness of the retrieved information. We quantify the utility of retrieval by the extent to which it reduces semantic perplexity post-retrieval. Extensive experiments demonstrate that SePer not only aligns closely with human preferences but also offers a more precise and efficient evaluation of retrieval utility across diverse RAG scenarios.

Understanding long video content is a complex endeavor that often relies on densely sampled frame captions or end-to-end feature selectors, yet these techniques commonly overlook the logical relationships between textual queries and visual elements. In practice, computational constraints necessitate coarse frame subsampling, a challenge analogous to ``finding a needle in a haystack.'' To address this issue, we introduce a semantics-driven search framework that reformulates keyframe selection under the paradigm of Visual Semantic-Logical Search. Specifically, we systematically define four fundamental logical dependencies: 1) spatial co-occurrence, 2) temporal proximity, 3) attribute dependency, and 4) causal order. These relations dynamically update frame sampling distributions through an iterative refinement process, enabling context-aware identification of semantically critical frames tailored to specific query requirements. Our method establishes new SOTA performance on the manually annotated benchmark in key-frame selection metrics. Furthermore, when applied to downstream video question-answering tasks, the proposed approach demonstrates the best performance gains over existing methods on LongVideoBench and Video-MME, validating its effectiveness in bridging the logical gap between textual queries and visual-temporal reasoning. The code will be publicly available.

As open-source large language models (LLMs) like Llama3 become more capable, it is crucial to develop watermarking techniques to detect their potential misuse. Existing watermarking methods either add watermarks during LLM inference, which is unsuitable for open-source LLMs, or primarily target classification LLMs rather than recent generative LLMs. Adapting these watermarks to open-source LLMs for misuse detection remains an open challenge. This work defines two misuse scenarios for open-source LLMs: intellectual property (IP) violation and LLM Usage Violation. Then, we explore the application of inference-time watermark distillation and backdoor watermarking in these contexts. We propose comprehensive evaluation methods to assess the impact of various real-world further fine-tuning scenarios on watermarks and the effect of these watermarks on LLM performance. Our experiments reveal that backdoor watermarking could effectively detect IP Violation, while inference-time watermark distillation is applicable in both scenarios but less robust to further fine-tuning and has a more significant impact on LLM performance compared to backdoor watermarking. Exploring more advanced watermarking methods for open-source LLMs to detect their misuse should be an important future direction.

Federated Learning (FL) has emerged as a promising privacy-preserving collaborative model training paradigm without sharing raw data. However, recent studies have revealed that private information can still be leaked through shared gradient information and attacked by Gradient Inversion Attacks (GIA). While many GIA methods have been proposed, a detailed analysis, evaluation, and summary of these methods are still lacking. Although various survey papers summarize existing privacy attacks in FL, few studies have conducted extensive experiments to unveil the effectiveness of GIA and their associated limiting factors in this context. To fill this gap, we first undertake a systematic review of GIA and categorize existing methods into three types, i.e., \textit{optimization-based} GIA (OP-GIA), \textit{generation-based} GIA (GEN-GIA), and \textit{analytics-based} GIA (ANA-GIA). Then, we comprehensively analyze and evaluate the three types of GIA in FL, providing insights into the factors that influence their performance, practicality, and potential threats. Our findings indicate that OP-GIA is the most practical attack setting despite its unsatisfactory performance, while GEN-GIA has many dependencies and ANA-GIA is easily detectable, making them both impractical. Finally, we offer a three-stage defense pipeline to users when designing FL frameworks and protocols for better privacy protection and share some future research directions from the perspectives of attackers and defenders that we believe should be pursued. We hope that our study can help researchers design more robust FL frameworks to defend against these attacks.

Large language models (LLMs) have greatly accelerated the automation of algorithm generation and optimization. However, current methods such as EoH and FunSearch mainly rely on predefined templates and expert-specified functions that focus solely on the local evolution of key functionalities. Consequently, they fail to fully leverage the synergistic benefits of the overall architecture and the potential of global optimization. In this paper, we introduce an end-to-end algorithm generation and optimization framework based on LLMs. Our approach utilizes the deep semantic understanding of LLMs to convert natural language requirements or human-authored papers into code solutions, and employs a two-dimensional co-evolution strategy to optimize both functional and structural aspects. This closed-loop process spans problem analysis, code generation, and global optimization, automatically identifying key algorithm modules for multi-level joint optimization and continually enhancing performance and design innovation. Extensive experiments demonstrate that our method outperforms traditional local optimization approaches in both performance and innovation, while also exhibiting strong adaptability to unknown environments and breakthrough potential in structural design. By building on human research, our framework generates and optimizes novel algorithms that surpass those designed by human experts, broadening the applicability of LLMs for algorithm design and providing a novel solution pathway for automated algorithm development.

However, high sequencing costs and technical challenges often result in Hi-C data with limited coverage, leading to imprecise estimates of chromatin interaction frequencies. To address this issue, we present a novel deep learning-based method HiCMamba to enhance the resolution of Hi-C contact maps using a state space model. We adopt the UNet-based auto-encoder architecture to stack the proposed holistic scan block, enabling the perception of both global and local receptive fields at multiple scales. Experimental results demonstrate that HiCMamba outperforms state-of-the-art methods while significantly reducing computational resources. Furthermore, the 3D genome structures, including topologically associating domains (TADs) and loops, identified in the contact maps recovered by HiCMamba are validated through associated epigenomic features. Our work demonstrates the potential of a state space model as foundational frameworks in the field of Hi-C resolution enhancement.

In recent years, the rapid advancement of Artificial Intelligence (AI) technologies, particularly Large Language Models (LLMs), has revolutionized the paradigm of scientific discovery, establishing AI-for-Science (AI4Science) as a dynamic and evolving field. However, there is still a lack of an effective framework for the overall assessment of AI4Science, particularly from a holistic perspective on data quality and model capability. Therefore, in this study, we propose SciHorizon, a comprehensive assessment framework designed to benchmark the readiness of AI4Science from both scientific data and LLM perspectives. First, we introduce a generalizable framework for assessing AI-ready scientific data, encompassing four key dimensions: Quality, FAIRness, Explainability, and Compliance which are subdivided into 15 sub-dimensions. Drawing on data resource papers published between 2018 and 2023 in peer-reviewed journals, we present recommendation lists of AI-ready datasets for both Earth and Life Sciences, making a novel and original contribution to the field. Concurrently, to assess the capabilities of LLMs across multiple scientific disciplines, we establish 16 assessment dimensions based on five core indicators Knowledge, Understanding, Reasoning, Multimodality, and Values spanning Mathematics, Physics, Chemistry, Life Sciences, and Earth and Space Sciences. Using the developed benchmark datasets, we have conducted a comprehensive evaluation of over 20 representative open-source and closed source LLMs. All the results are publicly available and can be accessed online at www.scihorizon.cn/en.

We present TimeFound, an encoder-decoder transformer-based time series foundation model for out-of-the-box zero-shot forecasting. To handle time series data from various domains, TimeFound employs a multi-resolution patching strategy to capture complex temporal patterns at multiple scales. We pre-train our model with two sizes (200M and 710M parameters) on a large time-series corpus comprising both real-world and synthetic datasets. Over a collection of unseen datasets across diverse domains and forecasting horizons, our empirical evaluations suggest that TimeFound can achieve superior or competitive zero-shot forecasting performance, compared to state-of-the-art time series foundation models.

Understanding and replicating the real world is a critical challenge in Artificial General Intelligence (AGI) research. To achieve this, many existing approaches, such as world models, aim to capture the fundamental principles governing the physical world, enabling more accurate simulations and meaningful interactions. However, current methods often treat different modalities, including 2D (images), videos, 3D, and 4D representations, as independent domains, overlooking their interdependencies. Additionally, these methods typically focus on isolated dimensions of reality without systematically integrating their connections. In this survey, we present a unified survey for multimodal generative models that investigate the progression of data dimensionality in real-world simulation. Specifically, this survey starts from 2D generation (appearance), then moves to video (appearance+dynamics) and 3D generation (appearance+geometry), and finally culminates in 4D generation that integrate all dimensions. To the best of our knowledge, this is the first attempt to systematically unify the study of 2D, video, 3D and 4D generation within a single framework. To guide future research, we provide a comprehensive review of datasets, evaluation metrics and future directions, and fostering insights for newcomers. This survey serves as a bridge to advance the study of multimodal generative models and real-world simulation within a unified framework.

Designing proper experiments and selecting optimal intervention targets is a longstanding problem in scientific or causal discovery. Identifying the underlying causal structure from observational data alone is inherently difficult. Obtaining interventional data, on the other hand, is crucial to causal discovery, yet it is usually expensive and time-consuming to gather sufficient interventional data to facilitate causal discovery. Previous approaches commonly utilize uncertainty or gradient signals to determine the intervention targets. However, numerical-based approaches may yield suboptimal results due to the inaccurate estimation of the guiding signals at the beginning when with limited interventional data. In this work, we investigate a different approach, whether we can leverage Large Language Models (LLMs) to assist with the intervention targeting in causal discovery by making use of the rich world knowledge about the experimental design in LLMs. Specifically, we present Large Language Model Guided Intervention Targeting (LeGIT) -- a robust framework that effectively incorporates LLMs to augment existing numerical approaches for the intervention targeting in causal discovery. Across 4 realistic benchmark scales, LeGIT demonstrates significant improvements and robustness over existing methods and even surpasses humans, which demonstrates the usefulness of LLMs in assisting with experimental design for scientific discovery.