AIMC Topic: Computational Biology

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Enhancing Spatial Domain Identification in Spatially Resolved Transcriptomics Using Graph Convolutional Networks With Adaptively Feature-Spatial Balance and Contrastive Learning.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Recent advancements in spatially transcriptomics (ST) technologies have enabled the comprehensive measurement of gene expression profiles while preserving the spatial information of cells. Combining gene expression profiles and spatial information ha...
Transcriptome Deep Learning Computational Biology Algorithms Humans Gene Expression Profiling Neural Networks, Computer
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A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Drug Target Interaction (DTI) prediction plays a crucial role in in-silico drug discovery, especially for deep learning (DL) models. Along this line, existing methods usually first extract features from drugs and target proteins, and use drug-target ...
Deep Learning Humans Computational Biology Algorithms Ligands Proteins Drug Discovery Databases, Protein
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Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Apple leaf diseases can seriously affect apple production and quality, and accurately detecting them can improve the efficiency of disease monitoring. Owing to the complex natural growth environment, apple leaf lesions may be easily confused with bac...
Malus Plant Leaves Plant Diseases Image Processing, Computer-Assisted Neural Networks, Computer Computational Biology Algorithms
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Improving Antifreeze Proteins Prediction With Protein Language Models and Hybrid Feature Extraction Networks.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Accurate identification of antifreeze proteins (AFPs) is crucial in developing biomimetic synthetic anti-icing materials and low-temperature organ preservation materials. Although numerous machine learning-based methods have been proposed for AFPs pr...
Neural Networks, Computer Deep Learning Computational Biology Algorithms Antifreeze Proteins Databases, Protein Sequence Analysis, Protein
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Reinforced Metapath Optimization in Heterogeneous Information Networks for Drug-Target Interaction Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Graph neural networks offer an effective avenue for predicting drug-target interactions. In this domain, researchers have found that constructing heterogeneous information networks based on metapaths using diverse biological datasets enhances predict...
Neural Networks, Computer Algorithms Markov Chains Humans Computational Biology
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GenoM7GNet: An Efficient N-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanw...
Sequence Analysis, RNA RNA Guanosine Deep Learning Computational Biology Neural Networks, Computer Algorithms Humans
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CTsynther: Contrastive Transformer Model for End-to-End Retrosynthesis Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Retrosynthesis prediction is a fundamental problem in organic chemistry and drug synthesis. We proposed an end-to-end deep learning model called CTsynther (Contrastive Transformer for single-step retrosynthesis prediction model) that could provide si...
Chemistry, Organic Deep Learning Computational Biology Algorithms
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Relation Extraction in Biomedical Texts: A Cross-Sentence Approach.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Relation extraction, a crucial task in understanding the intricate relationships between entities in biomedical domains, has predominantly focused on binary relations within single sentences. However, in practical biomedical scenarios, relationships ...
Humans Deep Learning Computational Biology Natural Language Processing Algorithms Databases, Factual Data Mining Semantics
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LKLPDA: A Low-Rank Fast Kernel Learning Approach for Predicting piRNA-Disease Associations.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Piwi-interacting RNAs (piRNAs) are increasingly recognized as potential biomarkers for various diseases. Investig-ating the complex relationship between piRNAs and diseases through computational methods can reduce the costs and risks associated with ...
Algorithms Genetic Predisposition to Disease RNA, Small Interfering Piwi-Interacting RNA Computational Biology Humans Machine Learning
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MMD-DTA: A Multi-Modal Deep Learning Framework for Drug-Target Binding Affinity and Binding Region Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
The prediction of drug-target affinity (DTA) plays a crucial role in drug development and the identification of potential drug targets. In recent years, computer-assisted DTA prediction has emerged as a significant approach in this field. In this stu...
Drug Discovery Deep Learning Humans Neural Networks, Computer Protein Binding Proteins Computational Biology Pharmaceutical Preparations Binding Sites
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