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SSRN 2023年

作者： Liang, Yanhua Qin, Guihe Sun, Minghui Qin, Jun Yan, Jie Zhang, Zhonghan College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China School of Computer Science and Technology Changchun University of Science and Technology Changchun130012 China

Salient object detection in optical remote sensing images (RSI-SOD) aims to locate and extract visually discriminative objects or regions, which has attracted more and more attention from the community. The key challenge of RSI-SOD lies in the characteristics of optical RSIs, such as scale diversification of salient objects, irregular edges, and cluttered backgrounds. In this paper, we strive to embrace challenges towards effective and efficient RSI-SOD. To this end, we develop a framework, termed Adversarial Complementary Erasing Network (ACENet), which comprehensively mines discriminative features of different layers from foreground, background, local and global perspectives to perform robust and accurate saliency detection. Specifically, ACENet is a typical encoder-decoder structure that embeds Adversarial Erasing Synthesis Module (AESM) in multi-scale encoding features to fully explore more useful and complete representations. In AESM, we introduce Adversarial Discriminant Information Mining (ADIM) component to facilitate adaptive adjustment between salient features and background, further enabling more representative and strong integrity feature generation. Experimental results on three datasets prove that our ACENet significantly outperforms cutting-edge SOD models both qualitatively and quantitatively with a quick reasoning speed of 76 FPS. Code will be available at https://***/Liangyh18/ACENet. © 2023, The Authors. All rights reserved.

关键词： Optical remote sensing

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PBCounter: Weighted Model Counting on Pseudo-Boolean Formulas

arXiv

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arXiv 2023年

作者： Lai, Yong Xu, Zhenghang Yin, Minghao College of Computer Science and Technology Jilin University Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130012 China School of Computer Science and Information Technology Northeast Normal University Changchun130017 China

In Weighted Model Counting (WMC), we assign weights to literals and compute the sum of the weights of the models of a given propositional formula where the weight of an assignment is the product of the weights of its literals. The current WMC solvers work on Conjunctive Normal Form (CNF) formulas. However, CNF is not a natural representation for human-being in many applications. Motivated by the stronger expressive power of pseudo-Boolean (PB) formulas than CNF, we propose to perform WMC on PB formulas. Based on a recent dynamic programming algorithm framework called ADDMC for WMC, we implement a weighted PB counting tool PBCounter. We compare PBCounter with the state-of-the-art weighted model counters SharpSAT-TD, ExactMC, D4, and ADDMC, where the latter tools work on CNF with encoding methods that convert PB constraints into a CNF formula. The experiments on three domains of benchmarks show that PBCounter is superior to the model counters on CNF formulas. Copyright © 2023, The Authors. All rights reserved.

关键词： Dynamic programming

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Complementary knowledge Compilation Using the Hyper Extension Rule

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Chinese Journal of Electronics 2019年第2期28卷 259-265页

作者： NIU Dangdang LIU Lei LYU Shuai XU Yue College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University

We introduce the concept of Complementary formula(COMF), which is a new and non-equivalent way for knowledge compilation(KC). Based on the Hyper extension rule(HER) which is an expansion of Extension rule(ER), we design a compilation algorithm which can formula compile each Conjunctive normal form(CNF)formula to complementary Fully complementary connected diagram(c-FCCD), named as C2C(CNF formula to cFCCD). Theoretically, c-FCCD is a kind of complementary formulae of the input formulae and can support all queries and partial transformations in KC map. Experimentally,C2C is competitive with the EPCCL compilers KCER,C2E, UKCHER, DKCHER and IKCHER.

关键词： knowledge compilation Extension rule Hyper extension rule Compilation language Each pair contains complementary literals(EPCCL) theory

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Multimodal Medical Image Feature Representation and Fusion for AD Early Diagnosis

Multimodal Medical Image Feature Representation and Fusion f...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jing Qu Ying Qu Xueliang Bai Lanxin Xu Han Wang Guixia Liu College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China College of Science North China University of Science and Technology Tangshan China School of Information Science and Technology Institute of Computational Biology Northeast Normal University Changchun China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Alzheimer's disease (AD) is progressive and gets worse with time. Early detection is an effective treatment for the disease, which can timely implement effective interventions. The multi-modal medical image contains more comprehensive and abundant information about the disease, which can reflect the different aspects of AD and reduce the potential bias in single-modal diagnosis. However, an effective and reliable solution is still lacking, which can integrate multimodal neuroimaging effectively for the precision diagnosis and treatment of AD. In this work, we proposed a feature representation and fusion model of MRI and PET scans based on a multiscale convolution network and cross-attention for AD early diagnosis, named camAD. Compared with the existing models, camAD performs better with fewer pre-processing steps. Using the Alzheimer’s disease neuroimaging initiative (ADNI) datasets, we demonstrated that integrating multi-modality data outperforms single-modality models in accuracy, specificity, sensitivity, AUC, and F1 scores. Our models exhibited significantly good accuracy and generality in four classification tasks, which provided a promising way to understand the underlying mechanisms of the disorder's progression.

关键词： Neuroimaging Accuracy Sensitivity Convolution Magnetic resonance imaging Feature extraction Data models Reliability Alzheimer's disease Medical diagnostic imaging

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Enhancing Long-and Short-Term Representations for Next POI Recommendations via Frequency and Hierarchical Contrastive Learning 39

Enhancing Long-and Short-Term Representations for Next POI R...

引用

39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Chen, Jiajie Sang, Yu Zhang, Peng-Fei Wang, Jiaan Qu, Jianfeng Li, Zhixu School of Computer Science and Technology Soochow University Suzhou China School of Artificial Intelligence and Computer Science Jiangnan University China School of Electrical Engineering and Computer Science University of Queensland Australia School of Information Renmin University of China Beijing China Renmin University of China Suzhou China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China

ISBN: (纸本)157735897X

Next POI recommendation aids users in predicting their destinations of interest and plays an increasingly vital role in location-based social services. Recent works focus on analyzing both long-term and short-term interests in POI recommendation to gain a deeper understanding of user profiles. However, these methods for modeling long-term user's sequences primarily rely on the Transformer model, which functions as a low-pass filter, often leading to the loss of high-frequency information. Additionally, long-term and short-term sequences are typically modeled independently, with short-term sequences often defined solely by the most recent check-ins, overlooking their interactions and dependencies. Therefore, we propose Enhancing Long-and Short-Term Representations for Next POI Recommendations via Frequency and Hierarchical Contrastive Learning (FHCRec). FHCRec captures both high-frequency and low-frequency information in long-term sequences to model richer long-term user's preference representations. Moreover, it harnesses the characteristics of the short-term subsequences embedded within long-term sequences to enhance short-term preference characterization via local and global hierarchical contrastive learning, resulting in more personalized short-term preferences. The enhanced long-term and short-term preferences are integrated to improve model recommendation performance. Extensive experiments on three real-world datasets demonstrate the effectiveness of our method. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Contrastive Learning

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AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

arXiv

引用

arXiv 2024年

作者： Li, Kewei Wu, Yuqian Li, Yinheng Guo, Yutong Wang, Yan Liang, Yiyang Fan, Yusi Huang, Lan Zhang, Ruochi Zhou, Fengfeng College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Software Jilin University Jilin Changchun130012 China School of Life Sciences Jilin University Jilin Changchun130012 China Department of Computer Science Columbia University 116th and Broadway New York CityNY10027 United States School of Artificial Intelligence Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China School of Biology and Engineering Guizhou Medical University Guizhou Guiyang550025 China School of Computer Engineering Changchun University of Engineering Jilin Changchun130103 China Changchun Wenli High School Jilin Changchun130062 China

Since the mechanism of action of drug molecules in the human body is difficult to reproduce in the in vitro environment, it becomes difficult to reveal the causes of the activity cliff phenomenon of drug molecules. We found out the AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in peptides with canonical amino acids. Understanding the mechanism of AC in canonical amino acids might help understand the one in drug molecules. This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the MIC, and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language model ESM2 demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient 0.4669 for the regression task of the MIC values on the benchmark dataset. Source code and additional resources are available at https://***/supp/or https://***/Kewei2023/AMPCliff-generation. © 2024, CC BY-NC-SA.

关键词： Deep learning

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Foundation models in bioinformatics

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National Science Review 2025年第4期 400-418页

作者： Fei Guo Renchu Guan Yaohang Li Qi Liu Xiaowo Wang Can Yang Jianxin Wang Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Xiangjiang Laboratory Key Laboratory for Symbol Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Department of Computer Science Old Dominion University School of Life Sciences and Technology Tongji University Department of Automation Tsinghua University Department of Mathematics State Key Laboratory of Molecular Neuroscience and Big Data Bio-Intelligence Lab The Hong Kong University of Science and Technology

With the adoption of foundation models(FMs),artificial intelligence(AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges,such as pre-training frameworks,model evaluation and *** demonstrate notable proficiency in managing large-scale,unlabeled datasets,because experimental procedures are costly and labor *** various downstream tasks,FMs have consistently achieved noteworthy results,demonstrating high levels of accuracy in representing biological entities.A new era in computational biology has been ushered in by the application of FMs,focusing on both general and specific biological *** this review,we introduce recent advancements in bioinformatics FMs employed in a variety of downstream tasks,including genomics,transcriptomics,proteomics,drug discovery and single-cell *** aim is to assist scientists in selecting appropriate FMs in bioinformatics,according to four model types:language FMs,vision FMs,graph FMs and multimodal *** addition to understanding molecular landscapes,AI technology can establish the theoretical and practical foundation for continued innovation in molecular biology.

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Medical Scene Graphs and Reasoning

Medical Scene Graphs and Reasoning

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Chuxue Cao Yiming He Yuzhen Chen Chunli Song Hao Ling Renchu Guan Xiaoyue Feng The Key Laboratory for Symbolic Computation and Knowledge Engineering of the Ministry of Education College of Software Jilin University Changchun China The Second Hospital of Jilin University Changchun China The Key Laboratory for Symbolic Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Changchun China

ISBN: (纸本)9781665429825

Medical scene graph contributes to cognitive tasks such as question answering. An automatic medical scene graph generator can annotate medical images with scene graphs conveniently. An end-to-end model is proposed, which contains an automatic medical scene graph generator based on medical images and surgery records. The novel model can extract symptom information of the images from surgery records via name entity recognition then convert it into scene graphs. The content and format of the scene graph are pre-defined according to the features of the images. A medical scene graph (MSG) dataset is also produced. The dataset contains 116 scene graphs where each graph includes 6 to 30 entities. Experiments show that our model performs well on making scene graphs of CT coronary angiography. Significantly, the scene graphs have the type, state, location, and index of arteries. To verify the practicability of the MSG dataset, We construct an intelligent model that can generate key diagnostic results. In addition, our medical scene graph generator can be applied to other medical areas to annotate different kinds of medical images intelligently. And the MSG dataset can directly be used in other cognitive visual tasks.

关键词： Visualization Computed tomography Angiography Surgery Medical services Generators Task analysis

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S3map: Semi-Supervised Aspect-Based Sentiment Analysis with Masked Aspect Prediction

SSRN

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SSRN 2022年

作者： Yang, Zhiyao Wang, Bing Li, Ximing Wang, Wenting Ouyang, Jihong College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China Department of Computer Science University of Texas Dallas United States

Aspect-Based Sentiment Analysis (ABSA) refers to a fine-grained task of detecting the sentiment polarities of sentences at the aspect level. To resolve this task, training samples of ABSA must be annotated with aspect words and the corresponding sentiment polarities. However, collecting such fine-grained training samples is expensive and time consuming. Therefore the available ABSA training samples are often scarce. To break the data scarcity challenge of ABSA, we investigate Semi-supervised Aspect-Based Sentiment Analysis (SemiABSA), which trains ABSA models by using a limited amount of expensive labeled sentences and more unlabeled-yet-cheaper ones. We propose a novel SemiABSA framework, namely Semi-supervised aspect-based Sentiment analysis with Masked aspect prediction (S3MAP), built on the self-training paradigm. For unlabeled sentences, we form pseudo-aspect words and pseudo-sentiment polarities and improve model training. Specifically, a BERT-Encoder-based Masked Aspect Prediction (MAP) task achieves the pseudo-aspect words generation. Based on S3MAP, we thoroughly investigate the potential of SemiABSA from various perspectives. Empirical results show that S3MAP can consistently improve the performance by leveraging unlabeled sentences even with those from different domains. © 2022, The Authors. All rights reserved.

关键词： Forecasting

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Variational Wasserstein Barycenters with c-Cyclical Monotonicity Regularization

arXiv

引用

arXiv 2021年

作者： Chi, Jinjin Yang, Zhiyao Li, Ximing Ouyang, Jihong Guan, Renchu College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China

Wasserstein barycenter, built on the theory of Optimal Transport (OT), provides a powerful framework to aggregate probability distributions, and it has increasingly attracted great attention within the machine learning community. However, it is often intractable to precisely compute, especially for high dimensional and continuous settings. To alleviate this problem, we develop a novel regularization by using the fact that c-cyclical monotonicity is often necessary and sufficient conditions for optimality in OT problems, and incorporate it into the dual formulation of Wasserstein barycenters. For efficient computations, we adopt a variational distribution as the approximation of the true continuous barycenter, so as to frame the Wasserstein barycenters problem as an optimization problem with respect to variational parameters. Upon those ideas, we propose a novel end-to-end continuous approximation method, namely Variational Wasserstein Barycenters with c-Cyclical Monotonicity Regularization (VWB-CMR), given sample access to the input distributions. We show theoretical convergence analysis and demonstrate the superior performance of VWB-CMR on synthetic data and real applications of subset posterior aggregation. Copyright © 2021, The Authors. All rights reserved.

关键词： Probability distributions

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