AIMC Topic: Computational Biology

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Noise-Consistent Hypergraph Autoencoder Based on Contrastive Learning for Cancer ceRNA Association Prediction in Complex Biological Regulatory Networks.

Journal of chemical information and modeling Jun 12, 2025
Competitive endogenous RNA (ceRNA) regulatory networks (CENA) have advanced our understanding of noncoding RNAs' roles in complex diseases, providing a theoretical basis for disease mechanisms. Existing ceRNA-disease association prediction methods ar...
Computational Biology Autoencoder RNA, Competitive Endogenous Neoplasms Gene Regulatory Networks Humans Machine Learning
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SCATrans: semantic cross-attention transformer for drug-drug interaction predication through multimodal biomedical data.

BMC bioinformatics Jun 10, 2025
Predicting potential drug-drug interactions (DDIs) from biomedical data plays a critical role in drug therapy, drug development, drug regulation, and public health. However, it remains challenging due to the large number of possible drug combinations...
Semantics Deep Learning Computational Biology Humans Drug Interactions Algorithms
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Fusing multisensory signals across channels and time.

PLoS computational biology Jun 6, 2025
Animals continuously combine information across sensory modalities and time, and use these combined signals to guide their behaviour. Picture a predator watching their prey sprint and screech through a field. To date, a range of multisensory algorith...
Computational Biology Models, Neurological Algorithms Animals Neural Networks, Computer
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The latest advances with natural products in drug discovery and opportunities for the future: a 2025 update.

Expert opinion on drug discovery Jun 5, 2025
INTRODUCTION: The landscape of drug discovery is rapidly evolving, with natural products (NPs) playing a pivotal role in the development of novel therapeutics. Despite their historical significance, challenges persist in fully harnessing their potent...
Animals Neoplasms Drug Discovery Humans Artificial Intelligence Molecular Targeted Therapy Immunoconjugates Biological Products Computational Biology High-Throughput Screening Assays Drug Development
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MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning.

Journal of chemical information and modeling Jun 5, 2025
Synonymous mutations do not change amino acid sequences, but they can drive cancer by influencing splicing, mRNA structure, translation efficiency, and other molecular mechanisms. Although driver synonymous mutations are significantly outnumbered by ...
Computational Biology Mutation Silent Mutation Machine Learning Neoplasms Humans
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Designing diverse and high-performance proteins with a large language model in the loop.

PLoS computational biology Jun 5, 2025
We present a protein engineering approach to directed evolution with machine learning that integrates a new semi-supervised neural network fitness prediction model, Seq2Fitness, and an innovative optimization algorithm, biphasic annealing for diverse...
Machine Learning Algorithms Neural Networks, Computer Mutation Computational Biology Protein Engineering Proteins Large Language Models
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A descriptor-free machine learning framework to improve antigen discovery for bacterial pathogens.

PloS one Jun 5, 2025
Identifying protective antigens (PAs), i.e., targets for bacterial vaccines, is challenging as conducting in-vivo tests at the proteome scale is impractical. Reverse Vaccinology (RV) aids in narrowing down the pool of candidates through computational...
Computational Biology Antigens, Bacterial Neural Networks, Computer Machine Learning Software Vaccinology Bacterial Vaccines Bacteria
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Predicting clinical prognosis in gastric cancer using deep learning-based analysis of tissue pathomics images.

Computer methods and programs in biomedicine Jun 4, 2025
OBJECTIVE: Evaluate the utility of a machine learning-based pathomics model in predicting overall survival (OS) post-surgery for gastric cancer patients.
Stomach Neoplasms Nomograms Female Prognosis Male Area Under Curve Retrospective Studies Aged Middle Aged Neoplasm Staging Humans Deep Learning Computational Biology
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GNNMutation: a heterogeneous graph-based framework for cancer detection.

BMC bioinformatics Jun 4, 2025
BACKGROUND: When genes are translated into proteins, mutations in the gene sequence can lead to changes in protein structure and function as well as in the interactions between proteins. These changes can disrupt cell function and contribute to the d...
Neoplasms Computational Biology Humans Mutation Neural Networks, Computer Exome Sequencing Algorithms
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HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction.

BMC bioinformatics Jun 4, 2025
BACKGROUND: Accurate identification of drug-drug interactions (DDIs) is critical in pharmacology, as DDIs can either enhance therapeutic efficacy or trigger adverse reactions when multiple medications are administered concurrently. Traditional method...
Drug Interactions Machine Learning Algorithms Computational Biology Humans
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