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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Wei, Shuoying Li, Songquan Guo, Yifei Zhu, Lida Wen, Xinlong Zhu, Rongbo College of Informatics Huazhong Agricultural University Wuhan430070 China Shenzhen Institute of Nutrition and Health Huazhong Agricultural University Shenzhen518000 China Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen518000 China Engineering Research Center of Intelligent Technology for Agriculture Ministry of Education Hubei Wuhan430074 China Key Laboratory of Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China

ISBN: (纸本)9798350337488

Obtaining accurate and effective information for drug molecules is a crucial and challenging task, which relies on high-quality chemical knowledge. However, chemical knowledge has been accumulated over the past 100 years from various regions, laboratories, and experimental purposes, which contains a lot of noise and inconsistency, leading to the out-of-distribution (OOD) problem. OOD may results in weak robustness and unsatisfied performance. In order to solve OOD learning problem with noise, a novel benchmark: ADMEOOD is proposed, which is a systematic OOD dataset curator and specifically designed for drug property prediction. ADMEOOD screens 27 Absorption, Distribution, Metabolism and Excretion (ADME) drug properties from Chembl and relevant literature. This paper explicitly make distinctions between two kinds of OOD data shifts: Noise Shift and Concept Conflict Drift (CCD). Overall, ADME contains 6 domain annotations combined with noise, CCD and no shifts, resulting in 18 different splits in total. ADMEOOD provides performance results on a variety of SOTA OOD models. The results demonstrate a significant difference performance between in-distribution and OOD data. Moreover, Empirical Risk Minimization and other models exhibit distinct trends in different domains and measurement types. The ADMEOOD benchmark can be accessed via https://***/qweasdzxc-wsy/ADMEOOD/. © 2023 IEEE.

关键词： ADME Benchmark Drug property prediction Out-of-distribution

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Causal Invariant Hierarchical Molecular Representation for Out-of-distribution Molecular Property Prediction

Causal Invariant Hierarchical Molecular Representation for O...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Wen, Xinlong Guo, Yifei Wei, Shuoying Long, Wenhan Zhu, Lida Zhu, Rongbo College of Informatics Huazhong Agricultural University Wuhan430070 China Shenzhen Institute of Nutrition and Health Huazhong Agricultural University Shenzhen518000 China Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen518000 China Engineering Research Center of Intelligent Technology for Agriculture Ministry of Education Hubei Wuhan430074 China Key Laboratory of Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China

ISBN: (纸本)9798350386226

Molecular representation learning is widely used in the field of drug discovery, due to its ability to accurately capture the complex features of compounds in high-dimensional space. However, existing molecular representation learning models are prone to be influenced by spurious parts during distribution shifts (also known as out-of-distribution, or OOD), which results in models mistakenly treating these spurious parts as crucial features of molecules, thereby limiting the generalization capability of the models. To tackle this issue, a novel invariant molecular representation learning model, called Causal Invariant Hierarchical Molecular Representation Graph Neural Networks (CHiMoGNN), is proposed for OOD molecular property prediction. In CHiMoGNN, a Feature Enhancement (FE) module is designed to leverage the multi-level molecular parts to enhance the expression of invariant features, thereby enhancing the model's capability to capture key molecular information. In addition, a Cartesian Product based Environmental Impact (EI) module is adopted to generate counterfactual samples with environmental diversity. Consequently, these samples are utilized to train a classifier that maintains consistent performance across various environments. Extensive experiments on seven real-world datasets demonstrate that CHiMoGNN outperforms 9 state-of-the-art models, achieving a 5.73% increase in average ROC-AUC, and the results also show that CHiMoGNN can effectively maintain generalization in various distribution shifts. Code and datasets are available at https://***/Chertuion/CHiMoGNN. © 2024 IEEE.

关键词： Graph neural networks

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Statistical Feasibility Robust Optimization for Hydrogen-Data Center Microgrid Operation

SSRN

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SSRN 2024年

作者： Duan, Juntao Li, Yuanzheng Li, Yang Liu, Zhiwei Zhao, Yong School of Artificial Intelligence and Automation Key Laboratory on Image Information Processing and Intelligent Control of Ministry of Education Huazhong University of Science and Technology Wuhan430074 China Key Laboratory of Modern Power System Simulation and Control & Renewable Energy Technology Ministry of Education Northeast Electric Power University Jilin132012 China

The increasing processing demands of information technology (IT) workloads cause the booming of data centers (DCs) in recent years. The servers in the DC emit much heat when processing the IT workloads and thus the DC temperature rises. The power consumption when controlling the DC temperature using the air conditioning (A/C) of the DC is high, which leads to expensive power bills. To reduce the power cost, using renewable energy (RE) to power DC has raised much attention in recent years. However, the intermittency of RE and the uncertainties of outside temperature pose operational challenges. Therefore, in this paper, a data-driven statistical-feasibility-based robust rolling optimization framework for the operation of hydrogen-DC microgrid (H2-DCMG) is proposed to control the DC temperature considering these uncertainties and the intermittency of RE. In the framework, the hydrogen energy storage system (HESS) is introduced to deal with the intermittency of RE, and robust optimization (RO) is adopted to deal with the uncertainty of outside temperature. The statistical feasibility is introduced into the framework to decrease the conservatism of RO, through relaxing the DC temperature constraints without harming normal DC operations. Moreover, we propose the Statistical-Guarantee-based Vertex Link (SGVL) algorithm to construct a polyhedron uncertain set of outside temperatures that can ensure the results of dispatch are economical and satisfy statistical feasibility. The constructed polyhedron uncertain set is linear, which reduces computational complexity in solving. A case study based on the real-world temperature dataset verifies the superiority of the SGVL algorithm on the aspect of the economic cost. It further validates the effectiveness of the proposed robust optimization framework for DC temperature control. © 2024, The Authors. All rights reserved.

关键词： Air conditioning

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Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

Isoform Function Prediction Based on Heterogeneous Graph Att...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kuo Guo Yifan Li Hao Chen Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function.

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Statistical Feasibility Robust Optimization for Hydrogen-Data Center Microgrid Operation

SSRN

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SSRN 2024年

关键词： Air conditioning

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Architectural distortion recognition based on a subclass technique and the sparse representation classifier

Architectural distortion recognition based on a subclass tec...

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International Congress on image and Signal processing, BioMedical Engineering and Informatics (CISP-BMEI)

作者： Xiaoming Liu Leilei Zhai Ting Zhu Zhou Yang School of Automation Huazhong University of Science and Technology Wuhan China Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System Wuhan China Key Laboratory of Image Processing and Intelligent Control of Education Ministry of China Wuhan China College of Computer Science and Technology Wuhan University of Science and Technology Wuhan China

ISBN: (纸本)9781509037117

Architectural distortion is the third most common sign of breast cancer in mammograms. The accurate recognition is important for computer aided diagnosis of breast cancer. However, due to the subtle symptom and complex structures in the mammogram images, it is difficult to recognize whether a region of interest (ROI) is truly an architectural distortion. In this paper, we proposed a new method for architectural distortion recognition. In the proposed method, several texture features are extracted for each region of interest, including features from GLCM matrix, spiculated related features, entropy features, etc. Feature selection is obtained by a sub-classes clustering based multi-task learning method (SMTL), which can utilize the discriminative label information and reflect the multi-clustering characteristic of the data samples. Finally, the powerful sparse representation based classifier is used for the classification of AD or non-AD. The proposed method has been tested on DDSM dataset and compared with several other methods, the experimental results showed the effectiveness of the proposed method.

关键词： Feature extraction Distortion Entropy Training Mammography Delta-sigma modulation Breast cancer

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Closer to Pre-trained Network Transfer Better

Closer to Pre-trained Network Transfer Better

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IEEE Joint International Information Technology and Artificial Intelligence Conference (ITAIC)

作者： Siyu Chen Wei Li School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan People’s Republic of China Image Processing and Intelligent Control Key Laboratory Education Ministry of China Wuhan People’s Republic of China

ISBN: (数字)9781728152448

ISBN: (纸本)9781728152455

In recent years, Deep Neural Network (DNN) has been widely used in the domain of computer vision, but its further development is restricted because of the lack of train samples. Fine-tuning is one of deep transfer learning methods to solve this problem. Nowadays, some existing Fine-tuning approaches assume that if the fine-tuned network could be as close to the pre-trained network as possible, the source knowledge would be fully utilized to improve the study effect. Although these approaches work pretty well, the assumptions on which they are based have not been systematically proved. Due to the complexity of DNNs, offering a reasonable and accurate explanation of the performance of the network is significant for designing new algorithms. In this paper, we design a series of experiments with or without transfer learning respectively, to characterize the relationship between network differences and network performance. The results show that there is an obvious negative correlation between them under certain circumstances. This conclusion can not only provide a more reasonable explanation for the relevant transfer learning algorithm, but also provide support and inspiration for the future work.

关键词： Knowledge engineering Correlation Transfer learning Neural networks Task analysis Information technology Knowledge transfer

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Fault detection and identification for a class of nonlinear systems with model uncertainty

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Applied Mathematical Modelling 2016年第15-16期40卷 7368-7381页

作者： Bingyong Yan Housheng Su Wei Ma School of Automation Key Laboratory of Advanced Control and Optimization for Chemical Process of Ministry of Education East China University of Science and Technology 130 Meilong Road Shanghai 200237 China School of Automation Key Laboratory of Image Processing and Intelligent Control of Ministry of Education of China Huazhong University of Science and Technology Wuhan 430074 China Key Laboratory for Advanced Materials & Institute of Fine Chemicals East China University of Science and Technology 130 Meilong Road Shanghai 200237 China

In this paper, we present a novel fault detection and identification (FDI) scheme for a class of nonlinear systems with model uncertainty. At the heart of this approach is an on-line approximator, referred to as fault tracking approximator (FTA). Differently from the other approximators, the FTA uses iterative algorithms to detect and identify nonlinear system faults, even in the presence of model uncertainty, which is motivated by predictive control theory and iterative learning control theory. The FTA can simultaneously detect and identify the shape and magnitude of the faults. The rigorous stability analysis and fault tracking properties of the FTA are also proved. Finally, two examples are given to illustrate the feasibility and effectiveness of the proposed approach.

关键词： Fault detection and identification Predictive control Iterative learning control

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Two-stage Train Components Defect Detection Based on Prior Knowledge

Two-stage Train Components Defect Detection Based on Prior K...

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IEEE/RSJ International Conference on intelligent Robots and Systems (IROS)

作者： Gang Peng Zhiyong Li Shaowei Wan Zhang Deng Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Wuhan Lisai Technology Co. Ltd. Wuhan China

The existing method of detecting defects in train components, which relies on visual identification, requires extensive involvement from inspectors and presents certain limitations. In this study, a two-stage defect detection based on prior knowledge was developed, which first detects the types and positions of components, and then conducts targeted detection of possible existing defect types. The algorithm introduces the prior knowledge of the relative spatial position relationship of components and optimizes the detection of sub-components by cascaded convolutional neural networks and local scale-up. In this study, three methods were used, including deep learning, template matching, and quantitative evaluation based on prior knowledge, to perform targeted detection of defect types that may occur in components. Experiments have verified the adaptability and accuracy of the method, demonstrating its high value for engineering applications.

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Transfer Learning for Motor imagery Based Brain-Computer Interfaces: A Complete Pipeline

arXiv

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arXiv 2020年

作者： Wu, Dongrui Jiang, Xue Peng, Ruimin Kong, Wanzeng Huang, Jian Zeng, Zhigang Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China Zhejiang Key Laboratory for Brain-Machine Collaborative Intelligence Hangzhou Dianzi University Hangzhou310018 China

Transfer learning (TL) has been widely used in motor imagery (MI) based brain-computer interfaces (BCIs) to reduce the calibration effort for a new subject, and demonstrated promising performance. While a closed-loop MI-based BCI system, after electroencephalogram (EEG) signal acquisition and temporal filtering, includes spatial filtering, feature engineering, and classification blocks before sending out the control signal to an external device, previous approaches only considered TL in one or two such components. This paper proposes that TL could be considered in all three components (spatial filtering, feature engineering, and classification) of MI-based BCIs. Furthermore, it is also very important to specifically add a data alignment component before spatial filtering to make the data from different subjects more consistent, and hence to facilitate subsequential TL. Offline calibration experiments on two MI datasets verified our proposal. Especially, integrating data alignment and sophisticated TL approaches can significantly improve the classification performance, and hence greatly reduces the calibration effort. Copyright © 2020, The Authors. All rights reserved.

关键词： Electroencephalography

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