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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Chen, Ke Han, Xiaosong Li, Xiaoran Liang, Yanchun Xu, Dong Guan, Renchu Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Changchun China Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Changchun China Zhuhai College of Science and Technology Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education School of Computer Science Zhuhai China University of Missouri Christopher S. Bond Life Sciences Center Department of Electrical Engineering and Computer Science Columbia United States

ISBN: (纸本)9798350386226

Drug-Drug Interaction (DDI) task plays a crucial role in clinical treatment and drug development. Recently, deep learning methods have been successfully applied for DDI prediction. However, training deep learning models always need large amount of data, while known DDIs are scarce. To address this challenge, a graph neural network-based DDI prediction model named PNESR-DDI is proposed, which compensates for the lack of DDIs by enriching drug representations. First, to obtain initial node representations that incorporate rich semantic information from the biomedical knowledge graph (KG), a link prediction pre-training method on external KG is proposed in the node embedding pre-training module. Then, considering the large scale of the KG, subgraph extraction for the target drug pairs is introduced to reduce noise and decrease computational complexity in the subgraph anchoring module. After that, the subgraph is updated, and node similarities are propagated in the subgraph reconstruction module. Based on the node similarity scores, the subgraph is pruned and reconstructed, which adjusts node representations to be more conducive to DDI prediction. Finally, the drug embeddings, subgraph representations, and drug fingerprint features are concatenated to predict DDIs. PNESRDDI is evaluated on two benchmark DDI datasets: DrugBank and TWOSIDES. Experiment results show that PNESR-DDI achieves better performance than baselines. Ablation results validate the effectiveness of the pre-training method and the adaptive subgraph reconstruction strategy. © 2024 IEEE.

关键词： knowledge graph

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2.5D ASF-UNet: Adjacent Slice Spatial Feature Fusion Model for WMH Segmentation from 3D MR Brain Image

2.5D ASF-UNet: Adjacent Slice Spatial Feature Fusion Model f...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Huang, Lan Sun, Yinglu Zhao, Ziqi Guo, Chunjie Wang, Yan College of Computer Science and Technology Jilin University Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education Changchun China The First Hospital of Jilin University Department of Radiology Changchun China

ISBN: (纸本)9798350386226

Segmenting brain white matter hyperintensities (WMH) from 3D Magnetic Resonance (MR) images is crucial for the diagnosis, treatment, and prognosis of Multiple Sclerosis (MS). Unlike common 2D images, this task is more challenging and time-consuming. Classical deep learning methods for 3D image segmentation face two main challenges: 1) Pure 3D networks have more parameters and are prone to overfitting. 2) When using 2D networks to segment slices of 3D images, the lack of 3D structural information results in suboptimal segmentation after reconstruction. To address these difficulties, we propose the 2.5D ASF-UNet, which employs the 2.5D workflow and uses adjacent slices as the input for 2D segmentation network ASF-UNet. In ASF-UNet, separate down-sampling paths are used for the adjacent slices, and the Local Spatial Attention Module (LSAM) is designed to more effectively integrate 3D spatial information into the 2D network. Additionally, the Conv-Spectral-Block (CSB) is designed to extract and integrate local and global features. It allows the model to capture global spatial structures while preserving detailed information. Experimental results on MICCAI MSSEG 2016 and Local MS datasets show that 2.5D ASF-UNet achieve better segmentation performance than other deep learning methods. © 2024 IEEE.

关键词： Image segmentation

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DeepHBSP:A Deep Learning Framework for Predicting Human Blood-Secretory Proteins Using Transfer Learning

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Journal of Computer Science & Technology 2021年第2期36卷 234-247页

作者： Wei Du Yu Sun Hui-Min Bao Liang Chen Ying Li Yan-Chun Liang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and TechnologyJilin UniversityChangchun 130012China Department of Computer Science College of EngineeringShantou UniversityShantou 515063China Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Zhuhai College of Jilin University Zhuhai 519041China

The identification of blood-secretory proteins and the detection of protein biomarkers in the blood have an important clinical application *** methods for predicting blood-secretory proteins are mainly based on traditional machine learning algorithms,and heavily rely on annotated protein *** traditional machine learning algorithms,deep learning algorithms can automatically learn better feature representations from raw data,and are expected to be more promising to predict blood-secretory *** present a novel deep learning model(DeepHBSP)combined with transfer learning by integrating a binary classification network and a ranking network to identify blood-secretory proteins from the amino acid sequence information *** loss function of DeepHBSP in the training step is designed to apply descriptive loss and compactness loss to the binary classification network and the ranking network,*** feature extraction subnetwork of DeepHBSP is composed of a multi-lane capsule ***,transfer learning is used to train a highly accurate generalized model with small samples of blood-secretory *** main contributions of this study are as follows:1)a novel deep learning architecture by integrating a binary classification network and a ranking network is proposed,superior to existing traditional machine learning algorithms and other state-of-the-art deep learning architectures for biological sequence analysis;2)the proposed model for blood-secretory protein prediction uses only amino acid sequences,overcoming the heavy dependence of existing methods on annotated protein features;3)the blood-secretory proteins predicted by our model are statistically significant compared with existing blood-based biomarkers of cancer.

关键词： blood-secretory protein deep learning capsule network transfer learning

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PNESR-DDI: An Effective Drug-Drug Interaction Prediction Model Based on Pretraining Method and Enhanced Subgraph Reconstruction

PNESR-DDI: An Effective Drug-Drug Interaction Prediction Mod...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Ke Chen Xiaosong Han Xiaoran Li Yanchun Liang Dong Xu Renchu Guan Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Jilin University Changchun China Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Jilin University Changchun China Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education School of Computer Science Zhuhai College of Science and Technology Zhuhai China Department of Electrical Engineering and Computer Science Christopher S. Bond Life Sciences Center University of Missouri Columbia USA

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

关键词： Drugs Deep learning Adaptation models Visualization Biological system modeling Noise knowledge graphs Predictive models Fingerprint recognition Transformers

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Independent and Collaborative Demosaicking Neural Networks 5

Independent and Collaborative Demosaicking Neural Networks

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5th ACM International Conference on Multimedia in Asia, MMAsia 2023

作者： Niu, Yan Zhang, Lixue Li, Chenlai State Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education College of Computer Science and Technology Jilin University Jilin Changchun China College of Computer Science and Technology Jilin University Changchun China School of Artificial Intelligence Shenzhen Polytechnic University Shenzhen China

ISBN: (纸本)9798400702051

Existing demosaicking neural models generally reconstruct the red, green and blue channels by one unified network. This has the advantage of allowing the RGB channels to share latent features. However, it is unnoticed that the training samples are severely unbalanced among the three channels. As a consequence, a unified model trained to fit the red or blue sample distributions is prone to under-fit the green samples. In this paper, we demonstrate the existence of such conflicts, and analyze the reason behind this phenomenon. To solve this disadvantage, we decouple the traditional three-in-one demosaicking to three independent but collaborative sub-tasks, respecting the distribution of samples in each spectrum. We show that, by our decoupling strategy, a very simple architecture can achieve high accuracy with high efficiency. For substantiation, we construct a model that has merely 1.3M parameters in total, and compares its accuracy to state of the art methods of similar or larger model size, across a wide variety of benchmark datasets. The proposed independent and collaborative architecture gains performance improvement over comparable models in both accuracy and inference time. © 2023 Copyright held by the owner/author(s).

关键词： Network architecture

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2.5D ASF-UNet: Adjacent Slice Spatial Feature Fusion Model for WMH Segmentation from 3D MR Brain Image

2.5D ASF-UNet: Adjacent Slice Spatial Feature Fusion Model f...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Lan Huang Yinglu Sun Ziqi Zhao Chunjie Guo Yan Wang Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University Changchun China Department of Radiology the First Hospital of Jilin University Changchun China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Segmenting brain white matter hyperintensities (WMH) from 3D Magnetic Resonance (MR) images is crucial for the diagnosis, treatment, and prognosis of Multiple Sclerosis (MS). Unlike common 2D images, this task is more challenging and time-consuming. Classical deep learning methods for 3D image segmentation face two main challenges: 1) Pure 3D networks have more parameters and are prone to overfitting. 2) When using 2D networks to segment slices of 3D images, the lack of 3D structural information results in suboptimal segmentation after reconstruction. To address these difficulties, we propose the 2.5D ASF-UNet, which employs the 2.5D workflow and uses adjacent slices as the input for 2D segmentation network ASF-UNet. In ASF-UNet, separate down-sampling paths are used for the adjacent slices, and the Local Spatial Attention Module (LSAM) is designed to more effectively integrate 3D spatial information into the 2D network. Additionally, the Conv_Spectral_Block (CSB) is designed to extract and integrate local and global features. It allows the model to capture global spatial structures while preserving detailed information. Experimental results on MICCAI MSSEG 2016 and Local MS datasets show that 2.5D ASF-UNet achieve better segmentation performance than other deep learning methods.

关键词： Deep learning Image segmentation Solid modeling Three-dimensional displays Multiple sclerosis Feature extraction Brain modeling White matter Prognostics and health management Overfitting

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Shortcut Learning in In-Context Learning: A Survey

arXiv

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arXiv 2024年

作者： Song, Rui Li, Yingji Shi, Lida Giunchiglia, Fausto Xu, Hao College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education Jilin University China Department of Information Engineering and Computer Science University of Trento Italy

Shortcut learning refers to the phenomenon where models employ simple, non-robust decision rules in practical tasks, which hinders their generalization and robustness. With the rapid development of Large Language Models (LLMs) in recent years, an increasing number of studies have shown the impact of shortcut learning on LLMs. This paper provides a novel perspective to review relevant research on shortcut learning in In-Context Learning (ICL). It conducts a detailed exploration of the types of shortcuts in ICL tasks, their causes, available benchmarks, and strategies for mitigating shortcuts. Based on the corresponding observations, we summarize the unresolved issues in existing research and attempts to outline the future research landscape of shortcut learning. © 2024, CC BY.

关键词： Contrastive Learning

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Toward Moiré-Free and Detail-Preserving Demosaicking

arXiv

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arXiv 2023年

作者： Li, Xuanchen Niu, Yan Zhao, Bo Shi, Haoyuan An, Zitong State Key Laboratory of Symbol Computation and Knowledge Engineering College of Computer Science and Technology Ministry of Education Jilin University Changchun China The College of Software Jilin University Changchun130012 China

3D convolutions are commonly employed by demosaicking neural models, in the same way as solving other image restoration problems. Counter-intuitively, we show that 3D convolutions implicitly impede the RGB color spectra from exchanging complementary information, resulting in spectral-inconsistent inference of the local spatial high frequency components. As a consequence, shallow 3D convolution networks suffer the Moiré artifacts, but deep 3D convolutions cause over-smoothness. We analyze the fundamental difference between demosaicking and other problems that predict lost pixels between available ones (e.g., super-resolution reconstruction), and present the underlying reasons for the confliction between Moiré-free and detail-preserving. From the new perspective, our work decouples the common standard convolution procedure to spectral and spatial feature aggregations, which allow strengthening global communication in the spectral dimension while respecting local contrast in the spatial dimension. We apply our demosaicking model to two tasks: Joint Demosaicking-Denoising and Independently Demosaicking. In both applications, our model substantially alleviates artifacts such as Moiré and over-smoothness at similar or lower computational cost to currently top-performing models, as validated by diverse evaluations. Source code will be released along with paper publication. Copyright © 2023, The Authors. All rights reserved.

关键词： Convolution

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Uncertainty-Aware Global-View Reconstruction for Multi-View Multi-Label Feature Selection

arXiv

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arXiv 2025年

作者： Hao, Pingting Liu, Kunpeng Gao, Wanfu 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 Portland State University PortlandOR97201 United States

In recent years, multi-view multi-label learning (MVML) has gained popularity due to its close resemblance to real-world scenarios. However, the challenge of selecting informative features to ensure both performance and efficiency remains a significant question in MVML. Existing methods often extract information separately from the consistency part and the complementary part, which may result in noise due to unclear segmentation. In this paper, we propose a unified model constructed from the perspective of global-view reconstruction. Additionally, while feature selection methods can discern the importance of features, they typically overlook the uncertainty of samples, which is prevalent in realistic scenarios. To address this, we incorporate the perception of sample uncertainty during the reconstruction process to enhance trustworthiness. Thus, the global-view is reconstructed through the graph structure between samples, sample confidence, and the view relationship. The accurate mapping is established between the reconstructed view and the label matrix. Experimental results demonstrate the superior performance of our method on multi-view datasets. Copyright © 2025, The Authors. All rights reserved.

关键词： Feature Selection

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Reconsidering Feature Structure Information and Latent Space Alignment in Partial Multi-label Feature Selection

arXiv

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arXiv 2025年

作者： Pan, Hanlin Liu, Kunpeng Gao, Wanfu 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 Portland State University PortlandOR97201 United States

The purpose of partial multi-label feature selection is to select the most representative feature subset, where the data comes from partial multi-label datasets that have label ambiguity issues. For label disambiguation, previous methods mainly focus on utilizing the information inside the labels and the relationship between the labels and features. However, the information existing in the feature space is rarely considered, especially in partial multi-label scenarios where the noises is considered to be concentrated in the label space while the feature information is correct. This paper proposes a method based on latent space alignment, which uses the information mined in feature space to disambiguate in latent space through the structural consistency between labels and features. In addition, previous methods overestimate the consistency of features and labels in the latent space after convergence. We comprehensively consider the similarity of latent space projections to feature space and label space, and propose new feature selection term. This method also significantly improves the positive label identification ability of the selected features. Comprehensive experiments demonstrate the superiority of the proposed method. Copyright © 2025, The Authors. All rights reserved.

关键词： Feature extraction

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