Dataset Information

Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns.

ABSTRACT: Identifying localization of proteins and their specific subpopulations associated with certain cellular compartments is crucial for understanding protein function and interactions with other macromolecules. Fluorescence microscopy is a powerful method to assess protein localizations, with increasing demand of automated high throughput analysis methods to supplement the technical advancements in high throughput imaging. Here, we study the applicability of deep neural network-based artificial intelligence in classification of protein localization in 13 cellular subcompartments. We use deep learning-based on convolutional neural network and fully convolutional network with similar architectures for the classification task, aiming at achieving accurate classification, but importantly, also comparison of the networks. Our results show that both types of convolutional neural networks perform well in protein localization classification tasks for major cellular organelles. Yet, in this study, the fully convolutional network outperforms the convolutional neural network in classification of images with multiple simultaneous protein localizations. We find that the fully convolutional network, using output visualizing the identified localizations, is a very useful tool for systematic protein localization assessment.

SUBMITTER: Liimatainen K

PROVIDER: S-EPMC7916854 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns.

Liimatainen Kaisa K Huttunen Riku R Latonen Leena L Ruusuvuori Pekka P

Biomolecules 20210211 2

Identifying localization of proteins and their specific subpopulations associated with certain cellular compartments is crucial for understanding protein function and interactions with other macromolecules. Fluorescence microscopy is a powerful method to assess protein localizations, with increasing demand of automated high throughput analysis methods to supplement the technical advancements in high throughput imaging. Here, we study the applicability of deep neural network-based artificial inte ...[more]

PMID: 33670112

Similar Datasets

Project description:BackgroundEarly diagnosis and accurate staging are important to improve the cure rate and prognosis for pancreatic cancer. This study was performed to develop an automatic and accurate imaging processing technique system, allowing this system to read computed tomography (CT) images correctly and make diagnosis of pancreatic cancer faster.MethodsThe establishment of the artificial intelligence (AI) system for pancreatic cancer diagnosis based on sequential contrast-enhanced CT images were composed of two processes: training and verification. During training process, our study used all 4385 CT images from 238 pancreatic cancer patients in the database as the training data set. Additionally, we used VGG16, which was pre-trained in ImageNet and contained 13 convolutional layers and three fully connected layers, to initialize the feature extraction network. In the verification experiment, we used sequential clinical CT images from 238 pancreatic cancer patients as our experimental data and input these data into the faster region-based convolution network (Faster R-CNN) model that had completed training. Totally, 1699 images from 100 pancreatic cancer patients were included for clinical verification.ResultsA total of 338 patients with pancreatic cancer were included in the study. The clinical characteristics (sex, age, tumor location, differentiation grade, and tumor-node-metastasis stage) between the two training and verification groups were insignificant. The mean average precision was 0.7664, indicating a good training effect of the Faster R-CNN. Sequential contrast-enhanced CT images of 100 pancreatic cancer patients were used for clinical verification. The area under the receiver operating characteristic curve calculated according to the trapezoidal rule was 0.9632. It took approximately 0.2 s for the Faster R-CNN AI to automatically process one CT image, which is much faster than the time required for diagnosis by an imaging specialist.ConclusionsFaster R-CNN AI is an effective and objective method with high accuracy for the diagnosis of pancreatic cancer.Trial registrationChiCTR1800017542; http://www.chictr.org.cn.

Dataset Information

Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns.

Publications

Convolutional Neural Network-Based Artificial Intelligence for Classification of Protein Localization Patterns.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets