AttriPrompter: Auto-Prompting with Attribute Semantics for Zero-shot Nuclei Detection via Visual-Language Pre-trained Models

Large-scale visual-language pre-trained models (VLPMs) have demonstrated exceptional performance in downstream object detection through text prompts for natural scenes. However, their application to zero-shot nuclei detection on histopathology images remains relatively unexplored, mainly due to the significant gap between the characteristics of medical images and the web-originated text-image pairs used for pre-training. This paper aims to investigate the potential of the object-level VLPM, Grounded Language-Image Pre-training (GLIP), for zero-shot nuclei detection. Specifically, we propose an innovative auto-prompting pipeline, named AttriPrompter, comprising attribute generation, attribute augmentation, and relevance sorting, to avoid subjective manual prompt design. AttriPrompter utilizes VLPMs' text-to-image alignment to create semantically rich text prompts, which are then fed into GLIP for initial zero-shot nuclei detection. Additionally, we propose a self-trained knowledge distillation framework, where GLIP serves as the teacher with its initial predictions used as pseudo labels, to address the challenges posed by high nuclei density, including missed detections, false positives, and overlapping instances. Our method exhibits remarkable performance in label-free nuclei detection, outperforming all existing unsupervised methods and demonstrating excellent generality. Notably, this work highlights the astonishing potential of VLPMs pre-trained on natural image-text pairs for downstream tasks in the medical field as well. Code will be released at https://github.com/wuyongjianCODE/AttriPrompter.

SDPT: Synchronous Dual Prompt Tuning for Fusion-based Visual-Language Pre-trained Models

Prompt tuning methods have achieved remarkable success in parameter-efficient fine-tuning on large pre-trained models. However, their application to dual-modal fusion-based visual-language pre-trained models (VLPMs), such as GLIP, has encountered issues. Existing prompt tuning methods have not effectively addressed the modal mapping and aligning problem for tokens in different modalities, leading to poor transfer generalization. To address this issue, we propose Synchronous Dual Prompt Tuning (SDPT). SDPT initializes a single set of learnable unified prototype tokens in the established modal aligning space to represent the aligned semantics of text and image modalities for downstream tasks. Furthermore, SDPT establishes inverse linear projections that require no training to embed the information of unified prototype tokens into the input space of different modalities. The inverse linear projections allow the unified prototype token to synchronously represent the two modalities and enable SDPT to share the unified semantics of text and image for downstream tasks across different modal prompts. Experimental results demonstrate that SDPT assists fusion-based VLPMs to achieve superior outcomes with only 0.04\% of model parameters for training across various scenarios, outperforming other single- or dual-modal methods. The code will be released at https://github.com/wuyongjianCODE/SDPT.

Restore-RWKV: Efficient and Effective Medical Image Restoration with RWKV

Transformers have revolutionized medical image restoration, but the quadratic complexity still poses limitations for their application to high-resolution medical images. The recent advent of RWKV in the NLP field has attracted much attention as it can process long sequences efficiently. To leverage its advanced design, we propose Restore-RWKV, the first RWKV-based model for medical image restoration. Since the original RWKV model is designed for 1D sequences, we make two necessary modifications for modeling spatial relations in 2D images. First, we present a recurrent WKV (Re-WKV) attention mechanism that captures global dependencies with linear computational complexity. Re-WKV incorporates bidirectional attention as basic for a global receptive field and recurrent attention to effectively model 2D dependencies from various scan directions. Second, we develop an omnidirectional token shift (Omni-Shift) layer that enhances local dependencies by shifting tokens from all directions and across a wide context range. These adaptations make the proposed Restore-RWKV an efficient and effective model for medical image restoration. Extensive experiments demonstrate that Restore-RWKV achieves superior performance across various medical image restoration tasks, including MRI image super-resolution, CT image denoising, PET image synthesis, and all-in-one medical image restoration. Code is available at: \href{https://github.com/Yaziwel/Restore-RWKV.git}{https://github.com/Yaziwel/Restore-RWKV}.

Region Attention Transformer for Medical Image Restoration

Transformer-based methods have demonstrated impressive results in medical image restoration, attributed to the multi-head self-attention (MSA) mechanism in the spatial dimension. However, the majority of existing Transformers conduct attention within fixed and coarsely partitioned regions (\text{e.g.} the entire image or fixed patches), resulting in interference from irrelevant regions and fragmentation of continuous image content. To overcome these challenges, we introduce a novel Region Attention Transformer (RAT) that utilizes a region-based multi-head self-attention mechanism (R-MSA). The R-MSA dynamically partitions the input image into non-overlapping semantic regions using the robust Segment Anything Model (SAM) and then performs self-attention within these regions. This region partitioning is more flexible and interpretable, ensuring that only pixels from similar semantic regions complement each other, thereby eliminating interference from irrelevant regions. Moreover, we introduce a focal region loss to guide our model to adaptively focus on recovering high-difficulty regions. Extensive experiments demonstrate the effectiveness of RAT in various medical image restoration tasks, including PET image synthesis, CT image denoising, and pathological image super-resolution. Code is available at \href{https://github.com/Yaziwel/Region-Attention-Transformer-for-Medical-Image-Restoration.git}{https://github.com/RAT}.

All-In-One Medical Image Restoration via Task-Adaptive Routing

Although single-task medical image restoration (MedIR) has witnessed remarkable success, the limited generalizability of these methods poses a substantial obstacle to wider application. In this paper, we focus on the task of all-in-one medical image restoration, aiming to address multiple distinct MedIR tasks with a single universal model. Nonetheless, due to significant differences between different MedIR tasks, training a universal model often encounters task interference issues, where different tasks with shared parameters may conflict with each other in the gradient update direction. This task interference leads to deviation of the model update direction from the optimal path, thereby affecting the model's performance. To tackle this issue, we propose a task-adaptive routing strategy, allowing conflicting tasks to select different network paths in spatial and channel dimensions, thereby mitigating task interference. Experimental results demonstrate that our proposed \textbf{A}ll-in-one \textbf{M}edical \textbf{I}mage \textbf{R}estoration (\textbf{AMIR}) network achieves state-of-the-art performance in three MedIR tasks: MRI super-resolution, CT denoising, and PET synthesis, both in single-task and all-in-one settings. The code and data will be available at \href{https://github.com/Yaziwel/All-In-One-Medical-Image-Restoration-via-Task-Adaptive-Routing.git}{https://github.com/Yaziwel/AMIR}.

DRMC: A Generalist Model with Dynamic Routing for Multi-Center PET Image Synthesis

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, \textit{i.e.} the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis.

Zero-shot Nuclei Detection via Visual-Language Pre-trained Models

Large-scale visual-language pre-trained models (VLPM) have proven their excellent performance in downstream object detection for natural scenes. However, zero-shot nuclei detection on H\&E images via VLPMs remains underexplored. The large gap between medical images and the web-originated text-image pairs used for pre-training makes it a challenging task. In this paper, we attempt to explore the potential of the object-level VLPM, Grounded Language-Image Pre-training (GLIP) model, for zero-shot nuclei detection. Concretely, an automatic prompts design pipeline is devised based on the association binding trait of VLPM and the image-to-text VLPM BLIP, avoiding empirical manual prompts engineering. We further establish a self-training framework, using the automatically designed prompts to generate the preliminary results as pseudo labels from GLIP and refine the predicted boxes in an iterative manner. Our method achieves a remarkable performance for label-free nuclei detection, surpassing other comparison methods. Foremost, our work demonstrates that the VLPM pre-trained on natural image-text pairs exhibits astonishing potential for downstream tasks in the medical field as well. Code will be released at https://github.com/wuyongjianCODE/VLPMNuD.

Cyclic Learning: Bridging Image-level Labels and Nuclei Instance Segmentation

Nuclei instance segmentation on histopathology images is of great clinical value for disease analysis. Generally, fully-supervised algorithms for this task require pixel-wise manual annotations, which is especially time-consuming and laborious for the high nuclei density. To alleviate the annotation burden, we seek to solve the problem through image-level weakly supervised learning, which is underexplored for nuclei instance segmentation. Compared with most existing methods using other weak annotations (scribble, point, etc.) for nuclei instance segmentation, our method is more labor-saving. The obstacle to using image-level annotations in nuclei instance segmentation is the lack of adequate location information, leading to severe nuclei omission or overlaps. In this paper, we propose a novel image-level weakly supervised method, called cyclic learning, to solve this problem. Cyclic learning comprises a front-end classification task and a back-end semi-supervised instance segmentation task to benefit from multi-task learning (MTL). We utilize a deep learning classifier with interpretability as the front-end to convert image-level labels to sets of high-confidence pseudo masks and establish a semi-supervised architecture as the back-end to conduct nuclei instance segmentation under the supervision of these pseudo masks. Most importantly, cyclic learning is designed to circularly share knowledge between the front-end classifier and the back-end semi-supervised part, which allows the whole system to fully extract the underlying information from image-level labels and converge to a better optimum. Experiments on three datasets demonstrate the good generality of our method, which outperforms other image-level weakly supervised methods for nuclei instance segmentation, and achieves comparable performance to fully-supervised methods.

Transformer based multiple instance learning for weakly supervised histopathology image segmentation

Hispathological image segmentation algorithms play a critical role in computer aided diagnosis technology. The development of weakly supervised segmentation algorithm alleviates the problem of medical image annotation that it is time-consuming and labor-intensive. As a subset of weakly supervised learning, Multiple Instance Learning (MIL) has been proven to be effective in segmentation. However, there is a lack of related information between instances in MIL, which limits the further improvement of segmentation performance. In this paper, we propose a novel weakly supervised method for pixel-level segmentation in histopathology images, which introduces Transformer into the MIL framework to capture global or long-range dependencies. The multi-head self-attention in the Transformer establishes the relationship between instances, which solves the shortcoming that instances are independent of each other in MIL. In addition, deep supervision is introduced to overcome the limitation of annotations in weakly supervised methods and make the better utilization of hierarchical information. The state-of-the-art results on the colon cancer dataset demonstrate the superiority of the proposed method compared with other weakly supervised methods. It is worth believing that there is a potential of our approach for various applications in medical images.

Group based Personalized Search by Integrating Search Behaviour and Friend Network

The key to personalized search is to build the user profile based on historical behaviour. To deal with the users who lack historical data, group based personalized models were proposed to incorporate the profiles of similar users when re-ranking the results. However, similar users are mostly found based on simple lexical or topical similarity in search behaviours. In this paper, we propose a neural network enhanced method to highlight similar users in semantic space. Furthermore, we argue that the behaviour-based similar users are still insufficient to understand a new query when user's historical activities are limited. To tackle this issue, we introduce the friend network into personalized search to determine the closeness between users in another way. Since the friendship is often formed based on similar background or interest, there are plenty of personalized signals hidden in the friend network naturally. Specifically, we propose a friend network enhanced personalized search model, which groups the user into multiple friend circles based on search behaviours and friend relations respectively. These two types of friend circles are complementary to construct a more comprehensive group profile for refining the personalization. Experimental results show the significant improvement of our model over existing personalized search models.