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DMNER: Biomedical Named Entity Recognition by Detection and Matching

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DMNER: Biomedical Named Entity Recognition by Detection and ...

2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Bian, Junyi Jiang, Rongze Zhai, Weiqi Huang, Tianyang Huang, Xiaodi Zhou, Hong Zhu, Shanfeng Fudan University School of Computer Science Shanghai China Fudan University Institute of Science and Technology for Brain-Inspired Intelligence Shanghai China Charles Sturt University School of Computing Mathematics and Engineering Nsw Australia Atypon Systems Llc United Kingdom Zhangjiang Fudan International Innovation Center Fudan University Institute of Science and Technology for Brain-Inspired Intelligence Moe Frontiers Center for Brain Science Shanghai Key Lab of Intelligent Information Processing Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Shanghai China

ISBN: (纸本)9798350386226

Biomedical Named Entity Recognition (NER) is a crucial task in extracting information from biomedical texts. However, the diversity of professional terminology, semantic complexity, and the widespread presence of synonyms pose significant challenges. Traditional methods that rely on sequence labeling training datasets often struggle to handle these complexities. To address this, we introduce a novel framework for BioNER, termed DMNER, which leverages external knowledge and operates in two steps: entity boundary detection and entity category identification through matching. The core of DMNER is its second step, which determines the entity category by retrieving similar entities and their categories from a knowledge dictionary using semantic similarity matching. Our experiments on 10 biomedical datasets demonstrate that DMNER outperforms baselines across these tasks, proving its effectiveness and adaptability. DMNER is versatile and can be applied to various NER tasks, including supervised NER, distantly supervised NER, and NER on multiple datasets with disjoint label sets. The DMNER code is publicly available. © 2024 IEEE.

关键词： Semantics

Evolutionary Multi-Objective Neural Architecture Search for Generalized Cognitive Diagnosis Models

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Evolutionary Multi-Objective Neural Architecture Search for ...

Data-driven Optimization of Complex Systems (DOCS), International Conference on

作者： Shangshang Yang Cheng Zhen Ye Tian Haiping Ma Yuanchao Liu Panpan Zhang Xingyi Zhang Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Artificial Intelligence Anhui University Hefei China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Institutes of Physical Science and Information Technology Anhui University Hefei China State Key Laboratory of Synthetical Automation for Process Industries Northeastern University Shenyang China

Cognitive diagnosis models (CDMs) with high generalization are essential for intelligent education systems to reveal students' knowledge states in multiple datasets. However, existing CDMs' architectures are designed dependent on researcher expertise and experience from observing and summarizing partial students' learning behaviors, which makes handcrafted models not cover all learning behaviors well and thus limits their generalization. To develop generalized CDMs, this paper proposes an evolutionary neural architecture search to design CDMs' architectures effective on multiple datasets automatically. Specifically, we first formulate the search task as a multi-objective optimization problem (MOP), which maximizes model performance on multiple datasets containing learning behaviors as many as possible to ensure model generalization. Then, an expressive search space is devised to contain as many potential architectures as possible, where each architecture is denoted by a unified form, taking three given inputs and integrating them in a linear or no-linear manner for prediction. Finally, an evolutionary algorithm with a tailored deduplication strategy is employed to solve the MOP, where each architecture is further represented by a single-root computation tree for easy optimization. Experiments on multiple datasets demonstrate the generalization and effectiveness of the best architecture searched by the proposed approach, and the searched architecture also holds as good interpretability as handcrafted architectures.

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Black⁃box adversarial attacks with imperceptible fake user profiles for recommender systems

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南京大学学报(自然科学版) 2024年第6期60卷 881-899页

作者： Qian Fulan Liu Jinggang Chen Hai Chen Wenbin Zhao Shu Zhang Yanping Artificial Intelligence Institute Anhui UniversityHefei230601China Key Laboratory of Intelligent Computing and Signal Processing Ministry of EducationAnhui UniversityHefei230601China Information Materials and Intelligent Sensing Laboratory of Anhui Province Anhui UniversityHefei230601China

Attackers inject the designed adversarial sample into the target recommendation system to achieve illegal goals,seriously affecting the security and reliability of the recommendation *** is difficult for attackers to obtain detailed knowledge of the target model in actual scenarios,so using gradient optimization to generate adversarial samples in the local surrogate model has become an effective black‐box attack ***,these methods suffer from gradients falling into local minima,limiting the transferability of the adversarial *** reduces the attack's effectiveness and often ignores the imperceptibility of the generated adversarial *** address these challenges,we propose a novel attack algorithm called PGMRS‐KL that combines pre‐gradient‐guided momentum gradient optimization strategy and fake user generation constrained by Kullback‐Leibler ***,the algorithm combines the accumulated gradient direction with the previous step's gradient direction to iteratively update the adversarial *** uses KL loss to minimize the distribution distance between fake and real user data,achieving high transferability and imperceptibility of the adversarial *** results demonstrate the superiority of our approach over state‐of‐the‐art gradient‐based attack algorithms in terms of attack transferability and the generation of imperceptible fake user data.

关键词： recommendation systems adversarial examples transferability imperceptible

SSFam: Scribble Supervised Salient Object Detection Family

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arXiv 2024年

作者： Liu, Zhengyi Deng, Sheng Wang, Xinrui Wang, Linbo Fang, Xianyong Tang, Bin Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China School of Artificial Intelligence and Big Data Hefei University Hefei China

Scribble supervised salient object detection (SSSOD) constructs segmentation ability of attractive objects from surroundings under the supervision of sparse scribble labels. For the better segmentation, depth and thermal infrared modalities serve as the supplement to RGB images in the complex scenes. Existing methods specifically design various feature extraction and multi-modal fusion strategies for RGB, RGB-Depth, RGB-Thermal, and Visual-Depth-Thermal image input respectively, leading to similar model flood. As the recently proposed Segment Anything Model (SAM) possesses extraordinary segmentation and prompt interactive capability, we propose an SSSOD family based on SAM, named SSFam, for the combination input with different modalities. Firstly, different modal-aware modulators are designed to attain modal-specific knowledge which cooperates with modal-agnostic information extracted from the frozen SAM encoder for the better feature ensemble. Secondly, a siamese decoder is tailored to bridge the gap between the training with scribble prompt and the testing with no prompt for the stronger decoding ability. Our model demonstrates the remarkable performance among combinations of different modalities and refreshes the highest level of scribble supervised methods and comes close to the ones of fully supervised methods. https://***/liuzywen/SSFam Copyright © 2024, The Authors. All rights reserved.

关键词： Image segmentation

MEFFGRN: Matrix enhancement and feature fusion-based method for reconstructing the gene regulatory network of epithelioma papulosum cyprini cells by spring viremia of carp virus infection

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Computers in Biology and Medicine 2024年 179卷 108835-108835页

作者： Wei, Pi-Jing Bao, Jin-Jin Gao, Zhen Tan, Jing-Yun Cao, Rui-Fen Su, Yansen Zheng, Chun-Hou Deng, Li Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education Institutes of Physical Science and Information Technology Anhui University 111 Jiulong Road HefeiAnhui230601 China Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University 111 Jiulong Road HefeiAnhui230601 China Shenzhen Key Laboratory of Microbial Genetic Engineering College of Life Sciences and Oceanology Shenzhen University Guangdong Shenzhen518055 China School of Artificial Intelligence Anhui University 111 Jiulong Road HefeiAnhui230601 China

Gene regulatory networks (GRNs) are crucial for understanding organismal molecular mechanisms and processes. Construction of GRN in the epithelioma papulosum cyprini (EPC) cells of cyprinid fish by spring viremia of carp virus (SVCV) infection helps understand the immune regulatory mechanisms that enhance the survival capabilities of cyprinid fish. Although many computational methods have been used to infer GRNs, specialized approaches for predicting the GRN of EPC cells following SVCV infection are lacking. In addition, most existing methods focus primarily on gene expression features, neglecting the valuable network structural information in known GRNs. In this study, we propose a novel supervised deep neural network, named MEFFGRN (Matrix Enhancement- and Feature Fusion-based method for Gene Regulatory Network inference), to accurately predict the GRN of EPC cells following SVCV infection. MEFFGRN considers both gene expression data and network structure information of known GRN and introduces a matrix enhancement method to address the sparsity issue of known GRN, extracting richer network structure information. To optimize the benefits of CNN (Convolutional Neural Network) in image processing, gene expression and enhanced GRN data were transformed into histogram images for each gene pair respectively. Subsequently, these histograms were separately fed into CNNs for training to obtain the corresponding gene expression and network structural features. Furthermore, a feature fusion mechanism was introduced to comprehensively integrate the gene expression and network structural features. This integration considers the specificity of each feature and their interactive information, resulting in a more comprehensive and precise feature representation during the fusion process. Experimental results from both real-world and benchmark datasets demonstrate that MEFFGRN achieves competitive performance compared with state-of-the-art computational methods. Furthermore, study

关键词： Gene expression

SwinNet: Swin Transformer Drives Edge-Aware RGB-D and RGB-T Salient Object Detection

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arXiv 2022年

作者： Liu, Zhengyi Tan, Yacheng He, Qian Xiao, Yun Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Artificial Intelligence Anhui University Hefei China

Convolutional neural networks (CNNs) are good at extracting contexture features within certain receptive fields, while transformers can model the global long-range dependency features. By absorbing the advantage of transformer and the merit of CNN, Swin Transformer shows strong feature representation ability. Based on it, we propose a cross-modality fusion model, SwinNet, for RGB-D and RGB-T salient object detection. It is driven by Swin Transformer to extract the hierarchical features, boosted by attention mechanism to bridge the gap between two modalities, and guided by edge information to sharp the contour of salient object. To be specific, two-stream Swin Transformer encoder first extracts multi-modality features, and then spatial alignment and channel re-calibration module is presented to optimize intra-level cross-modality features. To clarify the fuzzy boundary, edge-guided decoder achieves inter-level cross-modality fusion under the guidance of edge features. The proposed model outperforms the state-of-the-art models on RGB-D and RGB-T datasets, showing that it provides more insight into the cross-modality complementarity ***://***/liuzywen/SwinNet © 2022, CC0.

关键词： Convolutional neural networks

Learning Analysis of Kernel Ridgeless Regression with Asymmetric Kernel Learning

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arXiv 2024年

作者： He, Fan He, Mingzhen Shi, Lei Huang, Xiaolin Suykens, Johan A.K. STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium MOE Key Laboratory of System Control and Information Processing Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Shanghai Key Laboratory for Contemporary Applied Mathematics School of Mathematical Sciences Fudan University Shanghai200433 China Shanghai Artificial Intelligence Laboratory Shanghai200232 China MOE Key Laboratory of System Control and Information Processing Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai200240 China

Ridgeless regression has garnered attention among researchers, particularly in light of the "Benign Overfitting" phenomenon, where models interpolating noisy samples demonstrate robust generalization. However, kernel ridgeless regression does not always perform well due to the lack of flexibility. This paper enhances kernel ridgeless regression with Locally-Adaptive-Bandwidths (LAB) RBF kernels, incorporating kernel learning techniques to improve performance in both experiments and theory. For the first time, we demonstrate that functions learned from LAB RBF kernels belong to an integral space of Reproducible Kernel Hilbert Spaces (RKHSs). Despite the absence of explicit regularization in the proposed model, its optimization is equivalent to solving an 0-regularized problem in the integral space of RKHSs, elucidating the origin of its generalization ability. Taking an approximation analysis viewpoint, we introduce an lq-norm analysis technique (with 0 © 2024, CC BY.

关键词： Vector spaces

Transformer RGBT Tracking with Spatio-Temporal Multimodal Tokens

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arXiv 2024年

作者： Sun, Dengdi Pan, Yajie Lu, Andong Li, Chenglong Luo, Bin The Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education School of Artificial Intelligence Anhui University Hefei230601 China Institute of Artificial Intelligence Hefei Comprehensive National Science Center Hefei230026 China The Anhui Provincial Key Laboratory of Multimodal Cognitive Computation School of Computer Science and Technology Anhui University Hefei230601 China

Many RGBT tracking researches primarily focus on modal fusion design, while overlooking the effective handling of target appearance changes. While some approaches have introduced historical frames or fuse and replace initial templates to incorporate temporal information, they have the risk of disrupting the original target appearance and accumulating errors over time. To alleviate these limitations, we propose a novel Transformer RGBT tracking approach, which mixes spatio-temporal multimodal tokens from the static multimodal templates and multimodal search regions in Transformer to handle target appearance changes, for robust RGBT tracking. We introduce independent dynamic template tokens to interact with the search region, embedding temporal information to address appearance changes, while also retaining the involvement of the initial static template tokens in the joint feature extraction process to ensure the preservation of the original reliable target appearance information that prevent deviations from the target appearance caused by traditional temporal updates. We also use attention mechanisms to enhance the target features of multimodal template tokens by incorporating supplementary modal cues, and make the multimodal search region tokens interact with multimodal dynamic template tokens via attention mechanisms, which facilitates the conveyance of multimodal-enhanced target change information. Our module is inserted into the transformer backbone network and inherits joint feature extraction, search-template matching, and cross-modal interaction. Extensive experiments on three RGBT benchmark datasets show that the proposed approach maintains competitive performance compared to other state-of-the-art tracking algorithms while running at 39.1 FPS. Copyright © 2024, The Authors. All rights reserved.

关键词： Feature extraction

HRTransNet: HRFormer-Driven Two-Modality Salient Object Detection

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arXiv 2023年

作者： Tang, Bin Liu, Zhengyi Tan, Yacheng He, Qian School of Artificial Intelligence and Big Data Hefei University Hefei China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China

The High-Resolution Transformer (HRFormer) can maintain high-resolution representation and share global receptive fields. It is friendly towards salient object detection (SOD) in which the input and output have the same resolution. However, two critical problems need to be solved for two-modality SOD. One problem is two-modality fusion. The other problem is the HRFormer output’s fusion. To address the first problem, a supplementary modality is injected into the primary modality by using global optimization and an attention mechanism to select and purify the modality at the input level. To solve the second problem, a dual-direction short connection fusion module is used to optimize the output features of HRFormer, thereby enhancing the detailed representation of objects at the output level. The proposed model, named HRTransNet, first introduces an auxiliary stream for feature extraction of supplementary modality. Then, features are injected into the primary modality at the beginning of each multi-resolution branch. Next, HRFormer is applied to achieve forwarding propagation. Finally, all the output features with different resolutions are aggregated by intra-feature and inter-feature interactive transformers. Application of the proposed model results in impressive improvement for driving two-modality SOD tasks, e.g., RGB-D, RGB-T, and light field ***://***/liuzywen/HRTransNet Copyright © 2023, The Authors. All rights reserved.

关键词： Global optimization