arXiv subjects

Ya Zhang

Publications and source records attributed to Ya Zhang.

At least 109 records · Page 6Linked to original sources

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

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

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

ReMamber: Referring Image Segmentation with Mamba Twister

Referring Image Segmentation~(RIS) leveraging transformers has achieved great success on the interpretation of complex visual-language tasks. However, the quadratic computation cost makes it resource-consuming in capturing long-range visual-language dependencies. Fortunately, Mamba addresses this with efficient linear complexity in processing. However, directly applying Mamba to multi-modal interactions presents challenges, primarily due to inadequate channel interactions for the effective fusion of multi-modal data. In this paper, we propose ReMamber, a novel RIS architecture that integrates the power of Mamba with a multi-modal Mamba Twister block. The Mamba Twister explicitly models image-text interaction, and fuses textual and visual features through its unique channel and spatial twisting mechanism. We achieve competitive results on three challenging benchmarks with a simple and efficient architecture. Moreover, we conduct thorough analyses of ReMamber and discuss other fusion designs using Mamba. These provide valuable perspectives for future research. The code has been released at: https://github.com/yyh-rain-song/ReMamber.

cs.CV↗

arXiv2024

Multi-Sentence Grounding for Long-term Instructional Video

In this paper, we aim to establish an automatic, scalable pipeline for denoising the large-scale instructional dataset and construct a high-quality video-text dataset with multiple descriptive steps supervision, named HowToStep. We make the following contributions: (i) improving the quality of sentences in dataset by upgrading ASR systems to reduce errors from speech recognition and prompting a large language model to transform noisy ASR transcripts into descriptive steps; (ii) proposing a Transformer-based architecture with all texts as queries, iteratively attending to the visual features, to temporally align the generated steps to corresponding video segments. To measure the quality of our curated datasets, we train models for the task of multi-sentence grounding on it, i.e., given a long-form video, and associated multiple sentences, to determine their corresponding timestamps in the video simultaneously, as a result, the model shows superior performance on a series of multi-sentence grounding tasks, surpassing existing state-of-the-art methods by a significant margin on three public benchmarks, namely, 9.0% on HT-Step, 5.1% on HTM-Align and 1.9% on CrossTask. All codes, models, and the resulting dataset have been publicly released.

cs.CV↗

arXiv2024

Multi-Modal Prototypes for Open-World Semantic Segmentation

In semantic segmentation, generalizing a visual system to both seen categories and novel categories at inference time has always been practically valuable yet challenging. To enable such functionality, existing methods mainly rely on either providing several support demonstrations from the visual aspect or characterizing the informative clues from the textual aspect (e.g., the class names). Nevertheless, both two lines neglect the complementary intrinsic of low-level visual and high-level language information, while the explorations that consider visual and textual modalities as a whole to promote predictions are still limited. To close this gap, we propose to encompass textual and visual clues as multi-modal prototypes to allow more comprehensive support for open-world semantic segmentation, and build a novel prototype-based segmentation framework to realize this promise. To be specific, unlike the straightforward combination of bi-modal clues, we decompose the high-level language information as multi-aspect prototypes and aggregate the low-level visual information as more semantic prototypes, on basis of which, a fine-grained complementary fusion makes the multi-modal prototypes more powerful and accurate to promote the prediction. Based on an elastic mask prediction module that permits any number and form of prototype inputs, we are able to solve the zero-shot, few-shot and generalized counterpart tasks in one architecture. Extensive experiments on both PASCAL-$5^i$ and COCO-$20^i$ datasets show the consistent superiority of the proposed method compared with the previous state-of-the-art approaches, and a range of ablation studies thoroughly dissects each component in our framework both quantitatively and qualitatively that verify their effectiveness.

cs.CV↗

arXiv2024

Reprogramming Distillation for Medical Foundation Models

Medical foundation models pre-trained on large-scale datasets have demonstrated powerful versatile capabilities for various tasks. However, due to the gap between pre-training tasks (or modalities) and downstream tasks (or modalities), the real-world computation and speed constraints, it might not be straightforward to apply medical foundation models in the downstream scenarios. Previous methods, such as parameter efficient fine-tuning (PEFT) methods and knowledge distillation (KD) methods, are unable to simultaneously address the task (or modality) inconsistency and achieve personalized lightweight deployment under diverse real-world demands. To address the above issues, we propose a novel framework called Reprogramming Distillation (RD). On one hand, RD reprograms the original feature space of the foundation model so that it is more relevant to downstream scenarios, aligning tasks and modalities. On the other hand, through a co-training mechanism and a shared classifier, connections are established between the reprogrammed knowledge and the knowledge of student models, ensuring that the reprogrammed feature space can be smoothly mimic by the student model of different structures. Further, to reduce the randomness under different training conditions, we design a Centered Kernel Alignment (CKA) distillation to promote robust knowledge transfer. Empirically, we show that on extensive datasets, RD consistently achieve superior performance compared with previous PEFT and KD methods.

cs.CV↗

arXiv2024

Farey tree locking of terahertz semiconductor laser frequency combs

Frequency combs show various applications in molecular fingerprinting, imaging, communications, and so on. In the terahertz frequency range, semiconductor-based quantum cascade lasers (QCLs) are ideal platforms for realizing the frequency comb operation. Although self-started frequency comb operation can be obtained in free-running terahertz QCLs due to the four-wave mixing locking effects, resonant/off-resonant microwave injection, phase locking, and femtosecond laser based locking techniques have been widely used to broaden and stabilize terahertz QCL combs. These active locking methods indeed show significant effects on the frequency stabilization of terahertz QCL combs, but they simultaneously have drawbacks, such as introducing large phase noise and requiring complex optical coupling and/or electrical circuits. Here, we demonstrate Farey tree locking of terahertz QCL frequency combs under microwave injection. The frequency competition between the Farey fraction frequency and the cavity round-trip frequency results in the frequency locking of terahertz QCL combs, and the Farey fraction frequencies can be accurately anticipated based on the downward trend of the Farey tree hierarchy. Furthermore, dual-comb experimental results show that the phase noise of the dual-comb spectral lines is significantly reduced by employing the Farey tree locking method. These results pave the way to deploying compact and low phase noise terahertz frequency comb sources.

physics.optics↗

arXiv2024

Large-scale Long-tailed Disease Diagnosis on Radiology Images

Developing a generalist radiology diagnosis system can greatly enhance clinical diagnostics. In this paper, we introduce RadDiag, a foundational model supporting 2D and 3D inputs across various modalities and anatomies, using a transformer-based fusion module for comprehensive disease diagnosis. Due to patient privacy concerns and the lack of large-scale radiology diagnosis datasets, we utilize high-quality, clinician-reviewed radiological images available online with diagnosis labels. Our dataset, RP3D-DiagDS, contains 40,936 cases with 195,010 scans covering 5,568 disorders (930 unique ICD-10-CM codes). Experimentally, our RadDiag achieves 95.14% AUC on internal evaluation with the knowledge-enhancement strategy. Additionally, RadDiag can be zero-shot applied or fine-tuned to external diagnosis datasets sourced from various hospitals, demonstrating state-of-the-art results. In conclusion, we show that publicly shared medical data on the Internet is a tremendous and valuable resource that can potentially support building a generalist AI for healthcare.

cs.CV↗

arXiv2024

Exploring Training on Heterogeneous Data with Mixture of Low-rank Adapters

Training a unified model to take multiple targets into account is a trend towards artificial general intelligence. However, how to efficiently mitigate the training conflicts among heterogeneous data collected from different domains or tasks remains under-explored. In this study, we explore to leverage Mixture of Low-rank Adapters (MoLA) to mitigate conflicts in heterogeneous data training, which requires to jointly train the multiple low-rank adapters and their shared backbone. Specifically, we introduce two variants of MoLA, namely, MoLA-Grad and MoLA-Router, to respectively handle the target-aware and target-agnostic scenarios during inference. The former uses task identifiers to assign personalized low-rank adapters to each task, disentangling task-specific knowledge towards their adapters, thereby mitigating heterogeneity conflicts. The latter uses a novel Task-wise Decorrelation (TwD) loss to intervene the router to learn oriented weight combinations of adapters to homogeneous tasks, achieving similar effects. We conduct comprehensive experiments to verify the superiority of MoLA over previous state-of-the-art methods and present in-depth analysis on its working mechanism. Source code is available at: https://github.com/MediaBrain-SJTU/MoLA

cs.CV↗

arXiv2024

JointRF: End-to-End Joint Optimization for Dynamic Neural Radiance Field Representation and Compression

Neural Radiance Field (NeRF) excels in photo-realistically static scenes, inspiring numerous efforts to facilitate volumetric videos. However, rendering dynamic and long-sequence radiance fields remains challenging due to the significant data required to represent volumetric videos. In this paper, we propose a novel end-to-end joint optimization scheme of dynamic NeRF representation and compression, called JointRF, thus achieving significantly improved quality and compression efficiency against the previous methods. Specifically, JointRF employs a compact residual feature grid and a coefficient feature grid to represent the dynamic NeRF. This representation handles large motions without compromising quality while concurrently diminishing temporal redundancy. We also introduce a sequential feature compression subnetwork to further reduce spatial-temporal redundancy. Finally, the representation and compression subnetworks are end-to-end trained combined within the JointRF. Extensive experiments demonstrate that JointRF can achieve superior compression performance across various datasets.

cs.CV↗

arXiv2024

Diversified Batch Selection for Training Acceleration

The remarkable success of modern machine learning models on large datasets often demands extensive training time and resource consumption. To save cost, a prevalent research line, known as online batch selection, explores selecting informative subsets during the training process. Although recent efforts achieve advancements by measuring the impact of each sample on generalization, their reliance on additional reference models inherently limits their practical applications, when there are no such ideal models available. On the other hand, the vanilla reference-model-free methods involve independently scoring and selecting data in a sample-wise manner, which sacrifices the diversity and induces the redundancy. To tackle this dilemma, we propose Diversified Batch Selection (DivBS), which is reference-model-free and can efficiently select diverse and representative samples. Specifically, we define a novel selection objective that measures the group-wise orthogonalized representativeness to combat the redundancy issue of previous sample-wise criteria, and provide a principled selection-efficient realization. Extensive experiments across various tasks demonstrate the significant superiority of DivBS in the performance-speedup trade-off. The code is publicly available.

cs.LG↗

arXiv2024

Federated Learning under Partially Class-Disjoint Data via Manifold Reshaping

Statistical heterogeneity severely limits the performance of federated learning (FL), motivating several explorations e.g., FedProx, MOON and FedDyn, to alleviate this problem. Despite effectiveness, their considered scenario generally requires samples from almost all classes during the local training of each client, although some covariate shifts may exist among clients. In fact, the natural case of partially class-disjoint data (PCDD), where each client contributes a few classes (instead of all classes) of samples, is practical yet underexplored. Specifically, the unique collapse and invasion characteristics of PCDD can induce the biased optimization direction in local training, which prevents the efficiency of federated learning. To address this dilemma, we propose a manifold reshaping approach called FedMR to calibrate the feature space of local training. Our FedMR adds two interplaying losses to the vanilla federated learning: one is intra-class loss to decorrelate feature dimensions for anti-collapse; and the other one is inter-class loss to guarantee the proper margin among categories in the feature expansion. We conduct extensive experiments on a range of datasets to demonstrate that our FedMR achieves much higher accuracy and better communication efficiency. Source code is available at: https://github.com/MediaBrain-SJTU/FedMR.git.

cs.LG↗