arXiv subjects

Wenqi Shi

Publications and source records attributed to Wenqi Shi.

At least 37 records · Page 2Linked to original sources

arXiv2026

LLM-as-RNN: A Recurrent Language Model for Memory Updates and Sequence Prediction

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.

cs.CL↗

arXiv2026

MEDVISTAGYM: A Scalable Training Environment for Thinking with Medical Images via Tool-Integrated Reinforcement Learning

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.

cs.CV↗

arXiv2025

Developing Fairness-Aware Task Decomposition to Improve Equity in Post-Spinal Fusion Complication Prediction

Fairness in clinical prediction models remains a persistent challenge, particularly in high-stakes applications such as spinal fusion surgery for scoliosis, where patient outcomes exhibit substantial heterogeneity. Many existing fairness approaches rely on coarse demographic adjustments or post-hoc corrections, which fail to capture the latent structure of clinical populations and may unintentionally reinforce bias. We propose FAIR-MTL, a fairness-aware multitask learning framework designed to provide equitable and fine-grained prediction of postoperative complication severity. Instead of relying on explicit sensitive attributes during model training, FAIR-MTL employs a data-driven subgroup inference mechanism. We extract a compact demographic embedding, and apply k-means clustering to uncover latent patient subgroups that may be differentially affected by traditional models. These inferred subgroup labels determine task routing within a shared multitask architecture. During training, subgroup imbalance is mitigated through inverse-frequency weighting, and regularization prevents overfitting to smaller groups. Applied to postoperative complication prediction with four severity levels, FAIR-MTL achieves an AUC of 0.86 and an accuracy of 75%, outperforming single-task baselines while substantially reducing bias. For gender, the demographic parity difference decreases to 0.055 and equalized odds to 0.094; for age, these values reduce to 0.056 and 0.148, respectively. Model interpretability is ensured through SHAP and Gini importance analyses, which consistently highlight clinically meaningful predictors such as hemoglobin, hematocrit, and patient weight. Our findings show that incorporating unsupervised subgroup discovery into a multitask framework enables more equitable, interpretable, and clinically actionable predictions for surgical risk stratification.

cs.LG↗

arXiv2025

Scaling Agentic Reinforcement Learning for Tool-Integrated Reasoning in VLMs

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.

cs.AI↗

arXiv2025

AsyncHZP: Hierarchical ZeRO Parallelism with Asynchronous Scheduling for Scalable LLM Training

The training efficiency and scalability of language models on massive clusters currently remain a critical bottleneck. Mainstream approaches like ND parallelism are often cumbersome and complex, while flexible alternatives such as the Zero Redundancy Optimizer (ZeRO) are frequently hampered by communication overhead. In this paper, we propose Asynchronous Hierarchical Zero Parallelism (AsyncHZP), a novel asynchronous variant of ZeRO designed to achieve superior performance while maintaining simplicity and memory efficiency. Unlike traditional ZeRO, which employs over-fine-grained sharding that can lead to inefficient communication, AsyncHZP adaptively reshards parameters, gradients, and optimizer states across different replica groups. This strategy optimizes device memory utilization and significantly reduces communication overhead. In addition, we also design a multi-stream asynchronous scheduling method that executes parameter all-gather and gradient reduce-scatter operations in dedicated background threads, effectively overlapping communication with computation while incurring negligible memory fragmentation. Empirical evaluations on both Dense and Mixture-of-Experts (MoE) models confirm that AsyncHZP maintains robust stability at scale. It consistently outperforms classic ND parallelism, achieving state-of-the-art performance without complex strategic tuning, thereby simplifying the path to efficient large-scale training.

cs.DC↗

arXiv2025

MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science

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.

cs.CL↗

arXiv2025

On the Use of Weighting for Personalized and Transparent Evidence Synthesis

Over the past few decades, statistical methods for causal inference have made impressive strides, enabling progress across a range of scientific fields. However, much of this methodological development has been confined to individual studies, limiting its ability to draw more generalizable conclusions. Achieving a thorough understanding of cause and effect typically relies on the integration, reconciliation, and synthesis from diverse study designs and multiple data sources. Furthermore, it is crucial to direct this synthesis effort toward understanding the effect of treatments for specific patient populations. To address these challenges, we present a weighting framework for evidence synthesis that handles both individual- and aggregate-level data, encompassing and extending conventional regression-based meta-analysis methods. We use this approach to tailor meta-analyses, targeting the covariate profiles of patients in a target population in a sample-bounded manner, thereby enhancing their personalization and robustness. We propose a technique to detect studies that meaningfully deviate from the target population, suggesting when it might be prudent to exclude them from the analysis. We establish multiple consistency conditions and demonstrate asymptotic normality for the proposed estimator. We demonstrate the effectiveness of the method through a simulation study and two real-world case studies.

stat.ME↗

arXiv2025

AceSearcher: Bootstrapping Reasoning and Search for LLMs via Reinforced Self-Play

Search-augmented LLMs often struggle with complex reasoning tasks due to ineffective multi-hop retrieval and limited reasoning ability. We propose AceSearcher, a cooperative self-play framework that trains a single large language model (LLM) to alternate between two roles: a decomposer that breaks down complex queries and a solver that integrates retrieved contexts for answer generation. AceSearcher couples supervised fine-tuning on a diverse mixture of search, reasoning, and decomposition tasks with reinforcement fine-tuning optimized for final answer accuracy, eliminating the need for intermediate annotations. Extensive experiments on three reasoning-intensive tasks across 10 datasets show that AceSearcher outperforms state-of-the-art baselines, achieving an average exact match improvement of 7.6%. Remarkably, on document-level finance reasoning tasks, AceSearcher-32B matches the performance of the DeepSeek-V3 model using less than 5% of its parameters. Even at smaller scales (1.5B and 8B), AceSearcher often surpasses existing search-augmented LLMs with up to 9x more parameters, highlighting its exceptional efficiency and effectiveness in tackling complex reasoning tasks. Our code will be published at https://github.com/ritaranx/AceSearcher and https://huggingface.co/AceSearcher.

cs.CL↗

arXiv2025

Causal Machine Learning for Surgical Interventions

Surgical decision-making is complex and requires understanding causal relationships between patient characteristics, interventions, and outcomes. In high-stakes settings like spinal fusion or scoliosis correction, accurate estimation of individualized treatment effects (ITEs) remains limited due to the reliance on traditional statistical methods that struggle with complex, heterogeneous data. In this study, we develop a multi-task meta-learning framework, X-MultiTask, for ITE estimation that models each surgical decision (e.g., anterior vs. posterior approach, surgery vs. no surgery) as a distinct task while learning shared representations across tasks. To strengthen causal validity, we incorporate the inverse probability weighting (IPW) into the training objective. We evaluate our approach on two datasets: (1) a public spinal fusion dataset (1,017 patients) to assess the effect of anterior vs. posterior approaches on complication severity; and (2) a private AIS dataset (368 patients) to analyze the impact of posterior spinal fusion (PSF) vs. non-surgical management on patient-reported outcomes (PROs). Our model achieves the highest average AUC (0.84) in the anterior group and maintains competitive performance in the posterior group (0.77). It outperforms baselines in treatment effect estimation with the lowest overall $ε_{\text{NN-PEHE}}$ (0.2778) and $ε_{\text{ATE}}$ (0.0763). Similarly, when predicting PROs in AIS, X-MultiTask consistently shows superior performance across all domains, with $ε_{\text{NN-PEHE}}$ = 0.2551 and $ε_{\text{ATE}}$ = 0.0902. By providing robust, patient-specific causal estimates, X-MultiTask offers a powerful tool to advance personalized surgical care and improve patient outcomes. The code is available at https://github.com/Wizaaard/X-MultiTask.

cs.LG↗

arXiv2025

MENDR: Manifold Explainable Neural Data Representations

Foundation models for electroencephalography (EEG) signals have recently demonstrated success in learning generalized representations of EEGs, outperforming specialized models in various downstream tasks. However, many of these models lack transparency in their pretraining dynamics and offer limited insight into how well EEG information is preserved within their embeddings. For successful clinical integration, EEG foundation models must ensure transparency in pretraining, downstream fine-tuning, and the interpretability of learned representations. Current approaches primarily operate in the temporal domain, overlooking advancements in digital signal processing that enable the extraction of deterministic and traceable features, such as wavelet-based representations. We propose MENDR (Manifold Explainable Neural Data Representations), a filter bank-based EEG foundation model built on a novel Riemannian Manifold Transformer architecture to resolve these issues. MENDR learns symmetric positive definite matrix embeddings of EEG signals and is pretrained on a large corpus comprising over 4,000 hours of EEG data, decomposed via discrete wavelet packet transforms into multi-resolution coefficients. MENDR significantly enhances interpretability by visualizing symmetric positive definite embeddings as geometric ellipsoids and supports accurate reconstruction of EEG signals from learned embeddings. Evaluations across multiple clinical EEG tasks demonstrate that MENDR achieves near state-of-the-art performance with substantially fewer parameters, underscoring its potential for efficient, interpretable, and clinically applicable EEG analysis.

cs.LG↗

arXiv2025

RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieved at inference time. While RAG demonstrates strong performance on benchmarks largely derived from general-domain corpora like Wikipedia, its effectiveness under realistic, diverse retrieval scenarios remains underexplored. We evaluated RAG systems using MassiveDS, a large-scale datastore with mixture of knowledge, and identified critical limitations: retrieval mainly benefits smaller models, rerankers add minimal value, and no single retrieval source consistently excels. Moreover, current LLMs struggle to route queries across heterogeneous knowledge sources. These findings highlight the need for adaptive retrieval strategies before deploying RAG in real-world settings. Our code and data can be found at https://github.com/ritaranx/RAG_in_the_Wild.

cs.CL↗

arXiv2025

Large Language Models Powered Multiagent Ensemble for Mitigating Hallucination and Efficient Atrial Fibrillation Annotation of ECG Reports

This study introduces a LLMs powered multiagent ensemble method to address challenges in hallucination and data labeling, particularly in large-scale EHR datasets. Manual labeling of such datasets requires domain expertise and is labor-intensive, time-consuming, expensive, and error-prone. To overcome this bottleneck, we developed an ensemble LLMs method and demonstrated its effectiveness in two real-world tasks: (1) labeling a large-scale unlabeled ECG dataset in MIMIC-IV; (2) identifying social determinants of health (SDOH) from the clinical notes of EHR. Trading off benefits and cost, we selected a pool of diverse open source LLMs with satisfactory performance. We treat each LLM's prediction as a vote and apply a mechanism of majority voting with minimal winning threshold for ensemble. We implemented an ensemble LLMs application for EHR data labeling tasks. By using the ensemble LLMs and natural language processing, we labeled MIMIC-IV ECG dataset of 623,566 ECG reports with an estimated accuracy of 98.2%. We applied the ensemble LLMs method to identify SDOH from social history sections of 1,405 EHR clinical notes, also achieving competitive performance. Our experiments show that the ensemble LLMs can outperform individual LLM even the best commercial one, and the method reduces hallucination errors. From the research, we found that (1) the ensemble LLMs method significantly reduces the time and effort required for labeling large-scale EHR data, automating the process with high accuracy and quality; (2) the method generalizes well to other text data labeling tasks, as shown by its application to SDOH identification; (3) the ensemble of a group of diverse LLMs can outperform or match the performance of the best individual LLM; and (4) the ensemble method substantially reduces hallucination errors. This approach provides a scalable and efficient solution to data-labeling challenges.

cs.AI↗

arXiv2025

WorkForceAgent-R1: Incentivizing Reasoning Capability in LLM-based Web Agents via Reinforcement Learning

Large language models (LLMs)-empowered web agents enables automating complex, real-time web navigation tasks in enterprise environments. However, existing web agents relying on supervised fine-tuning (SFT) often struggle with generalization and robustness due to insufficient reasoning capabilities when handling the inherently dynamic nature of web interactions. In this study, we introduce WorkForceAgent-R1, an LLM-based web agent trained using a rule-based R1-style reinforcement learning framework designed explicitly to enhance single-step reasoning and planning for business-oriented web navigation tasks. We employ a structured reward function that evaluates both adherence to output formats and correctness of actions, enabling WorkForceAgent-R1 to implicitly learn robust intermediate reasoning without explicit annotations or extensive expert demonstrations. Extensive experiments on the WorkArena benchmark demonstrate that WorkForceAgent-R1 substantially outperforms SFT baselines by 10.26-16.59%, achieving competitive performance relative to proprietary LLM-based agents (gpt-4o) in workplace-oriented web navigation tasks.

cs.CL↗

arXiv2025

Novel Extraction of Discriminative Fine-Grained Feature to Improve Retinal Vessel Segmentation

Retinal vessel segmentation is a vital early detection method for several severe ocular diseases. Despite significant progress in retinal vessel segmentation with the advancement of Neural Networks, there are still challenges to overcome. Specifically, retinal vessel segmentation aims to predict the class label for every pixel within a fundus image, with a primary focus on intra-image discrimination, making it vital for models to extract more discriminative features. Nevertheless, existing methods primarily focus on minimizing the difference between the output from the decoder and the label, but ignore fully using feature-level fine-grained representations from the encoder. To address these issues, we propose a novel Attention U-shaped Kolmogorov-Arnold Network named AttUKAN along with a novel Label-guided Pixel-wise Contrastive Loss for retinal vessel segmentation. Specifically, we implement Attention Gates into Kolmogorov-Arnold Networks to enhance model sensitivity by suppressing irrelevant feature activations and model interpretability by non-linear modeling of KAN blocks. Additionally, we also design a novel Label-guided Pixel-wise Contrastive Loss to supervise our proposed AttUKAN to extract more discriminative features by distinguishing between foreground vessel-pixel pairs and background pairs. Experiments are conducted across four public datasets including DRIVE, STARE, CHASE_DB1, HRF and our private dataset. AttUKAN achieves F1 scores of 82.50%, 81.14%, 81.34%, 80.21% and 80.09%, along with MIoU scores of 70.24%, 68.64%, 68.59%, 67.21% and 66.94% in the above datasets, which are the highest compared to 11 networks for retinal vessel segmentation. Quantitative and qualitative results show that our AttUKAN achieves state-of-the-art performance and outperforms existing retinal vessel segmentation methods. Our code will be available at https://github.com/stevezs315/AttUKAN.

cs.CV↗

arXiv2025

Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration

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/.

cs.CL↗

arXiv2025

Multi-level Asymmetric Contrastive Learning for Volumetric Medical Image Segmentation Pre-training

Medical image segmentation is a fundamental yet challenging task due to the arduous process of acquiring large volumes of high-quality labeled data from experts. Contrastive learning offers a promising but still problematic solution to this dilemma. Firstly existing medical contrastive learning strategies focus on extracting image-level representation, which ignores abundant multi-level representations. Furthermore they underutilize the decoder either by random initialization or separate pre-training from the encoder, thereby neglecting the potential collaboration between the encoder and decoder. To address these issues, we propose a novel multi-level asymmetric contrastive learning framework named MACL for volumetric medical image segmentation pre-training. Specifically, we design an asymmetric contrastive learning structure to pre-train encoder and decoder simultaneously to provide better initialization for segmentation models. Moreover, we develop a multi-level contrastive learning strategy that integrates correspondences across feature-level, image-level, and pixel-level representations to ensure the encoder and decoder capture comprehensive details from representations of varying scales and granularities during the pre-training phase. Finally, experiments on 8 medical image datasets indicate our MACL framework outperforms existing 11 contrastive learning strategies. i.e. Our MACL achieves a superior performance with more precise predictions from visualization figures and 1.72%, 7.87%, 2.49% and 1.48% Dice higher than previous best results on ACDC, MMWHS, HVSMR and CHAOS with 10% labeled data, respectively. And our MACL also has a strong generalization ability among 5 variant U-Net backbones. Our code will be released at https://github.com/stevezs315/MACL.

cs.CV↗

arXiv2025

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models

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}.

cs.CL↗

arXiv2024

EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records

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.

cs.CL↗