A Retrieval-Augmented Knowledge Mining Method with Deep Thinking LLMs for Biomedical Research and Clinical Support

Knowledge graphs and large language models (LLMs) are key tools for biomedical knowledge integration and reasoning, facilitating structured organization of scientific articles and discovery of complex semantic relationships. However, current methods face challenges: knowledge graph construction is limited by complex terminology, data heterogeneity, and rapid knowledge evolution, while LLMs show limitations in retrieval and reasoning, making it difficult to uncover cross-document associations and reasoning pathways. To address these issues, we propose a pipeline that uses LLMs to construct a biomedical knowledge graph (BioStrataKG) from large-scale articles and builds a cross-document question-answering dataset (BioCDQA) to evaluate latent knowledge retrieval and multi-hop reasoning. We then introduce Integrated and Progressive Retrieval-Augmented Reasoning (IP-RAR) to enhance retrieval accuracy and knowledge reasoning. IP-RAR maximizes information recall through Integrated Reasoning-based Retrieval and refines knowledge via Progressive Reasoning-based Generation, using self-reflection to achieve deep thinking and precise contextual understanding. Experiments show that IP-RAR improves document retrieval F1 score by 20\% and answer generation accuracy by 25\% over existing methods. This framework helps doctors efficiently integrate treatment evidence for personalized medication plans and enables researchers to analyze advancements and research gaps, accelerating scientific discovery and decision-making.

UniHDSA: A Unified Relation Prediction Approach for Hierarchical Document Structure Analysis

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks.

DependEval: Benchmarking LLMs for Repository Dependency Understanding

While large language models (LLMs) have shown considerable promise in code generation, real-world software development demands advanced repository-level reasoning. This includes understanding dependencies, project structures, and managing multi-file changes. However, the ability of LLMs to effectively comprehend and handle complex code repositories has yet to be fully explored. To address challenges, we introduce a hierarchical benchmark designed to evaluate repository dependency understanding (DependEval). Benchmark is based on 15,576 repositories collected from real-world websites. It evaluates models on three core tasks: Dependency Recognition, Repository Construction, and Multi-file Editing, across 8 programming languages from actual code repositories. Our evaluation of over 25 LLMs reveals substantial performance gaps and provides valuable insights into repository-level code understanding.

TeraSim: Uncovering Unknown Unsafe Events for Autonomous Vehicles through Generative Simulation

Traffic simulation is essential for autonomous vehicle (AV) development, enabling comprehensive safety evaluation across diverse driving conditions. However, traditional rule-based simulators struggle to capture complex human interactions, while data-driven approaches often fail to maintain long-term behavioral realism or generate diverse safety-critical events. To address these challenges, we propose TeraSim, an open-source, high-fidelity traffic simulation platform designed to uncover unknown unsafe events and efficiently estimate AV statistical performance metrics, such as crash rates. TeraSim is designed for seamless integration with third-party physics simulators and standalone AV stacks, to construct a complete AV simulation system. Experimental results demonstrate its effectiveness in generating diverse safety-critical events involving both static and dynamic agents, identifying hidden deficiencies in AV systems, and enabling statistical performance evaluation. These findings highlight TeraSim's potential as a practical tool for AV safety assessment, benefiting researchers, developers, and policymakers. The code is available at https://github.com/mcity/TeraSim.

Digital Player: Evaluating Large Language Models based Human-like Agent in Games

With the rapid advancement of Large Language Models (LLMs), LLM-based autonomous agents have shown the potential to function as digital employees, such as digital analysts, teachers, and programmers. In this paper, we develop an application-level testbed based on the open-source strategy game "Unciv", which has millions of active players, to enable researchers to build a "data flywheel" for studying human-like agents in the "digital players" task. This "Civilization"-like game features expansive decision-making spaces along with rich linguistic interactions such as diplomatic negotiations and acts of deception, posing significant challenges for LLM-based agents in terms of numerical reasoning and long-term planning. Another challenge for "digital players" is to generate human-like responses for social interaction, collaboration, and negotiation with human players. The open-source project can be found at https:/github.com/fuxiAIlab/CivAgent.

Tarsier2: Advancing Large Vision-Language Models from Detailed Video Description to Comprehensive Video Understanding

We introduce Tarsier2, a state-of-the-art large vision-language model (LVLM) designed for generating detailed and accurate video descriptions, while also exhibiting superior general video understanding capabilities. Tarsier2 achieves significant advancements through three key upgrades: (1) Scaling pre-training data from 11M to 40M video-text pairs, enriching both volume and diversity; (2) Performing fine-grained temporal alignment during supervised fine-tuning; (3) Using model-based sampling to automatically construct preference data and applying DPO training for optimization. Extensive experiments show that Tarsier2-7B consistently outperforms leading proprietary models, including GPT-4o and Gemini 1.5 Pro, in detailed video description tasks. On the DREAM-1K benchmark, Tarsier2-7B improves F1 by 2.8\% over GPT-4o and 5.8\% over Gemini-1.5-Pro. In human side-by-side evaluations, Tarsier2-7B shows a +8.6\% performance advantage over GPT-4o and +24.9\% over Gemini-1.5-Pro. Tarsier2-7B also sets new state-of-the-art results across 15 public benchmarks, spanning tasks such as video question-answering, video grounding, hallucination test, and embodied question-answering, demonstrating its versatility as a robust generalist vision-language model.

Cascaded Self-Evaluation Augmented Training for Efficient Multimodal Large Language Models

Efficient Multimodal Large Language Models (EMLLMs) have rapidly advanced recently. Incorporating Chain-of-Thought (CoT) reasoning and step-by-step self-evaluation has improved their performance. However, limited parameters often hinder EMLLMs from effectively using self-evaluation during inference. Key challenges include synthesizing evaluation data, determining its quantity, optimizing training and inference strategies, and selecting appropriate prompts. To address these issues, we introduce Self-Evaluation Augmented Training (SEAT). SEAT uses more powerful EMLLMs for CoT reasoning, data selection, and evaluation generation, then trains EMLLMs with the synthesized data. However, handling long prompts and maintaining CoT reasoning quality are problematic. Therefore, we propose Cascaded Self-Evaluation Augmented Training (Cas-SEAT), which breaks down lengthy prompts into shorter, task-specific cascaded prompts and reduces costs for resource-limited settings. During data synthesis, we employ open-source 7B-parameter EMLLMs and annotate a small dataset with short prompts. Experiments demonstrate that Cas-SEAT significantly boosts EMLLMs' self-evaluation abilities, improving performance by 19.68%, 55.57%, and 46.79% on the MathVista, Math-V, and We-Math datasets, respectively. Additionally, our Cas-SEAT Dataset serves as a valuable resource for future research in enhancing EMLLM self-evaluation.

DeepSeek-V3 Technical Report

We present DeepSeek-V3, a strong Mixture-of-Experts (MoE) language model with 671B total parameters with 37B activated for each token. To achieve efficient inference and cost-effective training, DeepSeek-V3 adopts Multi-head Latent Attention (MLA) and DeepSeekMoE architectures, which were thoroughly validated in DeepSeek-V2. Furthermore, DeepSeek-V3 pioneers an auxiliary-loss-free strategy for load balancing and sets a multi-token prediction training objective for stronger performance. We pre-train DeepSeek-V3 on 14.8 trillion diverse and high-quality tokens, followed by Supervised Fine-Tuning and Reinforcement Learning stages to fully harness its capabilities. Comprehensive evaluations reveal that DeepSeek-V3 outperforms other open-source models and achieves performance comparable to leading closed-source models. Despite its excellent performance, DeepSeek-V3 requires only 2.788M H800 GPU hours for its full training. In addition, its training process is remarkably stable. Throughout the entire training process, we did not experience any irrecoverable loss spikes or perform any rollbacks. The model checkpoints are available at https://github.com/deepseek-ai/DeepSeek-V3.

DeepSeek-VL2: Mixture-of-Experts Vision-Language Models for Advanced Multimodal Understanding

We present DeepSeek-VL2, an advanced series of large Mixture-of-Experts (MoE) Vision-Language Models that significantly improves upon its predecessor, DeepSeek-VL, through two key major upgrades. For the vision component, we incorporate a dynamic tiling vision encoding strategy designed for processing high-resolution images with different aspect ratios. For the language component, we leverage DeepSeekMoE models with the Multi-head Latent Attention mechanism, which compresses Key-Value cache into latent vectors, to enable efficient inference and high throughput. Trained on an improved vision-language dataset, DeepSeek-VL2 demonstrates superior capabilities across various tasks, including but not limited to visual question answering, optical character recognition, document/table/chart understanding, and visual grounding. Our model series is composed of three variants: DeepSeek-VL2-Tiny, DeepSeek-VL2-Small and DeepSeek-VL2, with 1.0B, 2.8B and 4.5B activated parameters respectively. DeepSeek-VL2 achieves competitive or state-of-the-art performance with similar or fewer activated parameters compared to existing open-source dense and MoE-based models. Codes and pre-trained models are publicly accessible at https://github.com/deepseek-ai/DeepSeek-VL2.

CausalMob: Causal Human Mobility Prediction with LLMs-derived Human Intentions toward Public Events

Large-scale human mobility exhibits spatial and temporal patterns that can assist policymakers in decision making. Although traditional prediction models attempt to capture these patterns, they often interfered by non-periodic public events, such as disasters and occasional celebrations. Since regular human mobility patterns are heavily affected by these events, estimating their causal effects is critical to accurate mobility predictions. Although news articles provide unique perspectives on these events in an unstructured format, processing is a challenge. In this study, we propose a causality-augmented prediction model, called \textbf{CausalMob}, to analyze the causal effects of public events. We first utilize large language models (LLMs) to extract human intentions from news articles and transform them into features that act as causal treatments. Next, the model learns representations of spatio-temporal regional covariates from multiple data sources to serve as confounders for causal inference. Finally, we present a causal effect estimation framework to ensure event features remain independent of confounders during prediction. Based on large-scale real-world data, the experimental results show that the proposed model excels in human mobility prediction, outperforming state-of-the-art models.