RFC-Net: Learning High Resolution Global Features for Medical Image Segmentation on a Computational Budget

Learning High-Resolution representations is essential for semantic segmentation. Convolutional neural network (CNN)architectures with downstream and upstream propagation flow are popular for segmentation in medical diagnosis. However, due to performing spatial downsampling and upsampling in multiple stages, information loss is inexorable. On the contrary, connecting layers densely on high spatial resolution is computationally expensive. In this work, we devise a Loose Dense Connection Strategy to connect neurons in subsequent layers with reduced parameters. On top of that, using a m-way Tree structure for feature propagation we propose Receptive Field Chain Network (RFC-Net) that learns high resolution global features on a compressed computational space. Our experiments demonstrates that RFC-Net achieves state-of-the-art performance on Kvasir and CVC-ClinicDB benchmarks for Polyp segmentation.

Semi-supervised Contrastive Outlier removal for Pseudo Expectation Maximization (SCOPE)

Semi-supervised learning is the problem of training an accurate predictive model by combining a small labeled dataset with a presumably much larger unlabeled dataset. Many methods for semi-supervised deep learning have been developed, including pseudolabeling, consistency regularization, and contrastive learning techniques. Pseudolabeling methods however are highly susceptible to confounding, in which erroneous pseudolabels are assumed to be true labels in early iterations, thereby causing the model to reinforce its prior biases and thereby fail to generalize to strong predictive performance. We present a new approach to suppress confounding errors through a method we describe as Semi-supervised Contrastive Outlier removal for Pseudo Expectation Maximization (SCOPE). Like basic pseudolabeling, SCOPE is related to Expectation Maximization (EM), a latent variable framework which can be extended toward understanding cluster-assumption deep semi-supervised algorithms. However, unlike basic pseudolabeling which fails to adequately take into account the probability of the unlabeled samples given the model, SCOPE introduces an outlier suppression term designed to improve the behavior of EM iteration given a discrimination DNN backbone in the presence of outliers. Our results show that SCOPE greatly improves semi-supervised classification accuracy over a baseline, and furthermore when combined with consistency regularization achieves the highest reported accuracy for the semi-supervised CIFAR-10 classification task using 250 and 4000 labeled samples. Moreover, we show that SCOPE reduces the prevalence of confounding errors during pseudolabeling iterations by pruning erroneous high-confidence pseudolabeled samples that would otherwise contaminate the labeled set in subsequent retraining iterations.

Mitigating domain shift in AI-based tuberculosis screening with unsupervised domain adaptation

We demonstrate that Domain Invariant Feature Learning (DIFL) can improve the out-of-domain generalizability of a deep learning Tuberculosis screening algorithm. It is well known that state of the art deep learning algorithms often have difficulty generalizing to unseen data distributions due to "domain shift". In the context of medical imaging, this could lead to unintended biases such as the inability to generalize from one patient population to another. We analyze the performance of a ResNet-50 classifier for the purposes of Tuberculosis screening using the four most popular public datasets with geographically diverse sources of imagery. We show that without domain adaptation, ResNet-50 has difficulty in generalizing between imaging distributions from a number of public Tuberculosis screening datasets with imagery from geographically distributed regions. However, with the incorporation of DIFL, the out-of-domain performance is greatly enhanced. Analysis criteria includes a comparison of accuracy, sensitivity, specificity and AUC over both the baseline, as well as the DIFL enhanced algorithms. We conclude that DIFL improves generalizability of Tuberculosis screening while maintaining acceptable accuracy over the source domain imagery when applied across a variety of public datasets.

CCS-GAN: COVID-19 CT-scan classification with very few positive training images

We present a novel algorithm that is able to classify COVID-19 pneumonia from CT Scan slices using a very small sample of training images exhibiting COVID-19 pneumonia in tandem with a larger number of normal images. This algorithm is able to achieve high classification accuracy using as few as 10 positive training slices (from 10 positive cases), which to the best of our knowledge is one order of magnitude fewer than the next closest published work at the time of writing. Deep learning with extremely small positive training volumes is a very difficult problem and has been an important topic during the COVID-19 pandemic, because for quite some time it was difficult to obtain large volumes of COVID-19 positive images for training. Algorithms that can learn to screen for diseases using few examples are an important area of research. We present the Cycle Consistent Segmentation Generative Adversarial Network (CCS-GAN). CCS-GAN combines style transfer with pulmonary segmentation and relevant transfer learning from negative images in order to create a larger volume of synthetic positive images for the purposes of improving diagnostic classification performance. The performance of a VGG-19 classifier plus CCS-GAN was trained using a small sample of positive image slices ranging from at most 50 down to as few as 10 COVID-19 positive CT-scan images. CCS-GAN achieves high accuracy with few positive images and thereby greatly reduces the barrier of acquiring large training volumes in order to train a diagnostic classifier for COVID-19.

Person Re-Identification with a Locally Aware Transformer

Person Re-Identification is an important problem in computer vision-based surveillance applications, in which the same person is attempted to be identified from surveillance photographs in a variety of nearby zones. At present, the majority of Person re-ID techniques are based on Convolutional Neural Networks (CNNs), but Vision Transformers are beginning to displace pure CNNs for a variety of object recognition tasks. The primary output of a vision transformer is a global classification token, but vision transformers also yield local tokens which contain additional information about local regions of the image. Techniques to make use of these local tokens to improve classification accuracy are an active area of research. We propose a novel Locally Aware Transformer (LA-Transformer) that employs a Parts-based Convolution Baseline (PCB)-inspired strategy for aggregating globally enhanced local classification tokens into an ensemble of $\sqrt{N}$ classifiers, where $N$ is the number of patches. An additional novelty is that we incorporate blockwise fine-tuning which further improves re-ID accuracy. LA-Transformer with blockwise fine-tuning achieves rank-1 accuracy of $98.27 \%$ with standard deviation of $0.13$ on the Market-1501 and $98.7\%$ with standard deviation of $0.2$ on the CUHK03 dataset respectively, outperforming all other state-of-the-art published methods at the time of writing.

Toward Generating Synthetic CT Volumes using a 3D-Conditional Generative Adversarial Network

We present a novel conditional Generative Adversarial Network (cGAN) architecture that is capable of generating 3D Computed Tomography scans in voxels from noisy and/or pixelated approximations and with the potential to generate full synthetic 3D scan volumes. We believe conditional cGAN to be a tractable approach to generate 3D CT volumes, even though the problem of generating full resolution deep fakes is presently impractical due to GPU memory limitations. We present results for autoencoder, denoising, and depixelating tasks which are trained and tested on two novel COVID19 CT datasets. Our evaluation metrics, Peak Signal to Noise ratio (PSNR) range from 12.53 - 46.46 dB, and the Structural Similarity index ( SSIM) range from 0.89 to 1.

Deep Expectation-Maximization for Semi-Supervised Lung Cancer Screening

We present a semi-supervised algorithm for lung cancer screening in which a 3D Convolutional Neural Network (CNN) is trained using the Expectation-Maximization (EM) meta-algorithm. Semi-supervised learning allows a smaller labelled data-set to be combined with an unlabeled data-set in order to provide a larger and more diverse training sample. EM allows the algorithm to simultaneously calculate a maximum likelihood estimate of the CNN training coefficients along with the labels for the unlabeled training set which are defined as a latent variable space. We evaluate the model performance of the Semi-Supervised EM algorithm for CNNs through cross-domain training of the Kaggle Data Science Bowl 2017 (Kaggle17) data-set with the National Lung Screening Trial (NLST) data-set. Our results show that the Semi-Supervised EM algorithm greatly improves the classification accuracy of the cross-domain lung cancer screening, although results are lower than a fully supervised approach with the advantage of additional labelled data from the unsupervised sample. As such, we demonstrate that Semi-Supervised EM is a valuable technique to improve the accuracy of lung cancer screening models using 3D CNNs.

Generating Realistic COVID19 X-rays with a Mean Teacher + Transfer Learning GAN

COVID-19 is a novel infectious disease responsible for over 800K deaths worldwide as of August 2020. The need for rapid testing is a high priority and alternative testing strategies including X-ray image classification are a promising area of research. However, at present, public datasets for COVID19 x-ray images have low data volumes, making it challenging to develop accurate image classifiers. Several recent papers have made use of Generative Adversarial Networks (GANs) in order to increase the training data volumes. But realistic synthetic COVID19 X-rays remain challenging to generate. We present a novel Mean Teacher + Transfer GAN (MTT-GAN) that generates COVID19 chest X-ray images of high quality. In order to create a more accurate GAN, we employ transfer learning from the Kaggle Pneumonia X-Ray dataset, a highly relevant data source orders of magnitude larger than public COVID19 datasets. Furthermore, we employ the Mean Teacher algorithm as a constraint to improve stability of training. Our qualitative analysis shows that the MTT-GAN generates X-ray images that are greatly superior to a baseline GAN and visually comparable to real X-rays. Although board-certified radiologists can distinguish MTT-GAN fakes from real COVID19 X-rays. Quantitative analysis shows that MTT-GAN greatly improves the accuracy of both a binary COVID19 classifier as well as a multi-class Pneumonia classifier as compared to a baseline GAN. Our classification accuracy is favourable as compared to recently reported results in the literature for similar binary and multi-class COVID19 screening tasks.