Yuxing Lu

Yuxing Lu, Yushuhong Lin, Wenqi Shi et al.

Clinical practice is not the selection of an answer from enumerated options: a physician gathers heterogeneous information incrementally and commits to sequential, irreversible decisions under uncertainty. Static benchmarks cannot probe and existing interactive medical benchmarks each compromise on at least one of them. We present ClinEnv, an interactive benchmark that evaluates LLMs as attending physicians over real inpatient admissions under a paradigm we term Longitudinal Inpatient Simulation. Each case is automatically constructed into an ordered sequence of decision stages; at every stage the model must actively query four specialized agents before committing to medications, procedures, and diagnoses. ClinEnv scores both what the model decides, through deterministic ontology-grounded matching, and how it gathers information. Across seven models, the strongest reaches only 0.31 decision F1, and outcome quality is sharply decoupled from process quality. Difficulty concentrates in management decisions and later stages, where models recover discharge diagnoses far more reliably than management actions (0.51 vs. 0.17 F1) and continue to issue redundant queries as cases progress. ClinEnv makes this information-acquisition gap, invisible to outcome-only evaluation, directly measurable.

Meng Lu, Yuxing Lu, Yuchen Zhuang et al.

Vision language models (VLMs) achieve strong performance on general image understanding but struggle to think with medical images, especially when performing multi-step reasoning through iterative visual interaction. Medical VLMs often rely on static visual embeddings and single-pass inference, preventing models from re-examining, verifying, or refining visual evidence during reasoning. While tool-integrated reasoning offers a promising path forward, open-source VLMs lack the training infrastructure to learn effective tool selection, invocation, and coordination in multi-modal medical reasoning. We introduce MedVistaGym, a scalable and interactive training environment that incentivizes tool-integrated visual reasoning for medical image analysis. MedVistaGym equips VLMs to determine when and which tools to invoke, localize task-relevant image regions, and integrate single or multiple sub-image evidence into interleaved multimodal reasoning within a unified, executable interface for agentic training. Using MedVistaGym, we train MedVistaGym-R1 to interleave tool use with agentic reasoning through trajectory sampling and end-to-end reinforcement learning. Across six medical VQA benchmarks, MedVistaGym-R1-8B exceeds comparably sized tool-augmented baselines by 19.10% to 24.21%, demonstrating that structured agentic training--not tool access alone--unlocks effective tool-integrated reasoning for medical image analysis.

J. Ben Tamo, Yuxing Lu, Benoit L. Marteau et al.

Large Language Models (LLMs) are fluent but prone to hallucinations, producing answers that appear plausible yet are unsupported by available evidence. This failure is especially problematic in high-stakes domains where decisions must be justified by verifiable information. We introduce \textbf{EvidenceRL}, a reinforcement learning framework that enforces evidence adherence during training. EvidenceRL scores candidate responses for grounding (entailment with retrieved evidence and context) and correctness (agreement with reference answers) and optimizes the generator using Group Relative Policy Optimization (GRPO). We evaluate across two high-stakes domains, cardiac diagnosis and legal reasoning, where EvidenceRL consistently improves evidence grounding and faithfulness without sacrificing task accuracy. On cardiac diagnosis, F1@3 increases from 37.0 to 54.5 on Llama-3.2-3B while grounding ($G_{\max}@3$) rises from 47.6 to 78.2; hallucinations drop nearly 5$\times$ and evidence-supported diagnoses increase from 31.8\% to 61.6\%. On legal reasoning, EvidenceRL raises Faithfulness from 32.8\% to 67.6\% on Llama-3.1-8B, demonstrating consistent behavioral change across domains. Our code is open-sourced at https://github.com/Wizaaard/EvidenceRL.git.

Yucheng Hu, Yuxing Lu · pku

Large Language Models (LLMs) have catalyzed significant advancements in Natural Language Processing (NLP), yet they encounter challenges such as hallucination and the need for domain-specific knowledge. To mitigate these, recent methodologies have integrated information retrieved from external resources with LLMs, substantially enhancing their performance across NLP tasks. This survey paper addresses the absence of a comprehensive overview on Retrieval-Augmented Language Models (RALMs), both Retrieval-Augmented Generation (RAG) and Retrieval-Augmented Understanding (RAU), providing an in-depth examination of their paradigm, evolution, taxonomy, and applications. The paper discusses the essential components of RALMs, including Retrievers, Language Models, and Augmentations, and how their interactions lead to diverse model structures and applications. RALMs demonstrate utility in a spectrum of tasks, from translation and dialogue systems to knowledge-intensive applications. The survey includes several evaluation methods of RALMs, emphasizing the importance of robustness, accuracy, and relevance in their assessment. It also acknowledges the limitations of RALMs, particularly in retrieval quality and computational efficiency, offering directions for future research. In conclusion, this survey aims to offer a structured insight into RALMs, their potential, and the avenues for their future development in NLP. The paper is supplemented with a Github Repository containing the surveyed works and resources for further study: https://github.com/2471023025/RALM_Survey.

Shuang Zeng, Boxu Xie, Lei Zhu et al.

Deep learning has greatly advanced medical image segmentation, but its success relies heavily on fully supervised learning, which requires dense annotations that are costly and time-consuming for 3D volumetric scans. Barely-supervised learning reduces annotation burden by using only a few labeled slices per volume. Existing methods typically propagate sparse annotations to unlabeled slices through geometric continuity to generate pseudo-labels, but this strategy lacks semantic understanding, often resulting in low-quality pseudo-labels. Furthermore, medical image segmentation is inherently a pixel-level visual understanding task, where accuracy fundamentally depends on the quality of local, fine-grained visual features. Inspired by this, we propose RADA, a novel Region-Aware Dual-encoder Auxiliary learning pipeline which introduces a dual-encoder framework pre-trained on Alpha-CLIP to extract fine-grained, region-specific visual features from the original images and limited annotations. The framework combines image-level fine-grained visual features with text-level semantic guidance, providing region-aware semantic supervision that bridges image-level semantics and pixel-level segmentation. Integrated into a triple-view training framework, RADA achieves SOTA performance under extremely sparse annotation settings on LA2018, KiTS19 and LiTS, demonstrating robust generalization across diverse datasets.

Yuxing Lu, Yucheng Hu, Xukai Zhao et al.

Multi-agent systems built from prompted large language models can improve multi-round reasoning, yet most existing pipelines rely on fixed, trajectory-wide communication patterns that are poorly matched to the stage-dependent needs of iterative problem solving. We introduce DyTopo, a manager-guided multi-agent framework that reconstructs a sparse directed communication graph at each round. Conditioned on the manager's round goal, each agent outputs lightweight natural-language query (need) and \key (offer) descriptors; DyTopo embeds these descriptors and performs semantic matching, routing private messages only along the induced edges. Across code generation and mathematical reasoning benchmarks and four LLM backbones, DyTopo consistently outperforms over the strongest baseline (avg. +6.2). Beyond accuracy, DyTopo yields an interpretable coordination trace via the evolving graphs, enabling qualitative inspection of how communication pathways reconfigure across rounds.

Yuxing Lu, Xukai Zhao, Wei Wu et al.

The knowledge base in a retrieval-augmented generation (RAG) system is typically assembled once and never revised, even though the facts a query requires are often fragmented across documents and buried in irrelevant content. We argue that the knowledge base should be treated as a trainable component and propose WriteBack-RAG, a framework that uses labeled examples to identify where retrieval succeeds, isolate the relevant documents, and distill them into compact knowledge units that are indexed alongside the original corpus. Because the method modifies only the corpus, it can be applied once as an offline preprocessing step and combined with any RAG pipeline. Across four RAG methods, six benchmarks, and two LLM backbones, WriteBack-RAG improves every evaluated setting, with gains averaging +2.14%. Cross-method transfer experiments further show that the distilled knowledge benefits RAG pipelines other than the one used to produce it, confirming that the improvement resides in the corpus itself.

Yuxing Lu, Jinzhuo Wang · pku

Maintaining comprehensive and up-to-date knowledge graphs (KGs) is critical for modern AI systems, but manual curation struggles to scale with the rapid growth of scientific literature. This paper presents KARMA, a novel framework employing multi-agent large language models (LLMs) to automate KG enrichment through structured analysis of unstructured text. Our approach employs nine collaborative agents, spanning entity discovery, relation extraction, schema alignment, and conflict resolution that iteratively parse documents, verify extracted knowledge, and integrate it into existing graph structures while adhering to domain-specific schema. Experiments on 1,200 PubMed articles from three different domains demonstrate the effectiveness of KARMA in knowledge graph enrichment, with the identification of up to 38,230 new entities while achieving 83.1\% LLM-verified correctness and reducing conflict edges by 18.6\% through multi-layer assessments.

Yuxing Lu, Sin Yee Goi, Xukai Zhao et al. · pku

Biomedical knowledge graphs (BKGs) have emerged as powerful tools for organizing and leveraging the vast and complex data found across the biomedical field. Yet, current reviews of BKGs often limit their scope to specific domains or methods, overlooking the broader landscape and the rapid technological progress reshaping it. In this survey, we address this gap by offering a systematic review of BKGs from three core perspectives: domains, tasks, and applications. We begin by examining how BKGs are constructed from diverse data sources, including molecular interactions, pharmacological datasets, and clinical records. Next, we discuss the essential tasks enabled by BKGs, focusing on knowledge management, retrieval, reasoning, and interpretation. Finally, we highlight real-world applications in precision medicine, drug discovery, and scientific research, illustrating the translational impact of BKGs across multiple sectors. By synthesizing these perspectives into a unified framework, this survey not only clarifies the current state of BKG research but also establishes a foundation for future exploration, enabling both innovative methodological advances and practical implementations.

Yuxing Lu, Yucheng Hu, Nan Sun et al.

Configuration optimization remains a critical bottleneck in machine learning, requiring coordinated tuning across model architecture, training strategy, feature engineering, and hyperparameters. Traditional approaches treat these dimensions independently and lack interpretability, while recent automated methods struggle with dynamic adaptability and semantic reasoning about optimization decisions. We introduce Language-Guided Tuning (LGT), a novel framework that employs multi-agent Large Language Models to intelligently optimize configurations through natural language reasoning. We apply textual gradients - qualitative feedback signals that complement numerical optimization by providing semantic understanding of training dynamics and configuration interdependencies. LGT coordinates three specialized agents: an Advisor that proposes configuration changes, an Evaluator that assesses progress, and an Optimizer that refines the decision-making process, creating a self-improving feedback loop. Through comprehensive evaluation on six diverse datasets, LGT demonstrates substantial improvements over traditional optimization methods, achieving performance gains while maintaining high interpretability.

Nan Sun, Han Fang, Yuxing Lu et al.

DNN-based watermarking methods have rapidly advanced, with the ``Encoder-Noise Layer-Decoder'' (END) framework being the most widely used. To ensure end-to-end training, the noise layer in the framework must be differentiable. However, real-world distortions are often non-differentiable, leading to challenges in end-to-end training. Existing solutions only treat the distortion perturbation as additive noise, which does not fully integrate the effect of distortion in training. To better incorporate non-differentiable distortions into training, we propose a novel dual-decoder architecture (END$^2$). Unlike conventional END architecture, our method employs two structurally identical decoders: the Teacher Decoder, processing pure watermarked images, and the Student Decoder, handling distortion-perturbed images. The gradient is backpropagated only through the Teacher Decoder branch to optimize the encoder thus bypassing the problem of non-differentiability. To ensure resistance to arbitrary distortions, we enforce alignment of the two decoders' feature representations by maximizing the cosine similarity between their intermediate vectors on a hypersphere. Extensive experiments demonstrate that our scheme outperforms state-of-the-art algorithms under various non-differentiable distortions. Moreover, even without the differentiability constraint, our method surpasses baselines with a differentiable noise layer. Our approach is effective and easily implementable across all END architectures, enhancing practicality and generalizability.

Yuxing Lu, Yushuhong Lin, Jason Zhang

Large language models applied to clinical prediction exhibit case-level heterogeneity: simple cases yield consistent outputs, while complex cases produce divergent predictions under minor prompt changes. Existing single-agent strategies sample from one role-conditioned distribution, and multi-agent frameworks use fixed roles with flat majority voting, discarding the diagnostic signal in disagreement. We propose CAMP (Case-Adaptive Multi-agent Panel), where an attending-physician agent dynamically assembles a specialist panel tailored to each case's diagnostic uncertainty. Each specialist evaluates candidates via three-valued voting (KEEP/REFUSE/NEUTRAL), enabling principled abstention outside one's expertise. A hybrid router directs each diagnosis through strong consensus, fallback to the attending physician's judgment, or evidence-based arbitration that weighs argument quality over vote counts. On diagnostic prediction and brief hospital course generation from MIMIC-IV across four LLM backbones, CAMP consistently outperforms strong baselines while consuming fewer tokens than most competing multi-agent methods, with voting records and arbitration traces offering transparent decision audits.

Yuxing Lu, J. Ben Tamo, Weichen Zhao et al.

Large language models are strong sequence predictors, yet standard inference relies on immutable context histories. After making an error at generation step t, the model lacks an updatable memory mechanism that improves predictions for step t+1. We propose LLM-as-RNN, an inference-only framework that turns a frozen LLM into a recurrent predictor by representing its hidden state as natural-language memory. This state, implemented as a structured system-prompt summary, is updated at each timestep via feedback-driven text rewrites, enabling learning without parameter updates. Under a fixed token budget, LLM-as-RNN corrects errors and retains task-relevant patterns, effectively performing online learning through language. We evaluate the method on three sequential benchmarks in healthcare, meteorology, and finance across Llama, Gemma, and GPT model families. LLM-as-RNN significantly outperforms zero-shot, full-history, and MemPrompt baselines, improving predictive accuracy by 6.5% on average, while producing interpretable, human-readable learning traces absent in standard context accumulation.

Rui Peng, Ziru Liu, Lingyuan Ye et al.

Accurately modeling the relationship between perturbations, transcriptional responses, and phenotypic changes is essential for building an AI Virtual Cell (AIVC). However, existing methods typically constrained to modeling direct associations, such as Perturbation $\rightarrow$ RNA or Perturbation $\rightarrow$ Morphology, overlook the crucial causal link from RNA to morphology. To bridge this gap, we propose TRIDENT, a cascade generative framework that synthesizes realistic cellular morphology by conditioning on both the perturbation and the corresponding gene expression profile. To train and evaluate this task, we construct MorphoGene, a new dataset pairing L1000 gene expression with Cell Painting images for 98 compounds. TRIDENT significantly outperforms state-of-the-art approaches, achieving up to 7-fold improvement with strong generalization to unseen compounds. In a case study on docetaxel, we validate that RNA-guided synthesis accurately produces the corresponding phenotype. An ablation study further confirms that this RNA conditioning is essential for the model's high fidelity. By explicitly modeling transcriptome-phenome mapping, TRIDENT provides a powerful in silico tool and moves us closer to a predictive virtual cell.

Yuxing Lu, Xukai Zhao, J. Ben Tamo et al. · pku

Large Language Models (LLMs) have demonstrated remarkable capabilities on general text; however, their proficiency in specialized scientific domains that require deep, interconnected knowledge remains largely uncharacterized. Metabolomics presents unique challenges with its complex biochemical pathways, heterogeneous identifier systems, and fragmented databases. To systematically evaluate LLM capabilities in this domain, we introduce MetaBench, the first benchmark for metabolomics assessment. Curated from authoritative public resources, MetaBench evaluates five capabilities essential for metabolomics research: knowledge, understanding, grounding, reasoning, and research. Our evaluation of 25 open- and closed-source LLMs reveals distinct performance patterns across metabolomics tasks: while models perform well on text generation tasks, cross-database identifier grounding remains challenging even with retrieval augmentation. Model performance also decreases on long-tail metabolites with sparse annotations. With MetaBench, we provide essential infrastructure for developing and evaluating metabolomics AI systems, enabling systematic progress toward reliable computational tools for metabolomics research.

Yuxing Lu, Gecheng Fu, Wei Wu et al. · pku

Existing medical RAG systems mainly leverage knowledge from medical knowledge bases, neglecting the crucial role of experiential knowledge derived from similar patient cases -- a key component of human clinical reasoning. To bridge this gap, we propose DoctorRAG, a RAG framework that emulates doctor-like reasoning by integrating both explicit clinical knowledge and implicit case-based experience. DoctorRAG enhances retrieval precision by first allocating conceptual tags for queries and knowledge sources, together with a hybrid retrieval mechanism from both relevant knowledge and patient. In addition, a Med-TextGrad module using multi-agent textual gradients is integrated to ensure that the final output adheres to the retrieved knowledge and patient query. Comprehensive experiments on multilingual, multitask datasets demonstrate that DoctorRAG significantly outperforms strong baseline RAG models and gains improvements from iterative refinements. Our approach generates more accurate, relevant, and comprehensive responses, taking a step towards more doctor-like medical reasoning systems.

Qichen Sun, Yuxing Lu, Kun Xia et al. · pku

Rapid and efficient assessment of the future impact of research articles is a significant concern for both authors and reviewers. The most common standard for measuring the impact of academic papers is the number of citations. In recent years, numerous efforts have been undertaken to predict citation counts within various citation windows. However, most of these studies focus solely on a specific academic field or require early citation counts for prediction, rendering them impractical for the early-stage evaluation of papers. In this work, we harness Scopus to curate a significantly comprehensive and large-scale dataset of information from 69707 scientific articles sourced from 99 journals spanning multiple disciplines. We propose a deep learning methodology for the impact-based classification tasks, which leverages semantic features extracted from the manuscripts and paper metadata. To summarize the semantic features, such as titles and abstracts, we employ a Transformer-based language model to encode semantic features and design a text fusion layer to capture shared information between titles and abstracts. We specifically focus on the following impact-based prediction tasks using information of scientific manuscripts in pre-publication stage: (1) The impact of journals in which the manuscripts will be published. (2) The future impact of manuscripts themselves. Extensive experiments on our datasets demonstrate the superiority of our proposed model for impact-based prediction tasks. We also demonstrate potentials in generating manuscript's feedback and improvement suggestions.

Yang Zhang, Yuxing Lu, Guiyang Xin et al.

In this work, we present the design, development, and experimental validation of a custom-built quadruped robot, Ask1. The Ask1 robot shares similar morphology with the Unitree Go1, but features custom hardware components and a different control architecture. We transfer and extend previous reinforcement learning (RL)-based control methods to the Ask1 robot, demonstrating the applicability of our approach in real-world scenarios. By eliminating the need for Adversarial Motion Priors (AMP) and reference trajectories, we introduce a novel reward function to guide the robot's motion style. We demonstrate the generalization capability of the proposed RL algorithm by training it on both the Go1 and Ask1 robots. Simulation and real-world experiments validate the effectiveness of this method, showing that Ask1, like the Go1, is capable of navigating various rugged terrains.

Dengfeng Ke, Yuxing Lu, Xudong Liu et al.

With the rapid development of neural network architectures and speech processing models, singing voice synthesis with neural networks is becoming the cutting-edge technique of digital music production. In this work, in order to explore how to improve the quality and efficiency of singing voice synthesis, in this work, we use encoder-decoder neural models and a number of vocoders to achieve singing voice synthesis. We conduct experiments to demonstrate that the models can be trained using voice data with pitch information, lyrics and beat information, and the trained models can produce smooth, clear and natural singing voice that is close to real human voice. As the models work in the end-to-end manner, they allow users who are not domain experts to directly produce singing voice by arranging pitches, lyrics and beats.