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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Tong, Zhan Wu, Zhan Yang, Yang Mao, Weilong Wang, Shijie Li, Yinsheng Chen, Yang Southeast University Laboratory of Image Science and Technology Nanjing210096 China Southeast University Ministry of Education Key Laboratory of Computer Network and Information Integration Nanjing210096 China Chinese Academy of Sciences Research Center for Medical Artificial Intelligence Shenzhen Institutes of Advanced Technology Shenzhen518055 China School of Computer Science and Engineering Key Lab. of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing The Laboratory of Image Science and Technology Nanjing210096 China

ISBN: (纸本)9798350337488

Computed Tomography (CT) is an imaging technique widely used in clinical diagnosis. However, high-attenuation metallic implants result in the obstruction of low-energy Xrays and further lead to metal artifacts in the reconstructed CT images. Deep supervised model-based metal artifact reduction(MAR) approaches are limited in clinical applications due to the difficulty in obtaining paired artifact-affected and artifactfree data. Furthermore, these model-based methods lack the consideration of data consistency in the sinogram-domain to perform exact metal trace inpainting. To address these challenges, we propose a Data-consistent unsupErVised diffusiOn model for meTal artifact rEDuction, called DEVOTED-Net. First, DEVOTED-Net leverages prior knowledge to guide the conditional diffusion model for fine-grained metal trace inpainting. Second, an unsupervised MAR framework is designed in the reverse process for the unknown metal traces restoration in the sinogram domain. Third, to further enhance the sinogram-domain data consistency, physics-based consistency constraint loss including conjugateray consistency loss and accumulation-ray consistency loss is designed. Extensive experiments are carried out to verify the performance of our algorithm on the publicly available dataset and clinical experimental dataset. This efficient, accurate, and reliable MAR approach holds great potential in clinics. © 2023 IEEE.

关键词： computed tomography deep unsupervised learning denoising diffusion probabilistic model Metal artifact reduction physics-based consistency constraint

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eSROP Attack: Leveraging Signal Handler to Implement Turing-Complete Attack Under CFI Defense 1

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18th EAI International Conference on Security and Privacy in Communication Networks, SecureComm 2022

作者： Zhang, Tianning Cai, Miao Zhang, Diming Huang, Hao Department of Computer Science and Technology Nanjing University Nanjing China State Key Laboratory for Novel Software Technology Nanjing University Nanjing China Key Laboratory of Water Big Data Technology of Ministry of Water Resources Hohai University Nanjing China School of Computer and Information Hohai University Nanjing China College of Computer Engineering Jiangsu University of Science and Technology Nanjing China

ISBN: (数字)9783031255380

ISBN: (纸本)9783031255373

Signal Return Oriented Programming (SROP) is a dangerous code reuse attack method. Recently, defense techniques have been proposed to defeat SROP attacks. In this paper, we leverage the signal nesting mechanism provided by current operating systems and propose a new variant of SROP attack called enhanced SROP (eSROP) attack. eSROP provides the ability of invoking arbitrary system calls, simulating Turing-complete computation, and even bypassing the fine-grained label-based CFI defense, without modifying the return address and instruction register in the signal frame. Because the signal returns to the interrupted instruction, the shadow stack defense can hardly detect our attack. Signal has strong flexibility which can interrupt the normal control flow. We leverage such flexibility to design a new code reuse attack. To evaluate eSROP, we perform two exploits on two real-world programs, namely Proftpd and Wu-ftpd. In our attacks, adversaries can invoke arbitrary system calls and obtain a root shell. Both attacks succeed within 10 min under strict system defense such as data execution prevention, address space layout randomization, and coarse-grained control flow integrity. © 2023, ICST Institute for computer Sciences, Social Informatics and Telecommunications Engineering.

关键词： Network security

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AlphaFold2 and its applications in the fields of biology and medicine

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Signal Transduction and Targeted Therapy 2023年第4期8卷 1630-1643页

作者： Zhenyu Yang Xiaoxi Zeng Yi Zhao Runsheng Chen West China Biomedical Big Data Center West China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Intelligent Information Processing Advanced Computer Research CenterInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Pingshan Translational Medicine Center Shenzhen Bay LaboratoryShenzhen 518118China

AlphaFold2(AF2)is an artificial intelligence(AI)system developed by DeepMind that can predict three-dimensional(3D)structures of proteins from amino acid sequences with atomic-level *** structure prediction is one of the most challenging problems in computational biology and chemistry,and has puzzled scientists for 50 *** advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much *** release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community,especially in the fields of biology and ***2 is thought to have a significant impact on structural biology and research areas that need protein structure information,such as drug discovery,protein design,prediction of protein function,et *** the time is not long since AF2 was developed,there are already quite a few application studies of AF2 in the fields of biology and medicine,with many of them having preliminarily proved the potential of *** better understand AF2 and promote its applications,we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success,and particularly focus on reviewing its applications in the fields of biology and *** of current AF2 prediction will also be discussed.

关键词： system fields Fold

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VIDA: HOMEOSTATIC VISUAL DOMAIN ADAPTER FOR CONTINUAL TEST TIME ADAPTATION 12

VIDA: HOMEOSTATIC VISUAL DOMAIN ADAPTER FOR CONTINUAL TEST T...

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12th International Conference on Learning Representations, ICLR 2024

作者： Liu, Jiaming Yang, Senqiao Jia, Peidong Zhang, Renrui Lu, Ming Guo, Yandong Xue, Wei Zhang, Shanghang National Key Laboratory for Multimedia Information Processing School of Computer Science Peking University China AI2Robotics China The Chinese University of Hong Kong Hong Kong Hong Kong University of Science and Technology Hong Kong

Since real-world machine systems are running in non-stationary environments, Continual Test-Time Adaptation (CTTA) task is proposed to adapt the pre-trained model to continually changing target domains. Recently, existing methods mainly focus on model-based adaptation, which aims to leverage a self-training manner to extract the target domain knowledge. However, pseudo labels can be noisy and the updated model parameters are unreliable under dynamic data distributions, leading to error accumulation and catastrophic forgetting in the continual adaptation process. To tackle these challenges and maintain the model plasticity, we design a Visual Domain Adapter (ViDA) for CTTA, explicitly handling both domain-specific and domain-shared knowledge. Specifically, we first comprehensively explore the different domain representations of the adapters with trainable high-rank or low-rank embedding spaces. Then we inject ViDAs into the pre-trained model, which leverages high-rank and low-rank features to adapt the current domain distribution and maintain the continual domain-shared knowledge, respectively. To exploit the low-rank and high-rank ViDAs more effectively, we further propose a Homeostatic Knowledge Allotment (HKA) strategy, which adaptively combines different knowledge from each ViDA. Extensive experiments conducted on four widely used benchmarks demonstrate that our proposed method achieves state-of-the-art performance in both classification and segmentation CTTA tasks. Note that, our method can be regarded as a novel transfer paradigm for large-scale models, delivering promising results in adaptation to continually changing distributions. © 2024 12th International Conference on Learning Representations, ICLR 2024. All rights reserved.

关键词： Domain Knowledge

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Instance-Aware Diffusion Implicit Process for Box-Based Instance Segmentation 26

Instance-Aware Diffusion Implicit Process for Box-Based Inst...

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26th European Conference on Artificial Intelligence, ECAI 2023

作者： Ren, Hao Liu, Xingsong Huang, Junjian Wan, Ru Pu, Jian Lu, Hong Shanghai Key Laboratory of Intelligent Information Processing School of Computer Science Fudan University China Institute of Science and Technology for Brain-inspired Intelligence Fudan University China Mogo.ai Information and Technology Co. Ltd. Shanghai China

ISBN: (纸本)9781643684369

The diffusion model has demonstrated impressive performance in image generation, but its potential for discriminative tasks such as instance segmentation remains unexplored. In this paper, we propose an Instance-aware Diffusion Implicit Process (IDIP) framework for instance segmentation based on boxes. During training, IDIP diffuses ground-truth boxes across various time steps, extracting corresponding Region of Interest (RoI) features. Dynamic convolution is then used to predict boxes and categories for each RoI, and the mask head generates masks from these predictions. During inference, IDIP iteratively refines randomly generated boxes with the denoising diffusion implicit model, while the mask head derives final masks from RoIs based on the refined boxes. Our method surpasses existing approaches on the COCO benchmark, requiring fewer training steps and less memory resources due to its dynamic design and instance-aware characteristic. © 2023 The Authors.

关键词： Diffusion

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Three-Channel Graph Convolutional Network 24

Three-Channel Graph Convolutional Network

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24th IEEE International Conference on High Performance Computing and Communications, 8th IEEE International Conference on Data Science and Systems, 20th IEEE International Conference on Smart City and 8th IEEE International Conference on Dependability in Sensor, Cloud and Big Data Systems and Application, HPCC/DSS/SmartCity/DependSys 2022

作者： Meng, Lei Ye, Zhonglin Zhao, Haixing Yang, Yanlin Chen, Yang Wang, Zhaoyang College of Computer Qinghai Normal University Tibetan Information Processing Engineering Technology and Research Center of Qinghai Province The State Key Laboratory of Tibetan Intelligent Information Processing and Application Xining810008 China

ISBN: (纸本)9798350319934

At present, as an emerging direction of artificial intelligence, graph neural networks (GNNs) have developed rapidly and can solve many graph data problems efficiently. The real world is composed of a large number of networks. Compared with the widely studied single-relationship feature information networks, the real-world networks are mostly composed of multi-relationship feature information networks in which different types of objects are interconnected through complex relationships. Complex structural information and rich semantic information are included by multi-relationship feature information networks, thereby the real network can be restored more realistically. However, one type of relational feature of the network is merely considered by most of the existing GNNs, and the information of multi-relationship features and the hidden information between multi-relationship features are ignored in the network. In order to deal with these restrictions, a novel graph convolutional network (TCGCN) based on an attention mechanism is proposed, which aims to extract different relational features in multi-relationship feature networks and the hidden information between them more comprehensively, thereby improving the performance of GNNs in downstream tasks. In this paper, an improved attention mechanism is used to aggregate different types of single relational features, and the aggregated multiple single relational feature network information is fused with the mixed relational feature network information into the final node representation. The proposed TCGCN outperforms most other methods in extensive experiments conducted on three real-world datasets. © 2022 IEEE.

关键词： Graph neural networks

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Semantic Data Augmentation for Few-Shot Biomedical Named Entity Recognition

Semantic Data Augmentation for Few-Shot Biomedical Named Ent...

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2025 IEEE International Conference on Acoustics, Speech, and Signal processing, ICASSP 2025

作者： Zhang, Ying Wang, Weihua College of Computer Science Inner Mongolia University Hohhot China National and Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian Hohhot China Inner Mongolia Key Laboratory of Multilingual Artificial Intelligence Technology Hohhot China

ISBN: (纸本)9798350368741

Biomedical Named Entity Recognition (BioNER) aims to identify and classify entities in biomedical text. This task struggles with data scarcity due to limited annotated data. Although data augmentation is effective, existing methods fail to handle the complex semantic mappings on biomedical terminology, which results in the generated samples lacking semantic diversity. In this paper, we propose a data augmentation method to create semantically diverse and coherent training samples for few-shot BioNER. The method utilizes the Unified Medical Language System (UMLS) for entity replacement and combines with a Masked Language Model (MLM) to generate contextually relevant words. Experimental results show that our method improves BioNER performance in few-shot scenarios. Compared to all baseline models, our method achieves an average F1 score improvement of 7.6% and 11.6% on the NCBI and JNLPBA datasets, respectively. Our source code and data are available at https://***/ABC8184/SDA. © 2025 IEEE.

关键词： BioNER data augmentation few-shot learning masked language model UMLS

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DeepPointMap2: Accurate and Robust LiDAR-Visual SLAM with Neural Descriptors 24

DeepPointMap2: Accurate and Robust LiDAR-Visual SLAM with Ne...

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32nd ACM International Conference on Multimedia, MM 2024

作者： Zhang, Xiaze Ding, Ziheng Jing, Qi Cheng, Ying Ding, Wenchao Feng, Rui Fudan University Shanghai China The School of Computer Science Shanghai Key Laboratory of Intelligent Information Processing Fudan University China The Academy for Engineering and Technology Fudan University China The Shanghai Collaborative Innovation Center of Intelligent Visual Computing China

ISBN: (纸本)9798400706868

Simultaneous Localization and Mapping (SLAM) plays a pivotal role in autonomous driving and robotics. Existing methods often rely on hand-craft feature extraction and cross-modal fusion techniques, resulting in limited feature representation capability and reduced robustness. To address this challenge, we introduce DeepPointMap2, a novel learning-based LiDAR-Visual SLAM architecture that leverages neural descriptors to tackle multiple SLAM sub-tasks in a unified manner. Our approach employs neural networks to extract multi-modal tokens, which are then adaptively fused by the Visual-Point Fusion Module to generate sparse 3D neural descriptors, ensuring precise and robust performance. As a pioneering work, our method achieves state-of-the-art localization performance among various Visual-, LiDAR-, and Visual-LiDAR-based methods in widely-used benchmarks, as shown in the experiment results. Furthermore, the approach proves to be robust in scenarios involving camera failure and LiDAR obstruction. © 2024 ACM.

关键词： SLAM robotics

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Increasing Representative Ability for Topic Representation 34

Increasing Representative Ability for Topic Representation

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34th International Conference on Software Engineering and Knowledge Engineering, SEKE 2022

作者： Yan, Rong Tang, Ailing Zhang, Ziyi College of Computer Science Inner Mongolia University Inner Mongolia Key Laboratory of Mongolian Information Processing Technology National & Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian Hohhot010021 China

ISBN: (纸本)1891706543

As for standard topic model, such as LDA (Latent Dirichlet Allocation), each topic is generally depicted by a weighted word set, where the high-ranked words are deemed more representative. Meanwhile, the probability of each word is considered as the ability to represent the semantic contribution for the topic. However, few efforts are focused on enhancing the representative ability of the topic to support fine grained topic representation. In this paper, we propose a Word Topic Ware (WTW) model to take word inherent diversity characteristic into consideration, in order to screen out and enhance the more representative words for topic representation. Experimental results on three large datasets show that our proposed method can increase the representative ability for topic representation. In addition, our work will positively affect improving the quality of topic content analysis. © 2022 Knowledge Systems Institute Graduate School. All rights reserved.

关键词： Large dataset

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ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling 41

ESM All-Atom: Multi-scale Protein Language Model for Unified...

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41st International Conference on Machine Learning, ICML 2024

作者： Zheng, Kangjie Long, Siyu Lu, Tianyu Yang, Junwei Dai, Xinyu Zhang, Ming Nie, Zaiqing Ma, Wei-Ying Zhou, Hao School of Computer Science National Key Laboratory for Multimedia Information Processing Peking University Anker Embodied AI Lab Peking University Beijing100871 China School of Artificial Intelligence National Key Laboratory for Novel Software Technology Nanjing University China Department of Computer Science Tsinghua University China Tsinghua University China PharMolix Inc. China

Protein language models have demonstrated significant potential in the field of protein ***, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom *** limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small *** this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular ***-AA achieves this by pretraining on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and *** results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language *** investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins. Copyright 2024 by the author(s)

关键词： Molecular docking

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