Ran Xu

Ran Xu, Hejie Cui, Yue Yu et al. · gatech

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. Our code is available at \url{https://github.com/ritaranx/ClinGen}.

Jiayi Ni, Senqiao Yang, Ran Xu et al.

Since autonomous driving systems usually face dynamic and ever-changing environments, continual test-time adaptation (CTTA) has been proposed as a strategy for transferring deployed models to continually changing target domains. However, the pursuit of long-term adaptation often introduces catastrophic forgetting and error accumulation problems, which impede the practical implementation of CTTA in the real world. Recently, existing CTTA methods mainly focus on utilizing a majority of parameters to fit target domain knowledge through self-training. Unfortunately, these approaches often amplify the challenge of error accumulation due to noisy pseudo-labels, and pose practical limitations stemming from the heavy computational costs associated with entire model updates. In this paper, we propose a distribution-aware tuning (DAT) method to make the semantic segmentation CTTA efficient and practical in real-world applications. DAT adaptively selects and updates two small groups of trainable parameters based on data distribution during the continual adaptation process, including domain-specific parameters (DSP) and task-relevant parameters (TRP). Specifically, DSP exhibits sensitivity to outputs with substantial distribution shifts, effectively mitigating the problem of error accumulation. In contrast, TRP are allocated to positions that are responsive to outputs with minor distribution shifts, which are fine-tuned to avoid the catastrophic forgetting problem. In addition, since CTTA is a temporal task, we introduce the Parameter Accumulation Update (PAU) strategy to collect the updated DSP and TRP in target domain sequences. We conduct extensive experiments on two widely-used semantic segmentation CTTA benchmarks, achieving promising performance compared to previous state-of-the-art methods.

Ran Xu, Wenqi Shi, Yue Yu et al. · gatech

We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at \url{https://github.com/ritaranx/RAM-EHR}.

Ran Xu, Wenqi Shi, Yuchen Zhuang et al. · gatech

Retrieval-Augmented Generation (RAG) systems often struggle to handle multi-hop question-answering tasks accurately due to irrelevant context retrieval and limited complex reasoning capabilities. We introduce Collab-RAG, a collaborative training framework that leverages mutual enhancement between a white-box small language model (SLM) and a blackbox large language model (LLM) for RAG. Specifically, the SLM decomposes complex queries into simpler sub-questions, thus enhancing the accuracy of the retrieval and facilitating more effective reasoning by the black-box LLM. Concurrently, the black-box LLM provides feedback signals to improve the SLM's decomposition capability. We observe that Collab-RAG relies solely on supervision from an affordable black-box LLM without additional distillation from frontier LLMs, yet demonstrates strong generalization across multiple black-box LLMs. Experimental evaluations across five multi-hop QA datasets demonstrate that Collab-RAG substantially outperforms existing black-box-only and SLM fine-tuning baselines by 1.8%-14.2% on average. In particular, our fine-tuned 3B SLM surpasses a frozen 32B LLM in question decomposition, highlighting the efficiency of Collab-RAG in improving reasoning and retrieval for complex questions. The code of Collab-RAG is available on https://github.com/ritaranx/Collab-RAG/.

Ruiyu Wang, Tuan Vinh, Ran Xu et al.

Electronic health records (EHRs) support powerful clinical prediction models, but existing methods typically provide coarse, post hoc explanations that offer limited value for patient-level decision making. We introduce a knowledge graph (KG)-guided chain-of-thought (CoT) framework that generates clinically grounded and temporally consistent reasoning for visit-level disease prediction in MIMIC-III. ICD-9 codes are mapped to PrimeKG, from which disease-relevant nodes and multi-hop reasoning paths are extracted and used as scaffolds for CoT generation; only explanations whose conclusions match observed outcomes are retained. Lightweight LLaMA-3.1-Instruct-8B and Gemma-7B models are then fine-tuned on this supervision corpus. Across ten PrimeKG-mapped diseases and limited training cohorts (400 and 1000 cases), KG-guided models outperform strong classical baselines, achieving AUROC values of 0.66 to 0.70 and macro-AUPR values of 0.40 to 0.47. The models also transfer zero-shot to the CRADLE cohort, improving accuracy from approximately 0.40 to 0.51 up to 0.72 to 0.77. A blinded clinician evaluation shows consistent preference for KG-guided CoT explanations in clarity, relevance, and clinical correctness.

Meng Lu, Ran Xu, Yi Fang et al.

While recent vision-language models (VLMs) demonstrate strong image understanding, their ability to "think with images", i.e., to reason through multi-step visual interactions, remains limited. We introduce VISTA-Gym, a scalable training environment for incentivizing tool-integrated visual reasoning capabilities in VLMs. VISTA-Gym unifies diverse real-world multimodal reasoning tasks (7 tasks from 13 datasets in total) with a standardized interface for visual tools (e.g., grounding, parsing), executable interaction loops, verifiable feedback signals, and efficient trajectory logging, enabling visual agentic reinforcement learning at scale. While recent VLMs exhibit strong text-only reasoning, both proprietary and open-source models still struggle with tool selection, invocation, and coordination. With VISTA-Gym, we train VISTA-R1 to interleave tool-use with agentic reasoning via multi-turn trajectory sampling and end-to-end reinforcement learning. Extensive experiments across 11 public reasoning-intensive VQA benchmarks show that VISTA-R1-8B outperforms state-of-the-art baselines with similar sizes by 9.51%-18.72%, demonstrating VISTA-Gym as an effective training ground to unlock the tool-integrated reasoning capabilities for VLMs.

Haolin Chen, Shiyu Wang, Can Qin et al.

Diffusion language models promise bidirectional context and infilling capabilities that autoregressive coders lack, yet practical systems remain heavyweight. We introduce CoDA, a 1.7B-parameter diffusion coder trained on TPU with a fully open-source training pipeline. CoDA pairs large-scale diffusion pre-training with code-centric mid-training and instruction tuning, enabling confidence-guided sampling that keeps inference latency competitive. On Humaneval, MBPP, and EvalPlus, CoDA-1.7B-Instruct matches or surpasses diffusion models up to 7B parameters. Our release includes model checkpoints, evaluation harnesses, and TPU training pipelines to accelerate research on lightweight diffusion-based coding assistants.

Ran Xu, Yuchen Zhuang, Yishan Zhong et al. · gatech

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

Wenqi Shi, Ran Xu, Yuchen Zhuang et al. · gatech

Large language models (LLMs) have demonstrated exceptional capabilities in planning and tool utilization as autonomous agents, but few have been developed for medical problem-solving. We propose EHRAgent, an LLM agent empowered with a code interface, to autonomously generate and execute code for multi-tabular reasoning within electronic health records (EHRs). First, we formulate an EHR question-answering task into a tool-use planning process, efficiently decomposing a complicated task into a sequence of manageable actions. By integrating interactive coding and execution feedback, EHRAgent learns from error messages and improves the originally generated code through iterations. Furthermore, we enhance the LLM agent by incorporating long-term memory, which allows EHRAgent to effectively select and build upon the most relevant successful cases from past experiences. Experiments on three real-world multi-tabular EHR datasets show that EHRAgent outperforms the strongest baseline by up to 29.6% in success rate. EHRAgent leverages the emerging few-shot learning capabilities of LLMs, enabling autonomous code generation and execution to tackle complex clinical tasks with minimal demonstrations.

Wenqi Shi, Ran Xu, Yuchen Zhuang et al. · gatech

Despite their improved capabilities in generation and reasoning, adapting large language models (LLMs) to the biomedical domain remains challenging due to their immense size and corporate privacy. In this work, we propose MedAdapter, a unified post-hoc adapter for test-time adaptation of LLMs towards biomedical applications. Instead of fine-tuning the entire LLM, MedAdapter effectively adapts the original model by fine-tuning only a small BERT-sized adapter to rank candidate solutions generated by LLMs. Experiments demonstrate that MedAdapter effectively adapts both white-box and black-box LLMs in biomedical reasoning, achieving average performance improvements of 25.48% and 11.31%, respectively, without requiring extensive computational resources or sharing data with third parties. MedAdapter also yields superior performance when combined with train-time adaptation, highlighting a flexible and complementary solution to existing adaptation methods. Faced with the challenges of balancing model performance, computational resources, and data privacy, MedAdapter provides an efficient, privacy-preserving, cost-effective, and transparent solution for adapting LLMs to the biomedical domain.

Jiaming Liu, Ran Xu, Senqiao Yang et al.

Continual Test-Time Adaptation (CTTA) is proposed to migrate a source pre-trained model to continually changing target distributions, addressing real-world dynamism. Existing CTTA methods mainly rely on entropy minimization or teacher-student pseudo-labeling schemes for knowledge extraction in unlabeled target domains. However, dynamic data distributions cause miscalibrated predictions and noisy pseudo-labels in existing self-supervised learning methods, hindering the effective mitigation of error accumulation and catastrophic forgetting problems during the continual adaptation process. To tackle these issues, we propose a continual self-supervised method, Adaptive Distribution Masked Autoencoders (ADMA), which enhances the extraction of target domain knowledge while mitigating the accumulation of distribution shifts. Specifically, we propose a Distribution-aware Masking (DaM) mechanism to adaptively sample masked positions, followed by establishing consistency constraints between the masked target samples and the original target samples. Additionally, for masked tokens, we utilize an efficient decoder to reconstruct a hand-crafted feature descriptor (e.g., Histograms of Oriented Gradients), leveraging its invariant properties to boost task-relevant representations. Through conducting extensive experiments on four widely recognized benchmarks, our proposed method attains state-of-the-art performance in both classification and segmentation CTTA tasks. Our project page: https://sites.google.com/view/continual-mae/home.

Ran Xu, Hui Liu, Sreyashi Nag et al.

Retrieval-augmented generation (RAG) enhances the question-answering (QA) abilities of large language models (LLMs) by integrating external knowledge. However, adapting general-purpose RAG systems to specialized fields such as science and medicine poses unique challenges due to distribution shifts and limited access to domain-specific data. To tackle this, we propose SimRAG, a self-training approach that equips the LLM with joint capabilities of question answering and question generation for domain adaptation. Our method first fine-tunes the LLM on instruction-following, question-answering, and search-related data. Then, it prompts the same LLM to generate diverse domain-relevant questions from unlabeled corpora, with an additional filtering strategy to retain high-quality synthetic examples. By leveraging these self-generated synthetic examples, the LLM can improve their performance on domain-specific RAG tasks. Experiments on 11 datasets, spanning two backbone sizes and three domains, demonstrate that SimRAG outperforms baselines by 1.2\%--8.6\%.

Guohao Sun, Can Qin, Jiamian Wang et al.

Recent advances in vision-language models have shown notable generalization in broad tasks through visual instruction tuning. However, bridging the gap between the pre-trained vision encoder and the large language models (LLMs) becomes the whole network's bottleneck. To improve cross-modality alignment, existing works usually consider more visual instruction data covering a broader range of vision tasks to fine-tune the model for question-answering, which, however, is costly to obtain and has not thoroughly explored the rich contextual information contained in images. This paper first attempts to harness the overlooked context within visual instruction data, training the model to self-supervised "learning" how to ask high-quality questions. In this way, we introduce a novel framework named SQ-LLaVA: Self-Questioning for Large Vision-Language Assistant. SQ-LLaVA exhibits proficiency in generating flexible and meaningful image-related questions while analyzing the visual clue and prior language knowledge, signifying an advanced level of generalized visual understanding. Moreover, fine-tuning SQ-LLaVA on higher-quality instruction data shows a performance improvement compared with traditional visual-instruction tuning methods. This improvement highlights the efficacy of self-questioning techniques in achieving a deeper and more nuanced comprehension of visual content across various contexts.

Hejie Cui, Xinyu Fang, Ran Xu et al.

Electronic Health Records (EHRs) have become increasingly popular to support clinical decision-making and healthcare in recent decades. EHRs usually contain heterogeneous information, such as structural data in tabular form and unstructured data in textual notes. Different types of information in EHRs can complement each other and provide a more complete picture of the health status of a patient. While there has been a lot of research on representation learning of structured EHR data, the fusion of different types of EHR data (multimodal fusion) is not well studied. This is mostly because of the complex medical coding systems used and the noise and redundancy present in the written notes. In this work, we propose a new framework called MINGLE, which integrates both structures and semantics in EHR effectively. Our framework uses a two-level infusion strategy to combine medical concept semantics and clinical note semantics into hypergraph neural networks, which learn the complex interactions between different types of data to generate visit representations for downstream prediction. Experiment results on two EHR datasets, the public MIMIC-III and private CRADLE, show that MINGLE can effectively improve predictive performance by 11.83% relatively, enhancing semantic integration as well as multimodal fusion for structural and textual EHR data.

Yuzhen Du, Teng Hu, Jiangning Zhang et al. · tencent-ai

Image restoration (IR) aims to recover high-quality images from degraded inputs, with recent deep learning advancements significantly enhancing performance. However, existing methods lack a unified training benchmark for iterations and configurations. We also identify a bias in image complexity distributions between commonly used IR training and testing datasets, resulting in suboptimal restoration outcomes. To address this, we introduce a large-scale IR dataset called ReSyn, which employs a novel image filtering method based on image complexity to ensure a balanced distribution and includes both real and AIGC synthetic images. We establish a unified training standard that specifies iterations and configurations for image restoration models, focusing on measuring model convergence and restoration capability. Additionally, we enhance transformer-based image restoration models using linear attention mechanisms by proposing RWKV-IR, which integrates linear complexity RWKV into the transformer structure, allowing for both global and local receptive fields. Instead of directly using Vision-RWKV, we replace the original Q-Shift in RWKV with a Depth-wise Convolution shift to better model local dependencies, combined with Bi-directional attention for comprehensive linear attention. We also introduce a Cross-Bi-WKV module that merges two Bi-WKV modules with different scanning orders for balanced horizontal and vertical attention. Extensive experiments validate the effectiveness of our RWKV-IR model.