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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Chen, Ke Han, Xiaosong Li, Xiaoran Liang, Yanchun Xu, Dong Guan, Renchu Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Changchun China Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Changchun China Zhuhai College of Science and Technology Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education School of Computer Science Zhuhai China University of Missouri Christopher S. Bond Life Sciences Center Department of Electrical Engineering and Computer Science Columbia United States

ISBN: (纸本)9798350386226

Drug-Drug Interaction (DDI) task plays a crucial role in clinical treatment and drug development. Recently, deep learning methods have been successfully applied for DDI prediction. However, training deep learning models always need large amount of data, while known DDIs are scarce. To address this challenge, a graph neural network-based DDI prediction model named PNESR-DDI is proposed, which compensates for the lack of DDIs by enriching drug representations. First, to obtain initial node representations that incorporate rich semantic information from the biomedical knowledge graph (KG), a link prediction pre-training method on external KG is proposed in the node embedding pre-training module. Then, considering the large scale of the KG, subgraph extraction for the target drug pairs is introduced to reduce noise and decrease computational complexity in the subgraph anchoring module. After that, the subgraph is updated, and node similarities are propagated in the subgraph reconstruction module. Based on the node similarity scores, the subgraph is pruned and reconstructed, which adjusts node representations to be more conducive to DDI prediction. Finally, the drug embeddings, subgraph representations, and drug fingerprint features are concatenated to predict DDIs. PNESRDDI is evaluated on two benchmark DDI datasets: DrugBank and TWOSIDES. Experiment results show that PNESR-DDI achieves better performance than baselines. Ablation results validate the effectiveness of the pre-training method and the adaptive subgraph reconstruction strategy. © 2024 IEEE.

关键词： knowledge graph

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SMRI: A New Method for siRNA Design for COVID-19 Therapy

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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 13th, 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-19. 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-19 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-19.

关键词： COVID-19 SARS-CoV-2 RibonucleicAcid interference

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Semi-supervised Multi-label Learning with Balanced Binary Angular Margin Loss 38

Semi-supervised Multi-label Learning with Balanced Binary An...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Li, Ximing Liang, Silong Li, Changchun Wang, Pengfei Gu, Fangming College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China Computer Network Information Center Chinese Academy of Sciences China University of Chinese Academy of Sciences Chinese Academy of Sciences China

Semi-supervised multi-label learning (SSMLL) refers to inducing classifiers using a small number of samples with multiple labels and many unlabeled samples. The prevalent solution of SSMLL involves forming pseudo-labels for unlabeled samples and inducing classifiers using both labeled and pseudo-labeled samples in a self-training manner. Unfortunately, with the commonly used binary type of loss and negative sampling, we have empirically found that learning with labeled and pseudo-labeled samples can result in the variance bias problem between the feature distributions of positive and negative samples for each label. To alleviate this problem, we aim to balance the variance bias between positive and negative samples from the perspective of the feature angle distribution for each label. Specifically, we extend the traditional binary angular margin loss to a balanced extension with feature angle distribution transformations under the Gaussian assumption, where the distributions are iteratively updated during classifier training. We also suggest an efficient prototype-based negative sampling method to maintain high-quality negative samples for each label. With this insight, we propose a novel SSMLL method, namely Semi-Supervised Multi-Label Learning with Balanced Binary Angular Margin loss (S2ML2-BBAM). To evaluate the effectiveness of S2ML2-BBAM, we compare it with existing competitors on benchmark datasets. The experimental results validate that S2ML2-BBAM can achieve very competitive performance. © 2024 Neural information processing systems foundation. All rights reserved.

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An Automatic Solution in Security Inspection

An Automatic Solution in Security Inspection

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International Conference on Machine Vision and Information Technology (CMVIT)

作者： Hui Zhang Xiaoli Zhang Key Laboratory of Symbolic Computation and Knowledge Engineer Ministry of Education Changchun China

In this paper, we present a brand new dataset named cellphone buttery defects in X-ray(CBDx). CBDx consists of 300 X-ray images and 250 of them are anomaly free. We name them ‘good’. Others have some defects in the area of buttery. We name them ‘anomaly’, as Fig. 1. It raises a new task of detecting anomaly defects of cellphone butteries. But the challenge is how to distinguish the anomaly in the case of only training the ‘good’ cellphone. We define this task as an anomaly detection task. We propose an approach to deal with the task from the perspective of unbalanced classification. Specifically, we propose a data augmentation strategy that creates an anomaly sample mimic to the real defects. It helps the classifier to learn self-supervised deep representations and then make it an one-class classifier based on the representations. The classifier is well designed to discriminate the defect samples from the good ones. We evaluate different data augmentation strategies on CBDx. Our approach is more significant in this scenario with no defect training samples, which can be applied in real-world security inspection someday. Also, it can be used on the industrial texture anomaly detection, such as MVTec_AD.

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Decision mamba: reinforcement learning via hybrid selective sequence modeling 24

Decision mamba: reinforcement learning via hybrid selective ...

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Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Sili Huang Jifeng Hu Zhejian Yang Liwei Yang Tao Luo Hechang Chen Lichao Sun Bo Yang Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education and School of Artificial Intelligence Jilin University China School of Artificial Intelligence Jilin University China Institute of High Performance Computing Agency for Science Technology and Research Singapore Lehigh University Bethlehem Pennsylvania Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education

ISBN: (纸本)9798331314385

Recent works have shown the remarkable superiority of transformer models in reinforcement learning (RL), where the decision-making problem is formulated as sequential generation. Transformer-based agents could emerge with self-improvement in online environments by providing task contexts, such as multiple trajectories, called in-context RL. However, due to the quadratic computation complexity of attention in transformers, current in-context RL methods suffer from huge computational costs as the task horizon increases. In contrast, the Mamba model is renowned for its efficient ability to process long-term dependencies, which provides an opportunity for in-context RL to solve tasks that require long-term memory. To this end, we first implement Decision Mamba (DM) by replacing the backbone of Decision Transformer (DT). Then, we propose a Decision Mamba-Hybrid (DM-H) with the merits of transformers and Mamba in high-quality prediction and long-term memory. Specifically, DM-H first generates high-value sub-goals from long-term memory through the Mamba model. Then, we use sub-goals to prompt the transformer, establishing high-quality predictions. Experimental results demonstrate that DM-H achieves state-of-the-art in long and short-term tasks, such as D4RL, Grid World, and Tmaze benchmarks. Regarding efficiency, the online testing of DM-H in the long-term task is 28× times faster than the transformer-based baselines.

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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 Unified Loss for Handling Inter-Class and Intra-Class Imbalance in Medical Image Segmentation 39

A Unified Loss for Handling Inter-Class and Intra-Class Imba...

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39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Xu, Feilong Yang, Feiyang Li, Xiongfei Zhang, Xiaoli Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China College of Computer Science and Technology Jilin University China

ISBN: (纸本)157735897X

In utilizing deep learning techniques for medical image segmentation, two types of imbalance issues are observed: inter-class imbalance between majority and minority classes and intra-class imbalance between easy and hard samples. However, existing loss functions typically confuse these issues, leading to enhancements that cater to only one aspect. Moreover, loss functions optimized for specific tasks often exhibit limited generalizability. To address these issues, we propose Inter-class and Intra-class Balance loss, as well as a unified loss termed Balance loss. The Inter-class Balance loss controls the extent of hard sample mining for majority class samples by considering the frequency of minority classes present in each input image. This approach requires no manual adjustment weights and adapts automatically to different datasets. The Intra-class Balance loss enhances the network's ability to learn from hard samples by performing mining on hard samples within each class. We evaluate our loss functions on five segmentation tasks with varying degrees of class imbalance. The experimental results show that our proposed Balance loss enhances segmentation performance compared with the current loss functions and exhibits superior robustness. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Image segmentation

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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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A Simple Graph Contrastive Learning Framework for Short Text Classification 39

A Simple Graph Contrastive Learning Framework for Short Text...

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39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

ISBN: (纸本)157735897X

关键词： Contrastive Learning

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