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SMRI: A New Method for siRNA Design for COVID-1. Therapy

Journal of Computer Science & Technology 2022年第4期37卷 991-1002页

作者： Meng-Xin Chen Xiao-Dong Zhu Hao Zhang Zhen Liu Yuan-Ning Liu College of Software Jilin UniversityChangchun 130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Jilin UniversityChangchun 130012China College of Computer Science and Technology Jilin UniversityChangchun 130012China Graduate School of Engineering Nagasaki Institute of Applied ScienceNagasaki 851-0193Japan

First discovered in Wuhan, China, SARS-CoV-2 is a highly pathogenic novel coronavirus, which rapidly spreads globally and becomes a pandemic with no vaccine and limited distinctive clinical drugs available till March 1.th, 2020. Ribonucleic Acid interference (RNAi) technology, a gene-silencing technology that targets mRNA, can cause damage to RNA viruses effectively. Here, we report a new efficient small interfering RNA (siRNA) design method named Simple Multiple Rules Intelligent Method (SMRI) to propose a new solution of the treatment of COVID-1.. To be specific, this study proposes a new model named Base Preference and Thermodynamic Characteristic model (BPTC model) indicating the siRNA silencing efficiency and a new index named siRNA Extended Rules index (SER index) based on the BPTC model to screen high-efficiency siRNAs and filter out the siRNAs that are difficult to take effect or synthesize as a part of the SMRI method, which is more robust and efficient than the traditional statistical indicators under the same circumstances. Besides, to silence the spike protein of SARS-CoV-2 to invade cells, this study further puts forward the SMRI method to search candidate high-efficiency siRNAs on SARS-CoV-2's S gene. This study is one of the early studies applying RNAi therapy to the COVID-1. treatment. According to the analysis, the average value of predicted interference efficiency of the candidate siRNAs designed by the SMRI method is comparable to that of the mainstream siRNA design algorithms. Moreover, the SMRI method ensures that the designed siRNAs have more than three base mismatches with human genes, thus avoiding silencing normal human genes. This is not considered by other mainstream methods, thereby the five candidate high-efficiency siRNAs which are easy to take effect or synthesize and much safer for human body are obtained by our SMRI method, which provide a new safer, small dosage and long efficacy solution for the treatment of COVID-1..

关键词： COVID-1. SARS-CoV-2 RibonucleicAcid interference

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Measuring drug similarity using drug–drug interactions

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Quantitative Biology 2024年第2期12卷 164-172页

作者： Ji Lv Guixia Liu Yuan Ju Houhou Huang Ying Sun College of Computer Science and Technology Jilin UniversityChangchunChina Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin UniversityChangchunChina Sichuan University Library Sichuan UniversityChengduChina College of Chemistry Jilin UniversityChangchunChina Department of Respiratory Medicine The First Hospital of Jilin UniversityChangchunChina

Combination therapy is a promising approach to address the challenge of antimicrobial resistance,and computational models have been proposed for predicting drug–drug *** existing models rely on drug similarity measures based on characteristics such as chemical structure and the mechanism of *** this study,we focus on the network structure itself and propose a drug similarity measure based on drug–drug interaction *** explore the potential applications of this measure by combining it with unsupervised learning and semi-supervised learning *** unsupervised learning,drugs can be grouped based on their interactions,leading to almost monochromatic group–group *** addition,drugs within the same group tend to have similar mechanisms of action(MoA).In semi-supervised learning,the similarity measure can be utilized to construct affinity matrices,enabling the prediction of unknown drug–drug *** method exceeds existing approaches in terms of ***,our experiments demonstrate the effectiveness and practicability of the proposed similarity *** the one hand,when combined with clustering algorithms,it can be used for functional annotation of compounds with unknown *** the other hand,when combined with semi-supervised graph learning,it enables the prediction of unknown drug–drug interactions.

关键词： drug similarity drug–drug interactions drug combinations synergy effect clustering semi-supervised learning

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Injecting Revenue-awareness into Cold-start Recommendation: The Case of Online Insurance 29

Injecting Revenue-awareness into Cold-start Recommendation: ...

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29th IEEE International Conference on Parallel and Distributed Systems, ICPADS 2023

作者： Li, Yu Zhang, Yi Chang, Helen He Li, Qiang Jilin University College of Computer Science and Technology China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China WeSure Inc. Ping An Technology Shenzhen Co. Ltd China

ISBN: (纸本)9798350330717

In online insurance, one of the central challenges is the cold-starting of new insurance products, which means there are no previous samples to refer to. Previous studies have mainly focused on improving the prediction accuracy of new items, but they have failed to consider the revenue generated by existing items. As a result, the total revenue may suffer a loss even if new items get conversions. To address this issue, in this paper we propose RACRec, a Revenue-Aware Cold-start Recommendation framework for online insurance. Unlike previous works, RACRec uses a revenue-based objective function to ensure profitability when cold-starting new items. With this dedicated objective, RACRec orchestrates the cold-start and warm-start model by predicting their expected revenue from each user, thereby preserving the total profit. In order to accurately predict revenue, a double-ranking scheme is designed for the warm-start model to mitigate position bias, while an item embedding alignment algorithm is proposed for the cold-start model to learn the revenue of new items from similar old items. Furthermore, a reinforced orchestrate update scheme is designed to eliminate the impact of sparse conversions and continuously update revenue estimation. Extensive offline and online experiments have been conducted to validate the effectiveness of RACRec. © 2023 IEEE.

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A Simple Graph Contrastive Learning Framework for Short Text Classification

arXiv

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arXiv 2025年

作者： Liu, Yonghao Giunchiglia, Fausto Huang, Lan Li, Ximing Feng, Xiaoyue Guan, Renchu Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University China University of Trento Italy

Short text classification has gained significant attention in the information age due to its prevalence and real-world applications. Recent advancements in graph learning combined with contrastive learning have shown promising results in addressing the challenges of semantic sparsity and limited labeled data in short text classification. However, existing models have certain limitations. They rely on explicit data augmentation techniques to generate contrastive views, resulting in semantic corruption and noise. Additionally, these models only focus on learning the intrinsic consistency between the generated views, neglecting valuable discriminative information from other potential views. To address these issues, we propose a Simple graph contrastive learning framework for Short Text Classification (SimSTC). Our approach involves performing graph learning on multiple text-related component graphs to obtain multi-view text embeddings. Subsequently, we directly apply contrastive learning on these embeddings. Notably, our method eliminates the need for data augmentation operations to generate contrastive views while still leveraging the benefits of multi-view contrastive learning. Despite its simplicity, our model achieves outstanding performance, surpassing large language models on various datasets. Copyright © 2025, The Authors. All rights reserved.

关键词： Contrastive Learning

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Research on Ethnic Pattern Generation Based on Generative Adversarial Networks

Research on Ethnic Pattern Generation Based on Generative Ad...

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International Workshop on Advanced computational Intelligence (IWACI)

作者： Hao Wu Wenze He Xiongfei Li Yanchun Liang Zhuhai Sub Laboratory of Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Zhuhai College of Science and Technology Zhuhai China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Changchun China

In this paper, we take Mongolian ethnic patterns as the research object and conduct a technical study on ethnic pattern generation and super-resolution reconstruction based on deep learning generative adversarial networks to address the problems of low quality of ethnic pattern data collection and lack of innovation. In this paper, we use a database including 1.21.Mongolian ethnic patterns, train StyleGAN2 on the pre-processed images, and generate images After that, we use ESRGAN to perform super-resolution reconstruction on the generated images to generate high-resolution patterns with Mongolian style. The model designed in this paper can generate high quality images with ethnic characteristics in the case of insufficient original data. Compared with the time-consuming and labor-intensive traditional ethnic pattern design methods, the model designed in this paper lowers the threshold of ethnic pattern innovation and contributes to the innovative design of ethnic patterns to a certain extent, which has some positive significance for the protection and inheritance of ethnic patterns.

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2D-3D Feature Co-Embedding Network with Sparse Annotation for 3D Medical Image Segmentation

2D-3D Feature Co-Embedding Network with Sparse Annotation fo...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Zhu, Mingzhu Guo, Shuyu Wang, Ziwei Jiao, Jianhang Bai, Tian Jilin University College of Computer Science and Technology Changchun China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun China Jilin University College of Software Changchun China The Second Norman Bethune Hospital Jilin University Department of Orthopedics Changchun China

ISBN: (纸本)9798350386226

Supervised methods on 3D medical image segmentation need large amounts of annotated data, but annotating is time-consuming. Also, existing 3D segmentation methods capture more global structural information but overlook local detailed features, which negatively impacts the segmentation of small tissues. In this paper, we propose a novel weakly-supervised 2D-3D Feature Co-Embedding Network (2D-3D CoENet) that includes 2D and 3D encoding layers, simultaneously extracting 2D local detailed and 3D global structural features. To reduce annotation costs, we use fewer labeled slices as ground truth and pseudo-labels are generated by 2D-3D CoENet for other slices. Additionally, multi-view learning is introduced to capture more 2D local detailed information, and a Multi-view Semantic Consistency loss (MSC loss) is proposed to constrain features from multiple perspectives. To further enhance the local detailed texture features, we propose an Edge Enhancement Module (EEM) in the 3D segmentation network to enhance the edge detail features. Our experimental results on the SKI1. dataset and OAI ZIB dataset demonstrate that our method outperforms the SOTA weakly-supervised segmentation methods. Moreover, our approach achieves results that are comparable to the fully-supervised upper bound results. © 2024 IEEE.

关键词： Medical imaging

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A Method for Extracting Electronic Medical Record Entities by Fusing Multichannel Self-Attention Mechanism with Location Relationship Features

A Method for Extracting Electronic Medical Record Entities b...

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作者： Hongyan Xu Hong Wang Yong Feng Rongbing Wang Yonggang Zhang College of Information Liaoning University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University

With the implementation of the "Internet+" strategy, electronic medical records are generally applied in the medical field. Deep mining of electronic medical record content data is an effective means to obtain medical knowledge and analyse patients' states, but the existing methods for extracting entities from electronic medical records have problems of redundant information, overlapping entities, and low accuracy rates. Therefore, this paper proposes an entity extraction method for electronic medical records based on the network framework of BERT-Bi LSTM, which incorporates a multichannel self-attention mechanism and location relationship features. First, the text input sequence was encoded using the BERT-BiLSTM network framework, and the global semantic information of the sentence was mined more deeply using the multichannel self-attention mechanism. Then, the position relation characteristic was used to extract the local semantic message of the text, and the position relation characteristic of the word and the position embedding matrix of the whole sentence were obtained. Next, the extracted global semantic information was stitched with the positional embedding matrix of the sentence to obtain the current entity classification matrix. Finally,the proposed method was validated on the dataset of Chinese medical text entity relationship extraction and the 201.i2b2/VA relationship corpus, and the experimental results indicate that the proposed method surpasses existing methods in terms of precision, recall, F1.value and training time.

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Simple-Sampling and Hard-Mixup with Prototypes to Rebalance Contrastive Learning for Text Classification

arXiv

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arXiv 2024年

作者： Li, Mengyu Liu, Yonghao Giunchiglia, Fausto Feng, Xiaoyue Guan, Renchu Key Laboratory of Symbolic Computation and Knowledge Engineering The Ministry of Education College of Computer Science and Technology Jilin University China University of Trento Italy

Text classification is a crucial and fundamental task in natural language processing. Compared with the previous learning paradigm of pre-training and fine-tuning by cross entropy loss, the recently proposed supervised contrastive learning approach has received tremendous attention due to its powerful feature learning capability and robustness. Although several studies have incorporated this technique for text classification, some limitations remain. First, many text datasets are imbalanced, and the learning mechanism of supervised contrastive learning is sensitive to data imbalance, which may harm the model performance. Moreover, these models leverage separate classification branch with cross entropy and supervised contrastive learning branch without explicit mutual guidance. To this end, we propose a novel model named SharpReCL for imbalanced text classification tasks. First, we obtain the prototype vector of each class in the balanced classification branch to act as a representation of each class. Then, by further explicitly leveraging the prototype vectors, we construct a proper and sufficient target sample set with the same size for each class to perform the supervised contrastive learning procedure. The empirical results show the effectiveness of our model, which even outperforms popular large language models across several datasets. Copyright © 2024, The Authors. All rights reserved.

关键词： Classification (of information)

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Enabling Generalized Zero-Shot Vulnerability Classification

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IEEE Transactions on Dependable and Secure Computing 2025年

作者： Hu, Jinghao Guo, Jinsong Luo, Chen Hu, Yang Lanzinger, Matthias Li, Zhanshan Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education College of Software Changchun130012 China University College London Department of Computer Science United Kingdom Amazon United States United Kingdom University of Oxford Department of Computer Science United Kingdom Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education College of Computer Science and Technology Changchun130012 China

Regarding computer security, the growth of code vulnerability types presents a persistent challenge. These vulnerabilities, which may cause severe consequences, necessitate precise classification for effective mitigation. However, the rapid emergence of new vulnerability types complicates the classification process. Traditional methodologies, which often involve human expertise and the manual labeling or generation of example instances, are not only resource-intensive but also struggle to adapt to the dynamic nature of these vulnerabilities. This paper introduces VulnSense, an innovative method that harnesses the capabilities of Generalized Zero-Shot Learning (GZSL) to address the vulnerability classification problem. VulnSense learns about unseen vulnerability classes from the descriptions of these unseen classes, while not requiring to see any instances of these unseen classes. Specifically, VulnSense learns from three main resources: (1. seen classes with labeled code instances;(2) descriptions of these seen classes;and (3) descriptions of "unseen"classes which have no labeled instances. Our experiments underscore VulnSense's superiority over existing GZSL methods in classifying instances of unseen classes. Concurrently, it maintains a performance parity with traditional labeled-example based learning methods in classifying instances of seen vulnerabilities. VulnSense demonstrates the potential of using GZSL for vulnerability classification, while also highlighting challenges that inspire future work. © 2004-201. IEEE.

关键词： Zero-shot learning

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Underwater Target Detection Based on Reinforcement Learning and Ant Colony Optimization

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Journal of Ocean University of China 2022年第2期21卷 323-330页

作者： WANG Xinhua ZHU Yungang LI Dayu ZHANG Guang School of Computer Science Northeast Electric Power UniversityJilin 132012China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education College of Computer Science and TechnologyJilin UniversityChangchun 130012China State Key Laboratory of Applied Optics Changchun Institute of OpticsFine Mechanics and PhysicsChinese Academy of SciencesChangchun 130033China

Underwater optical imaging produces images with high resolution and abundant information and hence has outstanding advantages in short-distance underwater target ***,low-light and high-noise scenarios pose great challenges in un-derwater image and video *** improve the accuracy and anti-noise performance of underwater target image edge detection,an underwater target edge detection method based on ant colony optimization and reinforcement learning is proposed in this ***,the reinforcement learning concept is integrated into artificial ants’movements,and a variable radius sensing strategy is pro-posed to calculate the transition probability of each *** methods aim to avoid undetection and misdetection of some pixels in image ***,a double-population ant colony strategy is proposed,where the search process takes into account global search and local search *** results show that the algorithm can effectively extract the contour information of underwater targets and keep the image texture well and also has ideal anti-interference performance.

关键词： ant colony optimization reinforcement learning underwater target edge detection

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