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CSCL-DTI: predicting drug-target interaction through cross-view and self-supervised contrastive learning

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CSCL-DTI: predicting drug-target interaction through cross-v...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Xuan Lin Xi Zhang Zu-Guo Yu Yahui Long Xiangxiang Zeng Philip S. Yu College of Computer Science Xiangtan University China Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University China Singapore Immunology Network (SIgN) Agency for Science Technology and Research (A*STAR) Singapore College of Information Science and Engineering Hunan University China Department of Computer Science University of Illinois Chicago USA

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Accurately predicting drug-target interactions (DTI) is a critical step in drug discovery. Existing methods of DTI prediction primarily employ Simplified Molecular-Input Line-Entry System (SMILES) sequences or molecular graphs to learn drug representations. However, the features learned by such single-view approach is prone to incomplete. While some multiview methods that consider the views of both SMILES sequences and molecular graphs have been developed, these methods often fall in short in capturing potential interactions between views. In this work, we propose a novel dual contrastive learning framework CSCL-DTI for DTI prediction. First, we design a contrastive-enhanced cross-view representation learning (CVRL) to learn representations for drugs. In this module, Transformer-based and graph convolutional network (GCN)-based encoders are separately adopted to learn view-specific representations, followed by contrastive learning to enrich the representations by accounting for the potential interplay between local chemical context and topological structure. Second, we combine Transformer with self-supervised contrastive learning (SSCL) to learn representations for targets by modelling protein amino acids sequences. The scheme allows to effectively preserve the intrinsic characteristics of the sequences. Finally, we introduce a bilinear attention network to obtain an integrated representation by adaptively incorporating drug and target representations. Benchmarking experiments on two datasets demonstrated that CSCL-DTI 1 outperforms six state-of-the-art methods.

关键词： Drugs Proteins Representation learning Protein engineering Adaptation models Contrastive learning Predictive models Transformers Amino acids Diffusion tensor imaging

Low-rank alternating direction doubling algorithm for solving large-scale continuous time algebraic Riccati equations

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arXiv 2024年

This paper proposes an effective low-rank alternating direction doubling algorithm (R-ADDA) for computing numerical low-rank solutions to large-scale sparse continuous-time algebraic Riccati matrix equations. The method is based on the alternating direction doubling algorithm (ADDA), utilizing the low-rank property of matrices and employing Cholesky factorization for solving. The advantage of the new algorithm lies in computing only the 2k-th approximation during the iterative process, instead of every approximation. Its efficient low-rank formula saves storage space and is highly effective from a computational perspective. Finally, the effectiveness of the new algorithm is demonstrated through theoretical analysis and numerical experiments. Copyright © 2024, The Authors. All rights reserved.

关键词： Matrix algebra

Optimization methods for solving matrix equations

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arXiv 2024年

作者： Zhang, Juan Luo, Xiao Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan China School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan China

In this paper, we focus on using optimization methods to solve matrix equations by transforming the problem of solving the Sylvester matrix equation or continuous algebraic Riccati equation into an optimization problem. Initially, we use a constrained convex optimization method (CCOM) to solve the Sylvester matrix equation with 2,1-norm, where we provide a convergence analysis and numerical examples of CCOM;however, the results show that the algorithm is not efficient. To address this issue, we employ classical quasi-Newton methods such as DFP and BFGS algorithms to solve the Sylvester matrix equation and present the convergence and numerical results of the algorithm. Additionally, we compare these algorithms with the CG algorithm and AR algorithm, and our results demonstrate that the presented algorithms are effective. Furthermore, we propose a unified framework of the alternating direction multiplier method (ADMM) for directly solving the continuous algebraic Riccati equation (CARE), and we provide the convergence and numerical results of ADMM. Our experimental results indicate that ADMM is an effective optimization algorithm for solving CARE. Finally, to improve the effectiveness of the optimization method for solving Riccati equation, we propose the Newton-ADMM algorithm framework, where the outer iteration of this method is the classical Newton method, and the inner iteration involves using ADMM to solve Lyapunov matrix equations inexactly. We also provide the convergence and numerical results of this algorithm, which our results demonstrate are more efficient than ADMM for solving CARE. Copyright © 2024, The Authors. All rights reserved.

关键词： Newton-Raphson method

ReconBoost: boosting can achieve modality reconcilement 24

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ReconBoost: boosting can achieve modality reconcilement

Proceedings of the 41st International Conference on Machine Learning

作者： Cong Hua Qianqian Xu Shilong Bao Zhiyong Yang Qingming Huang Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China and School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China Institute of Information Engineering Chinese Academy of Sciences Beijing China and School of Cyber Security University of Chinese Academy of Sciences Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China and Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China and Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China

This paper explores a novel multi-modal alternating learning paradigm pursuing a reconciliation between the exploitation of uni-modal features and the exploration of cross-modal interactions. This is motivated by the fact that current paradigms of multi-modal learning tend to explore multi-modal features simultaneously. The resulting gradient prohibits further exploitation of the features in the weak modality, leading to modality competition, where the dominant modality overpowers the learning process. To address this issue, we study the modality-alternating learning paradigm to achieve reconcilement. Specifically, we propose a new method called ReconBoost to update a fixed modality each time. Herein, the learning objective is dynamically adjusted with a reconcilement regularization against competition with the historical models. By choosing a KL-based reconcilement, we show that the proposed method resembles Friedman's Gradient-Boosting (GB) algorithm, where the updated learner can correct errors made by others and help enhance the overall performance. The major difference with the classic GB is that we only preserve the newest model for each modality to avoid overfitting caused by ensembling strong learners. Furthermore, we propose a memory consolidation scheme and a global rectification scheme to make this strategy more effective. Experiments over six multi-modal benchmarks speak to the efficacy of the method. We release the code at https://***/huacong/ReconBoost.

关键词：

Using Rough Sets to Improve the High-dimensional Data Anomaly Detection Method Based on Extended Isolation Forest 26

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Using Rough Sets to Improve the High-dimensional Data Anomal...

26th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2023

作者： Liu, Hanlin Zhou, Jiantao Li, Hua Inner Mongolia University College of Computer Science Hohhot China Natl. Loc. Jt. Eng. Research Center of Intelligent Information Processing Technology for Mongolian Engineering Research Center of Ecological Big Data Ministry of Education Inner Mongolia Engineering Laboratory for Cloud Computing and Service Software Inner Mongolia Key Laboratory of Social Computing and Data Processing Inner Mongolia Key Laboratory of Discipline Inspection and Supervision Big Data Inner Mongolia Engineering Laboratory for Big Data Analysis Technology Hohhot China

ISBN: (纸本)9798350331684

Anomaly detection refers to the identification of data objects that deviate from the general data distribution. One of the important challenges in anomaly detection is handling high-dimensional data, especially when it contains a large number of redundant attributes. Although traditional Isolation Forest (iForest) and Extended Isolation Forest (EIF) have performed well in anomaly detection, the detection accuracy is still extremely influenced by redundant attributes. In this paper, we propose a two-tier architecture named RS-EIF, to alleviate the negative impact of redundant attributes. Specifically, the RS-EIF combines the rough set theory and EIF algorithm and provides an effective basis for the EIF-based anomaly detection method by removing redundant attributes with rough set theory. Experimental results show that the RS-EIF algorithm performs better than the iForest and EIF algorithms in terms of anomaly detection rate, and the results of the combination of rough set theory and EIF are more prominent compared to the other combination methods. © 2023 IEEE.

关键词： Anomaly detection

R-calculus for post three-valued description logic 7

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R-calculus for post three-valued description logic

7th International Conference on Fuzzy Systems and Data Mining, FSDM 2021

作者： Cao, Cungen Hu, Lanxi Sui, Yuefei Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences China School of Computer Science and Technology University of Chinese Academy of Sciences China

ISBN: (纸本)9781643682143

R-calculus is a belief revision operator satisfying AGM postulates, and belief revision in ontology engineering is ontology revision, which based logic is description logics. In Post three-valued description logic, a tableau proof system Tt will be given such that Tt is sound and complete for t-satisfiability, and nonmonotonic, that is, a theory Δis t-satisfiable if and only if Δis deducible in Tt. Based on the tableau proof system, an R-calculus Rt will be given such that a configuration Î"|C(a) is reducible to C(a),Δif and only if C(a) is t-satisfiable with Î", if and only if reduction Î"|C(a) â‡' C(a),Δis deducible in Rt. © 2021 The authors and IOS Press.

关键词： Ontology

Static for Dynamic: Towards a Deeper Understanding of Dynamic Facial Expressions Using Static Expression Data

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arXiv 2024年

作者： Chen, Yin Li, Jia Zhang, Yu Hu, Zhenzhen Shan, Shiguang Wang, Meng Hong, Richang School of Computer Science and Information Engineering Hefei University of Technology Hefei230601 China Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China University of Chinese Academy of Sciences Beijing100049 China

Dynamic facial expression recognition (DFER) infers emotions from the temporal evolution of expressions, unlike static facial expression recognition (SFER), which relies solely on a single snapshot. This temporal analysis provides richer information and promises greater recognition capability. However, current DFER methods often exhibit unsatisfied performance largely due to fewer training samples compared to SFER. Given the inherent correlation between static and dynamic expressions, we hypothesize that leveraging the abundant SFER data can enhance DFER. To this end, we propose Static-for-Dynamic (S4D), a unified dual-modal learning framework that integrates SFER data as a complementary resource for DFER. Specifically, S4D employs dual-modal self-supervised pre-training on facial images and videos using a shared Vision Transformer (ViT) encoder-decoder architecture, yielding improved spatiotemporal representations. The pre-trained encoder is then fine-tuned on static and dynamic expression datasets in a multi-task learning setup to facilitate emotional information interaction. Unfortunately, vanilla multitask learning in our study results in negative transfer. To address this, we propose an innovative Mixture of Adapter Experts (MoAE) module that facilitates task-specific knowledge acquisition while effectively extracting shared knowledge from both static and dynamic expression data. Extensive experiments demonstrate that S4D achieves a deeper understanding of DFER, setting new state-of-the-art performance on FERV39K, MAFW, and DFEW benchmarks, with weighted average recall (WAR) of 53.65%, 58.44%, and 76.68%, respectively. Additionally, a systematic correlation analysis between SFER and DFER tasks is presented, which further elucidates the potential benefits of leveraging SFER. Copyright © 2024, The Authors. All rights reserved.

关键词： Self-supervised learning

Deep progressive reinforcement learning-based flexible resource scheduling framework for IRS and UAV-assisted MEC system

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arXiv 2024年

作者： Dong, Li Jiang, Feibo Wang, Minjie Peng, Yubo Li, Xiaolong School of Computer Science Hunan University of Technology and Business Changsha China Xiangjiang Laboratory Changsha China Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing Hunan Normal University Changsha China College of Information Science and Engineering Hunan Normal University Changsha China

The intelligent reflection surface (IRS) and unmanned aerial vehicle (UAV)-assisted mobile edge computing (MEC) system is widely used in temporary and emergency scenarios. Our goal is to minimize the energy consumption of the MEC system by jointly optimizing UAV locations, IRS phase shift, task offloading, and resource allocation with a variable number of UAVs. To this end, we propose a Flexible REsource Scheduling (FRES) framework by employing a novel deep progressive reinforcement learning which includes the following innovations: Firstly, a novel multi-task agent is presented to deal with the mixed integer nonlinear programming (MINLP) problem. The multi-task agent has two output heads designed for different tasks, in which a classified head is employed to make offloading decisions with integer variables while a fitting head is applied to solve resource allocation with continuous variables. Secondly, a progressive scheduler is introduced to adapt the agent to the varying number of UAVs by progressively adjusting a part of neurons in the agent. This structure can naturally accumulate experiences and be immune to catastrophic forgetting. Finally, a light taboo search (LTS) is introduced to enhance the global search of the FRES. The numerical results demonstrate the superiority of the FRES framework which can make real-time and optimal resource scheduling even in dynamic MEC systems. Copyright © 2024, The Authors. All rights reserved.

关键词： Unmanned aerial vehicles (UAV)

General Sparse Normalization and Proportionate ASE Algorithms 5

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General Sparse Normalization and Proportionate ASE Algorithm...

5th IEEE International Conference on Electronic information and Communication Technology, ICEICT 2022

作者： Hadi, Abdul Peng, Yan Qadir, Abdul Li, Yingsong Khan, Khushal College of Information and Communication Engineering Harbin Engineering University Harbin China Anhui Province Key Laboratory of Target Recognition and Feature Extraction LuAn230088 China Anhui University Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education China College of Intelligent System and Control Science Engineering Harbin Engineering University China

ISBN: (数字)9781665472111

ISBN: (纸本)9781665472111

Andrew's Sine Estimator (ASE) has recently been used to invent adaptive filtering, which can combat more kind of noises than conventional estimators. Inspired by the LMS and its sparse forms, normalization and proportionate ASE algorithms with Lawson constraints are constructed with the respective given names of Lawson normalization ASE (LNASE) and Lawson proportionate NASE (LPNASE). Simulations are performed to analyze the performance of these algorithms under impulsive noise. © 2022 IEEE.

关键词： Impulse noise