arXiv subjects

Yefeng Zheng

Publications and source records attributed to Yefeng Zheng.

At least 91 records · Page 5Linked to original sources

arXiv2024

Unlocking the Potential of Weakly Labeled Data: A Co-Evolutionary Learning Framework for Abnormality Detection and Report Generation

Anatomical abnormality detection and report generation of chest X-ray (CXR) are two essential tasks in clinical practice. The former aims at localizing and characterizing cardiopulmonary radiological findings in CXRs, while the latter summarizes the findings in a detailed report for further diagnosis and treatment. Existing methods often focused on either task separately, ignoring their correlation. This work proposes a co-evolutionary abnormality detection and report generation (CoE-DG) framework. The framework utilizes both fully labeled (with bounding box annotations and clinical reports) and weakly labeled (with reports only) data to achieve mutual promotion between the abnormality detection and report generation tasks. Specifically, we introduce a bi-directional information interaction strategy with generator-guided information propagation (GIP) and detector-guided information propagation (DIP). For semi-supervised abnormality detection, GIP takes the informative feature extracted by the generator as an auxiliary input to the detector and uses the generator's prediction to refine the detector's pseudo labels. We further propose an intra-image-modal self-adaptive non-maximum suppression module (SA-NMS). This module dynamically rectifies pseudo detection labels generated by the teacher detection model with high-confidence predictions by the student.Inversely, for report generation, DIP takes the abnormalities' categories and locations predicted by the detector as input and guidance for the generator to improve the generated reports.

cs.CV↗

arXiv2024

GSCo: Towards Generalizable AI in Medicine via Generalist-Specialist Collaboration

Generalist foundation models (GFMs) are renowned for their exceptional capability and flexibility in effectively generalizing across diverse tasks and modalities. In the field of medicine, while GFMs exhibit superior generalizability based on their extensive intrinsic knowledge as well as proficiency in instruction following and in-context learning, specialist models excel in precision due to their domain knowledge. In this work, for the first time, we explore the synergy between the GFM and specialist models, to enable precise medical image analysis on a broader scope. Specifically, we propose a cooperative framework, Generalist-Specialist Collaboration (GSCo), which consists of two stages, namely the construction of GFM and specialists, and collaborative inference on downstream tasks. In the construction stage, we develop MedDr, the largest open-source GFM tailored for medicine, showcasing exceptional instruction-following and in-context learning capabilities. Meanwhile, a series of lightweight specialists are crafted for downstream tasks with low computational cost. In the collaborative inference stage, we introduce two cooperative mechanisms, Mixture-of-Expert Diagnosis and Retrieval-Augmented Diagnosis, to harvest the generalist's in-context learning abilities alongside the specialists' domain expertise. For a comprehensive evaluation, we curate a large-scale benchmark featuring 28 datasets and about 250,000 images. Extensive results demonstrate that MedDr consistently outperforms state-of-the-art GFMs on downstream datasets. Furthermore, GSCo exceeds both GFMs and specialists across all out-of-domain disease diagnosis datasets. These findings indicate a significant paradigm shift in the application of GFMs, transitioning from separate models for specific tasks to a collaborative approach between GFMs and specialists, thereby advancing the frontiers of generalizable AI in medicine.

cs.CV↗

arXiv2024

LLM-ESR: Large Language Models Enhancement for Long-tailed Sequential Recommendation

Sequential recommender systems (SRS) aim to predict users' subsequent choices based on their historical interactions and have found applications in diverse fields such as e-commerce and social media. However, in real-world systems, most users interact with only a handful of items, while the majority of items are seldom consumed. These two issues, known as the long-tail user and long-tail item challenges, often pose difficulties for existing SRS. These challenges can adversely affect user experience and seller benefits, making them crucial to address. Though a few works have addressed the challenges, they still struggle with the seesaw or noisy issues due to the intrinsic scarcity of interactions. The advancements in large language models (LLMs) present a promising solution to these problems from a semantic perspective. As one of the pioneers in this field, we propose the Large Language Models Enhancement framework for Sequential Recommendation (LLM-ESR). This framework utilizes semantic embeddings derived from LLMs to enhance SRS without adding extra inference load from LLMs. To address the long-tail item challenge, we design a dual-view modeling framework that combines semantics from LLMs and collaborative signals from conventional SRS. For the long-tail user challenge, we propose a retrieval augmented self-distillation method to enhance user preference representation using more informative interactions from similar users. To verify the effectiveness and versatility of our proposed enhancement framework, we conduct extensive experiments on three real-world datasets using three popular SRS models. The results show that our method surpasses existing baselines consistently, and benefits long-tail users and items especially. The implementation code is available at https://github.com/Applied-Machine-Learning-Lab/LLM-ESR.

cs.IR↗

arXiv2024

Large Language Models for Generative Information Extraction: A Survey

Information extraction (IE) aims to extract structural knowledge from plain natural language texts. Recently, generative Large Language Models (LLMs) have demonstrated remarkable capabilities in text understanding and generation. As a result, numerous works have been proposed to integrate LLMs for IE tasks based on a generative paradigm. To conduct a comprehensive systematic review and exploration of LLM efforts for IE tasks, in this study, we survey the most recent advancements in this field. We first present an extensive overview by categorizing these works in terms of various IE subtasks and techniques, and then we empirically analyze the most advanced methods and discover the emerging trend of IE tasks with LLMs. Based on a thorough review conducted, we identify several insights in technique and promising research directions that deserve further exploration in future studies. We maintain a public repository and consistently update related works and resources on GitHub (\href{https://github.com/quqxui/Awesome-LLM4IE-Papers}{LLM4IE repository})

cs.CL↗

arXiv2024

Mitigating Hallucinations of Large Language Models in Medical Information Extraction via Contrastive Decoding

The impressive capabilities of large language models (LLMs) have attracted extensive interests of applying LLMs to medical field. However, the complex nature of clinical environments presents significant hallucination challenges for LLMs, hindering their widespread adoption. In this paper, we address these hallucination issues in the context of Medical Information Extraction (MIE) tasks by introducing ALternate Contrastive Decoding (ALCD). We begin by redefining MIE tasks as an identify-and-classify process. We then separate the identification and classification functions of LLMs by selectively masking the optimization of tokens during fine-tuning. During the inference stage, we alternately contrast output distributions derived from sub-task models. This approach aims to selectively enhance the identification and classification capabilities while minimizing the influence of other inherent abilities in LLMs. Additionally, we propose an alternate adaptive constraint strategy to more effectively adjust the scale and scope of contrastive tokens. Through comprehensive experiments on two different backbones and six diverse medical information extraction tasks, ALCD demonstrates significant improvements in resolving hallucination issues compared to conventional decoding methods.

cs.CL↗

arXiv2024

PASS:Test-Time Prompting to Adapt Styles and Semantic Shapes in Medical Image Segmentation

Test-time adaptation (TTA) has emerged as a promising paradigm to handle the domain shifts at test time for medical images from different institutions without using extra training data. However, existing TTA solutions for segmentation tasks suffer from (1) dependency on modifying the source training stage and access to source priors or (2) lack of emphasis on shape-related semantic knowledge that is crucial for segmentation tasks.Recent research on visual prompt learning achieves source-relaxed adaptation by extended parameter space but still neglects the full utilization of semantic features, thus motivating our work on knowledge-enriched deep prompt learning. Beyond the general concern of image style shifts, we reveal that shape variability is another crucial factor causing the performance drop. To address this issue, we propose a TTA framework called PASS (Prompting to Adapt Styles and Semantic shapes), which jointly learns two types of prompts: the input-space prompt to reformulate the style of the test image to fit into the pretrained model and the semantic-aware prompts to bridge high-level shape discrepancy across domains. Instead of naively imposing a fixed prompt, we introduce an input decorator to generate the self-regulating visual prompt conditioned on the input data. To retrieve the knowledge representations and customize target-specific shape prompts for each test sample, we propose a cross-attention prompt modulator, which performs interaction between target representations and an enriched shape prompt bank. Extensive experiments demonstrate the superior performance of PASS over state-of-the-art methods on multiple medical image segmentation datasets. The code is available at https://github.com/EndoluminalSurgicalVision-IMR/PASS.

cs.CV↗

arXiv2024

Editing Factual Knowledge and Explanatory Ability of Medical Large Language Models

Model editing aims to precisely alter the behaviors of large language models (LLMs) in relation to specific knowledge, while leaving unrelated knowledge intact. This approach has proven effective in addressing issues of hallucination and outdated information in LLMs. However, the potential of using model editing to modify knowledge in the medical field remains largely unexplored, even though resolving hallucination is a pressing need in this area. Our observations indicate that current methods face significant challenges in dealing with specialized and complex knowledge in medical domain. Therefore, we propose MedLaSA, a novel Layer-wise Scalable Adapter strategy for medical model editing. MedLaSA harnesses the strengths of both adding extra parameters and locate-then-edit methods for medical model editing. We utilize causal tracing to identify the association of knowledge in neurons across different layers, and generate a corresponding scale set from the association value for each piece of knowledge. Subsequently, we incorporate scalable adapters into the dense layers of LLMs. These adapters are assigned scaling values based on the corresponding specific knowledge, which allows for the adjustment of the adapter's weight and rank. The more similar the content, the more consistent the scale between them. This ensures precise editing of semantically identical knowledge while avoiding impact on unrelated knowledge. To evaluate the editing impact on the behaviours of LLMs, we propose two model editing studies for medical domain: (1) editing factual knowledge for medical specialization and (2) editing the explanatory ability for complex knowledge. We build two novel medical benchmarking datasets and introduce a series of challenging and comprehensive metrics. Extensive experiments on medical LLMs demonstrate the editing efficiency of MedLaSA, without affecting unrelated knowledge.

cs.CL↗

arXiv2024

RSF-Conv: Rotation-and-Scale Equivariant Fourier Parameterized Convolution for Retinal Vessel Segmentation

Retinal vessel segmentation is of great clinical significance for the diagnosis of many eye-related diseases, but it is still a formidable challenge due to the intricate vascular morphology. With the skillful characterization of the translation symmetry existing in retinal vessels, convolutional neural networks (CNNs) have achieved great success in retinal vessel segmentation. However, the rotation-and-scale symmetry, as a more widespread image prior in retinal vessels, fails to be characterized by CNNs. Therefore, we propose a rotation-and-scale equivariant Fourier parameterized convolution (RSF-Conv) specifically for retinal vessel segmentation, and provide the corresponding equivariance analysis. As a general module, RSF-Conv can be integrated into existing networks in a plug-and-play manner while significantly reducing the number of parameters. For instance, we replace the traditional convolution filters in U-Net and Iter-Net with RSF-Convs, and faithfully conduct comprehensive experiments. RSF-Conv+U-Net and RSF-Conv+Iter-Net not only have slight advantages under in-domain evaluation, but more importantly, outperform all comparison methods by a significant margin under out-of-domain evaluation. It indicates the remarkable generalization of RSF-Conv, which holds greater practical clinical significance for the prevalent cross-device and cross-hospital challenges in clinical practice. To comprehensively demonstrate the effectiveness of RSF-Conv, we also apply RSF-Conv+U-Net and RSF-Conv+Iter-Net to retinal artery/vein classification and achieve promising performance as well, indicating its clinical application potential.

eess.IV↗

arXiv2024

Learning Spectral-Decomposed Tokens for Domain Generalized Semantic Segmentation

The rapid development of Vision Foundation Model (VFM) brings inherent out-domain generalization for a variety of down-stream tasks. Among them, domain generalized semantic segmentation (DGSS) holds unique challenges as the cross-domain images share common pixel-wise content information but vary greatly in terms of the style. In this paper, we present a novel Spectral-dEcomposed Token (SET) learning framework to advance the frontier. Delving into further than existing fine-tuning token & frozen backbone paradigm, the proposed SET especially focuses on the way learning style-invariant features from these learnable tokens. Particularly, the frozen VFM features are first decomposed into the phase and amplitude components in the frequency space, which mainly contain the information of content and style, respectively, and then separately processed by learnable tokens for task-specific information extraction. After the decomposition, style variation primarily impacts the token-based feature enhancement within the amplitude branch. To address this issue, we further develop an attention optimization method to bridge the gap between style-affected representation and static tokens during inference. Extensive cross-domain experiments show its state-of-the-art performance.

cs.CV↗

arXiv2024

A Survey of Large Language Models in Medicine: Progress, Application, and Challenge

Large language models (LLMs), such as ChatGPT, have received substantial attention due to their capabilities for understanding and generating human language. While there has been a burgeoning trend in research focusing on the employment of LLMs in supporting different medical tasks (e.g., enhancing clinical diagnostics and providing medical education), a review of these efforts, particularly their development, practical applications, and outcomes in medicine, remains scarce. Therefore, this review aims to provide a detailed overview of the development and deployment of LLMs in medicine, including the challenges and opportunities they face. In terms of development, we provide a detailed introduction to the principles of existing medical LLMs, including their basic model structures, number of parameters, and sources and scales of data used for model development. It serves as a guide for practitioners in developing medical LLMs tailored to their specific needs. In terms of deployment, we offer a comparison of the performance of different LLMs across various medical tasks, and further compare them with state-of-the-art lightweight models, aiming to provide an understanding of the advantages and limitations of LLMs in medicine. Overall, in this review, we address the following questions: 1) What are the practices for developing medical LLMs 2) How to measure the medical task performance of LLMs in a medical setting? 3) How have medical LLMs been employed in real-world practice? 4) What challenges arise from the use of medical LLMs? and 5) How to more effectively develop and deploy medical LLMs? By answering these questions, this review aims to provide insights into the opportunities for LLMs in medicine and serve as a practical resource. We also maintain a regularly updated list of practical guides on medical LLMs at https://github.com/AI-in-Health/MedLLMsPracticalGuide

cs.CL↗

arXiv2024

TAKT: Target-Aware Knowledge Transfer for Whole Slide Image Classification

Transferring knowledge from a source domain to a target domain can be crucial for whole slide image classification, since the number of samples in a dataset is often limited due to high annotation costs. However, domain shift and task discrepancy between datasets can hinder effective knowledge transfer. In this paper, we propose a Target-Aware Knowledge Transfer framework, employing a teacher-student paradigm. Our framework enables the teacher model to learn common knowledge from the source and target domains by actively incorporating unlabelled target images into the training of the teacher model. The teacher bag features are subsequently adapted to supervise the training of the student model on the target domain. Despite incorporating the target features during training, the teacher model tends to overlook them under the inherent domain shift and task discrepancy. To alleviate this, we introduce a target-aware feature alignment module to establish a transferable latent relationship between the source and target features by solving the optimal transport problem. Experimental results show that models employing knowledge transfer outperform those trained from scratch, and our method achieves state-of-the-art performance among other knowledge transfer methods on various datasets, including TCGA-RCC, TCGA-NSCLC, and Camelyon16.

cs.CV↗

arXiv2024

CTNeRF: Cross-Time Transformer for Dynamic Neural Radiance Field from Monocular Video

The goal of our work is to generate high-quality novel views from monocular videos of complex and dynamic scenes. Prior methods, such as DynamicNeRF, have shown impressive performance by leveraging time-varying dynamic radiation fields. However, these methods have limitations when it comes to accurately modeling the motion of complex objects, which can lead to inaccurate and blurry renderings of details. To address this limitation, we propose a novel approach that builds upon a recent generalization NeRF, which aggregates nearby views onto new viewpoints. However, such methods are typically only effective for static scenes. To overcome this challenge, we introduce a module that operates in both the time and frequency domains to aggregate the features of object motion. This allows us to learn the relationship between frames and generate higher-quality images. Our experiments demonstrate significant improvements over state-of-the-art methods on dynamic scene datasets. Specifically, our approach outperforms existing methods in terms of both the accuracy and visual quality of the synthesized views. Our code is available on https://github.com/xingy038/CTNeRF.

cs.CV↗

arXiv2024

QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.

eess.IV↗

arXiv2024

MoME: Mixture of Multimodal Experts for Cancer Survival Prediction

Survival analysis, as a challenging task, requires integrating Whole Slide Images (WSIs) and genomic data for comprehensive decision-making. There are two main challenges in this task: significant heterogeneity and complex inter- and intra-modal interactions between the two modalities. Previous approaches utilize co-attention methods, which fuse features from both modalities only once after separate encoding. However, these approaches are insufficient for modeling the complex task due to the heterogeneous nature between the modalities. To address these issues, we propose a Biased Progressive Encoding (BPE) paradigm, performing encoding and fusion simultaneously. This paradigm uses one modality as a reference when encoding the other. It enables deep fusion of the modalities through multiple alternating iterations, progressively reducing the cross-modal disparities and facilitating complementary interactions. Besides modality heterogeneity, survival analysis involves various biomarkers from WSIs, genomics, and their combinations. The critical biomarkers may exist in different modalities under individual variations, necessitating flexible adaptation of the models to specific scenarios. Therefore, we further propose a Mixture of Multimodal Experts (MoME) layer to dynamically selects tailored experts in each stage of the BPE paradigm. Experts incorporate reference information from another modality to varying degrees, enabling a balanced or biased focus on different modalities during the encoding process. Extensive experimental results demonstrate the superior performance of our method on various datasets, including TCGA-BLCA, TCGA-UCEC and TCGA-LUAD. Codes are available at https://github.com/BearCleverProud/MoME.

eess.IV↗

arXiv2024

UniHead: Unifying Multi-Perception for Detection Heads

The detection head constitutes a pivotal component within object detectors, tasked with executing both classification and localization functions. Regrettably, the commonly used parallel head often lacks omni perceptual capabilities, such as deformation perception, global perception and cross-task perception. Despite numerous methods attempting to enhance these abilities from a single aspect, achieving a comprehensive and unified solution remains a significant challenge. In response to this challenge, we develop an innovative detection head, termed UniHead, to unify three perceptual abilities simultaneously. More precisely, our approach (1) introduces deformation perception, enabling the model to adaptively sample object features; (2) proposes a Dual-axial Aggregation Transformer (DAT) to adeptly model long-range dependencies, thereby achieving global perception; and (3) devises a Cross-task Interaction Transformer (CIT) that facilitates interaction between the classification and localization branches, thus aligning the two tasks. As a plug-and-play method, the proposed UniHead can be conveniently integrated with existing detectors. Extensive experiments on the COCO dataset demonstrate that our UniHead can bring significant improvements to many detectors. For instance, the UniHead can obtain +2.7 AP gains in RetinaNet, +2.9 AP gains in FreeAnchor, and +2.1 AP gains in GFL. The code is available at https://github.com/zht8506/UniHead.

cs.CV↗

arXiv2024

Prototype Correlation Matching and Class-Relation Reasoning for Few-Shot Medical Image Segmentation

Few-shot medical image segmentation has achieved great progress in improving accuracy and efficiency of medical analysis in the biomedical imaging field. However, most existing methods cannot explore inter-class relations among base and novel medical classes to reason unseen novel classes. Moreover, the same kind of medical class has large intra-class variations brought by diverse appearances, shapes and scales, thus causing ambiguous visual characterization to degrade generalization performance of these existing methods on unseen novel classes. To address the above challenges, in this paper, we propose a \underline{\textbf{P}}rototype correlation \underline{\textbf{M}}atching and \underline{\textbf{C}}lass-relation \underline{\textbf{R}}easoning (i.e., \textbf{PMCR}) model. The proposed model can effectively mitigate false pixel correlation matches caused by large intra-class variations while reasoning inter-class relations among different medical classes. Specifically, in order to address false pixel correlation match brought by large intra-class variations, we propose a prototype correlation matching module to mine representative prototypes that can characterize diverse visual information of different appearances well. We aim to explore prototype-level rather than pixel-level correlation matching between support and query features via optimal transport algorithm to tackle false matches caused by intra-class variations. Meanwhile, in order to explore inter-class relations, we design a class-relation reasoning module to segment unseen novel medical objects via reasoning inter-class relations between base and novel classes. Such inter-class relations can be well propagated to semantic encoding of local query features to improve few-shot segmentation performance. Quantitative comparisons illustrates the large performance improvement of our model over other baseline methods.

cs.CV↗

arXiv2024

When MOE Meets LLMs: Parameter Efficient Fine-tuning for Multi-task Medical Applications

The recent surge in Large Language Models (LLMs) has garnered significant attention across numerous fields. Fine-tuning is often required to fit general LLMs for a specific domain, like the web-based healthcare system. However, two problems arise during fine-tuning LLMs for medical applications. One is the task variety problem, which involves distinct tasks in real-world medical scenarios. The variety often leads to sub-optimal fine-tuning for data imbalance and seesaw problems. Besides, the large amount of parameters in LLMs leads to huge time and computation consumption by fine-tuning. To address these two problems, we propose a novel parameter efficient fine-tuning framework for multi-task medical applications, dubbed as MOELoRA. The designed framework aims to absorb both the benefits of mixture-of-expert (MOE) for multi-task learning and low-rank adaptation (LoRA) for parameter efficient fine-tuning. For unifying MOE and LoRA, we devise multiple experts as the trainable parameters, where each expert consists of a pair of low-rank matrices to retain the small size of trainable parameters. Then, a task-motivated gate function for all MOELoRA layers is proposed, which can control the contributions of each expert and produce distinct parameters for various tasks. We conduct experiments on a multi-task medical dataset, indicating MOELoRA outperforms the existing parameter efficient fine-tuning methods. The code is available online.

cs.CL↗

arXiv2024

Wearable-based behaviour interpolation for semi-supervised human activity recognition

While traditional feature engineering for Human Activity Recognition (HAR) involves a trial-anderror process, deep learning has emerged as a preferred method for high-level representations of sensor-based human activities. However, most deep learning-based HAR requires a large amount of labelled data and extracting HAR features from unlabelled data for effective deep learning training remains challenging. We, therefore, introduce a deep semi-supervised HAR approach, MixHAR, which concurrently uses labelled and unlabelled activities. Our MixHAR employs a linear interpolation mechanism to blend labelled and unlabelled activities while addressing both inter- and intra-activity variability. A unique challenge identified is the activityintrusion problem during mixing, for which we propose a mixing calibration mechanism to mitigate it in the feature embedding space. Additionally, we rigorously explored and evaluated the five conventional/popular deep semi-supervised technologies on HAR, acting as the benchmark of deep semi-supervised HAR. Our results demonstrate that MixHAR significantly improves performance, underscoring the potential of deep semi-supervised techniques in HAR.

cs.CV↗