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Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules

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Drug3D-DTI: Improved Drug-target Interaction Prediction by I...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Zhirui Liao Xiaodi Huang Hiroshi Mamitsuka Shanfeng Zhu School of Computer Science Fudan University Shanghai China Institute of Artificial Intelligence Biomedicine Nanjing University Nanjing China School of Computing Mathematics and Engineering Charles Sturt University Albury NSW Australia Bioinformatics Center Institute for Chemical Research Kyoto University Uji Kyoto Japan Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University) Ministry of Education China MOE Frontiers Center for Brain Science Fudan University Shanghai China Zhangjiang Fudan International Innovation Center Shanghai China Shanghai Key Lab of Intelligent Information Processing Fudan University Shanghai China

ISBN: (纸本)9781665429825

A number of machine learning (ML) approaches for drug discovery have been available that rely only on sequential (1D) and planar (2D) information without effectively using the 3D information for generating features of drugs. However, 3D information of small molecules can reflect relative position of atoms more directly, which affects molecular properties. In this work, we present a new deep learning model called Drug3D-DTI for drug-target interaction prediction. Drug3D-DTI takes advantage of molecular spatial information, i.e., atom proximity in three-dimensional (3D) structures. We comprehensively evaluated the performance of Drug3D-DTI on two datasets with two tasks of regression and classification. In particular, we compared Drug3D-DTI with several existing methods including the two cutting-edge methods for compound-protein interaction prediction. From the experimental results, Drug3D-DTI clearly outperformed other methods under all settings. Further, this performance improvement was validated by ablation experiments and a case study. The implementation of Drug3D-DTI is available at (https://***/zhiruiliao/Drug3D-DTI).

关键词： Drugs Proteins Deep learning Solid modeling Three-dimensional displays Conferences Predictive models

The First GECAM Observation Results on Terrestrial Gamma-ray Flashes and Terrestrial Electron Beams

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arXiv 2023年

作者： Zhao, Y. Liu, J.C. Xiong, S.L. Xue, W.C. Yi, Q.B. Lu, G.P. Xu, W. Lyu, F.C. Sun, J.C. Peng, W.X. Zheng, C. Zhang, Y.Q. Cai, C. Xiao, S. Xie, S.L. Wang, C.W. Tan, W.J. An, Z.H. Chen, G. Du, Y.Q. Huang, Y. Gao, M. Gong, K. Guo, D.Y. He, J.J. Li, B. Li, G. Li, X.Q. Li, X.B. Liao, J.Y. Liang, J. Liang, X.H. Liu, Y.Q. Ma, X. Qiao, R. Song, L.M. Song, X.Y. Sun, X.L. Wang, J. Wang, J.Z. Wang, P. Wen, X.Y. Wu, H. Xu, Y.B. Yang, S. Zhang, B.X. Zhang, D.L. Zhang, F. Zhang, P. Zhang, H.M. Zhang, Z. Zhao, X.Y. Zheng, S.J. Zhang, K.K. Han, X.B. Wu, H.Y. Hu, T. Geng, H. Zhang, H.B. Lu, F.J. Zhang, S.N. Yu, H. Department of Astronomy Beijing Normal University Beijing Beijing100875 China Key Laboratory of Particle Astrophysics Institute of High Energy Physics Chinese Academy of Sciences Beijing Beijing100049 China University of Chinese Academy of Sciences Beijing Beijing100049 China School of Physics and Optoelectronics Xiangtan University Hunan Xiangtan411105 China School of Earth and Space Sciences University of Science and Technology of China Anhui Hefei230026 China Electronic Information School Wuhan University Hubei Wuhan430072 China Key Laboratory of Transportation Meteorology of China Meteorological Administration Nanjing Joint Institute for Atmospheric Sciences Jiangsu Nanjing210000 China College of Physics Hebei Key Laboratory of Photophysics Research and Application Hebei Normal University Hebei Shijiazhuang050024 China Guizhou Provincial Key Laboratory of Radio Astronomy and Data Processing Guizhou Normal University GuiZhou Guiyang550001 China School of Physics and Electronic Science Guizhou Normal University GuiZhou Guiyang550001 China Institute of Astrophysics Central China Normal University HuBei Wuhan430079 China School of Computing and Artificial Intelligence Southwest Jiaotong University SiChuan Chengdu611756 China College of Electronic and Information Engineering Tongji University Shanghai Shanghai201804 China Innovation Academy for Microsatellites Chinese Academy of Sciences Shanghai Shanghai201304 China National Space Science Center Chinese Academy of Sciences Beijing Beijing100190 China Key Laboratory of Middle Atmosphere and Global Environment Observation Institute of Atmospheric Physics Chinese Academy of Sciences Beijing Beijing100029 China

Gravitational-wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) is a space-borne instrument dedicated to monitoring high-energy transients, including Terrestrial Gamma-ray Flashes (TGFs) and Terrestrial Electron Beams (TEBs). We implemented a TGF/TEB search algorithm for GECAM, with which 147 bright TGFs, 2 typical TEBs and 2 special TEB-like events are identified during an effective observation time of ∼9 months. We show that, with gamma-ray and charged particle detectors, GECAM can effectively identify and distinguish TGFs and TEBs, and measure their temporal and spectral properties in detail. A very high TGF-lightning association rate of ∼80% is obtained between GECAM and GLD360 in east Asia region. Copyright © 2023, The Authors. All rights reserved.

关键词： Electron beams

AdaMMS: Model Merging for Heterogeneous Multimodal Large Language Models with Unsupervised Coefficient Optimization

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arXiv 2025年

作者： Du, Yiyang Wang, Xiaochen Chen, Chi Ye, Jiabo Wang, Yiru Li, Peng Yan, Ming Zhang, Ji Huang, Fei Sui, Zhifang Sun, Maosong Liu, Yang Dept. of Comp. Sci. & Tech. Institute for AI Tsinghua University Beijing China Tsinghua University Beijing China State Key Laboratory of Multimedia Information Processing Peking University Beijing China School of Software Microelectronics Peking University Beijing China Institute of Intelligent Computing Alibaba Group China Shanghai Artificial Intelligence Laboratory Shanghai China Jiangsu Collaborative Innovation Center for Language Competence Jiangsu China ModelTC Open Source Organization Beijing China

Recently, model merging methods have demonstrated powerful strengths in combining abilities on various tasks from multiple Large Language Models (LLMs). While previous model merging methods mainly focus on merging homogeneous models with identical architecture, they meet challenges when dealing with Multimodal Large Language Models (MLLMs) with inherent heterogeneous property, including differences in model architecture and the asymmetry in the parameter space. In this work, we propose AdaMMS1, a novel model merging method tailored for heterogeneous MLLMs. Our method tackles the challenges in three steps: mapping, merging and searching. Specifically, we first design mapping function between models to apply model merging on MLLMs with different architecture. Then we apply linear interpolation on model weights to actively adapt the asymmetry in the heterogeneous MLLMs. Finally in the hyper-parameter searching step, we propose an unsupervised hyper-parameter selection method for model merging. As the first model merging method capable of merging heterogeneous MLLMs without labeled data, extensive experiments on various model combinations demonstrated that AdaMMS outperforms previous model merging methods on various vision-language benchmarks. Copyright © 2025, The Authors. All rights reserved.

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Modal Analysis of Optical Waveguide using a Novel Symplectic Compact FDTD Schemes

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Modal Analysis of Optical Waveguide using a Novel Symplectic...

International Conference on Numerical Electromagnetic Modeling and Optimization for RF, Microwave, and Terahertz Applications (NEMO)

作者： Xiaojing Kuang Kong Meng Qi Qi Xin Zeng Zhixiang Huang Mingshen Chen The Anhui Province key laboratory of simulation & design for electronic information system Hefei Normal University Hefei China Digital circuit design east china institute of photo-electronic Suzhou China Key laboratory of intelligent & computing & signal processing Anhui University Hefei China School of Electronic Engineering Huainan Normal University Huainan China

ISBN: (数字)9781728169668

ISBN: (纸本)9781728169675

For modal analysis of longitudinally invariant optical devices, the compact-finite-difference time-domain is an efficient algorithm for alleviating the large amount of storage space and computing time under the 3D complex structure simulation. However, this algorithm needs to scale down the time step to mitigate the numerical dispersion errors while simulating optical waveguide working at high frequency. Here, a novel high-order symplectic compact FDTD scheme is proposed, which is attributed to the theory combination of the fast-spatial scheme and stable temporal scheme. The research results not only verify the effectiveness by numerical experiment on a planar dielectric waveguide with complex cross section, but also provide efficient theoretical guidance for the design and optimization of optical devices at the nanometer scale.

关键词： Electromagnetic waveguides Optical waveguide theory Adaptive optics Numerical models Time-domain analysis Optical waveguides Finite difference methods

Two-Stream Graph Convolutional Network for Intra-oral Scanner Image Segmentation

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arXiv 2022年

作者： Zhao, Yue Zhang, Lingming Liu, Yang Meng, Deyu Cui, Zhiming Gao, Chenqiang Gao, Xinbo Lian, Chunfeng Shen, Dinggang Chongqing University of Posts and Telecommunications School of Communication and Information Engineering Chongqing400065 China The Chongqing Key Laboratory of Signal and Information Processing Chongqing400065 China Department of Orthodontics Stomatological Hospital of Chongqing Medical University Chongqing401147 China Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences Chongqing401147 China Faculty of Information Technology Macau University of Science and Technology China School of Mathematics and Statistics Xi'an Jiaotong University Xian710049 China School of Biomedical Engineering ShanghaiTech University Shanghai201210 China Shanghai United Imaging Intelligence Co. Ltd. Shanghai200030 China The School of Computer Science The University of Hong Kong 999077 Hong Kong School of Computer Science and Technology Chongqing University of Posts and Telecommunications Chongqing400065 China

Precise segmentation of teeth from intra-oral scanner images is an essential task in computer-aided orthodontic surgical planning. The state-of-the-art deep learning-based methods often simply concatenate the raw geometric attributes (i.e., coordinates and normal vectors) of mesh cells to train a single-stream network for automatic intra-oral scanner image segmentation. However, since different raw attributes reveal completely different geometric information, the naive concatenation of different raw attributes at the (low-level) input stage may bring unnecessary confusion in describing and differentiating between mesh cells, thus hampering the learning of high-level geometric representations for the segmentation task. To address this issue, we design a two-stream graph convolutional network (i.e., TSGCN), which can effectively handle inter-view confusion between different raw attributes to more effectively fuse their complementary information and learn discriminative multi-view geometric representations. Specifically, our TSGCN adopts two input-specific graph-learning streams to extract complementary high-level geometric representations from coordinates and normal vectors, respectively. Then, these single-view representations are further fused by a self-attention module to adaptively balance the contributions of different views in learning more discriminative multi-view representations for accurate and fully automatic tooth segmentation. We have evaluated our TSGCN on a real-patient dataset of dental (mesh) models acquired by 3D intraoral scanners. Experimental results show that our TSGCN significantly outperforms state-of-the-art methods in 3D tooth (surface) segmentation. Github: https://***/ZhangLingMing1/TSGCNet. © 2022, CC BY.

关键词： Scanning

Multistage model for robust face alignment using deep neural networks

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arXiv 2020年

作者： Wang, Huabin Cheng, Rui Zhou, Jian Tao, Liang Kwan, Hon Keung MOE Key Laboratory of Intelligent Computing and Signal Processing School of Computer Science and Technology Anhui University Hefei Anhui230601 China Department of Electrical and Computer Engineering University of Windsor WindsorONN9B 3P4 Canada

An ability to generalize unconstrained conditions such as severe occlusions and large pose variations remains a challenging goal to achieve in face alignment. In this paper, a multistage model based on deep neural networks is proposed which takes advantage of spatial transformer networks, hourglass networks and exemplar-based shape constraints. First, a spatial transformer - generative adversarial network which consists of convolutional layers and residual units is utilized to solve the initialization issues caused by face detectors, such as rotation and scale variations, to obtain improved face bounding boxes for face alignment. Then, stacked hourglass network is employed to obtain preliminary locations of landmarks as well as their corresponding scores. In addition, an exemplar-based shape dictionary is designed to determine landmarks with low scores based on those with high scores. By incorporating face shape constraints, misaligned landmarks caused by occlusions or cluttered backgrounds can be considerably improved. Extensive experiments based on challenging benchmark datasets are performed to demonstrate the superior performance of the proposed method over other state-of-the-art methods. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep neural networks

An improved Gaussian Mixture Model algorithm for background representation

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An improved Gaussian Mixture Model algorithm for background ...

2019 International Conference on Artificial intelligence Technologies and Applications, ICAITA 2019

作者： Wang, Ping Dong, Shaoxiong School of Electrical Engineering and Electronic Information Xihua University Chengdu Sichuan610039 China Artificial Intelligence Key Laboratory of Sichuan Province Sichuan University of Science and Engineering Zigong Sichuan643000 China Science Computing Intelligent Information Processing GuangXi Higher Education Key Laboratory Guangxi Teachers Education University Nanning530023 China

Initializing a background frame for Gaussian Mixture Model requires no moving objects in the background scene. In this paper, in order to obtain an initial frame when there is a moving object in the background scene, filtering algorithm is used for background frame initialization. This paper proposes an improved method for updating Gaussian mixture models. In the initial stage of the GMM, the update rate of the mean and variance is taken as a larger value, so that the model mean and variance update speed becomes faster, and the model learning speed is accelerated;after training for a period of time with a large update rate, let The mean update rate is unchanged, and the variance update rate becomes smaller, so that the background model can be more stable. © 2019 IOP Publishing Ltd. All rights reserved.

关键词： Gaussian distribution

Multiplicative reconstruction based on the transport of intensity equation 4

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Multiplicative reconstruction based on the transport of inte...

4th International Conference on Fuzzy Systems and Data Mining, FSDM 2018

作者： Cheng, Hong Wang, Jincheng Shen, Chuan Zhang, Cheng Zhang, Fen Bao, Wenxia Education Ministry Key Laboratory of Intelligent Computing and Signal Processing Anhui University HefeiAnhui230039 China

ISBN: (纸本)9781614999270

In order to effectively recover the phase information of the object and reconstruct the three-dimensional shape of the object, a multiplicative reconstruction based on the transport of intensity equation (TIE) is proposed. Firstly, combining with the relationship between the light field moment imaging and the TIE, the phase information and the first moments of the light field are solved between the two differently focused intensity images, and the phase perspective can be recovered. In this way, the phase can be observed from different slight angles, and the three-dimensional shape of the phase of the object is reconstructed in combination with the multiplicative technique . At the same time, the object is rotated at different angles for the purpose of reconstructing the three-dimensional shape of the object phase under these angles. Finally, the correctness and effectiveness of the algorithm are verified by experimental results. © 2018 The authors and IOS Press. All rights reserved.

关键词： Fuzzy systems

Graphene based functional devices: A short review

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Frontiers of physics 2019年第1期14卷 23-42页

作者： Rong Wang Xin-Gang Ren Ze Yan Li-Jun Jiang Wei E. I. Sha Guang-Cun Shan Department of Electrical and Electronic Engineering The University of Hong Kong Pokfulam Road Hong Kong China Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei 230039 China School of Instrumentation Science & Opto-electronics Engineering Beihang University Beijing 100191 China Key Laboratory of Micro-nano Electronic Devices and Smart Systems of Zhejiang Province College of Information Science & Electronic Engineering Zhejiang University Hangzhou 310027 China California NanoSystem Institute and Department of Chemistry & Biochemistry University of California Los Angeles CA 90095 USA

Graphene is an ideal 2D material system bridging electronic and photonic devices. It also breaks the fundamental speed and size limits by electronics and photonics, respectively. Graphene offers multiple functions of signal transmission, emission, modulation, and detection in a broad band, high speed, compact size, and low loss. Here, we have a brief view of graphene based functional devices at microwave, terahertz, and optical frequencies. Their fundamental physics and computational models were discussed as well.

关键词： graphene terahertz antenna microwave