arXiv subjects

Yefeng Zheng

Publications and source records attributed to Yefeng Zheng.

At least 109 records · Page 6Linked to original sources

arXiv2024

Biomedical Entity Linking as Multiple Choice Question Answering

Although biomedical entity linking (BioEL) has made significant progress with pre-trained language models, challenges still exist for fine-grained and long-tailed entities. To address these challenges, we present BioELQA, a novel model that treats Biomedical Entity Linking as Multiple Choice Question Answering. BioELQA first obtains candidate entities with a fast retriever, jointly presents the mention and candidate entities to a generator, and then outputs the predicted symbol associated with its chosen entity. This formulation enables explicit comparison of different candidate entities, thus capturing fine-grained interactions between mentions and entities, as well as among entities themselves. To improve generalization for long-tailed entities, we retrieve similar labeled training instances as clues and concatenate the input with retrieved instances for the generator. Extensive experimental results show that BioELQA outperforms state-of-the-art baselines on several datasets.

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arXiv2024

LENAS: Learning-based Neural Architecture Search and Ensemble for 3D Radiotherapy Dose Prediction

Radiation therapy treatment planning requires balancing the delivery of the target dose while sparing normal tissues, making it a complex process. To streamline the planning process and enhance its quality, there is a growing demand for knowledge-based planning (KBP). Ensemble learning has shown impressive power in various deep learning tasks, and it has great potential to improve the performance of KBP. However, the effectiveness of ensemble learning heavily depends on the diversity and individual accuracy of the base learners. Moreover, the complexity of model ensembles is a major concern, as it requires maintaining multiple models during inference, leading to increased computational cost and storage overhead. In this study, we propose a novel learning-based ensemble approach named LENAS, which integrates neural architecture search with knowledge distillation for 3D radiotherapy dose prediction. Our approach starts by exhaustively searching each block from an enormous architecture space to identify multiple architectures that exhibit promising performance and significant diversity. To mitigate the complexity introduced by the model ensemble, we adopt the teacher-student paradigm, leveraging the diverse outputs from multiple learned networks as supervisory signals to guide the training of the student network. Furthermore, to preserve high-level semantic information, we design a hybrid-loss to optimize the student network, enabling it to recover the knowledge embedded within the teacher networks. The proposed method has been evaluated on two public datasets, OpenKBP and AIMIS. Extensive experimental results demonstrate the effectiveness of our method and its superior performance to the state-of-the-art methods.

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arXiv2024

AnomalyXFusion: Multi-modal Anomaly Synthesis with Diffusion

Anomaly synthesis is one of the effective methods to augment abnormal samples for training. However, current anomaly synthesis methods predominantly rely on texture information as input, which limits the fidelity of synthesized abnormal samples. Because texture information is insufficient to correctly depict the pattern of anomalies, especially for logical anomalies. To surmount this obstacle, we present the AnomalyXFusion framework, designed to harness multi-modality information to enhance the quality of synthesized abnormal samples. The AnomalyXFusion framework comprises two distinct yet synergistic modules: the Multi-modal In-Fusion (MIF) module and the Dynamic Dif-Fusion (DDF) module. The MIF module refines modality alignment by aggregating and integrating various modality features into a unified embedding space, termed X-embedding, which includes image, text, and mask features. Concurrently, the DDF module facilitates controlled generation through an adaptive adjustment of X-embedding conditioned on the diffusion steps. In addition, to reveal the multi-modality representational power of AnomalyXFusion, we propose a new dataset, called MVTec Caption. More precisely, MVTec Caption extends 2.2k accurate image-mask-text annotations for the MVTec AD and LOCO datasets. Comprehensive evaluations demonstrate the effectiveness of AnomalyXFusion, especially regarding the fidelity and diversity for logical anomalies. Project page: http:github.com/hujiecpp/MVTec-Caption

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arXiv2024

Learning Long-form Video Prior via Generative Pre-Training

Concepts involved in long-form videos such as people, objects, and their interactions, can be viewed as following an implicit prior. They are notably complex and continue to pose challenges to be comprehensively learned. In recent years, generative pre-training (GPT) has exhibited versatile capacities in modeling any kind of text content even visual locations. Can this manner work for learning long-form video prior? Instead of operating on pixel space, it is efficient to employ visual locations like bounding boxes and keypoints to represent key information in videos, which can be simply discretized and then tokenized for consumption by GPT. Due to the scarcity of suitable data, we create a new dataset called \textbf{Storyboard20K} from movies to serve as a representative. It includes synopses, shot-by-shot keyframes, and fine-grained annotations of film sets and characters with consistent IDs, bounding boxes, and whole body keypoints. In this way, long-form videos can be represented by a set of tokens and be learned via generative pre-training. Experimental results validate that our approach has great potential for learning long-form video prior. Code and data will be released at \url{https://github.com/showlab/Long-form-Video-Prior}.

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arXiv2024

NeRF2Points: Large-Scale Point Cloud Generation From Street Views' Radiance Field Optimization

Neural Radiance Fields (NeRF) have emerged as a paradigm-shifting methodology for the photorealistic rendering of objects and environments, enabling the synthesis of novel viewpoints with remarkable fidelity. This is accomplished through the strategic utilization of object-centric camera poses characterized by significant inter-frame overlap. This paper explores a compelling, alternative utility of NeRF: the derivation of point clouds from aggregated urban landscape imagery. The transmutation of street-view data into point clouds is fraught with complexities, attributable to a nexus of interdependent variables. First, high-quality point cloud generation hinges on precise camera poses, yet many datasets suffer from inaccuracies in pose metadata. Also, the standard approach of NeRF is ill-suited for the distinct characteristics of street-view data from autonomous vehicles in vast, open settings. Autonomous vehicle cameras often record with limited overlap, leading to blurring, artifacts, and compromised pavement representation in NeRF-based point clouds. In this paper, we present NeRF2Points, a tailored NeRF variant for urban point cloud synthesis, notable for its high-quality output from RGB inputs alone. Our paper is supported by a bespoke, high-resolution 20-kilometer urban street dataset, designed for point cloud generation and evaluation. NeRF2Points adeptly navigates the inherent challenges of NeRF-based point cloud synthesis through the implementation of the following strategic innovations: (1) Integration of Weighted Iterative Geometric Optimization (WIGO) and Structure from Motion (SfM) for enhanced camera pose accuracy, elevating street-view data precision. (2) Layered Perception and Integrated Modeling (LPiM) is designed for distinct radiance field modeling in urban environments, resulting in coherent point cloud representations.

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arXiv2024

Self-Supervised Learning for Medical Image Data with Anatomy-Oriented Imaging Planes

Self-supervised learning has emerged as a powerful tool for pretraining deep networks on unlabeled data, prior to transfer learning of target tasks with limited annotation. The relevance between the pretraining pretext and target tasks is crucial to the success of transfer learning. Various pretext tasks have been proposed to utilize properties of medical image data (e.g., three dimensionality), which are more relevant to medical image analysis than generic ones for natural images. However, previous work rarely paid attention to data with anatomy-oriented imaging planes, e.g., standard cardiac magnetic resonance imaging views. As these imaging planes are defined according to the anatomy of the imaged organ, pretext tasks effectively exploiting this information can pretrain the networks to gain knowledge on the organ of interest. In this work, we propose two complementary pretext tasks for this group of medical image data based on the spatial relationship of the imaging planes. The first is to learn the relative orientation between the imaging planes and implemented as regressing their intersecting lines. The second exploits parallel imaging planes to regress their relative slice locations within a stack. Both pretext tasks are conceptually straightforward and easy to implement, and can be combined in multitask learning for better representation learning. Thorough experiments on two anatomical structures (heart and knee) and representative target tasks (semantic segmentation and classification) demonstrate that the proposed pretext tasks are effective in pretraining deep networks for remarkably boosted performance on the target tasks, and superior to other recent approaches.

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arXiv2024

Federated Modality-specific Encoders and Multimodal Anchors for Personalized Brain Tumor Segmentation

Most existing federated learning (FL) methods for medical image analysis only considered intramodal heterogeneity, limiting their applicability to multimodal imaging applications. In practice, it is not uncommon that some FL participants only possess a subset of the complete imaging modalities, posing inter-modal heterogeneity as a challenge to effectively training a global model on all participants' data. In addition, each participant would expect to obtain a personalized model tailored for its local data characteristics from the FL in such a scenario. In this work, we propose a new FL framework with federated modality-specific encoders and multimodal anchors (FedMEMA) to simultaneously address the two concurrent issues. Above all, FedMEMA employs an exclusive encoder for each modality to account for the inter-modal heterogeneity in the first place. In the meantime, while the encoders are shared by the participants, the decoders are personalized to meet individual needs. Specifically, a server with full-modal data employs a fusion decoder to aggregate and fuse representations from all modality-specific encoders, thus bridging the modalities to optimize the encoders via backpropagation reversely. Meanwhile, multiple anchors are extracted from the fused multimodal representations and distributed to the clients in addition to the encoder parameters. On the other end, the clients with incomplete modalities calibrate their missing-modal representations toward the global full-modal anchors via scaled dot-product cross-attention, making up the information loss due to absent modalities while adapting the representations of present ones. FedMEMA is validated on the BraTS 2020 benchmark for multimodal brain tumor segmentation. Results show that it outperforms various up-to-date methods for multimodal and personalized FL and that its novel designs are effective. Our code is available.

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arXiv2024

Generation is better than Modification: Combating High Class Homophily Variance in Graph Anomaly Detection

Graph-based anomaly detection is currently an important research topic in the field of graph neural networks (GNNs). We find that in graph anomaly detection, the homophily distribution differences between different classes are significantly greater than those in homophilic and heterophilic graphs. For the first time, we introduce a new metric called Class Homophily Variance, which quantitatively describes this phenomenon. To mitigate its impact, we propose a novel GNN model named Homophily Edge Generation Graph Neural Network (HedGe). Previous works typically focused on pruning, selecting or connecting on original relationships, and we refer to these methods as modifications. Different from these works, our method emphasizes generating new relationships with low class homophily variance, using the original relationships as an auxiliary. HedGe samples homophily adjacency matrices from scratch using a self-attention mechanism, and leverages nodes that are relevant in the feature space but not directly connected in the original graph. Additionally, we modify the loss function to punish the generation of unnecessary heterophilic edges by the model. Extensive comparison experiments demonstrate that HedGe achieved the best performance across multiple benchmark datasets, including anomaly detection and edgeless node classification. The proposed model also improves the robustness under the novel Heterophily Attack with increased class homophily variance on other graph classification tasks.

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arXiv2024

MedKP: Medical Dialogue with Knowledge Enhancement and Clinical Pathway Encoding

With appropriate data selection and training techniques, Large Language Models (LLMs) have demonstrated exceptional success in various medical examinations and multiple-choice questions. However, the application of LLMs in medical dialogue generation-a task more closely aligned with actual medical practice-has been less explored. This gap is attributed to the insufficient medical knowledge of LLMs, which leads to inaccuracies and hallucinated information in the generated medical responses. In this work, we introduce the Medical dialogue with Knowledge enhancement and clinical Pathway encoding (MedKP) framework, which integrates an external knowledge enhancement module through a medical knowledge graph and an internal clinical pathway encoding via medical entities and physician actions. Evaluated with comprehensive metrics, our experiments on two large-scale, real-world online medical consultation datasets (MedDG and KaMed) demonstrate that MedKP surpasses multiple baselines and mitigates the incidence of hallucinations, achieving a new state-of-the-art. Extensive ablation studies further reveal the effectiveness of each component of MedKP. This enhancement advances the development of reliable, automated medical consultation responses using LLMs, thereby broadening the potential accessibility of precise and real-time medical assistance.

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arXiv2024

ConRF: Zero-shot Stylization of 3D Scenes with Conditioned Radiation Fields

Most of the existing works on arbitrary 3D NeRF style transfer required retraining on each single style condition. This work aims to achieve zero-shot controlled stylization in 3D scenes utilizing text or visual input as conditioning factors. We introduce ConRF, a novel method of zero-shot stylization. Specifically, due to the ambiguity of CLIP features, we employ a conversion process that maps the CLIP feature space to the style space of a pre-trained VGG network and then refine the CLIP multi-modal knowledge into a style transfer neural radiation field. Additionally, we use a 3D volumetric representation to perform local style transfer. By combining these operations, ConRF offers the capability to utilize either text or images as references, resulting in the generation of sequences with novel views enhanced by global or local stylization. Our experiment demonstrates that ConRF outperforms other existing methods for 3D scene and single-text stylization in terms of visual quality.

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arXiv2024

Multi-perspective Improvement of Knowledge Graph Completion with Large Language Models

Knowledge graph completion (KGC) is a widely used method to tackle incompleteness in knowledge graphs (KGs) by making predictions for missing links. Description-based KGC leverages pre-trained language models to learn entity and relation representations with their names or descriptions, which shows promising results. However, the performance of description-based KGC is still limited by the quality of text and the incomplete structure, as it lacks sufficient entity descriptions and relies solely on relation names, leading to sub-optimal results. To address this issue, we propose MPIKGC, a general framework to compensate for the deficiency of contextualized knowledge and improve KGC by querying large language models (LLMs) from various perspectives, which involves leveraging the reasoning, explanation, and summarization capabilities of LLMs to expand entity descriptions, understand relations, and extract structures, respectively. We conducted extensive evaluation of the effectiveness and improvement of our framework based on four description-based KGC models and four datasets, for both link prediction and triplet classification tasks.

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arXiv2024

K-Space-Aware Cross-Modality Score for Synthesized Neuroimage Quality Assessment

The problem of how to assess cross-modality medical image synthesis has been largely unexplored. The most used measures like PSNR and SSIM focus on analyzing the structural features but neglect the crucial lesion location and fundamental k-space speciality of medical images. To overcome this problem, we propose a new metric K-CROSS to spur progress on this challenging problem. Specifically, K-CROSS uses a pre-trained multi-modality segmentation network to predict the lesion location, together with a tumor encoder for representing features, such as texture details and brightness intensities. To further reflect the frequency-specific information from the magnetic resonance imaging principles, both k-space features and vision features are obtained and employed in our comprehensive encoders with a frequency reconstruction penalty. The structure-shared encoders are designed and constrained with a similarity loss to capture the intrinsic common structural information for both modalities. As a consequence, the features learned from lesion regions, k-space, and anatomical structures are all captured, which serve as our quality evaluators. We evaluate the performance by constructing a large-scale cross-modality neuroimaging perceptual similarity (NIRPS) dataset with 6,000 radiologist judgments. Extensive experiments demonstrate that the proposed method outperforms other metrics, especially in comparison with the radiologists on NIRPS.

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arXiv2024

Large Language Models Leverage External Knowledge to Extend Clinical Insight Beyond Language Boundaries

$\textbf{Objectives}$: Large Language Models (LLMs) such as ChatGPT and Med-PaLM have excelled in various medical question-answering tasks. However, these English-centric models encounter challenges in non-English clinical settings, primarily due to limited clinical knowledge in respective languages, a consequence of imbalanced training corpora. We systematically evaluate LLMs in the Chinese medical context and develop a novel in-context learning framework to enhance their performance. $\textbf{Materials and Methods}$: The latest China National Medical Licensing Examination (CNMLE-2022) served as the benchmark. We collected 53 medical books and 381,149 medical questions to construct the medical knowledge base and question bank. The proposed Knowledge and Few-shot Enhancement In-context Learning (KFE) framework leverages the in-context learning ability of LLMs to integrate diverse external clinical knowledge sources. We evaluated KFE with ChatGPT(GPT3.5), GPT4, Baichuan2(BC2)-7B, and BC2-13B in CNMLE-2022 and investigated the effectiveness of different pathways for incorporating LLMs with medical knowledge from 7 perspectives. $\textbf{Results}$: Directly applying ChatGPT failed to qualify for the CNMLE-2022 at a score of 51. Cooperated with the KFE, the LLMs with varying sizes yielded consistent and significant improvements. The ChatGPT's performance surged to 70.04 and GPT-4 achieved the highest score of 82.59. This surpasses the qualification threshold (60) and exceeds the average human score of 68.70. It also enabled a smaller BC2-13B to pass the examination, showcasing the great potential in low-resource settings. $\textbf{Conclusion}$: By synergizing medical knowledge through in-context learning, LLM can extend clinical insight beyond language barriers, significantly reducing language-related disparities of LLM applications and ensuring global benefit in healthcare.

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arXiv2024

Dynamically Masked Discriminator for Generative Adversarial Networks

Training Generative Adversarial Networks (GANs) remains a challenging problem. The discriminator trains the generator by learning the distribution of real/generated data. However, the distribution of generated data changes throughout the training process, which is difficult for the discriminator to learn. In this paper, we propose a novel method for GANs from the viewpoint of online continual learning. We observe that the discriminator model, trained on historically generated data, often slows down its adaptation to the changes in the new arrival generated data, which accordingly decreases the quality of generated results. By treating the generated data in training as a stream, we propose to detect whether the discriminator slows down the learning of new knowledge in generated data. Therefore, we can explicitly enforce the discriminator to learn new knowledge fast. Particularly, we propose a new discriminator, which automatically detects its retardation and then dynamically masks its features, such that the discriminator can adaptively learn the temporally-vary distribution of generated data. Experimental results show our method outperforms the state-of-the-art approaches.

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arXiv2023

Federated Learning via Input-Output Collaborative Distillation

Federated learning (FL) is a machine learning paradigm in which distributed local nodes collaboratively train a central model without sharing individually held private data. Existing FL methods either iteratively share local model parameters or deploy co-distillation. However, the former is highly susceptible to private data leakage, and the latter design relies on the prerequisites of task-relevant real data. Instead, we propose a data-free FL framework based on local-to-central collaborative distillation with direct input and output space exploitation. Our design eliminates any requirement of recursive local parameter exchange or auxiliary task-relevant data to transfer knowledge, thereby giving direct privacy control to local users. In particular, to cope with the inherent data heterogeneity across locals, our technique learns to distill input on which each local model produces consensual yet unique results to represent each expertise. Our proposed FL framework achieves notable privacy-utility trade-offs with extensive experiments on image classification and segmentation tasks under various real-world heterogeneous federated learning settings on both natural and medical images.

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arXiv2023

COOPER: Coordinating Specialized Agents towards a Complex Dialogue Goal

In recent years, there has been a growing interest in exploring dialogues with more complex goals, such as negotiation, persuasion, and emotional support, which go beyond traditional service-focused dialogue systems. Apart from the requirement for much more sophisticated strategic reasoning and communication skills, a significant challenge of these tasks lies in the difficulty of objectively measuring the achievement of their goals in a quantifiable way, making it difficult for existing research to directly optimize the dialogue procedure towards them. In our work, we emphasize the multifaceted nature of complex dialogue goals and argue that it is more feasible to accomplish them by comprehensively considering and jointly promoting their different aspects. To this end, we propose a novel dialogue framework, Cooper, which coordinates multiple specialized agents, each dedicated to a specific dialogue goal aspect separately, to approach the complex objective. Through this divide-and-conquer manner, we make complex dialogue goals more approachable and elicit greater intelligence via the collaboration of individual agents. Experiments on persuasion and emotional support dialogues demonstrate the superiority of our method over a set of competitive baselines.

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arXiv2023

Improving Biomedical Entity Linking with Retrieval-enhanced Learning

Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To address this limitation, we introduce a new scheme $k$NN-BioEL, which provides a BioEL model with the ability to reference similar instances from the entire training corpus as clues for prediction, thus improving the generalization capabilities. Moreover, we design a contrastive learning objective with dynamic hard negative sampling (DHNS) that improves the quality of the retrieved neighbors during inference. Extensive experimental results show that $k$NN-BioEL outperforms state-of-the-art baselines on several datasets.

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arXiv2023

Adversarial Medical Image with Hierarchical Feature Hiding

Deep learning based methods for medical images can be easily compromised by adversarial examples (AEs), posing a great security flaw in clinical decision-making. It has been discovered that conventional adversarial attacks like PGD which optimize the classification logits, are easy to distinguish in the feature space, resulting in accurate reactive defenses. To better understand this phenomenon and reassess the reliability of the reactive defenses for medical AEs, we thoroughly investigate the characteristic of conventional medical AEs. Specifically, we first theoretically prove that conventional adversarial attacks change the outputs by continuously optimizing vulnerable features in a fixed direction, thereby leading to outlier representations in the feature space. Then, a stress test is conducted to reveal the vulnerability of medical images, by comparing with natural images. Interestingly, this vulnerability is a double-edged sword, which can be exploited to hide AEs. We then propose a simple-yet-effective hierarchical feature constraint (HFC), a novel add-on to conventional white-box attacks, which assists to hide the adversarial feature in the target feature distribution. The proposed method is evaluated on three medical datasets, both 2D and 3D, with different modalities. The experimental results demonstrate the superiority of HFC, \emph{i.e.,} it bypasses an array of state-of-the-art adversarial medical AE detectors more efficiently than competing adaptive attacks, which reveals the deficiencies of medical reactive defense and allows to develop more robust defenses in future.

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