arXiv subjects

Yifan Peng

Publications and source records attributed to Yifan Peng.

At least 73 records · Page 4Linked to original sources

arXiv2025

A Multi-agent Large Language Model Framework to Automatically Assess Performance of a Clinical AI Triage Tool

Purpose: The purpose of this study was to determine if an ensemble of multiple LLM agents could be used collectively to provide a more reliable assessment of a pixel-based AI triage tool than a single LLM. Methods: 29,766 non-contrast CT head exams from fourteen hospitals were processed by a commercial intracranial hemorrhage (ICH) AI detection tool. Radiology reports were analyzed by an ensemble of eight open-source LLM models and a HIPAA compliant internal version of GPT-4o using a single multi-shot prompt that assessed for presence of ICH. 1,726 examples were manually reviewed. Performance characteristics of the eight open-source models and consensus were compared to GPT-4o. Three ideal consensus LLM ensembles were tested for rating the performance of the triage tool. Results: The cohort consisted of 29,766 head CTs exam-report pairs. The highest AUC performance was achieved with llama3.3:70b and GPT-4o (AUC= 0.78). The average precision was highest for Llama3.3:70b and GPT-4o (AP=0.75 & 0.76). Llama3.3:70b had the highest F1 score (0.81) and recall (0.85), greater precision (0.78), specificity (0.72), and MCC (0.57). Using MCC (95% CI) the ideal combination of LLMs were: Full-9 Ensemble 0.571 (0.552-0.591), Top-3 Ensemble 0.558 (0.537-0.579), Consensus 0.556 (0.539-0.574), and GPT4o 0.522 (0.500-0.543). No statistically significant differences were observed between Top-3, Full-9, and Consensus (p > 0.05). Conclusion: An ensemble of medium to large sized open-source LLMs provides a more consistent and reliable method to derive a ground truth retrospective evaluation of a clinical AI triage tool over a single LLM alone.

cs.CL↗

arXiv2025

Tensor Density Estimator by Convolution-Deconvolution

We propose a linear algebraic framework for performing density estimation. It consists of three simple steps: convolving the empirical distribution with certain smoothing kernels to remove the exponentially large variance; compressing the empirical distribution after convolution as a tensor train, with efficient tensor decomposition algorithms; and finally, applying a deconvolution step to recover the estimated density from such tensor-train representation. Numerical results demonstrate the high accuracy and efficiency of the proposed methods.

math.NA↗

arXiv2025

Gender Bias in Large Language Models for Healthcare: Assignment Consistency and Clinical Implications

The integration of large language models (LLMs) into healthcare holds promise to enhance clinical decision-making, yet their susceptibility to biases remains a critical concern. Gender has long influenced physician behaviors and patient outcomes, raising concerns that LLMs assuming human-like roles, such as clinicians or medical educators, may replicate or amplify gender-related biases. Using case studies from the New England Journal of Medicine Challenge (NEJM), we assigned genders (female, male, or unspecified) to multiple open-source and proprietary LLMs. We evaluated their response consistency across LLM-gender assignments regarding both LLM-based diagnosis and models' judgments on the clinical relevance or necessity of patient gender. In our findings, diagnoses were relatively consistent across LLM genders for most models. However, for patient gender's relevance and necessity in LLM-based diagnosis, all models demonstrated substantial inconsistency across LLM genders, particularly for relevance judgements. Some models even displayed a systematic female-male disparity in their interpretation of patient gender. These findings present an underexplored bias that could undermine the reliability of LLMs in clinical practice, underscoring the need for routine checks of identity-assignment consistency when interacting with LLMs to ensure reliable and equitable AI-supported clinical care.

cs.CL↗

arXiv2025

SynDoc: A Hybrid Discriminative-Generative Framework for Enhancing Synthetic Domain-Adaptive Document Key Information Extraction

Domain-specific Visually Rich Document Understanding (VRDU) presents significant challenges due to the complexity and sensitivity of documents in fields such as medicine, finance, and material science. Existing Large (Multimodal) Language Models (LLMs/MLLMs) achieve promising results but face limitations such as hallucinations, inadequate domain adaptation, and reliance on extensive fine-tuning datasets. This paper introduces SynDoc, a novel framework that combines discriminative and generative models to address these challenges. SynDoc employs a robust synthetic data generation workflow, using structural information extraction and domain-specific query generation to produce high-quality annotations. Through adaptive instruction tuning, SynDoc improves the discriminative model's ability to extract domain-specific knowledge. At the same time, a recursive inferencing mechanism iteratively refines the output of both models for stable and accurate predictions. This framework demonstrates scalable, efficient, and precise document understanding and bridges the gap between domain-specific adaptation and general world knowledge for document key information extraction tasks.

cs.CV↗

arXiv2025

Two-Stage Decoupling Framework for Variable-Length Glaucoma Prognosis

Glaucoma is one of the leading causes of irreversible blindness worldwide. Glaucoma prognosis is essential for identifying at-risk patients and enabling timely intervention to prevent blindness. Many existing approaches rely on historical sequential data but are constrained by fixed-length inputs, limiting their flexibility. Additionally, traditional glaucoma prognosis methods often employ end-to-end models, which struggle with the limited size of glaucoma datasets. To address these challenges, we propose a Two-Stage Decoupling Framework (TSDF) for variable-length glaucoma prognosis. In the first stage, we employ a feature representation module that leverages self-supervised learning to aggregate multiple glaucoma datasets for training, disregarding differences in their supervisory information. This approach enables datasets of varying sizes to learn better feature representations. In the second stage, we introduce a temporal aggregation module that incorporates an attention-based mechanism to process sequential inputs of varying lengths, ensuring flexible and efficient utilization of all available data. This design significantly enhances model performance while maintaining a compact parameter size. Extensive experiments on two benchmark glaucoma datasets:the Ocular Hypertension Treatment Study (OHTS) and the Glaucoma Real-world Appraisal Progression Ensemble (GRAPE),which differ significantly in scale and clinical settings,demonstrate the effectiveness and robustness of our approach.

cs.CV↗

arXiv2025

EventTracer: Fast Path Tracing-based Event Stream Rendering

Simulating event streams from 3D scenes has become a common practice in event-based vision research, as it meets the demand for large-scale, high temporal frequency data without setting up expensive hardware devices or undertaking extensive data collections. Yet existing methods in this direction typically work with noiseless RGB frames that are costly to render, and therefore they can only achieve a temporal resolution equivalent to 100-300 FPS, far lower than that of real-world event data. In this work, we propose EventTracer, a path tracing-based rendering pipeline that simulates high-fidelity event sequences from complex 3D scenes in an efficient and physics-aware manner. Specifically, we speed up the rendering process via low sample-per-pixel (SPP) path tracing, and train a lightweight event spiking network to denoise the resulting RGB videos into realistic event sequences. To capture the physical properties of event streams, the network is equipped with a bipolar leaky integrate-and-fired (BiLIF) spiking unit and trained with a bidirectional earth mover distance (EMD) loss. Our EventTracer pipeline runs at a speed of about 4 minutes per second of 720p video, and it inherits the merit of accurate spatiotemporal modeling from its path tracing backbone. We show in two downstream tasks that EventTracer captures better scene details and demonstrates a greater similarity to real-world event data than other event simulators, which establishes it as a promising tool for creating large-scale event-RGB datasets at a low cost, narrowing the sim-to-real gap in event-based vision, and boosting various application scenarios such as robotics, autonomous driving, and VRAR.

cs.CV↗

arXiv2025

Enhancing Health Fact-Checking with LLM-Generated Synthetic Data

Fact-checking for health-related content is challenging due to the limited availability of annotated training data. In this study, we propose a synthetic data generation pipeline that leverages large language models (LLMs) to augment training data for health-related fact checking. In this pipeline, we summarize source documents, decompose the summaries into atomic facts, and use an LLM to construct sentence-fact entailment tables. From the entailment relations in the table, we further generate synthetic text-claim pairs with binary veracity labels. These synthetic data are then combined with the original data to fine-tune a BERT-based fact-checking model. Evaluation on two public datasets, PubHealth and SciFact, shows that our pipeline improved F1 scores by up to 0.019 and 0.049, respectively, compared to models trained only on the original data. These results highlight the effectiveness of LLM-driven synthetic data augmentation in enhancing the performance of health-related fact-checkers.

cs.AI↗

arXiv2025

Extracting Post-Acute Sequelae of SARS-CoV-2 Infection Symptoms from Clinical Notes via Hybrid Natural Language Processing

Accurately and efficiently diagnosing Post-Acute Sequelae of COVID-19 (PASC) remains challenging due to its myriad symptoms that evolve over long- and variable-time intervals. To address this issue, we developed a hybrid natural language processing pipeline that integrates rule-based named entity recognition with BERT-based assertion detection modules for PASC-symptom extraction and assertion detection from clinical notes. We developed a comprehensive PASC lexicon with clinical specialists. From 11 health systems of the RECOVER initiative network across the U.S., we curated 160 intake progress notes for model development and evaluation, and collected 47,654 progress notes for a population-level prevalence study. We achieved an average F1 score of 0.82 in one-site internal validation and 0.76 in 10-site external validation for assertion detection. Our pipeline processed each note at $2.448\pm 0.812$ seconds on average. Spearman correlation tests showed $ρ>0.83$ for positive mentions and $ρ>0.72$ for negative ones, both with $P <0.0001$. These demonstrate the effectiveness and efficiency of our models and their potential for improving PASC diagnosis.

cs.CL↗

arXiv2025

A Multi-Stage Large Language Model Framework for Extracting Suicide-Related Social Determinants of Health

Background: Understanding social determinants of health (SDoH) factors contributing to suicide incidents is crucial for early intervention and prevention. However, data-driven approaches to this goal face challenges such as long-tailed factor distributions, analyzing pivotal stressors preceding suicide incidents, and limited model explainability. Methods: We present a multi-stage large language model framework to enhance SDoH factor extraction from unstructured text. Our approach was compared to other state-of-the-art language models (i.e., pre-trained BioBERT and GPT-3.5-turbo) and reasoning models (i.e., DeepSeek-R1). We also evaluated how the model's explanations help people annotate SDoH factors more quickly and accurately. The analysis included both automated comparisons and a pilot user study. Results: We show that our proposed framework demonstrated performance boosts in the overarching task of extracting SDoH factors and in the finer-grained tasks of retrieving relevant context. Additionally, we show that fine-tuning a smaller, task-specific model achieves comparable or better performance with reduced inference costs. The multi-stage design not only enhances extraction but also provides intermediate explanations, improving model explainability. Conclusions: Our approach improves both the accuracy and transparency of extracting suicide-related SDoH from unstructured texts. These advancements have the potential to support early identification of individuals at risk and inform more effective prevention strategies.

cs.CL↗

arXiv2025

AMD-Mamba: A Phenotype-Aware Multi-Modal Framework for Robust AMD Prognosis

Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss, making effective prognosis crucial for timely intervention. In this work, we propose AMD-Mamba, a novel multi-modal framework for AMD prognosis, and further develop a new AMD biomarker. This framework integrates color fundus images with genetic variants and socio-demographic variables. At its core, AMD-Mamba introduces an innovative metric learning strategy that leverages AMD severity scale score as prior knowledge. This strategy allows the model to learn richer feature representations by aligning learned features with clinical phenotypes, thereby improving the capability of conventional prognosis methods in capturing disease progression patterns. In addition, unlike existing models that use traditional CNN backbones and focus primarily on local information, such as the presence of drusen, AMD-Mamba applies Vision Mamba and simultaneously fuses local and long-range global information, such as vascular changes. Furthermore, we enhance prediction performance through multi-scale fusion, combining image information with clinical variables at different resolutions. We evaluate AMD-Mamba on the AREDS dataset, which includes 45,818 color fundus photographs, 52 genetic variants, and 3 socio-demographic variables from 2,741 subjects. Our experimental results demonstrate that our proposed biomarker is one of the most significant biomarkers for the progression of AMD. Notably, combining this biomarker with other existing variables yields promising improvements in detecting high-risk AMD patients at early stages. These findings highlight the potential of our multi-modal framework to facilitate more precise and proactive management of AMD.

eess.IV↗

arXiv2025

Enhanced Velocity Field Modeling for Gaussian Video Reconstruction

High-fidelity 3D video reconstruction is essential for enabling real-time rendering of dynamic scenes with realistic motion in virtual and augmented reality (VR/AR). The deformation field paradigm of 3D Gaussian splatting has achieved near-photorealistic results in video reconstruction due to the great representation capability of deep deformation networks. However, in videos with complex motion and significant scale variations, deformation networks often overfit to irregular Gaussian trajectories, leading to suboptimal visual quality. Moreover, the gradient-based densification strategy designed for static scene reconstruction proves inadequate to address the absence of dynamic content. In light of these challenges, we propose a flow-empowered velocity field modeling scheme tailored for Gaussian video reconstruction, dubbed FlowGaussian-VR. It consists of two core components: a velocity field rendering (VFR) pipeline which enables optical flow-based optimization, and a flow-assisted adaptive densification (FAD) strategy that adjusts the number and size of Gaussians in dynamic regions. We validate our model's effectiveness on multi-view dynamic reconstruction and novel view synthesis with multiple real-world datasets containing challenging motion scenarios, demonstrating not only notable visual improvements (over 2.5 dB gain in PSNR) and less blurry artifacts in dynamic textures, but also regularized and trackable per-Gaussian trajectories.

cs.CV↗

arXiv2025

Learned Off-aperture Encoding for Wide Field-of-view RGBD Imaging

End-to-end (E2E) designed imaging systems integrate coded optical designs with decoding algorithms to enhance imaging fidelity for diverse visual tasks. However, existing E2E designs encounter significant challenges in maintaining high image fidelity at wide fields of view, due to high computational complexity, as well as difficulties in modeling off-axis wave propagation while accounting for off-axis aberrations. In particular, the common approach of placing the encoding element into the aperture or pupil plane results in only a global control of the wavefront. To overcome these limitations, this work explores an additional design choice by positioning a DOE off-aperture, enabling a spatial unmixing of the degrees of freedom and providing local control over the wavefront over the image plane. Our approach further leverages hybrid refractive-diffractive optical systems by linking differentiable ray and wave optics modeling, thereby optimizing depth imaging quality and demonstrating system versatility. Experimental results reveal that the off-aperture DOE enhances the imaging quality by over 5 dB in PSNR at a FoV of approximately $45^\circ$ when paired with a simple thin lens, outperforming traditional on-aperture systems. Furthermore, we successfully recover color and depth information at nearly $28^\circ$ FoV using off-aperture DOE configurations with compound optics. Physical prototypes for both applications validate the effectiveness and versatility of the proposed method.

eess.IV↗

arXiv2025

Benchmarking Foundation Models with Multimodal Public Electronic Health Records

Foundation models have emerged as a powerful approach for processing electronic health records (EHRs), offering flexibility to handle diverse medical data modalities. In this study, we present a comprehensive benchmark that evaluates the performance, fairness, and interpretability of foundation models, both as unimodal encoders and as multimodal learners, using the publicly available MIMIC-IV database. To support consistent and reproducible evaluation, we developed a standardized data processing pipeline that harmonizes heterogeneous clinical records into an analysis-ready format. We systematically compared eight foundation models, encompassing both unimodal and multimodal models, as well as domain-specific and general-purpose variants. Our findings demonstrate that incorporating multiple data modalities leads to consistent improvements in predictive performance without introducing additional bias. Through this benchmark, we aim to support the development of effective and trustworthy multimodal artificial intelligence (AI) systems for real-world clinical applications. Our code is available at https://github.com/nliulab/MIMIC-Multimodal.

cs.LG↗

arXiv2025

OpusLM: A Family of Open Unified Speech Language Models

This paper presents Open Unified Speech Language Models (OpusLMs), a family of open foundational speech language models (SpeechLMs) up to 7B. Initialized from decoder-only text language models, the OpusLMs are continuously pre-trained on 213K hours of speech-text pairs and 292B text-only tokens. We demonstrate our OpusLMs achieve comparable (or even superior) performance with existing SpeechLMs in speech recognition, speech synthesis, and text-only capabilities. Technically, this paper articulates our SpeechLM designs on tokenization, multi-stream language models, and multi-stage training strategies. We experimentally demonstrate the importance of model size scaling and the effect of annealing data selection. The OpusLMs are all built from publicly available materials and are fully transparent models. We release our code, data, checkpoints, and training logs to facilitate open SpeechLM research

cs.CL↗

arXiv2025

Optimization-Free Diffusion Model -- A Perturbation Theory Approach

Diffusion models have emerged as a powerful framework in generative modeling, typically relying on optimizing neural networks to estimate the score function via forward SDE simulations. In this work, we propose an alternative method that is both optimization-free and forward SDE-free. By expanding the score function in a sparse set of eigenbasis of the backward Kolmogorov operator associated with the diffusion process, we reformulate score estimation as the solution to a linear system, avoiding iterative optimization and time-dependent sample generation. We analyze the approximation error using perturbation theory and demonstrate the effectiveness of our method on high-dimensional Boltzmann distributions and real-world datasets.

math.NA↗

arXiv2025

CXR-LT 2024: A MICCAI challenge on long-tailed, multi-label, and zero-shot disease classification from chest X-ray

The CXR-LT series is a community-driven initiative designed to enhance lung disease classification using chest X-rays (CXR). It tackles challenges in open long-tailed lung disease classification and enhances the measurability of state-of-the-art techniques. The first event, CXR-LT 2023, aimed to achieve these goals by providing high-quality benchmark CXR data for model development and conducting comprehensive evaluations to identify ongoing issues impacting lung disease classification performance. Building on the success of CXR-LT 2023, the CXR-LT 2024 expands the dataset to 377,110 chest X-rays (CXRs) and 45 disease labels, including 19 new rare disease findings. It also introduces a new focus on zero-shot learning to address limitations identified in the previous event. Specifically, CXR-LT 2024 features three tasks: (i) long-tailed classification on a large, noisy test set, (ii) long-tailed classification on a manually annotated "gold standard" subset, and (iii) zero-shot generalization to five previously unseen disease findings. This paper provides an overview of CXR-LT 2024, detailing the data curation process and consolidating state-of-the-art solutions, including the use of multimodal models for rare disease detection, advanced generative approaches to handle noisy labels, and zero-shot learning strategies for unseen diseases. Additionally, the expanded dataset enhances disease coverage to better represent real-world clinical settings, offering a valuable resource for future research. By synthesizing the insights and innovations of participating teams, we aim to advance the development of clinically realistic and generalizable diagnostic models for chest radiography.

cs.CV↗

arXiv2025

Seeing Far and Clearly: Mitigating Hallucinations in MLLMs with Attention Causal Decoding

Recent advancements in multimodal large language models (MLLMs) have significantly improved performance in visual question answering. However, they often suffer from hallucinations. In this work, hallucinations are categorized into two main types: initial hallucinations and snowball hallucinations. We argue that adequate contextual information can be extracted directly from the token interaction process. Inspired by causal inference in the decoding strategy, we propose to leverage causal masks to establish information propagation between multimodal tokens. The hypothesis is that insufficient interaction between those tokens may lead the model to rely on outlier tokens, overlooking dense and rich contextual cues. Therefore, we propose to intervene in the propagation process by tackling outlier tokens to enhance in-context inference. With this goal, we present FarSight, a versatile plug-and-play decoding strategy to reduce attention interference from outlier tokens merely by optimizing the causal mask. The heart of our method is effective token propagation. We design an attention register structure within the upper triangular matrix of the causal mask, dynamically allocating attention to capture attention diverted to outlier tokens. Moreover, a positional awareness encoding method with a diminishing masking rate is proposed, allowing the model to attend to further preceding tokens, especially for video sequence tasks. With extensive experiments, FarSight demonstrates significant hallucination-mitigating performance across different MLLMs on both image and video benchmarks, proving its effectiveness.

cs.CV↗

arXiv2025

AquaticVision: Benchmarking Visual SLAM in Underwater Environment with Events and Frames

Many underwater applications, such as offshore asset inspections, rely on visual inspection and detailed 3D reconstruction. Recent advancements in underwater visual SLAM systems for aquatic environments have garnered significant attention in marine robotics research. However, existing underwater visual SLAM datasets often lack groundtruth trajectory data, making it difficult to objectively compare the performance of different SLAM algorithms based solely on qualitative results or COLMAP reconstruction. In this paper, we present a novel underwater dataset that includes ground truth trajectory data obtained using a motion capture system. Additionally, for the first time, we release visual data that includes both events and frames for benchmarking underwater visual positioning. By providing event camera data, we aim to facilitate the development of more robust and advanced underwater visual SLAM algorithms. The use of event cameras can help mitigate challenges posed by extremely low light or hazy underwater conditions. The webpage of our dataset is https://sites.google.com/view/aquaticvision-lias.

cs.RO↗