scholarly journals Accurate classification of protein subcellular localization from high throughput microscopy images using deep learning

2016 ◽  
Author(s):  
Tanel Pärnamaa ◽  
Leopold Parts
Keyword(s):  
Deep Learning ◽  
Subcellular Localization ◽  
High Throughput ◽  
Single Cells ◽  
Cellular Compartment ◽  
Cell Localization ◽  
Image Characteristics ◽  
Basic Image ◽  
Training Examples

High throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high throughput microscopy.

scholarly journals High-throughput precision measurement of subcellular localization in single cells

2017 ◽  
Vol 91 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Tyler J. Burns ◽  
Andreas P. Frei ◽  
Pier F. Gherardini ◽  
Felice A. Bava ◽  
Jake E. Batchelder ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
High Throughput ◽  
Precision Measurement ◽  
Single Cells

scholarly journals Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

2021 ◽  
Author(s):  
Tomochika Fujisawa ◽  
Victor Noguerales ◽  
Emmanouil Meramveliotakis ◽  
Anna Papadopoulou ◽  
Alfried P Vogler
Keyword(s):  
Deep Learning ◽  
High Throughput ◽  
Domain Adaptation ◽  
Network Models ◽  
Neural Network Models ◽  
Data Set ◽  
Model Training ◽  
Trained Neural Network ◽  
Domain Transfer

Complex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. Yet the feasibility of transfer learning for the classification of unknown samples remains to be tested. Here, we assess the efficiency of deep learning and domain transfer algorithms for family-level classification of below-ground bulk samples of Coleoptera from understudied forests of Cyprus. We trained neural network models with images from local surveys versus global databases of above-ground samples from tropical forests and evaluated how prediction accuracy was affected by: (a) the quality and resolution of images, (b) the size and complexity of the training set and (c) the transferability of identifications across very disparate source-target pairs that do not share any species or genera. Within-dataset classification accuracy reached 98% and depended on the number and quality of training images and on dataset complexity. The accuracy of between-datasets predictions was reduced to a maximum of 82% and depended greatly on the standardisation of the imaging procedure. When the source and target images were of similar quality and resolution, albeit from different faunas, the reduction of accuracy was minimal. Application of algorithms for domain adaptation significantly improved the prediction performance of models trained by non-standardised, low-quality images. Our findings demonstrate that existing databases can be used to train models and successfully classify images from unexplored biota, when the imaging conditions and classification algorithms are carefully considered. Also, our results provide guidelines for data acquisition and algorithmic development for high-throughput image-based biodiversity surveys.

scholarly journals HD Spot: Interpretable Deep Learning Classification of Single Cell Transcript Data

2019 ◽  
Author(s):  
Eric Prince ◽  
Todd C. Hankinson
Keyword(s):  
Deep Learning ◽  
Single Cell ◽  
High Throughput ◽  
Ground Truth ◽  
Sequencing Technologies ◽  
Bioinformatic Tool ◽  
Complex Relationships ◽  
Insight Into ◽  
Generation Sequencing

ABSTRACTHigh throughput data is commonplace in biomedical research as seen with technologies such as single-cell RNA sequencing (scRNA-seq) and other Next Generation Sequencing technologies. As these techniques continue to be increasingly utilized it is critical to have analysis tools that can identify meaningful complex relationships between variables (i.e., in the case of scRNA-seq: genes) in a way such that human bias is absent. Moreover, it is equally paramount that both linear and non-linear (i.e., one-to-many) variable relationships be considered when contrasting datasets. HD Spot is a deep learning-based framework that generates an optimal interpretable classifier a given high-throughput dataset using a simple genetic algorithm as well as an autoencoder to classifier transfer learning approach. Using four unique publicly available scRNA-seq datasets with published ground truth, we demonstrate the robustness of HD Spot and the ability to identify ontologically accurate gene lists for a given data subset. HD Spot serves as a bioinformatic tool to allow novice and advanced analysts to gain complex insight into their respective datasets enabling novel hypotheses development.

scholarly journals Convolutional neural networks for high throughput screening of catalyst layer inks for polymer electrolyte fuel cells

RSC Advances ◽  
2021 ◽  
Vol 11 (51) ◽  
pp. 32126-32134
Author(s):  
Mohammad J. Eslamibidgoli ◽  
Fabian P. Tipp ◽  
Jenia Jitsev ◽  
Jasna Jankovic ◽  
Michael H. Eikerling ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Fuel Cells ◽  
Polymer Electrolyte ◽  
Convolutional Neural Networks ◽  
High Throughput ◽  
High Throughput Screening ◽  
Catalyst Layer ◽  
Polymer Electrolyte Fuel Cells

Deep learning enables the robust and accurate classification of the TEM images of catalyst layer inks for the polymer electrolyte fuel cells.

Convolutional Neural Network of Atomic Surface Structures to Predict Binding Energies for High-Throughput Screening of Catalysts

2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
High Throughput ◽  
High Throughput Screening ◽  
Binding Energies ◽  
Surface Structures ◽  
Voronoi Polyhedra ◽  
Atomic Surface

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.

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