SPDA: Superpixel-based Data Augmentation for Biomedical Image Segmentation

Supervised training a deep neural network aims to "teach" the network to mimic human visual perception that is represented by image-and-label pairs in the training data. Superpixelized (SP) images are visually perceivable to humans, but a conventionally trained deep learning model often performs poorly when working on SP images. To better mimic human visual perception, we think it is desirable for the deep learning model to be able to perceive not only raw images but also SP images. In this paper, we propose a new superpixel-based data augmentation (SPDA) method for training deep learning models for biomedical image segmentation. Our method applies a superpixel generation scheme to all the original training images to generate superpixelized images. The SP images thus obtained are then jointly used with the original training images to train a deep learning model. Our experiments of SPDA on four biomedical image datasets show that SPDA is effective and can consistently improve the performance of state-of-the-art fully convolutional networks for biomedical image segmentation in 2D and 3D images. Additional studies also demonstrate that SPDA can practically reduce the generalization gap.

Reducing Uncertainty in Undersampled MRI Reconstruction with Active Acquisition

The goal of MRI reconstruction is to restore a high fidelity image from partially observed measurements. This partial view naturally induces reconstruction uncertainty that can only be reduced by acquiring additional measurements. In this paper, we present a novel method for MRI reconstruction that, at inference time, dynamically selects the measurements to take and iteratively refines the prediction in order to best reduce the reconstruction error and, thus, its uncertainty. We validate our method on a large scale knee MRI dataset, as well as on ImageNet. Results show that (1) our system successfully outperforms active acquisition baselines; (2) our uncertainty estimates correlate with error maps; and (3) our ResNet-based architecture surpasses standard pixel-to-pixel models in the task of MRI reconstruction. The proposed method not only shows high-quality reconstructions but also paves the road towards more applicable solutions for accelerating MRI.

Squared English Word: A Method of Generating Glyph to Use Super Characters for Sentiment Analysis

The Super Characters method addresses sentiment analysis problems by first converting the input text into images and then applying 2D-CNN models to classify the sentiment. It achieves state of the art performance on many benchmark datasets. However, it is not as straightforward to apply in Latin languages as in Asian languages. Because the 2D-CNN model is designed to recognize two-dimensional images, it is better if the inputs are in the form of glyphs. In this paper, we propose SEW (Squared English Word) method generating a squared glyph for each English word by drawing Super Characters images of each English word at the alphabet level, combining the squared glyph together into a whole Super Characters image at the sentence level, and then applying the CNN model to classify the sentiment within the sentence. We applied the SEW method to Wikipedia dataset and obtained a 2.1% accuracy gain compared to the original Super Characters method. In the CL-Aff shared task on the HappyDB dataset, we applied Super Characters with SEW method and obtained 86.9% accuracy for agency classification and 85.8% for social accuracy classification on the validation set based on 80%:20% random split on the given labeled dataset.

Cascade Decoder: A Universal Decoding Method for Biomedical Image Segmentation

The Encoder-Decoder architecture is a main stream deep learning model for biomedical image segmentation. The encoder fully compresses the input and generates encoded features, and the decoder then produces dense predictions using encoded features. However, decoders are still under-explored in such architectures. In this paper, we comprehensively study the state-of-the-art Encoder-Decoder architectures, and propose a new universal decoder, called cascade decoder, to improve semantic segmentation accuracy. Our cascade decoder can be embedded into existing networks and trained altogether in an end-to-end fashion. The cascade decoder structure aims to conduct more effective decoding of hierarchically encoded features and is more compatible with common encoders than the known decoders. We replace the decoders of state-of-the-art models with our cascade decoder for several challenging biomedical image segmentation tasks, and the considerable improvements achieved demonstrate the efficacy of our new decoding method.

A New Ensemble Learning Framework for 3D Biomedical Image Segmentation

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.

Super Characters: A Conversion from Sentiment Classification to Image Classification

We propose a method named Super Characters for sentiment classification. This method converts the sentiment classification problem into image classification problem by projecting texts into images and then applying CNN models for classification. Text features are extracted automatically from the generated Super Characters images, hence there is no need of any explicit step of embedding the words or characters into numerical vector representations. Experimental results on large social media corpus show that the Super Characters method consistently outperforms other methods for sentiment classification and topic classification tasks on ten large social media datasets of millions of contents in four different languages, including Chinese, Japanese, Korean and English.

Dimensionality Reduction for Stationary Time Series via Stochastic Nonconvex Optimization

Stochastic optimization naturally arises in machine learning. Efficient algorithms with provable guarantees, however, are still largely missing, when the objective function is nonconvex and the data points are dependent. This paper studies this fundamental challenge through a streaming PCA problem for stationary time series data. Specifically, our goal is to estimate the principle component of time series data with respect to the covariance matrix of the stationary distribution. Computationally, we propose a variant of Oja's algorithm combined with downsampling to control the bias of the stochastic gradient caused by the data dependency. Theoretically, we quantify the uncertainty of our proposed stochastic algorithm based on diffusion approximations. This allows us to prove the asymptotic rate of convergence and further implies near optimal asymptotic sample complexity. Numerical experiments are provided to support our analysis.

ConvPath: A Software Tool for Lung Adenocarcinoma Digital Pathological Image Analysis Aided by Convolutional Neural Network

The spatial distributions of different types of cells could reveal a cancer cell growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key hallmarks of cancer. However, manually recognizing and localizing all the cells in pathology slides are almost impossible. In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor, stromal and lymphocytes classification, and extraction of tumor microenvironment related features for lung cancer pathology images. The overall classification accuracy is 92.9% and 90.1% in training and independent testing datasets, respectively. By identifying cells and classifying cell types, this pipeline can convert a pathology image into a spatial map of tumor, stromal and lymphocyte cells. From this spatial map, we can extracted features that characterize the tumor micro-environment. Based on these features, we developed an image feature-based prognostic model and validated the model in two independent cohorts. The predicted risk group serves as an independent prognostic factor, after adjusting for clinical variables that include age, gender, smoking status, and stage.

CT Image Enhancement Using Stacked Generative Adversarial Networks and Transfer Learning for Lesion Segmentation Improvement

Automated lesion segmentation from computed tomography (CT) is an important and challenging task in medical image analysis. While many advancements have been made, there is room for continued improvements. One hurdle is that CT images can exhibit high noise and low contrast, particularly in lower dosages. To address this, we focus on a preprocessing method for CT images that uses stacked generative adversarial networks (SGAN) approach. The first GAN reduces the noise in the CT image and the second GAN generates a higher resolution image with enhanced boundaries and high contrast. To make up for the absence of high quality CT images, we detail how to synthesize a large number of low- and high-quality natural images and use transfer learning with progressively larger amounts of CT images. We apply both the classic GrabCut method and the modern holistically nested network (HNN) to lesion segmentation, testing whether SGAN can yield improved lesion segmentation. Experimental results on the DeepLesion dataset demonstrate that the SGAN enhancements alone can push GrabCut performance over HNN trained on original images. We also demonstrate that HNN + SGAN performs best compared against four other enhancement methods, including when using only a single GAN.

Iterative Attention Mining for Weakly Supervised Thoracic Disease Pattern Localization in Chest X-Rays

Given image labels as the only supervisory signal, we focus on harvesting, or mining, thoracic disease localizations from chest X-ray images. Harvesting such localizations from existing datasets allows for the creation of improved data sources for computer-aided diagnosis and retrospective analyses. We train a convolutional neural network (CNN) for image classification and propose an attention mining (AM) strategy to improve the model's sensitivity or saliency to disease patterns. The intuition of AM is that once the most salient disease area is blocked or hidden from the CNN model, it will pay attention to alternative image regions, while still attempting to make correct predictions. However, the model requires to be properly constrained during AM, otherwise, it may overfit to uncorrelated image parts and forget the valuable knowledge that it has learned from the original image classification task. To alleviate such side effects, we then design a knowledge preservation (KP) loss, which minimizes the discrepancy between responses for X-ray images from the original and the updated networks. Furthermore, we modify the CNN model to include multi-scale aggregation (MSA), improving its localization ability on small-scale disease findings, e.g., lung nodules. We experimentally validate our method on the publicly-available ChestX-ray14 dataset, outperforming a class activation map (CAM)-based approach, and demonstrating the value of our novel framework for mining disease locations.