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Extended-wavelength diffuse reflectance spectroscopy with a machine-learning method for in vivo tissue classification.

PloS one 31600296
OBJECTIVES: An extended-wavelength diffuse reflectance spectroscopy (EWDRS) technique was evaluated for its ability to differentiate between and classify different skin and tissue types in an in vivo pig model.
Animals Machine Learning Organ Specificity Principal Component Analysis Spectrum Analysis Swine
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Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.

Scientific reports 30787315
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second appr...
Algorithms Cell Compartmentation Cells Deep Learning Gene Expression Profiling Humans Neural Networks, Computer Organ Specificity
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Separation of bones from soft tissue in chest radiographs: Anatomy-specific orientation-frequency-specific deep neural network convolution.

Medical physics 30848498
PURPOSE: Lung nodules that are missed by radiologists as well as by computer-aided detection (CAD) systems mostly overlap with ribs and clavicles. Removing the bony structures would result in better visualization of undetectable lesions. Our purpose ...
Clavicle Humans Image Processing, Computer-Assisted Neural Networks, Computer Organ Specificity Radiography, Thoracic Ribs
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ME-Class2 reveals context dependent regulatory roles for 5-hydroxymethylcytosine.

Nucleic acids research 30649543
Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the d...
5-Methylcytosine Animals Brain Databases, Genetic Datasets as Topic Genes Genome Humans Machine Learning Methylation Mice Organ Specificity Promoter Regions, Genetic Sequence Analysis, RNA Sulfites
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Development and Validation of a Bayesian Network Method to Detect External Beam Radiation Therapy Physician Order Errors.

International journal of radiation oncology, biology, physics 31158426
PURPOSE: To investigate a Bayesian network (BN)-based method to detect errors in external beam radiation therapy physician orders.
Algorithms Bayes Theorem Cohort Studies Datasets as Topic Dose Fractionation, Radiation False Negative Reactions False Positive Reactions Humans Medical Errors Neoplasms Neural Networks, Computer Organ Specificity Radiologists Radiotherapy Dosage Radiotherapy Planning, Computer-Assisted Radiotherapy Setup Errors Radiotherapy, Image-Guided ROC Curve Simulation Training Technology, Radiologic
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Improving prediction of phenotypic drug response on cancer cell lines using deep convolutional network.

BMC bioinformatics 31357929
BACKGROUND: Understanding the phenotypic drug response on cancer cell lines plays a vital role in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic...
Antineoplastic Agents Cell Line, Tumor Databases, Factual Deep Learning Genomics Humans Inhibitory Concentration 50 Neoplasms Neural Networks, Computer Organ Specificity Phenotype Regression Analysis
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Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.

International journal of molecular sciences 31336830
Transcription factor binding sites (TFBSs) play an important role in gene expression regulation. Many computational methods for TFBS prediction need sufficient labeled data. However, many transcription factors (TFs) lack labeled data in cell types. W...
Algorithms Binding Sites Computational Biology Deep Learning Gene Expression Regulation Neural Networks, Computer Organ Specificity Protein Binding ROC Curve Transcription Factors
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Cell Type Classification and Unsupervised Morphological Phenotyping From Low-Resolution Images Using Deep Learning.

Scientific reports 31530889
Convolutional neural networks (ConvNets) have proven to be successful in both the classification and semantic segmentation of cell images. Here we establish a method for cell type classification utilizing images taken with a benchtop microscope direc...
Algorithms Cell Tracking Deep Learning Microscopy Models, Theoretical Neural Networks, Computer Organ Specificity Phenotype Single-Cell Analysis
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DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome.

Scientific reports 31712594
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Network...
Algorithms Computational Biology Data Mining Deep Learning Disease Susceptibility Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Neoplasms Neural Networks, Computer Organ Specificity Pathology, Molecular Reproducibility of Results Transcriptome
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Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks.

IEEE/ACM transactions on computational biology and bioinformatics 31107658
Prediction of protein subcellular location has currently become a hot topic because it has been proven to be useful for understanding both the disease mechanisms and novel drug design. With the rapid development of automated microscopic imaging techn...
Algorithms Deep Learning Humans Image Processing, Computer-Assisted Intracellular Space Organ Specificity Proteins Proteomics
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