DeephESC 2.0: Deep Generative Multi Adversarial Networks for improving the classification of hESC

SinGAN-Seg: Synthetic training data generation for medical image segmentation

Analyzing medical data to find abnormalities is a time-consuming and costly task, particularly for rare abnormalities, requiring tremendous efforts from medical experts. Therefore, artificial intelligence has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. However, the machine learning models used to build these tools are highly dependent on the data used to train them. Large amounts of data can be difficult to obtain in medicine due to privacy reasons, expensive and time-consuming annotations, and a general lack of data samples for infrequent lesions. In this study, we present a novel synthetic data generation pipeline, called SinGAN-Seg, to produce synthetic medical images with corresponding masks using a single training image. Our method is different from the traditional generative adversarial networks (GANs) because our model needs only a single image and the corresponding ground truth to train. We also show that the synthetic data generation pipeline can be used to produce alternative artificial segmentation datasets with corresponding ground truth masks when real datasets are not allowed to share. The pipeline is evaluated using qualitative and quantitative comparisons between real data and synthetic data to show that the style transfer technique used in our pipeline significantly improves the quality of the generated data and our method is better than other state-of-the-art GANs to prepare synthetic images when the size of training datasets are limited. By training UNet++ using both real data and the synthetic data generated from the SinGAN-Seg pipeline, we show that the models trained on synthetic data have very close performances to those trained on real data when both datasets have a considerable amount of training data. In contrast, we show that synthetic data generated from the SinGAN-Seg pipeline improves the performance of segmentation models when training datasets do not have a considerable amount of data. All experiments were performed using an open dataset and the code is publicly available on GitHub.

Generative Adversarial Networks for Morphological-Temporal Classification of Stem Cell Images

Frequently, neural network training involving biological images suffers from a lack of data, resulting in inefficient network learning. This issue stems from limitations in terms of time, resources, and difficulty in cellular experimentation and data collection. For example, when performing experimental analysis, it may be necessary for the researcher to use most of their data for testing, as opposed to model training. Therefore, the goal of this paper is to perform dataset augmentation using generative adversarial networks (GAN) to increase the classification accuracy of deep convolutional neural networks (CNN) trained on induced pluripotent stem cell microscopy images. The main challenges are: 1. modeling complex data using GAN and 2. training neural networks on augmented datasets that contain generated data. To address these challenges, a temporally constrained, hierarchical classification scheme that exploits domain knowledge is employed for model learning. First, image patches of cell colonies from gray-scale microscopy images are generated using GAN, and then these images are added to the real dataset and used to address class imbalances at multiple stages of training. Overall, a 2% increase in both true positive rate and F1-score is observed using this method as compared to a straightforward, imbalanced classification network, with some greater improvements on a classwise basis. This work demonstrates that synergistic model design involving domain knowledge is key for biological image analysis and improves model learning in high-throughput scenarios.

Conditional Deep 3D-Convolutional Generative Adversarial Nets for RGB-D Generation

Generation of synthetic data is a challenging task. There are only a few significant works on RGB video generation and no pertinent works on RGB-D data generation. In the present work, we focus our attention on synthesizing RGB-D data which can further be used as dataset for various applications like object tracking, gesture recognition, and action recognition. This paper has put forward a proposal for a novel architecture that uses conditional deep 3D-convolutional generative adversarial networks to synthesize RGB-D data by exploiting 3D spatio-temporal convolutional framework. The proposed architecture can be used to generate virtually unlimited data. In this work, we have presented the architecture to generate RGB-D data conditioned on class labels. In the architecture, two parallel paths were used, one to generate RGB data and the second to synthesize depth map. The output from the two parallel paths is combined to generate RGB-D data. The proposed model is used for video generation at 30 fps (frames per second). The frame referred here is an RGB-D with the spatial resolution of 512 × 512.

Human embryonic stem cell classification: random network with autoencoded feature extractor

SIGNIFICANCE

Automated understanding of human embryonic stem cell (hESC) videos is essential for the quantified analysis and classification of various states of hESCs and their health for diverse applications in regenerative medicine.

AIM

This paper aims to develop an ensemble method and bagging of deep learning classifiers as a model for hESC classification on a video dataset collected using a phase contrast microscope.

APPROACH

The paper describes a deep learning-based random network (RandNet) with an autoencoded feature extractor for the classification of hESCs into six different classes, namely, (1) cell clusters, (2) debris, (3) unattached cells, (4) attached cells, (5) dynamically blebbing cells, and (6) apoptotically blebbing cells. The approach uses unlabeled data to pre-train the autoencoder network and fine-tunes it using the available annotated data.

RESULTS

The proposed approach achieves a classification accuracy of 97.23  ±  0.94  %   and outperforms the state-of-the-art methods. Additionally, the approach has a very low training cost compared with the other deep-learning-based approaches, and it can be used as a tool for annotating new videos, saving enormous hours of manual labor.

CONCLUSIONS

RandNet is an efficient and effective method that uses a combination of subnetworks trained using both labeled and unlabeled data to classify hESC images.