arXiv subjects

Ke Zou

Publications and source records attributed to Ke Zou.

At least 37 records · Page 2Linked to original sources

arXiv2025

Benchmarking Next-Generation Reasoning-Focused Large Language Models in Ophthalmology: A Head-to-Head Evaluation on 5,888 Items

Recent advances in reasoning-focused large language models (LLMs) mark a shift from general LLMs toward models designed for complex decision-making, a crucial aspect in medicine. However, their performance in specialized domains like ophthalmology remains underexplored. This study comprehensively evaluated and compared the accuracy and reasoning capabilities of four newly developed reasoning-focused LLMs, namely DeepSeek-R1, OpenAI o1, o3-mini, and Gemini 2.0 Flash-Thinking. Each model was assessed using 5,888 multiple-choice ophthalmology exam questions from the MedMCQA dataset in zero-shot setting. Quantitative evaluation included accuracy, Macro-F1, and five text-generation metrics (ROUGE-L, METEOR, BERTScore, BARTScore, and AlignScore), computed against ground-truth reasonings. Average inference time was recorded for a subset of 100 randomly selected questions. Additionally, two board-certified ophthalmologists qualitatively assessed clarity, completeness, and reasoning structure of responses to differential diagnosis questions.O1 (0.902) and DeepSeek-R1 (0.888) achieved the highest accuracy, with o1 also leading in Macro-F1 (0.900). The performance of models across the text-generation metrics varied: O3-mini excelled in ROUGE-L (0.151), o1 in METEOR (0.232), DeepSeek-R1 and o3-mini tied for BERTScore (0.673), DeepSeek-R1 (-4.105) and Gemini 2.0 Flash-Thinking (-4.127) performed best in BARTScore, while o3-mini (0.181) and o1 (0.176) led AlignScore. Inference time across the models varied, with DeepSeek-R1 being slowest (40.4 seconds) and Gemini 2.0 Flash-Thinking fastest (6.7 seconds). Qualitative evaluation revealed that DeepSeek-R1 and Gemini 2.0 Flash-Thinking tended to provide detailed and comprehensive intermediate reasoning, whereas o1 and o3-mini displayed concise and summarized justifications.

cs.CL↗

arXiv2025

Enhancing Diagnostic Accuracy in Rare and Common Fundus Diseases with a Knowledge-Rich Vision-Language Model

Previous foundation models for fundus images were pre-trained with limited disease categories and knowledge base. Here we introduce a knowledge-rich vision-language model (RetiZero) that leverages knowledge from more than 400 fundus diseases. For RetiZero's pretraining, we compiled 341,896 fundus images paired with texts, sourced from public datasets, ophthalmic literature, and online resources, encompassing a diverse range of diseases across multiple ethnicities and countries. RetiZero exhibits remarkable performance in several downstream tasks, including zero-shot disease recognition, image-to-image retrieval, AI-assisted clinical diagnosis,few-shot fine-tuning, and internal- and cross-domain disease identification. In zero-shot scenarios, RetiZero achieves Top-5 accuracies of 0.843 for 15 diseases and 0.756 for 52 diseases. For image retrieval, it achieves Top-5 scores of 0.950 and 0.886 for the same sets, respectively. AI-assisted clinical diagnosis results show that RetiZero's Top-3 zero-shot performance surpasses the average of 19 ophthalmologists from Singapore, China, and the United States. RetiZero substantially enhances clinicians' accuracy in diagnosing fundus diseases, in particularly rare ones. These findings underscore the value of integrating the RetiZero into clinical settings, where various fundus diseases are encountered.

eess.IV↗

arXiv2025

GEMeX: A Large-Scale, Groundable, and Explainable Medical VQA Benchmark for Chest X-ray Diagnosis

Medical Visual Question Answering (Med-VQA) combines computer vision and natural language processing to automatically answer clinical inquiries about medical images. However, current Med-VQA datasets exhibit two significant limitations: (1) they often lack visual and textual explanations for answers, hindering comprehension for patients and junior doctors; (2) they typically offer a narrow range of question formats, inadequately reflecting the diverse requirements in practical scenarios. These limitations pose significant challenges to the development of a reliable and user-friendly Med-VQA system. To address these challenges, we introduce a large-scale, Groundable, and Explainable Medical VQA benchmark for chest X-ray diagnosis (GEMeX), featuring several innovative components: (1) a multi-modal explainability mechanism that offers detailed visual and textual explanations for each question-answer pair, thereby enhancing answer comprehensibility; (2) four question types, open-ended, closed-ended, single-choice, and multiple-choice, to better reflect practical needs. With 151,025 images and 1,605,575 questions, GEMeX is the currently largest chest X-ray VQA dataset. Evaluation of 12 representative large vision language models (LVLMs) on GEMeX reveals suboptimal performance, underscoring the dataset's complexity. Meanwhile, we propose a strong model by fine-tuning an existing LVLM on the GEMeX training set. The substantial performance improvement showcases the dataset's effectiveness. The benchmark is available at https://www.med-vqa.com/GEMeX.

cs.CV↗

arXiv2025

LMOD: A Large Multimodal Ophthalmology Dataset and Benchmark for Large Vision-Language Models

The prevalence of vision-threatening eye diseases is a significant global burden, with many cases remaining undiagnosed or diagnosed too late for effective treatment. Large vision-language models (LVLMs) have the potential to assist in understanding anatomical information, diagnosing eye diseases, and drafting interpretations and follow-up plans, thereby reducing the burden on clinicians and improving access to eye care. However, limited benchmarks are available to assess LVLMs' performance in ophthalmology-specific applications. In this study, we introduce LMOD, a large-scale multimodal ophthalmology benchmark consisting of 21,993 instances across (1) five ophthalmic imaging modalities: optical coherence tomography, color fundus photographs, scanning laser ophthalmoscopy, lens photographs, and surgical scenes; (2) free-text, demographic, and disease biomarker information; and (3) primary ophthalmology-specific applications such as anatomical information understanding, disease diagnosis, and subgroup analysis. In addition, we benchmarked 13 state-of-the-art LVLM representatives from closed-source, open-source, and medical domains. The results demonstrate a significant performance drop for LVLMs in ophthalmology compared to other domains. Systematic error analysis further identified six major failure modes: misclassification, failure to abstain, inconsistent reasoning, hallucination, assertions without justification, and lack of domain-specific knowledge. In contrast, supervised neural networks specifically trained on these tasks as baselines demonstrated high accuracy. These findings underscore the pressing need for benchmarks in the development and validation of ophthalmology-specific LVLMs.

cs.CV↗

arXiv2025

Are Traditional Deep Learning Model Approaches as Effective as a Retinal-Specific Foundation Model for Ocular and Systemic Disease Detection?

Background: RETFound, a self-supervised, retina-specific foundation model (FM), showed potential in downstream applications. However, its comparative performance with traditional deep learning (DL) models remains incompletely understood. This study aimed to evaluate RETFound against three ImageNet-pretrained supervised DL models (ResNet50, ViT-base, SwinV2) in detecting ocular and systemic diseases. Methods: We fine-tuned/trained RETFound and three DL models on full datasets, 50%, 20%, and fixed sample sizes (400, 200, 100 images, with half comprising disease cases; for each DR severity class, 100 and 50 cases were used. Fine-tuned models were tested internally using the SEED (53,090 images) and APTOS-2019 (3,672 images) datasets and externally validated on population-based (BES, CIEMS, SP2, UKBB) and open-source datasets (ODIR-5k, PAPILA, GAMMA, IDRiD, MESSIDOR-2). Model performance was compared using area under the receiver operating characteristic curve (AUC) and Z-tests with Bonferroni correction (P<0.05/3). Interpretation: Traditional DL models are mostly comparable to RETFound for ocular disease detection with large datasets. However, RETFound is superior in systemic disease detection with smaller datasets. These findings offer valuable insights into the respective merits and limitation of traditional models and FMs.

cs.CV↗

arXiv2025

Can OpenAI o1 Reason Well in Ophthalmology? A 6,990-Question Head-to-Head Evaluation Study

Question: What is the performance and reasoning ability of OpenAI o1 compared to other large language models in addressing ophthalmology-specific questions? Findings: This study evaluated OpenAI o1 and five LLMs using 6,990 ophthalmological questions from MedMCQA. O1 achieved the highest accuracy (0.88) and macro-F1 score but ranked third in reasoning capabilities based on text-generation metrics. Across subtopics, o1 ranked first in ``Lens'' and ``Glaucoma'' but second to GPT-4o in ``Corneal and External Diseases'', ``Vitreous and Retina'' and ``Oculoplastic and Orbital Diseases''. Subgroup analyses showed o1 performed better on queries with longer ground truth explanations. Meaning: O1's reasoning enhancements may not fully extend to ophthalmology, underscoring the need for domain-specific refinements to optimize performance in specialized fields like ophthalmology.

cs.CL↗

arXiv2024

Temperature evolution of the Fermi surface of the FeSe monolayer on SrTiO$_3$

The origin of superconductivity in the FeSe monolayer on SrTiO$_3$ remains one of the unresolved mysteries in condensed-matter physics. Here by investigation of the temperature evolution of the dynamic charge response of FeSe/SrTiO$_3$ we infer that the response of the monolayer itself is nearly temperature independent. This indicates a constant Fermi surface over a wide range of temperature, in stark contrast to that of the bulk FeSe and other Fe-based superconductors. Our results, which manifest the peculiarity of the electronic structure of the FeSe monolayer, may help for a microscopic understanding of the superconductivity in Fe-chalcogenide monolayers on oxide surfaces in general.

cond-mat.supr-con↗

arXiv2024

Critical Role of Disorder for Superconductivity in the Series of Epitaxial Ti(O,N) Films

Realizing experimental control of superconductivity is of paramount importance to advancing both basic research and technological applications. Disorder, generally existing in most superconductors, intricately interacts with Cooper pairs and also impacts the performance of quantum devices. In this paper, we report the study of a series of Ti(O,N) crystalline films prepared via molecular beam epitaxy (MBE). We discover that substituting nitrogen (N) for oxygen (O) in TiO, namely TiO(N), considerably increases the normal-state conductivity and the superconducting transition temperature Tc. The Tc of TiO(N) falling between those of TiO (about 0.5 K) and TiN (about 6 K) is contrary to their comparable Tc predicted by the Migdal Eliasberg theory. It is found that their resistivity vs temperature obeys the Mooij rule, known as the characteristic of metallic glasses. Density functional theory (DFT) calculations demonstrate that strong disorder severely scatters the Bloch electron waves at nonzero momenta, which consequently weakens electron-phonon coupling in TiO(N).

cond-mat.supr-con↗

arXiv2024

MedSAM-U: Uncertainty-Guided Auto Multi-Prompt Adaptation for Reliable MedSAM

The Medical Segment Anything Model (MedSAM) has shown remarkable performance in medical image segmentation, drawing significant attention in the field. However, its sensitivity to varying prompt types and locations poses challenges. This paper addresses these challenges by focusing on the development of reliable prompts that enhance MedSAM's accuracy. We introduce MedSAM-U, an uncertainty-guided framework designed to automatically refine multi-prompt inputs for more reliable and precise medical image segmentation. Specifically, we first train a Multi-Prompt Adapter integrated with MedSAM, creating MPA-MedSAM, to adapt to diverse multi-prompt inputs. We then employ uncertainty-guided multi-prompt to effectively estimate the uncertainties associated with the prompts and their initial segmentation results. In particular, a novel uncertainty-guided prompts adaptation technique is then applied automatically to derive reliable prompts and their corresponding segmentation outcomes. We validate MedSAM-U using datasets from multiple modalities to train a universal image segmentation model. Compared to MedSAM, experimental results on five distinct modal datasets demonstrate that the proposed MedSAM-U achieves an average performance improvement of 1.7\% to 20.5\% across uncertainty-guided prompts.

cs.CV↗

arXiv2024

Enhancing Diagnostic Reliability of Foundation Model with Uncertainty Estimation in OCT Images

Inability to express the confidence level and detect unseen classes has limited the clinical implementation of artificial intelligence in the real-world. We developed a foundation model with uncertainty estimation (FMUE) to detect 11 retinal conditions on optical coherence tomography (OCT). In the internal test set, FMUE achieved a higher F1 score of 96.76% than two state-of-the-art algorithms, RETFound and UIOS, and got further improvement with thresholding strategy to 98.44%. In the external test sets obtained from other OCT devices, FMUE achieved an accuracy of 88.75% and 92.73% before and after thresholding. Our model is superior to two ophthalmologists with a higher F1 score (95.17% vs. 61.93% &71.72%). Besides, our model correctly predicts high uncertainty scores for samples with ambiguous features, of non-target-category diseases, or with low-quality to prompt manual checks and prevent misdiagnosis. FMUE provides a trustworthy method for automatic retinal anomalies detection in the real-world clinical open set environment.

eess.IV↗

arXiv2024

Confidence-aware multi-modality learning for eye disease screening

Multi-modal ophthalmic image classification plays a key role in diagnosing eye diseases, as it integrates information from different sources to complement their respective performances. However, recent improvements have mainly focused on accuracy, often neglecting the importance of confidence and robustness in predictions for diverse modalities. In this study, we propose a novel multi-modality evidential fusion pipeline for eye disease screening. It provides a measure of confidence for each modality and elegantly integrates the multi-modality information using a multi-distribution fusion perspective. Specifically, our method first utilizes normal inverse gamma prior distributions over pre-trained models to learn both aleatoric and epistemic uncertainty for uni-modality. Then, the normal inverse gamma distribution is analyzed as the Student's t distribution. Furthermore, within a confidence-aware fusion framework, we propose a mixture of Student's t distributions to effectively integrate different modalities, imparting the model with heavy-tailed properties and enhancing its robustness and reliability. More importantly, the confidence-aware multi-modality ranking regularization term induces the model to more reasonably rank the noisy single-modal and fused-modal confidence, leading to improved reliability and accuracy. Experimental results on both public and internal datasets demonstrate that our model excels in robustness, particularly in challenging scenarios involving Gaussian noise and modality missing conditions. Moreover, our model exhibits strong generalization capabilities to out-of-distribution data, underscoring its potential as a promising solution for multimodal eye disease screening.

eess.IV↗

arXiv2024

FRCNet Frequency and Region Consistency for Semi-supervised Medical Image Segmentation

Limited labeled data hinder the application of deep learning in medical domain. In clinical practice, there are sufficient unlabeled data that are not effectively used, and semi-supervised learning (SSL) is a promising way for leveraging these unlabeled data. However, existing SSL methods ignore frequency domain and region-level information and it is important for lesion regions located at low frequencies and with significant scale changes. In this paper, we introduce two consistency regularization strategies for semi-supervised medical image segmentation, including frequency domain consistency (FDC) to assist the feature learning in frequency domain and multi-granularity region similarity consistency (MRSC) to perform multi-scale region-level local context information feature learning. With the help of the proposed FDC and MRSC, we can leverage the powerful feature representation capability of them in an effective and efficient way. We perform comprehensive experiments on two datasets, and the results show that our method achieves large performance gains and exceeds other state-of-the-art methods.

cs.CV↗

arXiv2024

Reliable Source Approximation: Source-Free Unsupervised Domain Adaptation for Vestibular Schwannoma MRI Segmentation

Source-Free Unsupervised Domain Adaptation (SFUDA) has recently become a focus in the medical image domain adaptation, as it only utilizes the source model and does not require annotated target data. However, current SFUDA approaches cannot tackle the complex segmentation task across different MRI sequences, such as the vestibular schwannoma segmentation. To address this problem, we proposed Reliable Source Approximation (RSA), which can generate source-like and structure-preserved images from the target domain for updating model parameters and adapting domain shifts. Specifically, RSA deploys a conditional diffusion model to generate multiple source-like images under the guidance of varying edges of one target image. An uncertainty estimation module is then introduced to predict and refine reliable pseudo labels of generated images, and the prediction consistency is developed to select the most reliable generations. Subsequently, all reliable generated images and their pseudo labels are utilized to update the model. Our RSA is validated on vestibular schwannoma segmentation across multi-modality MRI. The experimental results demonstrate that RSA consistently improves domain adaptation performance over other state-of-the-art SFUDA methods. Code is available at https://github.com/zenghy96/Reliable-Source-Approximation.

eess.IV↗

arXiv2024

Training-free image style alignment for self-adapting domain shift on handheld ultrasound devices

Handheld ultrasound devices face usage limitations due to user inexperience and cannot benefit from supervised deep learning without extensive expert annotations. Moreover, the models trained on standard ultrasound device data are constrained by training data distribution and perform poorly when directly applied to handheld device data. In this study, we propose the Training-free Image Style Alignment (TISA) framework to align the style of handheld device data to those of standard devices. The proposed TISA can directly infer handheld device images without extra training and is suited for clinical applications. We show that TISA performs better and more stably in medical detection and segmentation tasks for handheld device data. We further validate TISA as the clinical model for automatic measurements of spinal curvature and carotid intima-media thickness. The automatic measurements agree well with manual measurements made by human experts and the measurement errors remain within clinically acceptable ranges. We demonstrate the potential for TISA to facilitate automatic diagnosis on handheld ultrasound devices and expedite their eventual widespread use.

eess.IV↗

arXiv2024

Reliable Joint Segmentation of Retinal Edema Lesions in OCT Images

Focusing on the complicated pathological features, such as blurred boundaries, severe scale differences between symptoms, background noise interference, etc., in the task of retinal edema lesions joint segmentation from OCT images and enabling the segmentation results more reliable. In this paper, we propose a novel reliable multi-scale wavelet-enhanced transformer network, which can provide accurate segmentation results with reliability assessment. Specifically, aiming at improving the model's ability to learn the complex pathological features of retinal edema lesions in OCT images, we develop a novel segmentation backbone that integrates a wavelet-enhanced feature extractor network and a multi-scale transformer module of our newly designed. Meanwhile, to make the segmentation results more reliable, a novel uncertainty segmentation head based on the subjective logical evidential theory is introduced to generate the final segmentation results with a corresponding overall uncertainty evaluation score map. We conduct comprehensive experiments on the public database of AI-Challenge 2018 for retinal edema lesions segmentation, and the results show that our proposed method achieves better segmentation accuracy with a high degree of reliability as compared to other state-of-the-art segmentation approaches. The code will be released on: https://github.com/LooKing9218/ReliableRESeg.

eess.IV↗

arXiv2023

Reliable Federated Disentangling Network for Non-IID Domain Feature

Federated learning (FL), as an effective decentralized distributed learning approach, enables multiple institutions to jointly train a model without sharing their local data. However, the domain feature shift caused by different acquisition devices/clients substantially degrades the performance of the FL model. Furthermore, most existing FL approaches aim to improve accuracy without considering reliability (e.g., confidence or uncertainty). The predictions are thus unreliable when deployed in safety-critical applications. Therefore, aiming at improving the performance of FL in non-Domain feature issues while enabling the model more reliable. In this paper, we propose a novel reliable federated disentangling network, termed RFedDis, which utilizes feature disentangling to enable the ability to capture the global domain-invariant cross-client representation and preserve local client-specific feature learning. Meanwhile, to effectively integrate the decoupled features, an uncertainty-aware decision fusion is also introduced to guide the network for dynamically integrating the decoupled features at the evidence level, while producing a reliable prediction with an estimated uncertainty. To the best of our knowledge, our proposed RFedDis is the first work to develop an FL approach based on evidential uncertainty combined with feature disentangling, which enhances the performance and reliability of FL in non-IID domain features. Extensive experimental results show that our proposed RFedDis provides outstanding performance with a high degree of reliability as compared to other state-of-the-art FL approaches.

cs.CV↗

arXiv2023

Reliable Multimodality Eye Disease Screening via Mixture of Student's t Distributions

Multimodality eye disease screening is crucial in ophthalmology as it integrates information from diverse sources to complement their respective performances. However, the existing methods are weak in assessing the reliability of each unimodality, and directly fusing an unreliable modality may cause screening errors. To address this issue, we introduce a novel multimodality evidential fusion pipeline for eye disease screening, EyeMoSt, which provides a measure of confidence for unimodality and elegantly integrates the multimodality information from a multi-distribution fusion perspective. Specifically, our model estimates both local uncertainty for unimodality and global uncertainty for the fusion modality to produce reliable classification results. More importantly, the proposed mixture of Student's $t$ distributions adaptively integrates different modalities to endow the model with heavy-tailed properties, increasing robustness and reliability. Our experimental findings on both public and in-house datasets show that our model is more reliable than current methods. Additionally, EyeMost has the potential ability to serve as a data quality discriminator, enabling reliable decision-making for multimodality eye disease screening.

eess.IV↗

arXiv2023

Uncertainty-inspired Open Set Learning for Retinal Anomaly Identification

Failure to recognize samples from the classes unseen during training is a major limitation of artificial intelligence in the real-world implementation for recognition and classification of retinal anomalies. We established an uncertainty-inspired open-set (UIOS) model, which was trained with fundus images of 9 retinal conditions. Besides assessing the probability of each category, UIOS also calculated an uncertainty score to express its confidence. Our UIOS model with thresholding strategy achieved an F1 score of 99.55%, 97.01% and 91.91% for the internal testing set, external target categories (TC)-JSIEC dataset and TC-unseen testing set, respectively, compared to the F1 score of 92.20%, 80.69% and 64.74% by the standard AI model. Furthermore, UIOS correctly predicted high uncertainty scores, which would prompt the need for a manual check in the datasets of non-target categories retinal diseases, low-quality fundus images, and non-fundus images. UIOS provides a robust method for real-world screening of retinal anomalies.

cs.LG↗