arXiv subjects

Yanfeng Wang

Publications and source records attributed to Yanfeng Wang.

At least 145 records · Page 8Linked to original sources

arXiv2024

RaTEScore: A Metric for Radiology Report Generation

This paper introduces a novel, entity-aware metric, termed as Radiological Report (Text) Evaluation (RaTEScore), to assess the quality of medical reports generated by AI models. RaTEScore emphasizes crucial medical entities such as diagnostic outcomes and anatomical details, and is robust against complex medical synonyms and sensitive to negation expressions. Technically, we developed a comprehensive medical NER dataset, RaTE-NER, and trained an NER model specifically for this purpose. This model enables the decomposition of complex radiological reports into constituent medical entities. The metric itself is derived by comparing the similarity of entity embeddings, obtained from a language model, based on their types and relevance to clinical significance. Our evaluations demonstrate that RaTEScore aligns more closely with human preference than existing metrics, validated both on established public benchmarks and our newly proposed RaTE-Eval benchmark.

cs.CL↗

arXiv2024

TAIA: Large Language Models are Out-of-Distribution Data Learners

Fine-tuning on task-specific question-answer pairs is a predominant method for enhancing the performance of instruction-tuned large language models (LLMs) on downstream tasks. However, in certain specialized domains, such as healthcare or harmless content generation, it is nearly impossible to obtain a large volume of high-quality data that matches the downstream distribution. To improve the performance of LLMs in data-scarce domains with domain-mismatched data, we re-evaluated the Transformer architecture and discovered that not all parameter updates during fine-tuning contribute positively to downstream performance. Our analysis reveals that within the self-attention and feed-forward networks, only the fine-tuned attention parameters are particularly beneficial when the training set's distribution does not fully align with the test set. Based on this insight, we propose an effective inference-time intervention method: Training All parameters but Inferring with only Attention (\trainallInfAttn). We empirically validate \trainallInfAttn using two general instruction-tuning datasets and evaluate it on seven downstream tasks involving math, reasoning, and knowledge understanding across LLMs of different parameter sizes and fine-tuning techniques. Our comprehensive experiments demonstrate that \trainallInfAttn achieves superior improvements compared to both the fully fine-tuned model and the base model in most scenarios, with significant performance gains. The high tolerance of \trainallInfAttn to data mismatches makes it resistant to jailbreaking tuning and enhances specialized tasks using general data. Code is available in \url{https://github.com/pixas/TAIA_LLM}.

cs.CL↗

arXiv2024

MedCare: Advancing Medical LLMs through Decoupling Clinical Alignment and Knowledge Aggregation

Large language models (LLMs) have shown substantial progress in natural language understanding and generation, proving valuable especially in the medical field. Despite advancements, challenges persist due to the complexity and diversity inherent in medical tasks, which can be categorized as knowledge-intensive tasks and alignment-required tasks. Previous approaches either ignore the latter task or focus on a minority of tasks and hence lose generalization. To address these drawbacks, we propose a progressive fine-tuning pipeline. This pipeline employs a Knowledge Aggregator and a Noise aggregator to encode diverse knowledge in the first stage and filter out detrimental information. In the second stage, we drop the Noise Aggregator to avoid the interference of suboptimal representation and leverage an additional alignment module optimized towards an orthogonal direction to the knowledge space to mitigate knowledge forgetting. Based on this two-stage paradigm, we proposed a Medical LLM through decoupling Clinical Alignment and Knowledge Aggregation (MedCare), which is designed to achieve state-of-the-art (SOTA) performance on over 20 medical tasks, as well as SOTA results on specific medical alignment tasks. Various model sizes of MedCare (1.8B, 7B, 14B) all demonstrate significant improvements over existing models with similar model sizes.

cs.CL↗

arXiv2024

KnowledgeSG: Privacy-Preserving Synthetic Text Generation with Knowledge Distillation from Server

The success of large language models (LLMs) facilitate many parties to fine-tune LLMs on their own private data. However, this practice raises privacy concerns due to the memorization of LLMs. Existing solutions, such as utilizing synthetic data for substitution, struggle to simultaneously improve performance and preserve privacy. They either rely on a local model for generation, resulting in a performance decline, or take advantage of APIs, directly exposing the data to API servers. To address this issue, we propose KnowledgeSG, a novel client-server framework which enhances synthetic data quality and improves model performance while ensuring privacy. We achieve this by learning local knowledge from the private data with differential privacy (DP) and distilling professional knowledge from the server. Additionally, inspired by federated learning, we transmit models rather than data between the client and server to prevent privacy leakage. Extensive experiments in medical and financial domains demonstrate the effectiveness of KnowledgeSG. Our code is now publicly available at https://github.com/wwh0411/KnowledgeSG.

cs.CR↗

arXiv2024

Few-Shot Anomaly Detection via Category-Agnostic Registration Learning

Most existing anomaly detection (AD) methods require a dedicated model for each category. Such a paradigm, despite its promising results, is computationally expensive and inefficient, thereby failing to meet the requirements for realworld applications. Inspired by how humans detect anomalies, by comparing a query image to known normal ones, this article proposes a novel few-shot AD (FSAD) framework. Using a training set of normal images from various categories, registration, aiming to align normal images of the same categories, is leveraged as the proxy task for self-supervised category-agnostic representation learning. At test time, an image and its corresponding support set, consisting of a few normal images from the same category, are supplied, and anomalies are identified by comparing the registered features of the test image to its corresponding support image features. Such a setup enables the model to generalize to novel test categories. It is, to our best knowledge, the first FSAD method that requires no model fine-tuning for novel categories: enabling a single model to be applied to all categories. Extensive experiments demonstrate the effectiveness of the proposed method. Particularly, it improves the current state-of-the-art (SOTA) for FSAD by 11.3% and 8.3% on the MVTec and MPDD benchmarks, respectively. The source code is available at https://github.com/Haoyan-Guan/CAReg.

cs.CV↗

arXiv2024

CliMedBench: A Large-Scale Chinese Benchmark for Evaluating Medical Large Language Models in Clinical Scenarios

With the proliferation of Large Language Models (LLMs) in diverse domains, there is a particular need for unified evaluation standards in clinical medical scenarios, where models need to be examined very thoroughly. We present CliMedBench, a comprehensive benchmark with 14 expert-guided core clinical scenarios specifically designed to assess the medical ability of LLMs across 7 pivot dimensions. It comprises 33,735 questions derived from real-world medical reports of top-tier tertiary hospitals and authentic examination exercises. The reliability of this benchmark has been confirmed in several ways. Subsequent experiments with existing LLMs have led to the following findings: (i) Chinese medical LLMs underperform on this benchmark, especially where medical reasoning and factual consistency are vital, underscoring the need for advances in clinical knowledge and diagnostic accuracy. (ii) Several general-domain LLMs demonstrate substantial potential in medical clinics, while the limited input capacity of many medical LLMs hinders their practical use. These findings reveal both the strengths and limitations of LLMs in clinical scenarios and offer critical insights for medical research.

cs.CL↗

arXiv2024

LoRKD: Low-Rank Knowledge Decomposition for Medical Foundation Models

The widespread adoption of large-scale pre-training techniques has significantly advanced the development of medical foundation models, enabling them to serve as versatile tools across a broad range of medical tasks. However, despite their strong generalization capabilities, medical foundation models pre-trained on large-scale datasets tend to suffer from domain gaps between heterogeneous data, leading to suboptimal performance on specific tasks compared to specialist models, as evidenced by previous studies. In this paper, we explore a new perspective called "Knowledge Decomposition" to improve the performance on specific medical tasks, which deconstructs the foundation model into multiple lightweight expert models, each dedicated to a particular anatomical region, with the aim of enhancing specialization and simultaneously reducing resource consumption. To accomplish the above objective, we propose a novel framework named Low-Rank Knowledge Decomposition (LoRKD), which explicitly separates gradients from different tasks by incorporating low-rank expert modules and efficient knowledge separation convolution. The low-rank expert modules resolve gradient conflicts between heterogeneous data from different anatomical regions, providing strong specialization at lower costs. The efficient knowledge separation convolution significantly improves algorithm efficiency by achieving knowledge separation within a single forward propagation. Extensive experimental results on segmentation and classification tasks demonstrate that our decomposed models not only achieve state-of-the-art performance but also exhibit superior transferability on downstream tasks, even surpassing the original foundation models in task-specific evaluations. The code is available at here.

cs.CV↗

arXiv2024

Knowledge-enhanced Visual-Language Pretraining for Computational Pathology

In this paper, we consider the problem of visual representation learning for computational pathology, by exploiting large-scale image-text pairs gathered from public resources, along with the domain-specific knowledge in pathology. Specifically, we make the following contributions: (i) We curate a pathology knowledge tree that consists of 50,470 informative attributes for 4,718 diseases requiring pathology diagnosis from 32 human tissues. To our knowledge, this is the first comprehensive structured pathology knowledge base; (ii) We develop a knowledge-enhanced visual-language pretraining approach, where we first project pathology-specific knowledge into latent embedding space via a language model, and use it to guide the visual representation learning; (iii) We conduct thorough experiments to validate the effectiveness of our proposed components, demonstrating significant performance improvement on various downstream tasks, including cross-modal retrieval, zero-shot classification on pathology patches, and zero-shot tumor subtyping on whole slide images (WSIs).

cs.CV↗

arXiv2024

Leveraging Unstructured Text Data for Federated Instruction Tuning of Large Language Models

Federated instruction tuning enables multiple clients to collaboratively fine-tune a shared large language model (LLM) that can follow humans' instructions without directly sharing raw data. However, existing literature impractically requires that all the clients readily hold instruction-tuning data (i.e., structured instruction-response pairs), which necessitates massive human annotations since clients' data is usually unstructured text instead. Addressing this, we propose a novel and flexible framework FedIT-U2S, which can automatically transform unstructured corpus into structured data for federated instruction tuning. FedIT-U2S consists two key steps: (1) few-shot instruction-tuning data generation, where each unstructured data piece together with several examples is combined to prompt an LLM in generating an instruction-response pair. To further enhance the flexibility, a retrieval-based example selection technique is proposed, where the examples are automatically selected based on the relatedness between the client's data piece and example pool, bypassing the need of determining examples in advance. (2) A typical federated instruction tuning process based on the generated data. Overall, FedIT-U2S can be applied to diverse scenarios as long as the client holds valuable text corpus, broadening the application scope of federated instruction tuning. We conduct a series of experiments on three domains (medicine, knowledge, and math), showing that our proposed FedIT-U2S can consistently and significantly brings improvement over the base LLM.

cs.CL↗

arXiv2024

PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering

Medical Visual Question Answering (MedVQA) presents a significant opportunity to enhance diagnostic accuracy and healthcare delivery by leveraging artificial intelligence to interpret and answer questions based on medical images. In this study, we reframe the problem of MedVQA as a generation task that naturally follows the human-machine interaction and propose a generative-based model for medical visual understanding by aligning visual information from a pre-trained vision encoder with a large language model. We establish a scalable pipeline to construct a large-scale medical visual question-answering dataset, named PMC-VQA, which contains 227k VQA pairs of 149k images that cover various modalities or diseases. We train the proposed model on PMC-VQA and then fine-tune it on multiple public benchmarks, e.g., VQA-RAD, SLAKE, and Image-Clef-2019, significantly outperforming existing MedVQA models in generating relevant, accurate free-form answers. In addition, we propose a test set that has undergone manual verification, which is significantly more challenging, serving to better monitor the development of generative MedVQA methods. To facilitate comprehensive evaluation and comparison, we have maintained a leaderboard at https://paperswithcode.com/paper/pmc-vqa-visual-instruction-tuning-for-medical, offering a centralized resource for tracking progress and benchmarking state-of-the-art approaches. The PMC-VQA dataset emerges as a vital resource for the field of research, and the MedVInT presents a significant breakthrough in the area of MedVQA.

cs.CV↗

arXiv2024

Towards Evaluating and Building Versatile Large Language Models for Medicine

In this study, we present MedS-Bench, a comprehensive benchmark designed to evaluate the performance of large language models (LLMs) in clinical contexts. Unlike existing benchmarks that focus on multiple-choice question answering, MedS-Bench spans 11 high-level clinical tasks, including clinical report summarization, treatment recommendations, diagnosis, named entity recognition, and medical concept explanation, among others. We evaluated six leading LLMs, e.g., MEDITRON, Mistral, InternLM 2, Llama 3, GPT-4, and Claude-3.5 using few-shot prompting, and found that even the most sophisticated models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 13.5 million samples across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models across nearly all clinical tasks. To promote further advancements in the application of LLMs to clinical challenges, we have made the MedS-Ins dataset fully accessible and invite the research community to contribute to its expansion.Additionally, we have launched a dynamic leaderboard for MedS-Bench, which we plan to regularly update the test set to track progress and enhance the adaptation of general LLMs to the medical domain. Leaderboard: https://henrychur.github.io/MedS-Bench/. Github: https://github.com/MAGIC-AI4Med/MedS-Ins.

cs.CL↗

arXiv2024

Self-supervised Anomaly Detection Pretraining Enhances Long-tail ECG Diagnosis

Current computer-aided ECG diagnostic systems struggle with the underdetection of rare but critical cardiac anomalies due to the imbalanced nature of ECG datasets. This study introduces a novel approach using self-supervised anomaly detection pretraining to address this limitation. The anomaly detection model is specifically designed to detect and localize subtle deviations from normal cardiac patterns, capturing the nuanced details essential for accurate ECG interpretation. Validated on an extensive dataset of over one million ECG records from clinical practice, characterized by a long-tail distribution across 116 distinct categories, the anomaly detection-pretrained ECG diagnostic model has demonstrated a significant improvement in overall accuracy. Notably, our approach yielded a 94.7% AUROC, 92.2% sensitivity, and 92.5\% specificity for rare ECG types, significantly outperforming traditional methods and narrowing the performance gap with common ECG types. The integration of anomaly detection pretraining into ECG analysis represents a substantial contribution to the field, addressing the long-standing challenge of long-tail data distributions in clinical diagnostics. Furthermore, prospective validation in real-world clinical settings revealed that our AI-driven approach enhances diagnostic efficiency, precision, and completeness by 32%, 6.7%, and 11.8% respectively, when compared to standard practices. This advancement marks a pivotal step forward in the integration of AI within clinical cardiology, with particularly profound implications for emergency care, where rapid and accurate ECG interpretation is crucial. The contributions of this study not only push the boundaries of current ECG diagnostic capabilities but also lay the groundwork for more reliable and accessible cardiovascular care.

cs.CV↗

arXiv2024

HSDreport: Heart Sound Diagnosis with Echocardiography Reports

Heart sound auscultation holds significant importance in the diagnosis of congenital heart disease. However, existing methods for Heart Sound Diagnosis (HSD) tasks are predominantly limited to a few fixed categories, framing the HSD task as a rigid classification problem that does not fully align with medical practice and offers only limited information to physicians. Besides, such methods do not utilize echocardiography reports, the gold standard in the diagnosis of related diseases. To tackle this challenge, we introduce HSDreport, a new benchmark for HSD, which mandates the direct utilization of heart sounds obtained from auscultation to predict echocardiography reports. This benchmark aims to merge the convenience of auscultation with the comprehensive nature of echocardiography reports. First, we collect a new dataset for this benchmark, comprising 2,275 heart sound samples along with their corresponding reports. Subsequently, we develop a knowledge-aware query-based transformer to handle this task. The intent is to leverage the capabilities of medically pre-trained models and the internal knowledge of large language models (LLMs) to address the task's inherent complexity and variability, thereby enhancing the robustness and scientific validity of the method. Furthermore, our experimental results indicate that our method significantly outperforms traditional HSD approaches and existing multimodal LLMs in detecting key abnormalities in heart sounds.

cs.SD↗

arXiv2024

Med-PMC: Medical Personalized Multi-modal Consultation with a Proactive Ask-First-Observe-Next Paradigm

The application of the Multi-modal Large Language Models (MLLMs) in medical clinical scenarios remains underexplored. Previous benchmarks only focus on the capacity of the MLLMs in medical visual question-answering (VQA) or report generation and fail to assess the performance of the MLLMs on complex clinical multi-modal tasks. In this paper, we propose a novel Medical Personalized Multi-modal Consultation (Med-PMC) paradigm to evaluate the clinical capacity of the MLLMs. Med-PMC builds a simulated clinical environment where the MLLMs are required to interact with a patient simulator to complete the multi-modal information-gathering and decision-making task. Specifically, the patient simulator is decorated with personalized actors to simulate diverse patients in real scenarios. We conduct extensive experiments to access 12 types of MLLMs, providing a comprehensive view of the MLLMs' clinical performance. We found that current MLLMs fail to gather multimodal information and show potential bias in the decision-making task when consulted with the personalized patient simulators. Further analysis demonstrates the effectiveness of Med-PMC, showing the potential to guide the development of robust and reliable clinical MLLMs. Code and data are available at https://github.com/LiuHC0428/Med-PMC.

cs.CL↗

arXiv2024

FedRSU: Federated Learning for Scene Flow Estimation on Roadside Units

Roadside unit (RSU) can significantly improve the safety and robustness of autonomous vehicles through Vehicle-to-Everything (V2X) communication. Currently, the usage of a single RSU mainly focuses on real-time inference and V2X collaboration, while neglecting the potential value of the high-quality data collected by RSU sensors. Integrating the vast amounts of data from numerous RSUs can provide a rich source of data for model training. However, the absence of ground truth annotations and the difficulty of transmitting enormous volumes of data are two inevitable barriers to fully exploiting this hidden value. In this paper, we introduce FedRSU, an innovative federated learning framework for self-supervised scene flow estimation. In FedRSU, we present a recurrent self-supervision training paradigm, where for each RSU, the scene flow prediction of points at every timestamp can be supervised by its subsequent future multi-modality observation. Another key component of FedRSU is federated learning, where multiple devices collaboratively train an ML model while keeping the training data local and private. With the power of the recurrent self-supervised learning paradigm, FL is able to leverage innumerable underutilized data from RSU. To verify the FedRSU framework, we construct a large-scale multi-modality dataset RSU-SF. The dataset consists of 17 RSU clients, covering various scenarios, modalities, and sensor settings. Based on RSU-SF, we show that FedRSU can greatly improve model performance in ITS and provide a comprehensive benchmark under diverse FL scenarios. To the best of our knowledge, we provide the first real-world LiDAR-camera multi-modal dataset and benchmark for the FL community.

cs.CV↗

arXiv2024

HPC: Hierarchical Progressive Coding Framework for Volumetric Video

Volumetric video based on Neural Radiance Field (NeRF) holds vast potential for various 3D applications, but its substantial data volume poses significant challenges for compression and transmission. Current NeRF compression lacks the flexibility to adjust video quality and bitrate within a single model for various network and device capacities. To address these issues, we propose HPC, a novel hierarchical progressive volumetric video coding framework achieving variable bitrate using a single model. Specifically, HPC introduces a hierarchical representation with a multi-resolution residual radiance field to reduce temporal redundancy in long-duration sequences while simultaneously generating various levels of detail. Then, we propose an end-to-end progressive learning approach with a multi-rate-distortion loss function to jointly optimize both hierarchical representation and compression. Our HPC trained only once can realize multiple compression levels, while the current methods need to train multiple fixed-bitrate models for different rate-distortion (RD) tradeoffs. Extensive experiments demonstrate that HPC achieves flexible quality levels with variable bitrate by a single model and exhibits competitive RD performance, even outperforming fixed-bitrate models across various datasets.

cs.CV↗

arXiv2024

AutoRG-Brain: Grounded Report Generation for Brain MRI

Radiologists are tasked with interpreting a large number of images in a daily base, with the responsibility of generating corresponding reports. This demanding workload elevates the risk of human error, potentially leading to treatment delays, increased healthcare costs, revenue loss, and operational inefficiencies. To address these challenges, we initiate a series of work on grounded Automatic Report Generation (AutoRG), starting from the brain MRI interpretation system, which supports the delineation of brain structures, the localization of anomalies, and the generation of well-organized findings. We make contributions from the following aspects, first, on dataset construction, we release a comprehensive dataset encompassing segmentation masks of anomaly regions and manually authored reports, termed as RadGenome-Brain MRI. This data resource is intended to catalyze ongoing research and development in the field of AI-assisted report generation systems. Second, on system design, we propose AutoRG-Brain, the first brain MRI report generation system with pixel-level grounded visual clues. Third, for evaluation, we conduct quantitative assessments and human evaluations of brain structure segmentation, anomaly localization, and report generation tasks to provide evidence of its reliability and accuracy. This system has been integrated into real clinical scenarios, where radiologists were instructed to write reports based on our generated findings and anomaly segmentation masks. The results demonstrate that our system enhances the report-writing skills of junior doctors, aligning their performance more closely with senior doctors, thereby boosting overall productivity.

eess.IV↗

arXiv2024

Decoding Linguistic Representations of Human Brain

Language, as an information medium created by advanced organisms, has always been a concern of neuroscience regarding how it is represented in the brain. Decoding linguistic representations in the evoked brain has shown groundbreaking achievements, thanks to the rapid improvement of neuroimaging, medical technology, life sciences and artificial intelligence. In this work, we present a taxonomy of brain-to-language decoding of both textual and speech formats. This work integrates two types of research: neuroscience focusing on language understanding and deep learning-based brain decoding. Generating discernible language information from brain activity could not only help those with limited articulation, especially amyotrophic lateral sclerosis (ALS) patients but also open up a new way for the next generation's brain-computer interface (BCI). This article will help brain scientists and deep-learning researchers to gain a bird's eye view of fine-grained language perception, and thus facilitate their further investigation and research of neural process and language decoding.

cs.CL↗