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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

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 1 .

关键词： Training Dictionaries Codes Semantics Named entity recognition Complexity theory Labeling Data mining Bioinformatics

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A Two-Stage Graph Computation Model with Communication Equilibrium 15th

A Two-Stage Graph Computation Model with Communication Equil...

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15th CCF Conference on Computer Supported Cooperative Work and Social computing, Chinese CSCW 2020

作者： Dong, Yanmei Chen, Rongwang Guo, Kun College of Mathematics and Computer Science Fuzhou University Fuzhou350108 China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou China Key Laboratory of Spatial Data Mining and Information Sharing Ministry of Education Fuzhou350108 China College of Mathematics and Computer Science Wuyi University Wuyishan Fujian354300 China Digital Fujian Tourism Big Data Institute Wuyishan Fujian354300 China

ISBN: (纸本)9789811625398

Distributed graph computing aims at performing in-depth analysis on large networks in a parallel manner. Iterative communication computation is an important model to perform graph analysis. Moreover, high-efficiency iterative communication computation is necessary for assuring the quality of graph partitioning. Many strategies to improve graph computing are usually based on the hypothesis of single communication iteration which focuses on the optimization of load balance in a single graph partitioning and the improvement of parallel granularity or communication manners. However, a graph in the real-world usually requires complex communication iterations to achieve good analysis results, which often have the problems of data and communication tilting and low analysis efficiency. In this paper, we propose a two-stage graph computing model with communication equilibrium (TSMCE). The model employs a communication-equilibrated graph partitioning strategy (CEGP) for load balancing and a two-stage graph computing mode (TS) to reduce the crossing-partition communication. With the change of graph density, various factors such as load balancing, communication balancing, cross-partition transmission traffic, communication delay, and convergence speed can always maintain an efficient balance. The experiments conducted on the real-world datasets show that the communication-equilibrated graph partitioning strategy can divide a graph with high quality compared with Hash and Metis. Besides, the overall performance of our two-stage graph computing model with communication equilibrium is higher than that of the BSP model. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Efficiency

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Quantum Circuits for the Heat Equation with Physical Boundary Conditions Via Schrödingerisation

SSRN

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SSRN 2024年

作者： Jin, Shi Liu, Nana Yu, Yue School of Mathematical Sciences Institute of Natural Sciences MOE-LSC Shanghai Jiao Tong University Shanghai200240 China University of Michigan Shanghai Jiao Tong University Joint Institute Shanghai200240 China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education National Center for Applied Mathematics in Hunan Xiangtan University Hunan Xiangtan411105 China

This paper explores the explicit design of quantum circuits for quantum simulation of partial differential equations (PDEs) with physical boundary conditions. These equations and/or their discretized forms usually do not evolve via unitary dynamics, thus are not suitable for quantum simulation. Boundary conditions (either time-dependent or independent) make the problem more difficult. To tackle this challenge, the Schrödingerisation method can be employed, which converts linear partial and ordinary differential equations with non-unitary dynamics into systems of Schrödinger-type equations, via the so-called warped phase transformation that maps the equation into one higher dimension. Despite advancements in Schrödingerisation techniques, the explicit implementation of quantum circuits for solving general PDEs, especially with physical boundary conditions, remains underdeveloped. We present two methods for handling the inhomogeneous terms arising from time-dependent physical boundary conditions. One approach utilizes Duhamel's principle to express the solution in integral form and employs linear combination of unitaries (LCU) for coherent state preparation. Another method applies an augmentation to transform the inhomogeneous problem into a homogeneous one. We then apply the quantum simulation technique from [CJL23] to transform the resulting non-autonomous system to an autonomous system in one higher dimension. We provide detailed implementations of these two methods and conduct a comprehensive complexity analysis in terms of queries to the time evolution input oracle. © 2024, The Authors. All rights reserved.

关键词： Boundary conditions

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Quantum Circuits for the heat equation with physical boundary conditions via Schrödingerisation

arXiv

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arXiv 2024年

This paper explores the explicit design of quantum circuits for quantum simulation of partial differential equations (PDEs) with physical boundary conditions. These equations and/or their discretized forms usually do not evolve via unitary dynamics, thus are not suitable for quantum simulation. Boundary conditions (either time-dependent or independent) make the problem more difficult. To tackle this challenge, the Schrödingerisation method can be employed, which converts linear partial and ordinary differential equations with non-unitary dynamics into systems of Schrödinger-type equations, via the so-called warped phase transformation that maps the equation into one higher dimension. Despite advancements in Schrödingerisation techniques, the explicit implementation of quantum circuits for solving general PDEs, especially with physical boundary conditions, remains underdeveloped. We present two methods for handling the inhomogeneous terms arising from time-dependent physical boundary conditions. One approach utilizes Duhamel’s principle to express the solution in integral form and employs linear combination of unitaries (LCU) for coherent state preparation. Another method applies an augmentation to transform the inhomogeneous problem into a homogeneous one. We then apply the quantum simulation technique from [CJL23] to transform the resulting non-autonomous system to an autonomous system in one higher dimension. We provide detailed implementations of these two methods and conduct a comprehensive complexity analysis in terms of queries to the time evolution input oracle. © 2024, CC BY-NC-ND.

关键词： Ordinary differential equations

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CRSOT: Cross-Resolution Object Tracking using Unaligned Frame and Event Cameras

arXiv

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arXiv 2024年

作者： Zhu, Yabin Wang, Xiao Li, Chenglong Jiang, Bo Zhu, Lin Huang, Zhixiang Tian, Yonghong Tang, Jin Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University China School of Computer Science and Technology Anhui University China School of Artificial Intelligence Anhui University China Beijing Institute of Technology Beijing China School of Electronic and Information Engineering Anhui University China Peng Cheng Laboratory Shenzhen China School of Computer Science Peking University Beijing China School of Electronic and Computer Engineering Peking University Shenzhen China

Existing datasets for RGB-DVS tracking are collected with DVS346 camera and their resolution (346 × 260) is low for practical applications. Actually, only visible cameras are deployed in many practical systems, and the newly designed neuromorphic cameras may have different resolutions. The latest neuromorphic sensors can output high-definition event streams, but it is very difficult to achieve strict alignment between events and frames on both spatial and temporal views. Therefore, how to achieve accurate tracking with unaligned neuromorphic and visible sensors is a valuable but unresearched problem. In this work, we formally propose the task of object tracking using unaligned neuromorphic and visible cameras. We build the first unaligned frame-event dataset CRSOT collected with a specially built data acquisition system, which contains 1,030 high-definition RGB-Event video pairs, 304,974 video frames. In addition, we propose a novel unaligned object tracking framework that can realize robust tracking even using the loosely aligned RGB-Event data. Specifically, we extract the template and search regions of RGB and Event data and feed them into a unified ViT backbone for feature embedding. Then, we propose uncertainty perception modules to encode the RGB and Event features, respectively, then, we propose a modality uncertainty fusion module to aggregate the two modalities. These three branches are jointly optimized in the training phase. Extensive experiments demonstrate that our tracker can collaborate the dual modalities for high-performance track- Copyright © 2024, The Authors. All rights reserved.

关键词： Cameras

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A Reconstruction Method for Cross-Cut Shredded Documents Based on the Extreme Learning Machine Algorithm

Research Square

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Research Square 2022年

作者： Zhang, Zhenghui Zou, Juan Zheng, Jinhua Yang, Shengxiang Gong, Dunwei Pei, Tingrui Key Laboratory of Hunan Province for Internet of Things and Information Security Xiangtan University Hunan Xiangtan411105 China Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Information Engineering College of Xiangtan University Hunan Xiangtan411105 China Hunan Provincial Key Laboratory of Intelligent Information Processing and Application Hengyang421002 China School of Computer Science and Informatics De Montfort University LeicesterLE1 9BH United Kingdom School of Information and Electronic Engineering China University of Mining and Technology Xuzhou221116 China

Reconstruction of cross-cut shredded text documents (RCCSTD) has important applications for information security and judicial evidence collection. The traditional method of manual construction is a very time-consuming task, so the use of computer-assisted efficient reconstruction is a crucial research topic. Fragment consensus information extraction and fragment pair compatibility measurement are two fundamental processes in RCCSTD. Due to the limitations of the existing classical methods of these two steps, only documents with specific structures or characteristics can be spliced, and pairing error is larger when the cutting is more fine-grained. In order to reconstruct the fragments more effectively, this paper improves the extraction method for consensus information and constructs a new global pairwise compatibility measurement model based on the extreme learning machine algorithm. The purpose of the algorithm’s design is to exploit all available information and computationally suggest matches to increase the algorithm’s ability to discriminate between data in various complex situations, then find the best neighbor of each fragment for splicing according to pairwise compatibility. The overall performance of our approach in several practical experiments is illustrated. The results indicate that the matching accuracy of the proposed algorithm is better than that of the previously published classical algorithms and still ensures a higher matching accuracy in the noisy datasets, which can provide a feasible method for RCCSTD intelligent systems in real scenarios. © 2022, CC BY.

关键词： Knowledge acquisition

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Understanding the Robustness of 3D Object Detection with Bird'View Representations in Autonomous Driving

Understanding the Robustness of 3D Object Detection with Bir...

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Zijian Zhu Yichi Zhang Hai Chen Yinpeng Dong Shu Zhao Wenbo Ding Jiachen Zhong Shibao Zheng Institute of Image Communication and Network Engineering Shanghai Jiao Tong University Dept. of Comp. Sci. and Tech. THBI Lab Institute for AI Tsinghua University BNRist Center Zhongguancun Laboratory Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Information Materials and Intelligent Sensing Laboratory of Anhui Province School of Computer Science and Technology Anhui University SAIC Motor AI Lab

3D object detection is an essential perception task in autonomous driving to understand the environments. The Bird's-Eye-View (BEV) representations have significantly improved the performance of 3D detectors with camera inputs on popular benchmarks. However, there still lacks a systematic understanding of the robustness of these vision-dependent BEV models, which is closely related to the safety of autonomous driving systems. In this paper, we evaluate the natural and adversarial robustness of various representative models under extensive settings, to fully understand their behaviors influenced by explicit BEV features compared with those without BEV. In addition to the classic settings, we propose a 3D consistent patch attack by applying adversarial patches in the 3D space to guarantee the spatiotemporal consistency, which is more realistic for the scenario of autonomous driving. With substantial experiments, we draw several findings: 1) BEV models tend to be more stable than previous methods under different natural conditions and common corruptions due to the expressive spatial representations; 2) BEV models are more vulnerable to adversarial noises, mainly caused by the redundant BEV features; 3) Camera-LiDARfusion models have superior performance under different settings with multi-modal inputs, but BEV fusion model is still vulnerable to adversarial noises of both point cloud and image. These findings alert the safety issue in the applications of BEV detectors and could facilitate the development of more robust models.

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A Unified Generalization Analysis of Re-Weighting and Logit-Adjustment for Imbalanced Learning

arXiv

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arXiv 2023年

作者： Wang, Zitai Xu, Qianqian Yang, Zhiyong He, Yuan Cao, Xiaochun Huang, Qingming SKLOIS Institute of Information Engineering CAS China School of Cyber Security University of Chinese Academy of Sciences China Key Lab. of Intelligent Information Processing Institute of Computing Tech. CAS China School of Computer Science and Tech. University of Chinese Academy of Sciences China Alibaba Group China School of Cyber Science and Tech. Shenzhen Campus Sun Yat-sen University China BDKM University of Chinese Academy of Sciences China

Real-world datasets are typically imbalanced in the sense that only a few classes have numerous samples, while many classes are associated with only a few samples. As a result, a naïve ERM learning process will be biased towards the majority classes, making it difficult to generalize to the minority classes. To address this issue, one simple but effective approach is to modify the loss function to emphasize the learning on minority classes, such as re-weighting the losses or adjusting the logits via class-dependent terms. However, existing generalization analysis of such losses is still coarse-grained and fragmented, failing to explain some empirical results. To bridge this gap, we propose a novel technique named data-dependent contraction to capture how these modified losses handle different classes. On top of this technique, a fine-grained generalization bound is established for imbalanced learning, which helps reveal the mystery of re-weighting and logit-adjustment in a unified manner. Furthermore, a principled learning algorithm is developed based on the theoretical insights. Finally, the empirical results on benchmark datasets not only validate the theoretical results but also demonstrate the effectiveness of the proposed method. © 2023, CC BY.

关键词： Learning algorithms

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Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction

arXiv

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arXiv 2023年

作者： Lin, Xuan Dai, Lichang Zhou, Yafang Yu, Zu-Guo Zhang, Wen Shi, Jian-Yu Cao, Dong-Sheng Zeng, Li Chen, Haowen Song, Bosheng Yu, Philip S. Zeng, Xiangxiang Xiangtan China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University China College of Informatics Huazhong Agricultural University China The Northwestern Polytechnical University Xi’an China The Xiangya School of Pharmaceutical Sciences Central South University China AIDD Department of Yuyao Biotech Shanghai China Hunan University China The College of Information Science and Engineering Hunan University Changsha China Computer Science The University of Illinois Chicago United States

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in the effect of one drug to the presence of another drug in the human body, which plays an essential role in drug discovery and clinical research. DDIs prediction through traditional clinical trials and experiments is an expensive and time-consuming process. To correctly apply the advanced AI and deep learning, the developer and user meet various challenges such as the availability and encoding of data resources, and the design of computational methods. This review summarizes chemical structure based, network based, NLP based and hybrid methods, providing an updated and accessible guide to the broad researchers and development community with different domain knowledge. We introduce widely-used molecular representation and describe the theoretical frameworks of graph neural network models for representing molecular structures. We present the advantages and disadvantages of deep and graph learning methods by performing comparative experiments. We discuss the potential technical challenges and highlight future directions of deep and graph learning models for accelerating DDIs prediction. Copyright © 2023, The Authors. All rights reserved.

关键词： Forecasting

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Optimizing Neighborhood Area Network Topology for Enhanced Communication in Smart Grid

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IEEE Transactions on Consumer Electronics 2025年

作者： Li, Jian-Hui Ding, Yuemin Yu, Zu-Guo Zhang, Weizhe Ren, Honglin Tian, Yu-Chu Xiangtan University National Center for Applied Mathematics in Hunan Key Laboratory of Intelligent Computing and Information Processing of the Ministry of Education of China Xiangtan University Hunan 411105 China Queensland University of Technology School of Computer Science Brisbane QLD Australia University of Navarra Ikerbasque Foundation Tecnun School of Engineering San Sebastián Spain Bilbao Spain Harbin Institute of Technology School of Computer Science and Technology Shenzhen China

In modern power grids, smart meters, as a type of consumer electronics, act as metering and communication nodes, which form Neighborhood Area Networks (NANs) spanning electricity distribution networks from substations to energy producers and consumers. In smart meter communication, wireless technologies have been widely adopted due to their inherent advantages of easier installation, flexibility, and low cost. For achieving low-latency communications in NANs, it is crucial to optimize the existing topology to enhance communication efficiency. However, optimizing the NAN topology is a challenging task due to the computational infeasibility of obtaining the optimal solution. To tackle this challenge, topology optimization in NANs is first formulated into a combinatorial optimization problem. After that, a heuristic solution driven by complex network theory is presented to solve the formulated optimization problem. The proposed heuristic solution consists of an effective network rewiring scheme and a long-range edge connection strategy. The rewiring optimizes the topology of wireless NANs to reduce local network length, whilst the long-range edge connection best pairs a small number of NAN nodes to reduce global network length. Numerical studies are conducted on diverse case studies to demonstrate the presented solution to enhance communication efficiency in smart grid NANs, outperforming the benchmark schemes. © 1975-2011 IEEE.

关键词： communication efficiency neighborhood area network network rewiring network topological optimization Network topology smart grid smart meter

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