A Foundation Model for Chest X-ray Interpretation with Grounded Reasoning via Online Reinforcement Learning

Medical foundation models (FMs) have shown tremendous promise amid the rapid advancements in artificial intelligence (AI) technologies. However, current medical FMs typically generate answers in a black-box manner, lacking transparent reasoning processes and locally grounded interpretability, which hinders their practical clinical deployments. To this end, we introduce DeepMedix-R1, a holistic medical FM for chest X-ray (CXR) interpretation. It leverages a sequential training pipeline: initially fine-tuned on curated CXR instruction data to equip with fundamental CXR interpretation capabilities, then exposed to high-quality synthetic reasoning samples to enable cold-start reasoning, and finally refined via online reinforcement learning to enhance both grounded reasoning quality and generation performance. Thus, the model produces both an answer and reasoning steps tied to the image's local regions for each query. Quantitative evaluation demonstrates substantial improvements in report generation (e.g., 14.54% and 31.32% over LLaVA-Rad and MedGemma) and visual question answering (e.g., 57.75% and 23.06% over MedGemma and CheXagent) tasks. To facilitate robust assessment, we propose Report Arena, a benchmarking framework using advanced language models to evaluate answer quality, further highlighting the superiority of DeepMedix-R1. Expert review of generated reasoning steps reveals greater interpretability and clinical plausibility compared to the established Qwen2.5-VL-7B model (0.7416 vs. 0.2584 overall preference). Collectively, our work advances medical FM development toward holistic, transparent, and clinically actionable modeling for CXR interpretation.

OS-R1: Agentic Operating System Kernel Tuning with Reinforcement Learning

Linux kernel tuning is essential for optimizing operating system (OS) performance. However, existing methods often face challenges in terms of efficiency, scalability, and generalization. This paper introduces OS-R1, an agentic Linux kernel tuning framework powered by rule-based reinforcement learning (RL). By abstracting the kernel configuration space as an RL environment, OS-R1 facilitates efficient exploration by large language models (LLMs) and ensures accurate configuration modifications. Additionally, custom reward functions are designed to enhance reasoning standardization, configuration modification accuracy, and system performance awareness of the LLMs. Furthermore, we propose a two-phase training process that accelerates convergence and minimizes retraining across diverse tuning scenarios. Experimental results show that OS-R1 significantly outperforms existing baseline methods, achieving up to 5.6% performance improvement over heuristic tuning and maintaining high data efficiency. Notably, OS-R1 is adaptable across various real-world applications, demonstrating its potential for practical deployment in diverse environments. Our dataset and code are publicly available at https://github.com/LHY-24/OS-R1.

Graph-R1: Towards Agentic GraphRAG Framework via End-to-end Reinforcement Learning

Retrieval-Augmented Generation (RAG) mitigates hallucination in LLMs by incorporating external knowledge, but relies on chunk-based retrieval that lacks structural semantics. GraphRAG methods improve RAG by modeling knowledge as entity-relation graphs, but still face challenges in high construction cost, fixed one-time retrieval, and reliance on long-context reasoning and prompt design. To address these challenges, we propose Graph-R1, an agentic GraphRAG framework via end-to-end reinforcement learning (RL). It introduces lightweight knowledge hypergraph construction, models retrieval as a multi-turn agent-environment interaction, and optimizes the agent process via an end-to-end reward mechanism. Experiments on standard RAG datasets show that Graph-R1 outperforms traditional GraphRAG and RL-enhanced RAG methods in reasoning accuracy, retrieval efficiency, and generation quality.

HyperGraphRAG: Retrieval-Augmented Generation with Hypergraph-Structured Knowledge Representation

While standard Retrieval-Augmented Generation (RAG) based on chunks, GraphRAG structures knowledge as graphs to leverage the relations among entities. However, previous GraphRAG methods are limited by binary relations: one edge in the graph only connects two entities, which cannot well model the n-ary relations among more than two entities that widely exist in reality. To address this limitation, we propose HyperGraphRAG, a novel hypergraph-based RAG method that represents n-ary relational facts via hyperedges, modeling the complicated n-ary relations in the real world. To retrieve and generate over hypergraphs, we introduce a complete pipeline with a hypergraph construction method, a hypergraph retrieval strategy, and a hypergraph-guided generation mechanism. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms standard RAG and GraphRAG in accuracy and generation quality.

KGCompiler: Deep Learning Compilation Optimization for Knowledge Graph Complex Logical Query Answering

Complex Logical Query Answering (CLQA) involves intricate multi-hop logical reasoning over large-scale and potentially incomplete Knowledge Graphs (KGs). Although existing CLQA algorithms achieve high accuracy in answering such queries, their reasoning time and memory usage scale significantly with the number of First-Order Logic (FOL) operators involved, creating serious challenges for practical deployment. In addition, current research primarily focuses on algorithm-level optimizations for CLQA tasks, often overlooking compiler-level optimizations, which can offer greater generality and scalability. To address these limitations, we introduce a Knowledge Graph Compiler, namely KGCompiler, the first deep learning compiler specifically designed for CLQA tasks. By incorporating KG-specific optimizations proposed in this paper, KGCompiler enhances the reasoning performance of CLQA algorithms without requiring additional manual modifications to their implementations. At the same time, it significantly reduces memory usage. Extensive experiments demonstrate that KGCompiler accelerates CLQA algorithms by factors ranging from 1.04x to 8.26x, with an average speedup of 3.71x. We also provide an interface to enable hands-on experience with KGCompiler.

A Cognitive Writing Perspective for Constrained Long-Form Text Generation

Like humans, Large Language Models (LLMs) struggle to generate high-quality long-form text that adheres to strict requirements in a single pass. This challenge is unsurprising, as successful human writing, according to the Cognitive Writing Theory, is a complex cognitive process involving iterative planning, translating, reviewing, and monitoring. Motivated by these cognitive principles, we aim to equip LLMs with human-like cognitive writing capabilities through CogWriter, a novel training-free framework that transforms LLM constrained long-form text generation into a systematic cognitive writing paradigm. Our framework consists of two key modules: (1) a Planning Agent that performs hierarchical planning to decompose the task, and (2) multiple Generation Agents that execute these plans in parallel. The system maintains quality via continuous monitoring and reviewing mechanisms, which evaluate outputs against specified requirements and trigger necessary revisions. CogWriter demonstrates exceptional performance on LongGenBench, a benchmark for complex constrained long-form text generation. Even when using Qwen-2.5-14B as its backbone, CogWriter surpasses GPT-4o by 22% in complex instruction completion accuracy while reliably generating texts exceeding 10,000 words. We hope this cognitive science-inspired approach provides a paradigm for LLM writing advancements: \href{https://github.com/KaiyangWan/CogWriter}{CogWriter}.

SQL-o1: A Self-Reward Heuristic Dynamic Search Method for Text-to-SQL

The Text-to-SQL(Text2SQL) task aims to convert natural language queries into executable SQL queries. Thanks to the application of large language models (LLMs), significant progress has been made in this field. However, challenges such as model scalability, limited generation space, and coherence issues in SQL generation still persist. To address these issues, we propose SQL-o1, a Self-Reward-based heuristic search method designed to enhance the reasoning ability of LLMs in SQL query generation. SQL-o1 combines Monte Carlo Tree Search (MCTS) for heuristic process-level search and constructs a Schema-Aware dataset to help the model better understand database schemas. Extensive experiments on the Bird and Spider datasets demonstrate that SQL-o1 improves execution accuracy by 10.8\% on the complex Bird dataset compared to the latest baseline methods, even outperforming GPT-4-based approaches. Additionally, SQL-o1 excels in few-shot learning scenarios and shows strong cross-model transferability. Our code is publicly available at:https://github.com/ShuaiLyu0110/SQL-o1.

KBQA-o1: Agentic Knowledge Base Question Answering with Monte Carlo Tree Search

Knowledge Base Question Answering (KBQA) aims to answer natural language questions with a large-scale structured knowledge base (KB). Despite advancements with large language models (LLMs), KBQA still faces challenges in weak KB awareness, imbalance between effectiveness and efficiency, and high reliance on annotated data. To address these challenges, we propose KBQA-o1, a novel agentic KBQA method with Monte Carlo Tree Search (MCTS). It introduces a ReAct-based agent process for stepwise logical form generation with KB environment exploration. Moreover, it employs MCTS, a heuristic search method driven by policy and reward models, to balance agentic exploration's performance and search space. With heuristic exploration, KBQA-o1 generates high-quality annotations for further improvement by incremental fine-tuning. Experimental results show that KBQA-o1 outperforms previous low-resource KBQA methods with limited annotated data, boosting Llama-3.1-8B model's GrailQA F1 performance to 78.5% compared to 48.5% of the previous sota method with GPT-3.5-turbo.

TSVC:Tripartite Learning with Semantic Variation Consistency for Robust Image-Text Retrieval

Cross-modal retrieval maps data under different modality via semantic relevance. Existing approaches implicitly assume that data pairs are well-aligned and ignore the widely existing annotation noise, i.e., noisy correspondence (NC). Consequently, it inevitably causes performance degradation. Despite attempts that employ the co-teaching paradigm with identical architectures to provide distinct data perspectives, the differences between these architectures are primarily stemmed from random initialization. Thus, the model becomes increasingly homogeneous along with the training process. Consequently, the additional information brought by this paradigm is severely limited. In order to resolve this problem, we introduce a Tripartite learning with Semantic Variation Consistency (TSVC) for robust image-text retrieval. We design a tripartite cooperative learning mechanism comprising a Coordinator, a Master, and an Assistant model. The Coordinator distributes data, and the Assistant model supports the Master model's noisy label prediction with diverse data. Moreover, we introduce a soft label estimation method based on mutual information variation, which quantifies the noise in new samples and assigns corresponding soft labels. We also present a new loss function to enhance robustness and optimize training effectiveness. Extensive experiments on three widely used datasets demonstrate that, even at increasing noise ratios, TSVC exhibits significant advantages in retrieval accuracy and maintains stable training performance.

MVKTrans: Multi-View Knowledge Transfer for Robust Multiomics Classification

The distinct characteristics of multiomics data, including complex interactions within and across biological layers and disease heterogeneity (e.g., heterogeneity in etiology and clinical symptoms), drive us to develop novel designs to address unique challenges in multiomics prediction. In this paper, we propose the multi-view knowledge transfer learning (MVKTrans) framework, which transfers intra- and inter-omics knowledge in an adaptive manner by reviewing data heterogeneity and suppressing bias transfer, thereby enhancing classification performance. Specifically, we design a graph contrastive module that is trained on unlabeled data to effectively learn and transfer the underlying intra-omics patterns to the supervised task. This unsupervised pretraining promotes learning general and unbiased representations for each modality, regardless of the downstream tasks. In light of the varying discriminative capacities of modalities across different diseases and/or samples, we introduce an adaptive and bi-directional cross-omics distillation module. This module automatically identifies richer modalities and facilitates dynamic knowledge transfer from more informative to less informative omics, thereby enabling a more robust and generalized integration. Extensive experiments on four real biomedical datasets demonstrate the superior performance and robustness of MVKTrans compared to the state-of-the-art. Code and data are available at https://github.com/Yaolab-fantastic/MVKTrans.