AIMC Topic: Computational Biology

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Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data.

PLoS computational biology Jun 20, 2024
Computational fluid dynamics (CFD) can be used for non-invasive evaluation of hemodynamics. However, its routine use is limited by labor-intensive manual segmentation, CFD mesh creation, and time-consuming simulation. This study aims to train a deep ...
Pulmonary Artery Hemodynamics Deep Learning Blood Flow Velocity Imaging, Three-Dimensional Computational Biology Humans Hydrodynamics Magnetic Resonance Imaging Neural Networks, Computer Models, Cardiovascular Proof of Concept Study
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Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets.

BMC bioinformatics Jun 19, 2024
BACKGROUND: Compared to traditional supervised machine learning approaches employing fully labeled samples, positive-unlabeled (PU) learning techniques aim to classify "unlabeled" samples based on a smaller proportion of known positive examples. This...
Supervised Machine Learning Machine Learning Algorithms Computational Biology Humans
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NNBGWO-BRCA marker: Neural Network and binary grey wolf optimization based Breast cancer biomarker discovery framework using multi-omics dataset.

Computer methods and programs in biomedicine Jun 18, 2024
BACKGROUND AND OBJECTIVE: Breast cancer is a multifaceted condition characterized by diverse features and a substantial mortality rate, underscoring the imperative for timely detection and intervention. The utilization of multi-omics data has gained ...
Biomarkers, Tumor Algorithms Humans Computational Biology Deep Learning Female Neural Networks, Computer Multiomics Breast Neoplasms Support Vector Machine
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Precision Drug Repurposing: A Deep Learning Toolkit for Identifying 34 Hyperpigmentation-Associated Genes and Optimizing Treatment Selection.

Annals of plastic surgery Jun 18, 2024
BACKGROUND: Hyperpigmentation is a skin disorder characterized by a localized darkening of the skin due to increased melanin production. When patients fail first line topical treatments, secondary treatments such as chemical peels and lasers are offe...
Humans Precision Medicine Deep Learning Computational Biology Data Mining Drug Repositioning Hyperpigmentation
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EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction.

BMC bioinformatics Jun 18, 2024
BACKGROUND: Recognition of enhancer-promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating transcription. However, experimental approaches for classifying EPIs are too expensive in terms of eff...
Computational Biology Cell Line Promoter Regions, Genetic Enhancer Elements, Genetic Humans Neural Networks, Computer Deep Learning
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NNICE: a deep quantile neural network algorithm for expression deconvolution.

Scientific reports Jun 18, 2024
The composition of cell-type is a key indicator of health. Advancements in bulk gene expression data curation, single cell RNA-sequencing technologies, and computational deconvolution approaches offer a new perspective to learn about the composition ...
RNA-Seq Computational Biology Sequence Analysis, RNA Transcriptome Deep Learning Single-Cell Analysis Algorithms Gene Expression Profiling Humans Neural Networks, Computer
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Missing data in amortized simulation-based neural posterior estimation.

PLoS computational biology Jun 17, 2024
Amortized simulation-based neural posterior estimation provides a novel machine learning based approach for solving parameter estimation problems. It has been shown to be computationally efficient and able to handle complex models and data sets. Yet,...
Computational Biology Data Interpretation, Statistical Bayes Theorem Algorithms Computer Simulation Humans Neural Networks, Computer Machine Learning
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A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation.

BMC bioinformatics Jun 14, 2024
BACKGROUND: The exploration of gene-disease associations is crucial for understanding the mechanisms underlying disease onset and progression, with significant implications for prevention and treatment strategies. Advances in high-throughput biotechn...
Deep Learning Protein Interaction Maps Genetic Predisposition to Disease Humans Neural Networks, Computer Algorithms Genetic Association Studies Computational Biology
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Big data and deep learning for RNA biology.

Experimental & molecular medicine Jun 14, 2024
The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depe...
Humans Big Data Computational Biology RNA Algorithms Animals Deep Learning
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Mining key circadian biomarkers for major depressive disorder by integrating bioinformatics and machine learning.

Aging Jun 13, 2024
OBJECTIVE: This study aimed to identify key clock genes closely associated with major depressive disorder (MDD) using bioinformatics and machine learning approaches.
Computational Biology Circadian Rhythm Case-Control Studies Gene Regulatory Networks Female Humans Middle Aged Adult Machine Learning Depressive Disorder, Major Male Biomarkers Gene Expression Profiling
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