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Development of a Universal RNA Dual-Terminal Labeling Method for Sensing RNA-Ligand Interactions

CCS Chemistry 2023年第1期5卷 221-233页

作者： Longhuai Cheng Dejun Ma Jie Zhang Xueying Kang Yang Wu Yi Zhao Long Yi Zhen Xi State Key Laboratory of Elemento-Organic Chemistry Department of Chemical BiologyCollege of ChemistryNational Pesticide Engineering Research CenterCollaborative Innovation Center of Chemical Science and EngineeringNankai UniversityTianjin 300071 State Key Laboratory of Organic-Inorganic Composites and Beijing Key Laboratory of Bioprocess Beijing University of Chemical Technology(BUCT)Beijing 100029 Key Laboratory of Intelligent Information Processing Research Center for Ubiquitous Computing SystemsInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190

Dual labeling of an RNA can provide Förster resonance energy transfer(FRET)sensors for studying RNA folding,miRNA maturation,and RNA-protein ***,we report the development of a highly efficient strategy for direct dual-terminal labeling of any RNA of *** explored new Michael cycloaddition for facile labeling of 5′-terminal RNA with improved *** chemical tetrazinylation of RNA at the 3′-terminus was achieved with the highly efficient and catalysis-free tetrazine-cycloalkyne *** single-terminal labeling methods were combined for dual-terminal labeling of an RNA including short hairpin RNA,pre-miRNA,riboswitch,and noncoding ***,these dual-labeled RNA-based FRET sensors were used to monitor RNA-ligand interactions in vitro and in live *** is anticipated that these universal RNA labeling strategies will be useful to study RNA structures and functions.

关键词： dual labeling Förster resonance energy transfer sensor Michael cycloaddition tetrazinecycloalkyne ligation RNA-ligand interaction

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Text-Driven Generative Domain Adaptation with Spectral Consistency Regularization

Text-Driven Generative Domain Adaptation with Spectral Consi...

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International Conference on Computer Vision (ICCV)

作者： Zhenhuan Liu Liang Li Jiayu Xiao Zheng-Jun Zha Qingming Huang Institute of Computing Technology Key Laboratory of Intelligent Information Processing CAS University of Chinese Academy of Sciences University of Science and Technology of China Peng Cheng Laboratory

Combined with the generative prior of pre-trained models and the flexibility of text, text-driven generative domain adaptation can generate images from a wide range of target domains. However, current methods still suffer from overfitting and the mode collapse problem. In this paper, we analyze the mode collapse from the geometric point of view and reveal its relationship to the Hessian matrix of generator. To alleviate it, we propose the spectral consistency regularization to preserve the diversity of source domain without restricting the semantic adaptation to target domain. We also design granularity adaptive regularization to flexibly control the balance between diversity and stylization for target model. We conduct experiments for broad target domains compared with state-of-the-art methods and extensive ablation studies. The experiments demonstrate the effectiveness of our method to preserve the diversity of source domain and generate high fidelity target images. Source code has been released in https://***/Victarry/Adaptation-SCR.

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Integrating Multi-scale Contextualized information for Byte-based Neural Machine Translation

arXiv

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arXiv 2024年

作者： Huang, Langlin Feng, Yang Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences China Key Laboratory of AI Safety Chinese Academy of Sciences China University of Chinese Academy of Sciences China

Subword tokenization is a common method for vocabulary building in Neural Machine Translation (NMT) models. However, increasingly complex tasks have revealed its disadvantages. First, a vocabulary cannot be modified once it is learned, making it hard to adapt to new words. Second, in multilingual translation, the imbalance in data volumes across different languages spreads to the vocabulary, exacerbating translations involving low-resource languages. While byte-based tokenization addresses these issues, byte-based models struggle with the low information density inherent in UTF-8 byte sequences. Previous works enhance token semantics through local contextualization but fail to select an appropriate contextualizing scope based on the input. Consequently, we propose the Multi-Scale Contextualization (MSC) method, which learns contextualized information of varying scales across different hidden state dimensions. It then leverages the attention module to dynamically integrate the multi-scale contextualized information. Experiments show that MSC significantly outperforms subword-based and other byte-based methods in both multilingual and out-of-domain scenarios. We have uploaded the code to github1 © 2024, CC BY-NC-ND.

关键词： Neural machine translation

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Combination of graphics, uncertainty, and semantics: A survey

Combination of graphics, uncertainty, and semantics: A surve...

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作者： Gao, Yuan Rafi, Muhammad Adnan Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Chinese Academy of Sciences Beijing China Department of Computer Science Aston University Birmingham United Kingdom

Graphics, uncertainty, and semantics are three approaches to building models. The combination of the three approaches is a way to develop a stronger modeling method. This article surveys the research efforts toward combining these aspects, which can be divided into two routes: One is to combine graphics and uncertainty as probabilistic graphical models and then incorporate semantics, and the other is to combine graphics and semantics and then incorporate probability to handle uncertainty. The models and methods involved in these efforts are introduced and their expressiveness, pros, and cons are discussed. © 2021 John Wiley & Sons Ltd.

关键词： Semantics

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Variational Clustering and Denoising of Spatial Transcriptomics

Variational Clustering and Denoising of Spatial Transcriptom...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Li, Cuiyuan Zhang, Fa Hu, Kai Cui, Xuefeng Shandong University School of Computer Science and Technology Qingdao China Beijing Institute of Technology School of Medical Technology Beijing China Xiangtan University Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan China Xiangnan University Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province Chenzhou China

ISBN: (纸本)9798350337488

Spatial transcriptomics data provides a unique opportunity to investigate both gene expression and spatial structure in tissues at the same time. However, incorporating spatial information to accurately identify spatial domains is difficult due to factors such as high-dimensionality, sparsity, noise, and dropout events. To address these issues, we introduce vGraphST, a novel graph-based deep learning approach tailored for spatial transcriptomics data. Our method combines auto-encoder and contrastive learning techniques to process high-dimensional data and generate meaningful low-dimensional embeddings. Additionally, we use continuous distributions instead of discrete values in both the latent space and the denoised gene expression space. Specifically, Gaussian distributions are used to model the latent space, while zero-inflated Poisson distributions are used to model the denoised gene expression space. Experimental results demonstrate the effectiveness of vGraphST in accurately representing and analyzing spatial transcriptomics data. When compared to other methods using the DLPFC dataset, vGraphST achieves an average Adjusted Rand Index (ARI) of 0.58, demonstrating its superiority in segmenting spatial domains and recognizing biologically relevant spatiotemporal patterns. © 2023 IEEE.

关键词： clustering contrastive learning denoising spatial transcriptomics variational auto-encoder

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Variant quantifiers in L_(3)-valued first-order logic

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Frontiers of Computer Science 2021年第5期15卷 151-159页

作者： Wei LI Yuefei SUI State Key Laboratory of Software Development Environment Beihang UniversityBeijing 100083China Key Laboratory of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China

Traditional first-order logic has four definitions for quantifiers,which are defined by universal and existential *** L_(3)-valued(three-valued)first-order logic,there are eight kinds of definitions for quantifiers;and corresponding Gentzen deduction systems will be given and their soundness and completeness theorems will be proved.

关键词： L_(3)-valued(three-valued)first-order logic sequent quantifier soundness theorem completeness theorem

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Facial Expression Recognition With Vision Transformer Using Fused Shifted Windows

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IEEE Transactions on affective computing 2024年

作者： Sun, Xiao Wang, Rui Chen, Shaokai Wang, Meng Hefei University of Technology Anhui Province Key Laboratory of Affective Computing and Advanced Intelligent Machines School of Computer Science and Information Engineering China Institute of Artificial Intelligence Hefei Comprehensive National Science Center Hefei China University of Science and Technology of China Institute of Advanced Technology China Hefei University of Technology School of Computer Science and Information Engineering Hefei China

Facial expressions contain massive affective information. Previous methods have focused on using diverse models based on CNN or Transformer to handle the facial expression recognition(FER) task. However, most of them treat the FER task as a general image classification task and neglect the impact of regions of interest (ROIs) for the performance of FER. To verify the influence of different ROIs, in this paper, we propose a vision Transformer based on Fused Shifted windows (FSwin), called FSwin Transformer. The semantic information of the face, obtained by ROIs, guides the FSwin Transformer to focus more on the key regions. The fused shifted windows enable the model to perform global semantic interactions, allowing it to concentrate on key regions without losing the topological structural information of the entire face. Additionally, learnable parameters are introduced to learn the feature weights expressed by each ROI, helping the model dynamically adjust the attention distribution. We have conducted controlled experiments to quantitatively verify the impact of ROIs. And the experimental results show that with the increase of the number of ROIs, the accuracy of FER is significantly improved, demonstrating that the key ROIs play an important role in feature extraction. The results on Jaffe, CK+, FER2013, AffectNet have reached 99.8%, 99.0%, 74.8%, and 68.9%, respectively, which all set new state-of-the-art. Extensive cross-dataset experiments also show that the FSwin Transformer has good generalization ability, proving that our proposed model has a beneficial effect on FER tasks. © 2010-2012 IEEE.

关键词： Feature extraction

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SELF-SUPERVISED DIFFUSION MRI DENOISING VIA ITERATIVE AND STABLE REFINEMENT

arXiv

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arXiv 2025年

作者： Wu, Chenxu Kong, Qingpeng Jiang, Zihang Kevin Zhou, S. School of Biomedical Engineering Division of Life Sciences and Medicine USTC China MIRACLE Center Suzhou Institute for Advance Research USTC China State Key Laboratory of Precision and Intelligent Chemistry USTC China Key Laboratory of Intelligent Information Processing of CAS Institute of Computing Technology CAS China

Magnetic Resonance Imaging (MRI), including diffusion MRI (dMRI), serves as a "microscope" for anatomical structures and routinely mitigates the influence of low signal-to-noise ratio scans by compromising temporal or spatial resolution. However, these compromises fail to meet clinical demands for both efficiency and precision. Consequently, denoising is a vital preprocessing step, particularly for dMRI, where clean data is unavailable. In this paper, we introduce Di-Fusion, a fully self-supervised denoising method that leverages the latter diffusion steps and an adaptive sampling process. Unlike previous approaches, our single-stage framework achieves efficient and stable training without extra noise model training and offers adaptive and controllable results in the sampling process. Our thorough experiments on real and simulated data demonstrate that Di-Fusion achieves state-of-the-art performance in microstructure modeling, tractography tracking, and other downstream tasks. Code is available at https://***/FouierL/Di-Fusion. Copyright © 2025, The Authors. All rights reserved.

关键词： Signal to noise ratio

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DASC-SPT: Towards Self-Supervised Panoramic Semantic Segmentation

DASC-SPT: Towards Self-Supervised Panoramic Semantic Segment...

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IEEE Workshop on Applications of Computer Vision (WACV)

作者： Tianlong Tan Bin Chen Hongliang Cao Chenggang Yan Yike Ma Feng Dai Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology Chinese Academy of Sciences Beijing China Shandong University University of Chinese Academy of Sciences Beijing China Hangzhou Dianzi University

ISBN: (数字)9798331510831

ISBN: (纸本)9798331510848

Self-Supervised Semantic Segmentation, aiming to leverage masses of unlabeled data for boosting semantic segmentation, has been rapidly emerging as an active task in recent years. However, existing self-supervised semantic segmentation approaches mainly focus on planar images, leaving multiple distorted objects encountered in panoramic images unexplored due to the formidable challenge of handling heterogeneous degrees of distortions across different locations. In this paper, we propose a novel Self-Supervised Panoramic Semantic Segmentation model, termed DASC-SPT, built upon the mainstream contrastive learning framework. Towards distortions in panoramic images, we present two structures to better learn from distorted features by applying planar images. For the input images of self-supervision, we design a Spherical Projection Transformation (SPT) strategy that involves randomly projecting planar images onto various locations of the sphere to introduce the distortions. For pixel-wise distorted features, we construct a Deformation-aware Sampling Consistency (DASC) framework to further utilize the shared content and discrepancies caused by different distortions of paired views, where the deformation-aware consistency can be quantified on pixel-wise features. Both of the two components facilitate the model to adapt to distortions and boost panoramic semantic segmentation. Extensive comprehensive experiments on three panoramic datasets demonstrate the effectiveness and superiority of DASC-SPT approach.

关键词： Training Deformable models Adaptation models Computer vision Semantic segmentation Computational modeling Crops Contrastive learning Distortion Boosting

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Top-ambiguity samples matter: understanding why deep ensemble works in selective classification 23

Top-ambiguity samples matter: understanding why deep ensembl...

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Proceedings of the 37th International Conference on Neural information processing Systems

作者： Qiang Ding Yixuan Cao Ping Luo Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS) Institute of Computing Technology CAS Beijing China and University of Chinese Academy of Sciences Beijing China Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS) Institute of Computing Technology CAS Beijing China and University of Chinese Academy of Sciences Beijing China and Peng Cheng Laboratory Shenzhen China

Selective classification allows a machine learning model to reject some hard inputs and thus improve the reliability of its predictions. In this area, the ensemble method is powerful in practice, but there has been no solid analysis on why the ensemble method works. Inspired by an interesting empirical result that the improvement of the ensemble largely comes from top-ambiguity samples where its member models diverge, we prove that, based on some assumptions, the ensemble has a lower selective risk than the member model for any coverage within a range. The proof is nontrivial since the selective risk is a non-convex function of the model prediction. The assumptions and the theoretical results are supported by systematic experiments on both computer vision and natural language processing tasks.

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