Retrieval-Augmented Generation (RAG) provides additional contextual knowledge to complement the parametric knowledge in Large Language Models (LLMs). These two knowledge interweave to enhance the accuracy and timeliness of LLM responses. However, the internal mechanisms by which LLMs utilize these knowledge remain unclear. We propose modeling the forward propagation of knowledge as an entity flow, employing this framework to trace LLMs' internal behaviors when processing mixed-source knowledge. Linear probing utilizes a trainable linear classifier to detect specific attributes in hidden layers.

The detection of ligand binding sites for proteins is a fundamental step in StructureBased Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-theart methods in ligand binding site detection.

Large Language Models (LLMs) have shown remarkable progress across domains, yet their ability to perform inductive reasoning--inferring latent rules from sparse examples--remains limited. It is often assumed that chain-of-thought (CoT) prompting, as used in Large Reasoning Models (LRMs), enhances such reasoning. We investigate this assumption with creating four controlled, diagnostic game-based tasks--chess, Texas Hold'em, dice games, and blackjack--with hidden humandefined rules. We find that CoT reasoning can degrade inductive performance, with LRMs often underperforming their non-reasoning counterparts. To explain this, we present a theoretical framework that reveals how reasoning steps can amplify error through three failure modes: incorrect sub-task decomposition, incorrect sub-task solving, and incorrect final answer summarization. Based on our theoretical and empirical analysis, we introduce structured interventions that adapt CoT generation according to our identified failure types. These interventions improve inductive accuracy without retraining. Our findings suggest that effective (CoT) reasoning depends not only on taking more steps but also on ensuring those steps are well-structured.

Articulated objects, as prevalent entities in human life, their 3D representations play crucial roles across various applications. However, achieving both high-fidelity textured surface reconstruction and dynamic generation for articulated objects remains challenging for existing methods. In this paper, we present REArtGS, a novel framework that introduces additional geometric and motion constraints to 3DGaussian primitives, enabling realistic surface reconstruction and generation for articulated objects. Specifically, given multi-view RGB images of arbitrary two states of articulated objects, we first introduce an unbiased Signed Distance Field (SDF) guidance to regularize Gaussian opacity fields, enhancing geometry constraints and improving surface reconstruction quality. Then we establish deformable fields for 3DGaussians constrained by the kinematic structures of articulated objects, achieving unsupervised generation of surface meshes in unseen states. Extensive experiments on both synthetic and real datasets demonstrate our approach achieves high-quality textured surface reconstruction for given states, and enables high-fidelity surface generation for unseen states.

Vision-language-action (VLA) models provide a powerful approach to training control policies for physical systems, such as robots, by combining end-to-end learning with transfer of semantic knowledge from web-scale vision-language model (VLM) training. However, the constraints of real-time control are often at odds with the design of VLMs: the most powerful VLMs have tens or hundreds of billions of parameters, presenting an obstacle to real-time inference, and operate on discrete tokens rather than the continuous-valued outputs that are required for controlling robots. To address this challenge, recent VLA models have used specialized modules for efficient continuous control, such as action experts or continuous output heads, which typically require adding new untrained parameters to the pretrained VLM backbone. While these modules improve real-time and control capabilities, it remains an open question whether they preserve or degrade the semantic knowledge contained in the pretrained VLM, and what effect they have on the VLA training dynamics. In this paper, we study this question in the context of VLAs that include a continuous diffusion or flow matching action expert, showing that naively including such experts significantly harms both training speed and knowledge transfer. We provide an extensive analysis of various design choices, their impact on performance and knowledge transfer, and propose a technique for insulating the VLM backbone during VLA training that mitigates this issue.

We present a novel video generation framework that integrates 3-dimensional geometry and dynamic awareness. To achieve this, we augment 2D videos with 3D point trajectories and align them in pixel space. The resulting 3D-aware video dataset, PointVid, is then used to fine-tune a latent diffusion model, enabling it to track 2D objects with 3DCartesian coordinates. Building on this, we regularize the shape and motion of objects in the video to eliminate undesired artifacts, e.g., non-physical deformation. Consequently, we enhance the quality of generated RGB videos and alleviate common issues like object morphing, which are prevalent in current video models due to a lack of shape awareness. With our 3D augmentation and regularization, our model is capable of handling contact-rich scenarios such as task-oriented videos, where 3D information is essential for perceiving shape and motion of interacting solids. Our method can be seamlessly integrated into existing video diffusion models to improve their visual plausibility.

Recent studies show that the reasoning capabilities of Large Language Models (LLMs) can be improved by applying Reinforcement Learning (RL) to questionanswering (QA) tasks in areas such as math and coding. With a long context length, LLMs may learn to perform search, as indicated by the self-correction behavior observed in DeepSeek R1. However, this search behavior is often imprecise and lacks confidence, resulting in long, redundant responses and highlighting deficiencies in intuition and verification. Inspired by the Dual Process Theory in psychology, we introduce a simple modification to the QA task that includes four stages: Fast Thinking, where the LLM must answer within a strict token budget; Verification, where the model evaluates its initial response; Slow Thinking, where it refines the initial response with more deliberation; and Summarization, where it distills the refinement from the previous stage into precise steps. Our proposed task improves average accuracy from 25.6% to 27.3% for Qwen2.5-1.5B, and from 45.9% to 51.0% for DeepSeek-R1-Qwen-1.5B. Notably, for Qwen2.5-1.5B, the Fast Thinking mode alone achieves 25.2% accuracy using fewer than 1000 tokens, demonstrating substantial inference efficiency gains. These findings suggest that intuition and deliberative reasoning are distinct, complementary systems benefiting from targeted training. Additionally, we have open-sourced both the trained models and the source code.

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Long-form video understanding poses a significant challenge for video large language models (VideoLLMs) due to prohibitively high computational and memory demands. In this paper, We propose FlexSelect, a flexible and efficient token selection strategy for processing long videos. FlexSelect identifies and retains the most semantically relevant content by leveraging cross-modal attention patterns from a reference transformer layer. It comprises two key components: (1) a training-free token ranking pipeline that leverages faithful cross-modal attention weights to estimate each video token's importance, and (2) a rank-supervised lightweight selector that is trained to replicate these rankings and filter redundant tokens. This generic approach can be seamlessly integrated into various VideoLLM architectures, such as LLaVA-Video, InternVL and Qwen-VL, serving as a plug-and-play module to extend their temporal context length. Empirically, FlexSelect delivers strong gains across multiple long-video benchmarks - including VideoMME, MLVU, LongVB, and LVBench. Morever, it achieves significant speed-ups (e.g., up to 9 on a LLaVA-Video-7B model), highlighting FlexSelect's promise for efficient long-form video understanding.

Aligning large language models with pointwise absolute rewards has so far required online, on-policy algorithms such as PPO and GRPO. In contrast, simpler methods that can leverage offline or off-policy data, such as DPO and REBEL, are limited to learning from preference pairs or relative signals. To bridge this gap, we introduce Quantile Reward Policy Optimization (QRPO), which learns from pointwise absolute rewards while preserving the simplicity and offline applicability of DPO-like methods. QRPO uses quantile rewards to enable regression to the closed-form solution of the KL-regularized RL objective. This reward yields an analytically tractable partition function, removing the need for relative signals to cancel this term. Moreover, QRPO scales with increased compute to estimate quantile rewards, opening a new dimension for pre-computation scaling.