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

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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

Implicit knowledge discovery in biomedical ontologies: computing interesting relatednesses

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Implicit knowledge discovery in biomedical ontologies: Compu...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Tian Bai Leiguang Gong Casimir A. Kulikowski Lan Huang Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China College of Computer Science and Technology Jilin University Changchun China Yantai Intelligent Information Technologies Ltd. Yantai China Department of Computer Science Rutgers The State University of New Jersey Piscataway NJ USA

Ontologies, seen as effective representations for sharing and reusing knowledge, have become increasingly important in biomedicine, usually focusing on taxonomic knowledge specific to a subject. Efforts have been made to uncover implicit knowledge within large biomedical ontologies by exploring semantic similarity and relatedness between concepts. However, much less attention has been paid to another potentially helpful approach: discovering implicit knowledge across multiple ontologies of different types, such as disease ontologies, symptom ontologies, and gene ontologies. In this paper, we propose a unified approach to the problem of ontology based implicit knowledge discovery - a Multi-Ontology Relatedness Model (MORM), which includes the formation of multiple related ontologies, a relatedness network and a formal inference mechanism based on set-theoretic operations. Experiments for biomedical applications have been carried out, and preliminary results show the potential value of the proposed approach for biomedical knowledge discovery.

关键词： Biological system modeling Biomedical measurement Ontologies Arthritis Diseases

A Multi-Agent Deep Reinforcement Learning Method for Fully Noisy Observations

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SSRN

SSRN 2023年

作者： Wang, Kaiyu Zhang, Menglin Qu, Bohao Wang, Xianchang College of Computer Science and Technology Jilin University Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin Changchun130012 China School of Artificial Intelligence Jilin University Jilin Changchun130012 China Chengdu Kestrel Artificial Intelligence Institute Chengdu611730 China

Multi-agent reinforcement learning (MARL) algorithms have achieved great breakthroughs in many aspects. The MARL algorithms can learn effective policies in ideal simulation environments. But different from the ideal simulation environments, noise is unavoidable in the real world. MARL algorithms need to learn effective policies in unavoidable fully noisy environments. In this paper, we consider a challenging multi-agent reinforcement learning problem: All agents cannot observe any noiseless observations from environments during the whole training process and MARL algorithms cannot learn effective policies in these fully noisy observation environments. To solve this problem, we propose a method called Robust Policy Learning under Fully Noisy Observation viA DeNoising REpresentation NeTwork (PLANET), which enables MARL algorithms learning effective policies in fully noisy observation environments. The PLANET method learns the effective policy through two steps. (1) Extracting the noise characteristics and motion laws information from fully noisy observation histories. (2) Making MARL algorithms extract information from the noise characteristics and motion laws information and learn effective policies. The results of a series of exhaustive experiments show that our method can eliminate the effects of noise and learn effective policies in fully noisy observation environments. © 2023, The Authors. All rights reserved.

关键词： Learning algorithms

Biogeography-based optimization for cluster analysis

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Biogeography-based optimization for cluster analysis

International Conference on Computer, Communication and Computational Sciences, ICCCCS 2016

作者： Wu, Xueyan Wang, Hainan Chen, Zhimin Lu, Zhihai Phillips, Preetha Wang, Shuihua Zhang, Yudong School of Computer Science and Technology Nanjing Normal University NanjingJiangsu210023 China Key Laboratory of Statistical Information Technology & Data Mining State Statistics Bureau ChengduSichuan610225 China School of Computer and Information Engineering Henan Normal University XinxiangHenan453000 China School of Electronic Information Shanghai Dianji University Shanghai200240 China Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education Jilin University ChangchunJilin130012 China Guangxi Key Laboratory of Manufacturing System & Advanced Manufacturing Technology GuilinGuangxi541004 China School of Natural Sciences and Mathematics Shepherd University ShepherdstownWV25443 United States West Virginia School of Osteopathic Medicine 400 N Lee St LewisburgWV24901 United States Department of Electrical Engineering The City College of New York CUNY New YorkNY10031 United States State Key Lab of CAD & CG Zhejiang University HangzhouZhejiang310027 China Manchester Metropolitan University ManchesterM156BH United Kingdom

ISBN: (纸本)9789811037696

With the aim of resolving the issue of cluster analysis more precisely and validly, a new approach was proposed based on biogeography-based optimization (abbreviated as BBO) algorithm. (Method) First, we reformulated the problem with an optimization model based on the variance ratio criterion (VARAC). Then, BBO was presented to search the optimal solution of the VARAC. There are 400 data of four groups in the experimental dataset, which have the degrees of overlapping of three distinct scales. The first one is nonoverlapping, the second one is partial overlapping, and the last is severely overlapping. BBO algorithm was compared with three different state-of-the-art approaches. We ran every algorithm 20 times. In this experiment, our results demonstrate the maximum VARAC values that can be found by BBO. The conclusion is that BBO is predominant which is extremely quick for the issue of clustering analysis. © Springer Nature Singapore Pte Ltd. 2017.

关键词： Cluster analysis

Joint-Motion Mutual Learning for Pose Estimation in Videos

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arXiv 2024年

作者： Wu, Sifan Chen, Haipeng Yin, Yifang Hu, Sihao Feng, Runyang Jiao, Yingying Yang, Ziqi Liu, Zhenguang College of Computer Science and Technology Jilin University Changchun China A*STAR Singapore Georgia Institute of Technology Atlanta United States School of Artificial Intelligence Jilin University Changchun China The State Key Laboratory of Blockchain and Data Security Zhejiang University Hangzhou China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China Institute of Blockchain and Data Security Hangzhou China

Human pose estimation in videos has long been a compelling yet challenging task within the realm of computer vision. Nevertheless, this task remains difficult because of the complex video scenes, such as video defocus and self-occlusion. Recent methods strive to integrate multi-frame visual features generated by a backbone network for pose estimation. However, they often ignore the useful joint information encoded in the initial heatmap, which is a byproduct of the backbone generation. Comparatively, methods that attempt to refine the initial heatmap fail to consider any spatiotemporal motion features. As a result, the performance of existing methods for pose estimation falls short due to the lack of ability to leverage both local joint (heatmap) information and global motion (feature) dynamics. To address this problem, we propose a novel joint-motion mutual learning framework for pose estimation, which effectively concentrates on both local joint dependency and global pixel-level motion dynamics. Specifically, we introduce a context-aware joint learner that adaptively leverages initial heatmaps and motion flow to retrieve robust local joint feature. Given that local joint feature and global motion flow are complementary, we further propose a progressive joint-motion mutual learning that synergistically exchanges information and interactively learns between joint feature and motion flow to improve the capability of the model. More importantly, to capture more diverse joint and motion cues, we theoretically analyze and propose an information orthogonality objective to avoid learning redundant information from multi-cues. Empirical experiments show our method outperforms prior arts on three challenging benchmarks. Copyright © 2024, The Authors. All rights reserved.

关键词： Motion estimation

Distantly Supervised Relation Extraction via Recursive Hierarchy-Interactive Attention and Entity-Order Perception

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arXiv 2021年

作者： Han, Ridong Peng, Tao Han, Jiayu Cui, Hai Liu, Lu College of Computer Science and Technology Jilin University Jilin Changchun130012 China College of Software Jilin University Jilin Changchun130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Jilin Changchun130012 China Department of Linguistics University of Washington SeattleWA98195 United States

Wrong-labeling problem and long-tail relations severely affect the performance of distantly supervised relation extraction task. Many studies mitigate the effect of wrong-labeling through selective attention mechanism and handle long-tail relations by introducing relation hierarchies to share knowledge. However, almost all existing studies ignore the fact that, in a sentence, the appearance order of two entities contributes to the understanding of its semantics. Furthermore, they only utilize each relation level of relation hierarchies separately, but do not exploit the heuristic effect between relation levels, i.e., higher-level relations can give useful information to the lower ones. Based on the above, in this paper, we design a novel Recursive Hierarchy-Interactive Attention network (RHIA) to further handle long-tail relations, which models the heuristic effect between relation levels. From the top down, it passes relation-related information layer by layer, which is the most significant difference from existing models, and generates relation-augmented sentence representations for each relation level in a recursive structure. Besides, we introduce a newfangled training objective, called Entity-Order Perception (EOP), to make the sentence encoder retain more entity appearance information. Substantial experiments on the popular New York Times (NYT) dataset are conducted. Compared to prior baselines, our RHIA-EOP achieves state-of-the-art performance in terms of precision-recall (P-R) curves, AUC, Top-N precision and other evaluation metrics. Insightful analysis also demonstrates the necessity and effectiveness of each component of RHIA-EOP. © 2021, CC BY.

关键词： Semantics

U-HRMLP: Refining Segmentation Boundaries in Histopathology Images

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U-HRMLP: Refining Segmentation Boundaries in Histopathology ...

IEEE International Symposium on Biomedical Imaging

作者： Tao Wang Kai Zhang Weijie Wang Mingrui Ma Ye Zhang He Zhao Guixia Liu College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China School of Information Science and Engineering Shandong Normal University China Department of Information Engineering and Computer Science University of Trento Italy Faculty of Information Engineering and Automation Kunming University of Science and Technology China School of Information Science and Technology Northeast Normal University China

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

Segmenting regions of interest in histopathology images is a critical prerequisite for biomedical applications. CNN-based models have advanced medical image segmentation, yet accurately delineating boundaries is still challenging. This challenge arises from the loss of spatial resolution due to downsampling and the complexity of capturing contextual information when upsampling to the original resolution. To address these issues, we design U-HRMLP, a U-shaped network based on a hybrid combination of HRNet and Multi-Layer Perceptron (MLP). Specifically, we propose a multi-scale feature fusion module to avoid the loss of image resolution in the encoding stage as much as possible. Simultaneously, we propose an MLP-based decoding block to recover image details and resolution progressively, alleviating the issues related to the inadequate segmentation of smaller objects and the blurring of tissue boundaries. Results on the MoNuSeg and GlaS datasets demonstrate that U-HRMLP outperforms conventional or transformer-based methods and achieves state-of- the-art performance.

关键词： Measurement Image segmentation Histopathology Biological system modeling Semantics Refining Transformers

SLMP: A Scientific Literature Management Platform Based on Large Language Models

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SLMP: A Scientific Literature Management Platform Based on L...

IEEE International Conference on Big knowledge (ICBK)

作者： Menghao Guo Jinling Jiang Fan Wu Shanxin Sun Chen Zhang Wenhui Li Zeyi Sun Guangyong Chen Xindong Wu Research Center for Life Sciences Computing Zhejiang Lab Hangzhou China Research Center for Data Hub and Security Zhejiang Lab Hangzhou China Research Center for High Efficiency Computing System Zhejiang Lab Hangzhou China Key Laboratory of Knowledge Engineering With Big Data Hefei University of Technology Hefei China

ISBN: (数字)9798331508821

ISBN: (纸本)9798331508838

This paper presents a Scientific Literature Management Platform (SLMP, demo link 1 ) based on large language models (LLMs). The platform consists of four modules: literature management, literature extraction, literature retrieval, and question answering. The core techniques used to support the four modules across the platform include a fine-tuned model PaperExtractGPT and a continual pre-training model ChatPaperGPT based on ChatGLM 2 using the data from scientific research literature, responsible for information extraction and communication, respectively. Due to their powerful capabilities in natural language understanding and generation, LLMs can understand complex scientific concepts based on the provided contexts, and thus generate high-quality texts and conduct in-depth information retrieval and question answering. Our platform can help researchers manage and utilize literature more effectively and efficiently for finding relevant literature, obtaining required information, and generating new knowledge.

关键词： Training Large language models knowledge graphs Information retrieval Data models Question answering (information retrieval)

Document-level Relation Extraction with Relation Correlations

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arXiv 2022年

作者： Han, Ridong Peng, Tao Wang, Benyou Liu, Lu Wan, Xiang College of Computer Science and Technology Jilin University China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education China College of Software Jilin University China Shenzhen Research Institute of Big Data The Chinese University of Hong Kong Shenzhen China School of Data Science The Chinese University of Hong Kong Shenzhen China

Document-level relation extraction faces two overlooked challenges: long-tail problem and multi-label problem. Previous work focuses mainly on obtaining better contextual representations for entity pairs, hardly address the above challenges. In this paper, we analyze the co-occurrence correlation of relations, and introduce it into DocRE task for the first time. We argue that the correlations can not only transfer knowledge between data-rich relations and data-scarce ones to assist in the training of tailed relations, but also reflect semantic distance guiding the classifier to identify semantically close relations for multi-label entity pairs. Specifically, we use relation embedding as a medium, and propose two co-occurrence prediction sub-tasks from both coarse- and fine-grained perspectives to capture relation correlations. Finally, the learned correlation-aware embeddings are used to guide the extraction of relational facts. Substantial experiments on two popular DocRE datasets are conducted, and our method achieves superior results compared to baselines. Insightful analysis also demonstrates the potential of relation correlations to address the above challenges. Copyright © 2022, The Authors. All rights reserved.

关键词： Extraction