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EXSEQREG: Explaining sequence-based NLP tasks with regions with a case study using morphological features for named entity recognition.

PloS one Dec 30, 2020
The state-of-the-art systems for most natural language engineering tasks employ machine learning methods. Despite the improved performances of these systems, there is a lack of established methods for assessing the quality of their predictions. This ...
Machine Learning Software Natural Language Processing
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Developing a Qualification and Verification Strategy for Digital Tissue Image Analysis in Toxicological Pathology.

Toxicologic pathology Dec 29, 2020
Digital tissue image analysis is a computational method for analyzing whole-slide images and extracting large, complex, and quantitative data sets. However, as with any analysis method, the quality of generated results is dependent on a well-designed...
Humans Artificial Intelligence Microscopy Image Interpretation, Computer-Assisted Software Image Processing, Computer-Assisted
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Template-based prediction of protein structure with deep learning.

BMC genomics Dec 29, 2020
BACKGROUND: Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary struct...
Proteins Databases, Protein Protein Conformation Software Algorithms Deep Learning Sequence Analysis, Protein
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Network-based drug sensitivity prediction.

BMC medical genomics Dec 28, 2020
BACKGROUND: Drug sensitivity prediction and drug responsive biomarker selection on high-throughput genomic data is a critical step in drug discovery. Many computational methods have been developed to serve this purpose including several deep neural n...
Carcinoma, Non-Small-Cell Lung Lung Neoplasms Computational Biology Gene Expression Regulation, Neoplastic Gene Expression Profiling Deep Learning Gene Regulatory Networks Software Biomarkers, Tumor Humans Prognosis Antineoplastic Agents Neural Networks, Computer
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Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs.

Scientific reports Dec 23, 2020
The global population is at present suffering from a pandemic of Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The goal of this study was to use artificial intellige...
Amino Acid Sequence Haplotypes Immunogenicity, Vaccine HLA Antigens Drug Evaluation, Preclinical Alleles SARS-CoV-2 Epitopes, T-Lymphocyte COVID-19 Vaccines Proteome Pandemics Mutation Humans COVID-19 Spike Glycoprotein, Coronavirus Machine Learning Algorithms Software Proteomics
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Interactive Classification of Whole-Slide Imaging Data for Cancer Researchers.

Cancer research Dec 21, 2020
Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists...
Breast Neoplasms Biomedical Research Neoplasms Skin Neoplasms Reproducibility of Results Sensitivity and Specificity Melanoma, Cutaneous Malignant Image Interpretation, Computer-Assisted Medical Oncology Datasets as Topic Image Processing, Computer-Assisted Lymphocytes, Tumor-Infiltrating Predictive Value of Tests Humans Machine Learning Software Female Melanoma Algorithms Prognosis
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DeepCLA: A Hybrid Deep Learning Approach for the Identification of Clathrin.

Journal of chemical information and modeling Dec 21, 2020
Clathrin is a highly evolutionarily conserved protein, which can affect membrane cleavage and membrane release of vesicles. The absence of clathrin in the cellular system affects a variety of human diseases. Effective recognition of clathrin plays an...
Deep Learning Computational Biology Clathrin Humans Neural Networks, Computer Software
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RAM-PGK: Prediction of Lysine Phosphoglycerylation Based on Residue Adjacency Matrix.

Genes Dec 20, 2020
BACKGROUND: Post-translational modification (PTM) is a biological process that is associated with the modification of proteome, which results in the alteration of normal cell biology and pathogenesis. There have been numerous PTM reports in recent ye...
Support Vector Machine Protein Processing, Post-Translational Amino Acid Sequence Datasets as Topic Lysine Glyceric Acids Software Algorithms ROC Curve
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Three-Dimensional Vessel Segmentation in Whole-Tissue and Whole-Block Imaging Using a Deep Neural Network: Proof-of-Concept Study.

The American journal of pathology Dec 18, 2020
In the field of pathology, micro-computed tomography (micro-CT) has become an attractive imaging modality because it enables full analysis of the three-dimensional characteristics of a tissue sample or organ in a noninvasive manner. However, because ...
Humans Neural Networks, Computer Software X-Ray Microtomography Paraffin Embedding Imaging, Three-Dimensional Proof of Concept Study
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Cellpose: a generalist algorithm for cellular segmentation.

Nature methods Dec 14, 2020
Many biological applications require the segmentation of cell bodies, membranes and nuclei from microscopy images. Deep learning has enabled great progress on this problem, but current methods are specialized for images that have large training datas...
Algorithms Female Animals Humans Neural Networks, Computer Software Mice Mice, Inbred C57BL Neurons Cell Nucleus Male Deep Learning Image Processing, Computer-Assisted
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