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The chordata olfactory receptor database

Protein & Cell 2025年第4期16卷 283-292页

作者： Wei Han Siyu Bao Jintao Liu Yiran Wu Liting Zeng Tao Zhang Ningmeng Chen Kai Yao Shunguo Fan Aiping Huang Yuanyuan Feng Guiquan Zhang Ruiyi Zhang Hongjin Zhu Tian Hua Zhijie Liu Lina Cao Xingxu Huang Suwen Zhao Human Institute ShanghaiTech UniversityShanghai 201210China Research Center for Life Sciences Computing Zhejiang LabHangzhou 311121China Department of Intelligent Edge Cloud China Telecom Cloud Technology Co.Ltd.Shanghai 200120China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China School of Information Science and Technology Shanghai Tech UniversityShanghai 201210China Shanghai Key Laboratory of High-Resolution Electron Microscopy Shanghai Tech UniversityShanghai 201210China Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated Hospitaland Institute of Translational MedicineZhejiang University School of MedicineHangzhou 310029China Shanghai Clinical Research and Trial Center Shanghai 201210China

Introduction of database Olfaction is one of the oldest chemosensory systems in chordates,playing crucial roles in their foraging,predator evasion,social communication,mating and parental care(Guo et al.,2023;Li and Liberles,2015;Liberles,2014).The initial step of olfaction is the binding and activation of olfactory receptors(ORs)by odorants in a combinatorial way(Malnic et al.,1999).

关键词： chordates chemosensory systems introduction database olfaction foraging olfaction binding activation olfactory olfactory receptors odorants

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Disentangled latent factors for muti-cause treatment effect estimation 6

Disentangled latent factors for muti-cause treatment effect ...

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2024 6th International Conference on Artificial Intelligence Technologies and Applications, ICAITA 2024

作者： Zhao, Zhuoyue Wang, Haotian Xu, Liyang Wang, Qian Tang, Yuhua Department of Intelligent Data Science National University of Defense Technology Changsha410073 China Intelligent Game and Decision Lab. Academy of Military Science Beijing100071 China Institute for Quantum Information State Key Laboratory of High-Performance Computing College of Computer Science and Technology National University of Defense Technology Changsha410073 China

Existing methods estimate treatment effects from observational data and assume that covariates are all confounders. However, observed covariates may not directly represent confounding variables that influence both treatment and outcome. They always include variables that only affect the treatment or the outcome. In addition, for multi-dimensional binary treatments, disentangled methods are mainly designed for binary variables and ignore the impact of multi-cause treatment variables on the inference of latent factors. To address these two issues, based on variable decomposition and proxy inference, we propose the Disentangled Latent Factors for Multi-cause Treatment Estimation (DEMTE) algorithm. It utilizes an identifiable autoencoder to infer and disentangle latent factors based on the joint distribution of variables in observational data. DEMTE evaluates the treatment effect on the disentangled factors. Synthetic experiments and semi-synthetic experiments demonstrate the effectiveness of the inference and disentanglement techniques and our method achieves more accurate treatment effect estimation. © 2024 Institute of Physics Publishing. All rights reserved.

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AUCSeg: AUC-oriented Pixel-level Long-tail Semantic Segmentation 38

AUCSeg: AUC-oriented Pixel-level Long-tail Semantic Segmenta...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Han, Boyu Xu, Qianqian Yang, Zhiyong Bao, Shilong Wen, Peisong Jiang, Yangbangyan Huang, Qingming Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS China School of Computer Science and Tech. University of Chinese Academy of Sciences China Peng Cheng Laboratory China Key Laboratory of Big Data Mining and Knowledge Management CAS China

The Area Under the ROC Curve (AUC) is a well-known metric for evaluating instance-level long-tail learning problems. In the past two decades, many AUC optimization methods have been proposed to improve model performance under long-tail distributions. In this paper, we explore AUC optimization methods in the context of pixel-level long-tail semantic segmentation, a much more complicated scenario. This task introduces two major challenges for AUC optimization techniques. On one hand, AUC optimization in a pixel-level task involves complex coupling across loss terms, with structured inner-image and pairwise inter-image dependencies, complicating theoretical analysis. On the other hand, we find that mini-batch estimation of AUC loss in this case requires a larger batch size, resulting in an unaffordable space complexity. To address these issues, we develop a pixel-level AUC loss function and conduct a dependency-graph-based theoretical analysis of the algorithm's generalization ability. Additionally, we design a Tail-Classes Memory Bank (T-Memory Bank) to manage the significant memory demand. Finally, comprehensive experiments across various benchmarks confirm the effectiveness of our proposed AUCSeg method. The code is availab.e at https://***/boyuh/AUCSeg. © 2024 Neural information processing systems foundation. All rights reserved.

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ETS: An Error Tolerable System for Coreference Resolution 15

ETS: An Error Tolerable System for Coreference Resolution

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15th Conference on Computational Natural Language Learning, CoNLL 2011

作者： Xiong, Hao Song, Linfeng Meng, Fandong Liu, Yang Liu, Qun Lü, Yajuan Key Lab. of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences P.O. Box 2704 Beijing100190 China

ISBN: (纸本)9781937284084

This paper presents our error tolerable system for coreference resolution in CoNLL-2011(Pradhan et al., 2011) shared task (closed track). Different from most previous reported work, we detect mention candidates based on packed forest instead of single parse tree, and we use beam search algorithm based on the Bell Tree to create entities. Experimental results show that our methods achieve promising results on the development set. © 2011 Association for Computational Linguistics

关键词： Forestry

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AUCSeg: AUC-oriented pixel-level long-tail semantic segmentation 24

AUCSeg: AUC-oriented pixel-level long-tail semantic segmenta...

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

作者： Boyu Han Qianqian Xu Zhiyong Yang Shilong Bao Peisong Wen Yangbangyan Jiang Qingming Huang Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and School of Computer Science and Tech. University of Chinese Academy of Sciences Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Peng Cheng Laboratory School of Computer Science and Tech. University of Chinese Academy of Sciences School of Computer Science and Tech. University of Chinese Academy of Sciences and Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Key Laboratory of Big Data Mining and Knowledge Management CAS

ISBN: (纸本)9798331314385

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Not all diffusion model activations have been evaluated as discriminative features 24

Not all diffusion model activations have been evaluated as d...

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

作者： Benyuan Meng Qianqian Xu Zitai Wang Xiaochun Cao Qingming Huang Institute of Information Engineering CAS and School of Cyber Security University of Chinese Academy of Sciences Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Peng Cheng Laboratory Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS School of Cyber Science and Tech. Shenzhen Campus of Sun Yat-sen University School of Computer Science and Tech. University of Chinese Academy of Sciences and Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Key Laboratory of Big Data Mining and Knowledge Management CAS

ISBN: (纸本)9798331314385

Diffusion models are initially designed for image generation. Recent research shows that the internal signals within their backbones, named activations, can also serve as dense features for various discriminative tasks such as semantic segmentation. Given numerous activations, selecting a small yet effective subset poses a fundamental problem. To this end, the early study of this field performs a large-scale quantitative comparison of the discriminative ability of the activations. However, we find that many potential activations have not been evaluated, such as the queries and keys used to compute attention scores. Moreover, recent advancements in diffusion architectures bring many new activations, such as those within embedded ViT modules. Both combined, activation selection remains unresolved but overlooked. To tackle this issue, this paper takes a further step with a much broader range of activations evaluated. Considering the significant increase in activations, a full-scale quantitative comparison is no longer operational. Instead, we seek to understand the properties of these activations, such that the activations that are clearly inferior can be filtered out in advance via simple qualitative evaluation. After careful analysis, we discover three properties universal among diffusion models, enabling this study to go beyond specific models. On top of this, we present effective feature selection solutions for several popular diffusion models. Finally, the experiments across multiple discriminative tasks validate the superiority of our method over the SOTA competitors. Our code is availab.e at https://***/Darkbblue/generic-diffusion-feature.

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Uncertainty-aware complementary lab.l queries for active learning

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Frontiers of Information technology & Electronic Engineering 2023年第10期24卷 1497-1503页

作者： Shengyuan LIU Ke CHEN Tianlei HU Yunqing MAO Key Lab of Intelligent Computing Based Big Data of Zhejiang Province Zhejiang UniversityHangzhou 310027China State Key Laboratory of Blockchain and Data Security Zhejiang UniversityHangzhou 310027China City Cloud Technology(China)Co. Ltd.Hangzhou 310000China

Many active learning methods assume that a learner can simply ask for the full annotations of some training data from *** methods mainly try to cut the annotation costs by minimizing the number of annotation ***,annotating instances exactly in many realworld classification tasks is still *** reduce the cost of a single annotation action,we try to tackle a novel active learning setting,named active learning with complementary lab.ls(ALCL).ALCL learners ask only yes/no questions in some *** receiving answers from annotators,ALCL learners obtain a few supervised instances and more training instances with complementary lab.ls,which specify only one of the classes to which the pattern does not *** are two challenging issues in ALCL:one is how to sample instances to be queried,and the other is how to learn from these complementary lab.ls and ordinary accurate *** the first issue,we propose an uncertainty-based sampling strategy under this novel setup.

关键词： complementary instance ordinary

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Suppress content shift: better diffusion features via off-the-shelf generation techniques 24

Suppress content shift: better diffusion features via off-th...

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

作者： Benyuan Meng Qianqian Xu Zitai Wang Zhiyong Yang Xiaochun Cao Qingming Huang Institute of Information Engineering CAS and School of Cyber Security University of Chinese Academy of Sciences Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Peng Cheng Laboratory Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS School of Computer Science and Tech. University of Chinese Academy of Sciences School of Cyber Science and Tech. Shenzhen Campus of Sun Yat-sen University School of Computer Science and Tech. University of Chinese Academy of Sciences and Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS and Key Laboratory of Big Data Mining and Knowledge Management CAS

ISBN: (纸本)9798331314385

Diffusion models are powerful generative models, and this capability can also be applied to discrimination. The inner activations of a pre-trained diffusion model can serve as features for discriminative tasks, namely, diffusion feature. We discover that diffusion feature has been hindered by a hidden yet universal phenomenon that we call content shift. To be specific, there are content differences between features and the input image, such as the exact shape of a certain object. We locate the cause of content shift as one inherent characteristic of diffusion models, which suggests the broad existence of this phenomenon in diffusion feature. Further empirical study also indicates that its negative impact is not negligible even when content shift is not visually perceivable. Hence, we propose to suppress content shift to enhance the overall quality of diffusion features. Specifically, content shift is related to the information drift during the process of recovering an image from the noisy input, pointing out the possibility of turning off-the-shelf generation techniques into tools for content shift suppression. We further propose a practical guideline named GATE to efficiently evaluate the potential benefit of a technique and provide an implementation of our methodology. Despite the simplicity, the proposed approach has achieved superior results on various tasks and datasets, validating its potential as a generic booster for diffusion features. Our code is availab.e at https://***/Darkbblue/diffusion-content-shift.

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Suppress Content Shift: Better Diffusion Features via Off-the-Shelf Generation Techniques 38

Suppress Content Shift: Better Diffusion Features via Off-th...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Meng, Benyuan Xu, Qianqian Wang, Zitai Yang, Zhiyong Cao, Xiaochun Huang, Qingming Institute of Information Engineering CAS China School of Cyber Security University of Chinese Academy of Sciences China Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS China Peng Cheng Laboratory China School of Computer Science and Tech. University of Chinese Academy of Sciences China School of Cyber Science and Tech. Shenzhen Campus of Sun Yat-sen University China Key Laboratory of Big Data Mining and Knowledge Management CAS China

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Not All Diffusion Model Activations Have Been Evaluated as Discriminative Features 38

Not All Diffusion Model Activations Have Been Evaluated as D...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Meng, Benyuan Xu, Qianqian Wang, Zitai Cao, Xiaochun Huang, Qingming Institute of Information Engineering CAS China School of Cyber Security University of Chinese Academy of Sciences China Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS China Peng Cheng Laboratory China School of Cyber Science and Tech. Shenzhen Campus of Sun Yat-sen University China School of Computer Science and Tech. University of Chinese Academy of Sciences China Key Laboratory of Big Data Mining and Knowledge Management CAS China

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