arXiv subjects

Ke Yan

Publications and source records attributed to Ke Yan.

At least 55 records · Page 3Linked to original sources

arXiv2024

Med-Query: Steerable Parsing of 9-DoF Medical Anatomies with Query Embedding

Automatic parsing of human anatomies at the instance-level from 3D computed tomography (CT) is a prerequisite step for many clinical applications. The presence of pathologies, broken structures or limited field-of-view (FOV) can all make anatomy parsing algorithms vulnerable. In this work, we explore how to leverage and implement the successful detection-then-segmentation paradigm for 3D medical data, and propose a steerable, robust, and efficient computing framework for detection, identification, and segmentation of anatomies in CT scans. Considering the complicated shapes, sizes, and orientations of anatomies, without loss of generality, we present a nine degrees of freedom (9-DoF) pose estimation solution in full 3D space using a novel single-stage, non-hierarchical representation. Our whole framework is executed in a steerable manner where any anatomy of interest can be directly retrieved to further boost inference efficiency. We have validated our method on three medical imaging parsing tasks: ribs, spine, and abdominal organs. For rib parsing, CT scans have been annotated at the rib instance-level for quantitative evaluation, similarly for spine vertebrae and abdominal organs. Extensive experiments on 9-DoF box detection and rib instance segmentation demonstrate the high efficiency and effectiveness of our framework (with the identification rate of 97.0% and the segmentation Dice score of 90.9%), compared favorably against several strong baselines (e.g., CenterNet, FCOS, and nnU-Net). For spine parsing and abdominal multi-organ segmentation, our method achieves competitive results on par with state-of-the-art methods on the public CTSpine1K dataset and FLARE22 competition, respectively. Our annotations, code, and models are available at: https://github.com/alibaba-damo-academy/Med_Query.

cs.CV↗

arXiv2024

SGTC: Semantic-Guided Triplet Co-training for Sparsely Annotated Semi-Supervised Medical Image Segmentation

Although semi-supervised learning has made significant advances in the field of medical image segmentation, fully annotating a volumetric sample slice by slice remains a costly and time-consuming task. Even worse, most of the existing approaches pay much attention to image-level information and ignore semantic features, resulting in the inability to perceive weak boundaries. To address these issues, we propose a novel Semantic-Guided Triplet Co-training (SGTC) framework, which achieves high-end medical image segmentation by only annotating three orthogonal slices of a few volumetric samples, significantly alleviating the burden of radiologists. Our method consist of two main components. Specifically, to enable semantic-aware, fine-granular segmentation and enhance the quality of pseudo-labels, a novel semantic-guided auxiliary learning mechanism is proposed based on the pretrained CLIP. In addition, focusing on a more challenging but clinically realistic scenario, a new triple-view disparity training strategy is proposed, which uses sparse annotations (i.e., only three labeled slices of a few volumes) to perform co-training between three sub-networks, significantly improving the robustness. Extensive experiments on three public medical datasets demonstrate that our method outperforms most state-of-the-art semi-supervised counterparts under sparse annotation settings. The source code is available at https://github.com/xmeimeimei/SGTC.

cs.CV↗

arXiv2024

Towards a Comprehensive, Efficient and Promptable Anatomic Structure Segmentation Model using 3D Whole-body CT Scans

Segment anything model (SAM) demonstrates strong generalization ability on natural image segmentation. However, its direct adaptation in medical image segmentation tasks shows significant performance drops. It also requires an excessive number of prompt points to obtain a reasonable accuracy. Although quite a few studies explore adapting SAM into medical image volumes, the efficiency of 2D adaptation methods is unsatisfactory and 3D adaptation methods are only capable of segmenting specific organs/tumors. In this work, we propose a comprehensive and scalable 3D SAM model for whole-body CT segmentation, named CT-SAM3D. Instead of adapting SAM, we propose a 3D promptable segmentation model using a (nearly) fully labeled CT dataset. To train CT-SAM3D effectively, ensuring the model's accurate responses to higher-dimensional spatial prompts is crucial, and 3D patch-wise training is required due to GPU memory constraints. Therefore, we propose two key technical developments: 1) a progressively and spatially aligned prompt encoding method to effectively encode click prompts in local 3D space; and 2) a cross-patch prompt scheme to capture more 3D spatial context, which is beneficial for reducing the editing workloads when interactively prompting on large organs. CT-SAM3D is trained using a curated dataset of 1204 CT scans containing 107 whole-body anatomies and extensively validated using five datasets, achieving significantly better results against all previous SAM-derived models. Code, data, and our 3D interactive segmentation tool with quasi-real-time responses are available at https://github.com/alibaba-damo-academy/ct-sam3d.

cs.CV↗

arXiv2024

Decision Transformer vs. Decision Mamba: Analysing the Complexity of Sequential Decision Making in Atari Games

This work analyses the disparity in performance between Decision Transformer (DT) and Decision Mamba (DM) in sequence modelling reinforcement learning tasks for different Atari games. The study first observed that DM generally outperformed DT in the games Breakout and Qbert, while DT performed better in more complicated games, such as Hero and Kung Fu Master. To understand these differences, we expanded the number of games to 12 and performed a comprehensive analysis of game characteristics, including action space complexity, visual complexity, average trajectory length, and average steps to the first non-zero reward. In order to further analyse the key factors that impact the disparity in performance between DT and DM, we employ various approaches, including quantifying visual complexity, random forest regression, correlation analysis, and action space simplification strategies. The results indicate that the performance gap between DT and DM is affected by the complex interaction of multiple factors, with the complexity of the action space and visual complexity (particularly evaluated by compression ratio) being the primary determining factors. DM performs well in environments with simple action and visual elements, while DT shows an advantage in games with higher action and visual complexity. Our findings contribute to a deeper understanding of how the game characteristics affect the performance difference in sequential modelling reinforcement learning, potentially guiding the development of future model design and applications for diverse and complex environments.

cs.LG↗

arXiv2024

SAFE: Slow and Fast Parameter-Efficient Tuning for Continual Learning with Pre-Trained Models

Continual learning aims to incrementally acquire new concepts in data streams while resisting forgetting previous knowledge. With the rise of powerful pre-trained models (PTMs), there is a growing interest in training incremental learning systems using these foundation models, rather than learning from scratch. Existing works often view PTMs as a strong initial point and directly apply parameter-efficient tuning (PET) in the first session for adapting to downstream tasks. In the following sessions, most methods freeze model parameters for tackling forgetting issues. However, applying PET directly to downstream data cannot fully explore the inherent knowledge in PTMs. Additionally, freezing the parameters in incremental sessions hinders models' plasticity to novel concepts not covered in the first session. To solve the above issues, we propose a Slow And Fast parameter-Efficient tuning (SAFE) framework. In particular, to inherit general knowledge from foundation models, we include a transfer loss function by measuring the correlation between the PTM and the PET-applied model. After calibrating in the first session, the slow efficient tuning parameters can capture more informative features, improving generalization to incoming classes. Moreover, to further incorporate novel concepts, we strike a balance between stability and plasticity by fixing slow efficient tuning parameters and continuously updating the fast ones. Specifically, a cross-classification loss with feature alignment is proposed to circumvent catastrophic forgetting. During inference, we introduce an entropy-based aggregation strategy to dynamically utilize the complementarity in the slow and fast learners. Extensive experiments on seven benchmark datasets verify the effectiveness of our method by significantly surpassing the state-of-the-art.

cs.LG↗

arXiv2024

End-to-end Multi-source Visual Prompt Tuning for Survival Analysis in Whole Slide Images

Survival analysis using pathology images poses a considerable challenge, as it requires the localization of relevant information from the multitude of tiles within whole slide images (WSIs). Current methods typically resort to a two-stage approach, where a pre-trained network extracts features from tiles, which are then used by survival models. This process, however, does not optimize the survival models in an end-to-end manner, and the pre-extracted features may not be ideally suited for survival prediction. To address this limitation, we present a novel end-to-end Visual Prompt Tuning framework for survival analysis, named VPTSurv. VPTSurv refines feature embeddings through an efficient encoder-decoder framework. The encoder remains fixed while the framework introduces tunable visual prompts and adaptors, thus permitting end-to-end training specifically for survival prediction by optimizing only the lightweight adaptors and the decoder. Moreover, the versatile VPTSurv framework accommodates multi-source information as prompts, thereby enriching the survival model. VPTSurv achieves substantial increases of 8.7% and 12.5% in the C-index on two immunohistochemical pathology image datasets. These significant improvements highlight the transformative potential of the end-to-end VPT framework over traditional two-stage methods.

eess.IV↗

arXiv2024

Model-agnostic explainable artificial intelligence for object detection in image data

In recent years, deep neural networks have been widely used for building high-performance Artificial Intelligence (AI) systems for computer vision applications. Object detection is a fundamental task in computer vision, which has been greatly progressed through developing large and intricate AI models. However, the lack of transparency is a big challenge that may not allow the widespread adoption of these models. Explainable artificial intelligence is a field of research where methods are developed to help users understand the behavior, decision logics, and vulnerabilities of AI systems. Previously, few explanation methods were developed for object detection based on random masking. However, random masks may raise some issues regarding the actual importance of pixels within an image. In this paper, we design and implement a black-box explanation method named Black-box Object Detection Explanation by Masking (BODEM) through adopting a hierarchical random masking approach for object detection systems. We propose a hierarchical random masking framework in which coarse-grained masks are used in lower levels to find salient regions within an image, and fine-grained mask are used to refine the salient regions in higher levels. Experimentations on various object detection datasets and models showed that BODEM can effectively explain the behavior of object detectors. Moreover, our method outperformed Detector Randomized Input Sampling for Explanation (D-RISE) and Local Interpretable Model-agnostic Explanations (LIME) with respect to different quantitative measures of explanation effectiveness. The experimental results demonstrate that BODEM can be an effective method for explaining and validating object detection systems in black-box testing scenarios.

cs.CV↗

arXiv2024

Improved Esophageal Varices Assessment from Non-Contrast CT Scans

Esophageal varices (EV), a serious health concern resulting from portal hypertension, are traditionally diagnosed through invasive endoscopic procedures. Despite non-contrast computed tomography (NC-CT) imaging being a less expensive and non-invasive imaging modality, it has yet to gain full acceptance as a primary clinical diagnostic tool for EV evaluation. To overcome existing diagnostic challenges, we present the Multi-Organ-cOhesion-Network (MOON), a novel framework enhancing the analysis of critical organ features in NC-CT scans for effective assessment of EV. Drawing inspiration from the thorough assessment practices of radiologists, MOON establishes a cohesive multiorgan analysis model that unifies the imaging features of the related organs of EV, namely esophagus, liver, and spleen. This integration significantly increases the diagnostic accuracy for EV. We have compiled an extensive NC-CT dataset of 1,255 patients diagnosed with EV, spanning three grades of severity. Each case is corroborated by endoscopic diagnostic results. The efficacy of MOON has been substantiated through a validation process involving multi-fold cross-validation on 1,010 cases and an independent test on 245 cases, exhibiting superior diagnostic performance compared to methods focusing solely on the esophagus (for classifying severe grade: AUC of 0.864 versus 0.803, and for moderate to severe grades: AUC of 0.832 versus 0.793). To our knowledge, MOON is the first work to incorporate a synchronized multi-organ NC-CT analysis for EV assessment, providing a more acceptable and minimally invasive alternative for patients compared to traditional endoscopy.

eess.IV↗

arXiv2024

LIDIA: Precise Liver Tumor Diagnosis on Multi-Phase Contrast-Enhanced CT via Iterative Fusion and Asymmetric Contrastive Learning

The early detection and precise diagnosis of liver tumors are tasks of critical clinical value, yet they pose significant challenges due to the high heterogeneity and variability of liver tumors. In this work, a precise LIver tumor DIAgnosis network on multi-phase contrast-enhance CT, named LIDIA, is proposed for real-world scenario. To fully utilize all available phases in contrast-enhanced CT, LIDIA first employs the iterative fusion module to aggregate variable numbers of image phases, thereby capturing the features of lesions at different phases for better tumor diagnosis. To effectively mitigate the high heterogeneity problem of liver tumors, LIDIA incorporates asymmetric contrastive learning to enhance the discriminability between different classes. To evaluate our method, we constructed a large-scale dataset comprising 1,921 patients and 8,138 lesions. LIDIA has achieved an average AUC of 93.6% across eight different types of lesions, demonstrating its effectiveness. Besides, LIDIA also demonstrated strong generalizability with an average AUC of 89.3% when tested on an external cohort of 828 patients.

cs.CV↗

arXiv2024

Image steganography based on generative implicit neural representation

In the realm of advanced steganography, the scale of the model typically correlates directly with the resolution of the fundamental grid, necessitating the training of a distinct neural network for message extraction. This paper proposes an image steganography based on generative implicit neural representation. This approach transcends the constraints of image resolution by portraying data as continuous functional expressions. Notably, this method permits the utilization of a diverse array of multimedia data as cover images, thereby broadening the spectrum of potential carriers. Additionally, by fixing a neural network as the message extractor, we effectively redirect the training burden to the image itself, resulting in both a reduction in computational overhead and an enhancement in steganographic speed. This approach also circumvents potential transmission challenges associated with the message extractor. Experimental findings reveal that this methodology achieves a commendable optimization efficiency, achieving a completion time of just 3 seconds for 64x64 dimensional images, while concealing only 1 bpp of information. Furthermore, the accuracy of message extraction attains an impressive mark of 100%.

cs.CR↗

arXiv2024

Dual Relation Mining Network for Zero-Shot Learning

Zero-shot learning (ZSL) aims to recognize novel classes through transferring shared semantic knowledge (e.g., attributes) from seen classes to unseen classes. Recently, attention-based methods have exhibited significant progress which align visual features and attributes via a spatial attention mechanism. However, these methods only explore visual-semantic relationship in the spatial dimension, which can lead to classification ambiguity when different attributes share similar attention regions, and semantic relationship between attributes is rarely discussed. To alleviate the above problems, we propose a Dual Relation Mining Network (DRMN) to enable more effective visual-semantic interactions and learn semantic relationship among attributes for knowledge transfer. Specifically, we introduce a Dual Attention Block (DAB) for visual-semantic relationship mining, which enriches visual information by multi-level feature fusion and conducts spatial attention for visual to semantic embedding. Moreover, an attribute-guided channel attention is utilized to decouple entangled semantic features. For semantic relationship modeling, we utilize a Semantic Interaction Transformer (SIT) to enhance the generalization of attribute representations among images. Additionally, a global classification branch is introduced as a complement to human-defined semantic attributes, and we then combine the results with attribute-based classification. Extensive experiments demonstrate that the proposed DRMN leads to new state-of-the-art performances on three standard ZSL benchmarks, i.e., CUB, SUN, and AwA2.

cs.CV↗

arXiv2024

Anchor-based Robust Finetuning of Vision-Language Models

We aim at finetuning a vision-language model without hurting its out-of-distribution (OOD) generalization. We address two types of OOD generalization, i.e., i) domain shift such as natural to sketch images, and ii) zero-shot capability to recognize the category that was not contained in the finetune data. Arguably, the diminished OOD generalization after finetuning stems from the excessively simplified finetuning target, which only provides the class information, such as ``a photo of a [CLASS]''. This is distinct from the process in that CLIP was pretrained, where there is abundant text supervision with rich semantic information. Therefore, we propose to compensate for the finetune process using auxiliary supervision with rich semantic information, which acts as anchors to preserve the OOD generalization. Specifically, two types of anchors are elaborated in our method, including i) text-compensated anchor which uses the images from the finetune set but enriches the text supervision from a pretrained captioner, ii) image-text-pair anchor which is retrieved from the dataset similar to pretraining data of CLIP according to the downstream task, associating with the original CLIP text with rich semantics. Those anchors are utilized as auxiliary semantic information to maintain the original feature space of CLIP, thereby preserving the OOD generalization capabilities. Comprehensive experiments demonstrate that our method achieves in-distribution performance akin to conventional finetuning while attaining new state-of-the-art results on domain shift and zero-shot learning benchmarks.

cs.CV↗

arXiv2024

CycleINR: Cycle Implicit Neural Representation for Arbitrary-Scale Volumetric Super-Resolution of Medical Data

In the realm of medical 3D data, such as CT and MRI images, prevalent anisotropic resolution is characterized by high intra-slice but diminished inter-slice resolution. The lowered resolution between adjacent slices poses challenges, hindering optimal viewing experiences and impeding the development of robust downstream analysis algorithms. Various volumetric super-resolution algorithms aim to surmount these challenges, enhancing inter-slice resolution and overall 3D medical imaging quality. However, existing approaches confront inherent challenges: 1) often tailored to specific upsampling factors, lacking flexibility for diverse clinical scenarios; 2) newly generated slices frequently suffer from over-smoothing, degrading fine details, and leading to inter-slice inconsistency. In response, this study presents CycleINR, a novel enhanced Implicit Neural Representation model for 3D medical data volumetric super-resolution. Leveraging the continuity of the learned implicit function, the CycleINR model can achieve results with arbitrary up-sampling rates, eliminating the need for separate training. Additionally, we enhance the grid sampling in CycleINR with a local attention mechanism and mitigate over-smoothing by integrating cycle-consistent loss. We introduce a new metric, Slice-wise Noise Level Inconsistency (SNLI), to quantitatively assess inter-slice noise level inconsistency. The effectiveness of our approach is demonstrated through image quality evaluations on an in-house dataset and a downstream task analysis on the Medical Segmentation Decathlon liver tumor dataset.

eess.IV↗

arXiv2024

Modality-Agnostic Structural Image Representation Learning for Deformable Multi-Modality Medical Image Registration

Establishing dense anatomical correspondence across distinct imaging modalities is a foundational yet challenging procedure for numerous medical image analysis studies and image-guided radiotherapy. Existing multi-modality image registration algorithms rely on statistical-based similarity measures or local structural image representations. However, the former is sensitive to locally varying noise, while the latter is not discriminative enough to cope with complex anatomical structures in multimodal scans, causing ambiguity in determining the anatomical correspondence across scans with different modalities. In this paper, we propose a modality-agnostic structural representation learning method, which leverages Deep Neighbourhood Self-similarity (DNS) and anatomy-aware contrastive learning to learn discriminative and contrast-invariance deep structural image representations (DSIR) without the need for anatomical delineations or pre-aligned training images. We evaluate our method on multiphase CT, abdomen MR-CT, and brain MR T1w-T2w registration. Comprehensive results demonstrate that our method is superior to the conventional local structural representation and statistical-based similarity measures in terms of discriminability and accuracy.

cs.CV↗

arXiv2024

SAME++: A Self-supervised Anatomical eMbeddings Enhanced medical image registration framework using stable sampling and regularized transformation

Image registration is a fundamental medical image analysis task. Ideally, registration should focus on aligning semantically corresponding voxels, i.e., the same anatomical locations. However, existing methods often optimize similarity measures computed directly on intensities or on hand-crafted features, which lack anatomical semantic information. These similarity measures may lead to sub-optimal solutions where large deformations, complex anatomical differences, or cross-modality imagery exist. In this work, we introduce a fast and accurate method for unsupervised 3D medical image registration building on top of a Self-supervised Anatomical eMbedding (SAM) algorithm, which is capable of computing dense anatomical correspondences between two images at the voxel level. We name our approach SAM-Enhanced registration (SAME++), which decomposes image registration into four steps: affine transformation, coarse deformation, deep non-parametric transformation, and instance optimization. Using SAM embeddings, we enhance these steps by finding more coherent correspondence and providing features with better semantic guidance. We extensively evaluated SAME++ using more than 50 labeled organs on three challenging inter-subject registration tasks of different body parts. As a complete registration framework, SAME++ markedly outperforms leading methods by $4.2\%$ - $8.2\%$ in terms of Dice score while being orders of magnitude faster than numerical optimization-based methods. Code is available at \url{https://github.com/alibaba-damo-academy/same}.

cs.CV↗

arXiv2024

Model Tailor: Mitigating Catastrophic Forgetting in Multi-modal Large Language Models

Catastrophic forgetting emerges as a critical challenge when fine-tuning multi-modal large language models (MLLMs), where improving performance on unseen tasks often leads to a significant performance drop on the original tasks. This paper presents a comprehensive analysis of catastrophic forgetting in MLLMs and introduces a post-training adjustment method called Model Tailor. Our method primarily preserves the pre-trained parameters while replacing a small number ($\leq$ 10\%) of fine-tuned parameters, maintaining $\sim$ 99\% effectiveness on original tasks versus pre-training, and achieving $\sim$ 97\% on new tasks compared to standard fine-tuning. Specifically, we derive a sparse mask to identify the "model patch", based on a fusion strategy that integrates salience and sensitivity analysis. Subsequently, a compensation mechanism is introduced to "decorate the patch", enhancing the model's performance on both target and original tasks. Additionally, our method is adaptable to multi-task scenarios. Through extensive experiments on InstructBLIP and LLaVA-1.5 in both image captioning and visual question answering tasks, our approach demonstrates significant task adaptability while preserving inherent pre-trained capabilities.

cs.CL↗

arXiv2024

Surface mobility gradient and emergent facilitation in glassy films

Confining glassy polymer into films can substantially modify their local and film-averaged properties. We present a lattice model of film geometry with void-mediated facilitation behaviors but free from any elasticity effect. We analyze the spatially varying viscosity to delineate the transport property of glassy films. The film mobility measurements reported by [Yang et. al., Science, 2010, 328, 1676] are successfully reproduced. The flow exhibits a crossover from simple viscous flow to a surface-dominated regime as temperature decreases. The propagation of a highly mobile front induced by the free surface is visualized in real space. Our approach provides a microscopic treatment of the observed glassy phenomena.

cond-mat.soft↗

arXiv2024

UAE: Universal Anatomical Embedding on Multi-modality Medical Images

Identifying specific anatomical structures (\textit{e.g.}, lesions or landmarks) in medical images plays a fundamental role in medical image analysis. Exemplar-based landmark detection methods are receiving increasing attention since they can detect arbitrary anatomical points in inference while do not need landmark annotations in training. They use self-supervised learning to acquire a discriminative embedding for each voxel within the image. These approaches can identify corresponding landmarks through nearest neighbor matching and has demonstrated promising results across various tasks. However, current methods still face challenges in: (1) differentiating voxels with similar appearance but different semantic meanings (\textit{e.g.}, two adjacent structures without clear borders); (2) matching voxels with similar semantics but markedly different appearance (\textit{e.g.}, the same vessel before and after contrast injection); and (3) cross-modality matching (\textit{e.g.}, CT-MRI landmark-based registration). To overcome these challenges, we propose universal anatomical embedding (UAE), which is a unified framework designed to learn appearance, semantic, and cross-modality anatomical embeddings. Specifically, UAE incorporates three key innovations: (1) semantic embedding learning with prototypical contrastive loss; (2) a fixed-point-based matching strategy; and (3) an iterative approach for cross-modality embedding learning. We thoroughly evaluated UAE across intra- and inter-modality tasks, including one-shot landmark detection, lesion tracking on longitudinal CT scans, and CT-MRI affine/rigid registration with varying field of view. Our results suggest that UAE outperforms state-of-the-art methods, offering a robust and versatile approach for landmark based medical image analysis tasks. Code and trained models are available at: \href{https://shorturl.at/bgsB3}

cs.CV↗