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arXiv 2023年

作者： Wang, Lean Li, Lei Dai, Damai Chen, Deli Zhou, Hao Meng, Fandong Zhou, Jie Sun, Xu National Key Laboratory for Multimedia Information Processing School of Computer Science Peking University China Pattern Recognition Center WeChat AI Tencent Inc. China

In-context learning (ICL) emerges as a promising capability of large language models (LLMs) by providing them with demonstration examples to perform diverse tasks. However, the underlying mechanism of how LLMs learn from the provided context remains under-explored. In this paper, we investigate the working mechanism of ICL through an information flow lens. Our findings reveal that label words in the demonstration examples function as anchors: (1) semantic information aggregates into label word representations during the shallow computation layers' processing;(2) the consolidated information in label words serves as a reference for LLMs' final predictions. Based on these insights, we introduce an anchor re-weighting method to improve ICL performance, a demonstration compression technique to expedite inference, and an analysis framework for diagnosing ICL errors in GPT2-XL. The promising applications of our findings again validate the uncovered ICL working mechanism and pave the way for future studies. © 2023, CC BY.

关键词： Demonstrations

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Low-light image enhancement model based on self-calibration illumination and color adjustment 2

Low-light image enhancement model based on self-calibration ...

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2nd International Conference on Algorithms, High Performance Computing and Artificial Intelligence, AHPCAI 2022

作者： Zhang, Guiwen Li, Qishen Li, Qiufeng Wu, Taida School of Information Engineering Nanchang Hangkong University Jiangxi Nanchang China Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition Jiangxi Nanchang China School of Software Nanchang Hangkong University Jiangxi Nanchang China Jiangxi Nanchang China

ISBN: (纸本)9798350334784

to improve the clarity of objects in a dark-light environment, and to facilitate the identification and detection of targets behind. People perceive the color and brightness of a point not only depending on the pixel value of the point but also the absolute light entering the human eye is related to the color and brightness around the point. The self-calibration model we used considers the surrounding information, which avoids the information pollution, such as large regions of dark background information. In this model, we introduce a heterogeneous convolution filter, which makes reasonable use of different parts of the filter. Through this operation, information from multiple different scale spaces can be fused, and the field of view when applying the convolution layer is greatly increased without increasing the hyper-parameters, thus producing a more distinctive feature representation. Then the self-calibration model is combined with the backbone reinforcement network, which can not only retain the information of the original scale space but also efficiently collect the latent space information to guide the feature transformation in the original space. After the different channels of the image are processed separately, the dependency between the channels can be established by using the heterogeneous convolution filter. Finally, the test on the ExDark data set proves that our dark target enhancement effect has been significantly improved. © 2022 IEEE.

关键词： Convolution

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Abundant Semantic Information Module for Object Detection 2

Abundant Semantic Information Module for Object Detection

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2nd International Conference on Algorithms, High Performance Computing and Artificial Intelligence, AHPCAI 2022

作者： Wu, Taida Li, Qishen Li, Qiufeng Gao, Jun School of Information Engineering Nanchang Hangkong University Jiangxi Nanchang China School of Software Nanchang Hangkong University Jiangxi Nanchang China Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition Jiangxi Nanchang China Jiangxi Nanchang China

ISBN: (纸本)9798350334784

Nowadays, with the high-speed iteration of convolution neural network, the efficient object detector emerges one after another. As an important branch of computer vision, object detection aims to detect where and what the object is. However, nowadays, many detector cannot extract abundant semantic information to discriminate the location and size of the objects, resulting in poor performance of the network. In this paper, a new module is proposed, named Abundant Semantic Information Module (ASIM), to enrich and expand the semantic information of the object with more and larger receptive fields. In ASIM, we blend the extracted feature maps to different degrees with different blending factors and fuse them so that all object information is given full attention. Compared to the baseline method, a wealth of experiments show that our module has achieved a significant performance improvement. © 2022 IEEE.

关键词： Object detection

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An Improved Embedding Model for Zero-Shot Classification based on Attention Mechanism 5

An Improved Embedding Model for Zero-Shot Classification bas...

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5th IEEE Advanced Information Technology, Electronic and Automation Control Conference, IAEAC 2021

作者： Wu, Zongfeng Li, Qishen Yu, Xiao Peng, Xu Nanchang Hangkong University School of Information Engineering Nanchang Jiangxi China Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition Nanchang Jiangxi China

It is well-known that the auxiliary information plays a key role in zero-shot classification. However, most of the existing popular methods do not make effective use of auxiliary information. To address this issue, we propose an improved embedding model for zero-shot classification based on attention mechanism, called EMAM. In the proposed EMAM, we first add an attention mechanism to effectively extract the key information of auxiliary information in zero-shot classification. Then optimizes the objective function to improve the recognition rate of this model. Finally the experimental comparison is implemented on the standard zero-shot learning datasets. The experimental results demonstrate that our proposed EMAM not only verifies its validity, but also achieves good results. © 2021 IEEE.

关键词： Zero-shot learning

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Room Layout Estimation based on Planar Semantic Segmentation

Room Layout Estimation based on Planar Semantic Segmentation

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2022 IEEE World Conference on Applied Intelligence and Computing, AIC 2022

作者： Huang, Shizhong Miao, Jun Yao, Hui Zheng, Yilin Chu, Jun Zhang, Guoxiang Nanchang Hangkong University School of Aeronautical Manufacturing Engineering Nanchang330063 China Nanchang Hangkong University Department of Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition Nanchang330063 China University of California MercedCA95343 United States

ISBN: (数字)9781665479882

ISBN: (纸本)9781509050017

Layout estimation is one of fundamental tasks for understanding indoor scenes. In a single image of indoor scenes, key information, such as key points and boundaries for inferring the layout is often severely occluded or completely invisible. In this paper, a novel end-to-end deep learning network, which is extended from Xception module, is constructed for segmentation of semantic planes to infer the room layout structure. Moreover, the network contains an optimized depth wise separable convolution (DSC) in Xception module and a reinforced spatial attention module (SAM), so that it obtained good learning ability in severely occluded areas. Tests on public datasets show that the proposed network has a lower pixel error (PE) and higher generalization compared with existing algorithms. Ablation experiments prove that optimized DSC and SAM in the network are effective in improving the accuracy of layout estimation. © 2022 IEEE.

关键词： Semantic Segmentation

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RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs

RBP-Former: Joint Prediction of RNA-protein Binding Sites on...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yichong Li Xiaojian Liu Fan Cheng Xiaoyong Pan Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

RNA-binding proteins (RBPs) are essential for gene expression, and the complex RNA-protein interaction mechanisms require analysis of global RNA information. Therefore, accurate prediction of RBP binding sites on full-length RNA transcripts is crucial for understanding these mechanisms and their roles in diseases. While machine learning methods can predict RBP binding to RNA fragments, extending this to full-length transcripts presents challenges due to sequence length and data imbalance. In this paper, we introduce RBP-Former, a binding site joint prediction model designed specifically for full-length RNA transcripts that can be used for multiple RBPs. This model processes information at both coarse and fine-grained levels to fully exploit sequence data and its interactions with multiple RBPs. We develop multi-level imbalance learning strategies, achieving favorable results on imbalanced data. Our method outperforms existing methods in predicting binding sites on full-length RNA transcripts for multiple RBPs, demonstrating its effectiveness in handling imbalanced label and sample distributions.

关键词： Proteins Protein engineering Accuracy RNA Machine learning Predictive models Data models Gene expression Bioinformatics Diseases

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Simultaneously Infer Cell Pseudotime,Velocity Field and Gene Interaction from Multi-Branch scRNA-seq Data with scPN

arXiv

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arXiv 2024年

作者： Zhou, Zhen Li, Jiachen Xin, Hongyi Pan, Xiaoyong Shen, Hong-Bin Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Global Institute of Future Technology Shanghai Jiao Tong University Shanghai200240 China

Modeling cellular dynamics from single-cell RNA sequencing (scRNA-seq) data is critical for understanding cell development and underlying gene regulatory relationships. Many current methods rely on single-cell velocity to obtain pseudotime, which can lead to inconsistencies between pseudotime and velocity. It is challenging to simultaneously infer cell pseudotime and gene interaction networks, especially in multi-branch differentiation scenarios. We present single-cell Piecewise Network (scPN), a novel high-dimensional dynamical modeling approach that iteratively extracts temporal patterns and inter-gene relationships from scRNA-seq data. To tackle multi-branch differentiation challenges, scPN models gene regulatory dynamics using piecewise gene-gene interaction networks, offering an interpretable framework for deciphering complex gene regulation patterns over time. Results on synthetic data and multiple scRNA-seq datasets demonstrate the superior performance of scPN in reconstructing cellular dynamics and identifying key transcription factors involved in development compared to existing methods. To the best of our knowledge, scPN is the first attempt at modeling that can recover pseudotime, velocity fields, and gene interactions all at once on multi-branch datasets. Copyright © 2024, The Authors. All rights reserved.

关键词： Transcription

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Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

Isoform Function Prediction Based on Heterogeneous Graph Att...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Guo, Kuo Li, Yifan Chen, Hao Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai200240 China Carnegie Mellon University School of Computer Science Computational Biology Department PittsburghPA15213 United States

ISBN: (纸本)9798350337488

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function. © 2023 IEEE.

关键词： alternative splicing gene ontology heterogeneous graph attention network isoform function prediction protein language model

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SliceProp: A Slice-Wise Bidirectional Propagation Model for Interactive 3D Medical Image Segmentation 1

SliceProp: A Slice-Wise Bidirectional Propagation Model for ...

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1st IEEE International Conference on Medical Artificial Intelligence, MedAI 2023

作者： Xu, Xin Lu, Wenjing Lei, Jiahao Qiu, Peng Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine Department of Vascular Surgery China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China

ISBN: (纸本)9798350358780

Interactive medical image segmentation methods have become increasingly popular in recent years. These methods combine manual labeling and automatic segmentation, reducing the workload of annotation while maintaining high accuracy. However, most current interactive segmentation frameworks are limited to 2D image data, and are not suitable for 3D image data due to the large size and high complexity of 3D data, as well as the challenges posed by information asymmetry and sparse annotation. In this paper, we propose SliceProp, an interactive segmentation framework that implements slice-wise Label Bidirectional Propagation (LBP) for 3D medical image segmentation. SliceProp extends the interactive 2D image segmentation algorithm to 3D image segmentation, and can handle 3D data with large size and high complexity. Moreover, equipped with a Backtracking Feedback Check (BFC) module, SliceProp effectively addresses the issues of information asymmetry and spatial sparse annotation in 3D medical image segmentation. Additionally, we adopt an uncertainty-based criterion to pri-oritize the slices to be refined interactively, which enhances the efficiency of the interaction process by enabling the model to focus on the regions with the most unreliable predictions. SliceProp is evaluated on two datasets and achieves promising results compared to state-of-the-art methods. © 2023 IEEE.

关键词： Medical imaging

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Semantic Transformation-Based Data Augmentation for Few-Shot Learning

SSRN

引用

SSRN 2023年

作者： Pan, Mei-Hong Xin, Hong-Yi Shen, Hong-Bin Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Shanghai Jiaotong University Shanghai200240 China

Few-shot learning (FSL) as a data-scarce method, aims to recognize instances of unseen classes solely based on very few examples. However, the model can easily become overfitted due to the biased distribution formed with extremely limited training data. This paper presents a task specific data augmentation approach by transferring samples from base dataset to the novel tasks in an encoder-decoder paradigm, which guarantees generating semantically meaningful features. Specifically, the feature transfer process is carried out in semantic space. We further impose a compactness constraint to the generated features with the prototypes working as the reference points, which ensures the generated features distribute around the class centers. Moreover, we incorporate the cluster centers of the query set with the prototypes of the support set to reduce the bias of the class centers. With the supervision of the compactness loss, the model is encouraged to generate discriminative features with high inter-class dispersion and intra-class compactness. Extensive experiments show that our method outperforms the state-of-the-arts on four benchmarks, namely MiniImageNet, TieredImageNet, CUB and CIFAR-FS. © 2023, The Authors. All rights reserved.

关键词： Motion planning

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