Triplet-Net Classification of Contiguous Stem Cell Microscopy Images.

Cellular microscopy imaging is a common form of data acquisition for biological experimentation. Observation of gray-level morphological features allows for the inference of useful biological information such as cellular health and growth status. Cellular colonies can contain multiple cell types, making colony level classification very difficult. Additionally, cell types growing in a hierarchical, downstream fashion, can often look visually similar, although biologically distinct. In this paper, it is determined empirically that traditional deep Convolutional Neural Networks (CNN) and classical object recognition techniques are not sufficient to distinguish between these subtle visual differences, resulting in misclassifications. Instead, Triplet-net CNN learning is employed in a hierarchical classification scheme to improve the ability of the model to discern distinct, fine-grain features of two commonly confused morphological image-patch classes, namely Dense and Spread colonies. The Triplet-net method improves classification accuracy over a four-class deep neural network by  âˆ¼  3 %, a value that was determined to be statistically significant, as well as existing state-of-the-art image patch classification approaches and standard template matching. These findings allow for the accurate classification of multi-class cell colonies with contiguous boundaries, and increased reliability and efficiency of automated, high-throughput experimental quantification using non-invasive microscopy.

Privacy Preserving Defense For Black Box Classifiers Against On-Line Adversarial Attacks.

Deep learning models have been shown to be vulnerable to adversarial attacks. Adversarial attacks are imperceptible perturbations added to an image such that the deep learning model misclassifies the image with a high confidence. Existing adversarial defenses validate their performance using only the classification accuracy. However, classification accuracy by itself is not a reliable metric to determine if the resulting image is "adversarial-free". This is a foundational problem for online image recognition applications where the ground-truth of the incoming image is not known and hence we cannot compute the accuracy of the classifier or validate if the image is "adversarial-free" or not. This paper proposes a novel privacy preserving framework for defending Black box classifiers from adversarial attacks using an ensemble of iterative adversarial image purifiers whose performance is continuously validated in a loop using Bayesian uncertainties. The proposed approach can convert a single-step black box adversarial defense into an iterative defense and proposes three novel privacy preserving Knowledge Distillation (KD) approaches that use prior meta-information from various datasets to mimic the performance of the Black box classifier. Additionally, this paper proves the existence of an optimal distribution for the purified images that can reach a theoretical lower bound, beyond which the image can no longer be purified. Experimental results on six public benchmark datasets namely: 1) Fashion-MNIST, 2) CIFAR-10, 3) GTSRB, 4) MIO-TCD, 5) Tiny-ImageNet, and 6) MS-Celeb show that the proposed approach can consistently detect adversarial examples and purify or reject them against a variety of adversarial attacks.

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.

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

Human embryonic stem cells (hESC), derived from the blastocysts, provide unique cellular models for numerous potential applications. They have great promise in the treatment of diseases such as Parkinson's, Huntington's, diabetes mellitus, etc. hESC are a reliable developmental model for early embryonic growth because of their ability to divide indefinitely (pluripotency), and differentiate, or functionally change, into any adult cell type. Their adaptation to toxicological studies is particularly attractive as pluripotent stem cells can be used to model various stages of prenatal development. Automated detection and classification of human embryonic stem cell in videos is of great interest among biologists for quantified analysis of various states of hESC in experimental work. Currently video annotation is done by hand, a process which is very time consuming and exhaustive. To solve this problem, this paper introduces DeephESC 2.0 an automated machine learning approach consisting of two parts: (a) Generative Multi Adversarial Networks (GMAN) for generating synthetic images of hESC, (b) a hierarchical classification system consisting of Convolution Neural Networks (CNN) and Triplet CNNs to classify phase contrast hESC images into six different classes namely: Cell clusters, Debris, Unattached cells, Attached cells, Dynamically Blebbing cells and Apoptically Blebbing cells. The approach is totally non-invasive and does not require any chemical or staining of hESC. DeephESC 2.0 is able to classify hESC images with an accuracy of 93.23% out performing state-of-the-art approaches by at least 20%. Furthermore, DeephESC 2.0 is able to generate large number of synthetic images which can be used for augmenting the dataset. Experimental results show that training DeephESC 2.0 exclusively on a large amount of synthetic images helps to improve the performance of the classifier on original images from 93.23% to 94.46%. This paper also evaluates the quality of the generated synthetic images using the Structural SIMilarity (SSIM) index, Peak Signal to Noise ratio (PSNR) and statistical p-value metrics and compares them with state-of-the-art approaches for generating synthetic images. DeephESC 2.0 saves hundreds of hours of manual labor which would otherwise be spent on manually/semi-manually annotating more and more videos.