Mingrui Ma

Mingrui Ma, Lei Song, Yuanbo Xu et al.

Medical image registration is a fundamental and critical task in medical image analysis. With the rapid development of deep learning, convolutional neural networks (CNN) have dominated the medical image registration field. Due to the disadvantage of the local receptive field of CNN, some recent registration methods have focused on using transformers for non-local registration. However, the standard Transformer has a vast number of parameters and high computational complexity, which causes Transformer can only be applied at the bottom of the registration models. As a result, only coarse information is available at the lowest resolution, limiting the contribution of Transformer in their models. To address these challenges, we propose a convolution-based efficient multi-head self-attention (CEMSA) block, which reduces the parameters of the traditional Transformer and captures local spatial context information for reducing semantic ambiguity in the attention mechanism. Based on the proposed CEMSA, we present a novel Symmetric Transformer-based model (SymTrans). SymTrans employs the Transformer blocks in the encoder and the decoder respectively to model the long-range spatial cross-image relevance. We apply SymTrans to the displacement field and diffeomorphic registration. Experimental results show that our proposed method achieves state-of-the-art performance in image registration. Our code is publicly available at \url{https://github.com/MingR-Ma/SymTrans}.

Mingrui Ma, Weijie Wang, Jie Ning et al.

The challenge of Multimodal Deformable Image Registration (MDIR) lies in the conversion and alignment of features between images of different modalities. Generative models (GMs) cannot retain the necessary information enough from the source modality to the target one, while non-GMs struggle to align features across these two modalities. In this paper, we propose a novel coarse-to-fine MDIR framework,LLM-Morph, which is applicable to various pre-trained Large Language Models (LLMs) to solve these concerns by aligning the deep features from different modal medical images. Specifically, we first utilize a CNN encoder to extract deep visual features from cross-modal image pairs, then we use the first adapter to adjust these tokens, and use LoRA in pre-trained LLMs to fine-tune their weights, both aimed at eliminating the domain gap between the pre-trained LLMs and the MDIR task. Third, for the alignment of tokens, we utilize other four adapters to transform the LLM-encoded tokens into multi-scale visual features, generating multi-scale deformation fields and facilitating the coarse-to-fine MDIR task. Extensive experiments in MR-CT Abdomen and SR-Reg Brain datasets demonstrate the effectiveness of our framework and the potential of pre-trained LLMs for MDIR task. Our code is availabel at: https://github.com/ninjannn/LLM-Morph.

Mingrui Ma, Tao Wang, Lei Song et al.

The Swin transformer has recently attracted attention in medical image analysis due to its computational efficiency and long-range modeling capability. Owing to these properties, the Swin Transformer is suitable for establishing more distant relationships between corresponding voxels in different positions in complex abdominal image registration tasks. However, the registration models based on transformers combine multiple voxels into a single semantic token. This merging process limits the transformers to model and generate coarse-grained spatial information. To address this issue, we propose Recovery Feature Resolution Network (RFRNet), which allows the transformer to contribute fine-grained spatial information and rich semantic correspondences to higher resolution levels. Furthermore, shifted window partitioning operations are inflexible, indicating that they cannot perceive the semantic information over uncertain distances and automatically bridge the global connections between windows. Therefore, we present a Weighted Window Attention (WWA) to build global interactions between windows automatically. It is implemented after the regular and cyclic shift window partitioning operations within the Swin transformer block. The proposed unsupervised deformable image registration model, named RFR-WWANet, detects the long-range correlations, and facilitates meaningful semantic relevance of anatomical structures. Qualitative and quantitative results show that RFR-WWANet achieves significant improvements over the current state-of-the-art methods. Ablation experiments demonstrate the effectiveness of the RFRNet and WWA designs. Our code is available at \url{https://github.com/MingR-Ma/RFR-WWANet}.

Mingrui Ma, Chentao Li, Pan Huang et al.

Whole slide images (WSIs) are the gold standard for pathological diagnosis and sub-typing. Current main-stream two-step frameworks employ offline feature encoders trained without domain-specific knowledge. Among them, attention-based multiple instance learning (MIL) methods are outcome-oriented and offer limited interpretability. Clustering-based approaches can provide explainable decision-making process but suffer from high dimension features and semantically ambiguous centroids. To this end, we propose an end-to-end MIL framework that integrates Grassmann re-embedding and manifold adaptive clustering, where the manifold geometric structure facilitates robust clustering results. Furthermore, we design a prior knowledge guiding proxy instance labeling and aggregation strategy to approximate patch labels and focus on pathologically relevant tumor regions. Experiments on multicentre WSI datasets demonstrate that: 1) our cluster-incorporated model achieves superior performance in both grading accuracy and interpretability; 2) end-to-end learning refines better feature representations and it requires acceptable computation resources.

Mingrui Ma, Lansheng Han, Chunjie Zhou

Transformer, as one of the most advanced neural network models in Natural Language Processing (NLP), exhibits diverse applications in the field of anomaly detection. To inspire research on Transformer-based anomaly detection, this review offers a fresh perspective on the concept of anomaly detection. We explore the current challenges of anomaly detection and provide detailed insights into the operating principles of Transformer and its variants in anomaly detection tasks. Additionally, we delineate various application scenarios for Transformer-based anomaly detection models and discuss the datasets and evaluation metrics employed. Furthermore, this review highlights the key challenges in Transformer-based anomaly detection research and conducts a comprehensive analysis of future research trends in this domain. The review includes an extensive compilation of over 100 core references related to Transformer-based anomaly detection. To the best of our knowledge, this is the first comprehensive review that focuses on the research related to Transformer in the context of anomaly detection. We hope that this paper can provide detailed technical information to researchers interested in Transformer-based anomaly detection tasks.

Mingrui Ma, Lansheng Han, Chunjie Zhou

Webshell, as the "culprit" behind numerous network attacks, is one of the research hotspots in the field of cybersecurity. However, the complexity, stealthiness, and confusing nature of webshells pose significant challenges to the corresponding detection schemes. With the rise of Artificial Intelligence (AI) technology, researchers have started to apply different intelligent algorithms and neural network architectures to the task of webshell detection. However, the related research still lacks a systematic and standardized methodological process, which is confusing and redundant. Therefore, following the development timeline, we carefully summarize the progress of relevant research in this field, dividing it into three stages: Start Stage, Initial Development Stage, and In-depth Development Stage. We further elaborate on the main characteristics and core algorithms of each stage. In addition, we analyze the pain points and challenges that still exist in this field and predict the future development trend of this field from our point of view. To the best of our knowledge, this is the first review that details the research related to AI-based webshell detection. It is also hoped that this paper can provide detailed technical information for more researchers interested in AI-based webshell detection tasks.

Mingrui Ma, Lansheng Han, Chunjie Zhou

The frequent occurrence of cyber-attacks has made webshell attacks and defense gradually become a research hotspot in the field of network security. However, the lack of publicly available benchmark datasets and the over-reliance on manually defined rules for webshell escape sample generation have slowed down the progress of research related to webshell escape sample generation and artificial intelligence (AI)-based webshell detection. To address the drawbacks of weak webshell sample escape capabilities, the lack of webshell datasets with complex malicious features, and to promote the development of webshell detection, we propose the Hybrid Prompt algorithm for webshell escape sample generation with the help of large language models. As a prompt algorithm specifically developed for webshell sample generation, the Hybrid Prompt algorithm not only combines various prompt ideas including Chain of Thought, Tree of Thought, but also incorporates various components such as webshell hierarchical module and few-shot example to facilitate the LLM in learning and reasoning webshell escape strategies. Experimental results show that the Hybrid Prompt algorithm can work with multiple LLMs with excellent code reasoning ability to generate high-quality webshell samples with high Escape Rate (88.61% with GPT-4 model on VirusTotal detection engine) and (Survival Rate 54.98% with GPT-4 model).