Predicting Goal-directed Human Attention Using Inverse Reinforcement Learning

Being able to predict human gaze behavior has obvious importance for behavioral vision and for computer vision applications. Most models have mainly focused on predicting free-viewing behavior using saliency maps, but these predictions do not generalize to goal-directed behavior, such as when a person searches for a visual target object. We propose the first inverse reinforcement learning (IRL) model to learn the internal reward function and policy used by humans during visual search. The viewer's internal belief states were modeled as dynamic contextual belief maps of object locations. These maps were learned by IRL and then used to predict behavioral scanpaths for multiple target categories. To train and evaluate our IRL model we created COCO-Search18, which is now the largest dataset of high-quality search fixations in existence. COCO-Search18 has 10 participants searching for each of 18 target-object categories in 6202 images, making about 300,000 goal-directed fixations. When trained and evaluated on COCO-Search18, the IRL model outperformed baseline models in predicting search fixation scanpaths, both in terms of similarity to human search behavior and search efficiency. Finally, reward maps recovered by the IRL model reveal distinctive target-dependent patterns of object prioritization, which we interpret as a learned object context.

Towards Better Opioid Antagonists Using Deep Reinforcement Learning

Naloxone, an opioid antagonist, has been widely used to save lives from opioid overdose, a leading cause for death in the opioid epidemic. However, naloxone has short brain retention ability, which limits its therapeutic efficacy. Developing better opioid antagonists is critical in combating the opioid epidemic.Instead of exhaustively searching in a huge chemical space for better opioid antagonists, we adopt reinforcement learning which allows efficient gradient-based search towards molecules with desired physicochemical and/or biological properties. Specifically, we implement a deep reinforcement learning framework to discover potential lead compounds as better opioid antagonists with enhanced brain retention ability. A customized multi-objective reward function is designed to bias the generation towards molecules with both sufficient opioid antagonistic effect and enhanced brain retention ability. Thorough evaluation demonstrates that with this framework, we are able to identify valid, novel and feasible molecules with multiple desired properties, which has high potential in drug discovery.

Dataset of Segmented Nuclei in Hematoxylin and Eosin Stained Histopathology Images of 10 Cancer Types

The distribution and appearance of nuclei are essential markers for the diagnosis and study of cancer. Despite the importance of nuclear morphology, there is a lack of large scale, accurate, publicly accessible nucleus segmentation data. To address this, we developed an analysis pipeline that segments nuclei in whole slide tissue images from multiple cancer types with a quality control process. We have generated nucleus segmentation results in 5,060 Whole Slide Tissue images from 10 cancer types in The Cancer Genome Atlas. One key component of our work is that we carried out a multi-level quality control process (WSI-level and image patch-level), to evaluate the quality of our segmentation results. The image patch-level quality control used manual segmentation ground truth data from 1,356 sampled image patches. The datasets we publish in this work consist of roughly 5 billion quality controlled nuclei from more than 5,060 TCGA WSIs from 10 different TCGA cancer types and 1,356 manually segmented TCGA image patches from the same 10 cancer types plus additional 4 cancer types.

Self-supervised Deformation Modeling for Facial Expression Editing

Recent advances in deep generative models have demonstrated impressive results in photo-realistic facial image synthesis and editing. Facial expressions are inherently the result of muscle movement. However, existing neural network-based approaches usually only rely on texture generation to edit expressions and largely neglect the motion information. In this work, we propose a novel end-to-end network that disentangles the task of facial editing into two steps: a " "motion-editing" step and a "texture-editing" step. In the "motion-editing" step, we explicitly model facial movement through image deformation, warping the image into the desired expression. In the "texture-editing" step, we generate necessary textures, such as teeth and shading effects, for a photo-realistic result. Our physically-based task-disentanglement system design allows each step to learn a focused task, removing the need of generating texture to hallucinate motion. Our system is trained in a self-supervised manner, requiring no ground truth deformation annotation. Using Action Units [8] as the representation for facial expression, our method improves the state-of-the-art facial expression editing performance in both qualitative and quantitative evaluations.

Exascale Deep Learning to Accelerate Cancer Research

Deep learning, through the use of neural networks, has demonstrated remarkable ability to automate many routine tasks when presented with sufficient data for training. The neural network architecture (e.g. number of layers, types of layers, connections between layers, etc.) plays a critical role in determining what, if anything, the neural network is able to learn from the training data. The trend for neural network architectures, especially those trained on ImageNet, has been to grow ever deeper and more complex. The result has been ever increasing accuracy on benchmark datasets with the cost of increased computational demands. In this paper we demonstrate that neural network architectures can be automatically generated, tailored for a specific application, with dual objectives: accuracy of prediction and speed of prediction. Using MENNDL--an HPC-enabled software stack for neural architecture search--we generate a neural network with comparable accuracy to state-of-the-art networks on a cancer pathology dataset that is also $16\times$ faster at inference. The speedup in inference is necessary because of the volume and velocity of cancer pathology data; specifically, the previous state-of-the-art networks are too slow for individual researchers without access to HPC systems to keep pace with the rate of data generation. Our new model enables researchers with modest computational resources to analyze newly generated data faster than it is collected.

Shadow Removal via Shadow Image Decomposition

We propose a novel deep learning method for shadow removal. Inspired by physical models of shadow formation, we use a linear illumination transformation to model the shadow effects in the image that allows the shadow image to be expressed as a combination of the shadow-free image, the shadow parameters, and a matte layer. We use two deep networks, namely SP-Net and M-Net, to predict the shadow parameters and the shadow matte respectively. This system allows us to remove the shadow effects on the images. We train and test our framework on the most challenging shadow removal dataset (ISTD). Compared to the state-of-the-art method, our model achieves a 40% error reduction in terms of root mean square error (RMSE) for the shadow area, reducing RMSE from 13.3 to 7.9. Moreover, we create an augmented ISTD dataset based on an image decomposition system by modifying the shadow parameters to generate new synthetic shadow images. Training our model on this new augmented ISTD dataset further lowers the RMSE on the shadow area to 7.4.

Learning from Thresholds: Fully Automated Classification of Tumor Infiltrating Lymphocytes for Multiple Cancer Types

Deep learning classifiers for characterization of whole slide tissue morphology require large volumes of annotated data to learn variations across different tissue and cancer types. As is well known, manual generation of digital pathology training data is time consuming and expensive. In this paper, we propose a semi-automated method for annotating a group of similar instances at once, instead of collecting only per-instance manual annotations. This allows for a much larger training set, that reflects visual variability across multiple cancer types and thus training of a single network which can be automatically applied to each cancer type without human adjustment. We apply our method to the important task of classifying Tumor Infiltrating Lymphocytes (TILs) in H&E images. Prior approaches were trained for individual cancer types, with smaller training sets and human-in-the-loop threshold adjustment. We utilize these thresholded results as large scale "semi-automatic" annotations. Combined with existing manual annotations, our trained deep networks are able to automatically produce better TIL prediction results in 12 cancer types, compared to the human-in-the-loop approach.

Topology-Preserving Deep Image Segmentation

Segmentation algorithms are prone to make topological errors on fine-scale structures, e.g., broken connections. We propose a novel method that learns to segment with correct topology. In particular, we design a continuous-valued loss function that enforces a segmentation to have the same topology as the ground truth, i.e., having the same Betti number. The proposed topology-preserving loss function is differentiable and we incorporate it into end-to-end training of a deep neural network. Our method achieves much better performance on the Betti number error, which directly accounts for the topological correctness. It also performs superiorly on other topology-relevant metrics, e.g., the Adjusted Rand Index and the Variation of Information. We illustrate the effectiveness of the proposed method on a broad spectrum of natural and biomedical datasets.

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer

Quantitative assessment of Tumor-TIL spatial relationships is increasingly important in both basic science and clinical aspects of breast cancer research. We have developed and evaluated convolutional neural network (CNN) analysis pipelines to generate combined maps of cancer regions and tumor infiltrating lymphocytes (TILs) in routine diagnostic breast cancer whole slide tissue images (WSIs). We produce interactive whole slide maps that provide 1) insight about the structural patterns and spatial distribution of lymphocytic infiltrates and 2) facilitate improved quantification of TILs. We evaluated both tumor and TIL analyses using three CNN networks - Resnet-34, VGG16 and Inception v4, and demonstrated that the results compared favorably to those obtained by what believe are the best published methods. We have produced open-source tools and generated a public dataset consisting of tumor/TIL maps for 1,015 TCGA breast cancer images. We also present a customized web-based interface that enables easy visualization and interactive exploration of high-resolution combined Tumor-TIL maps for 1,015TCGA invasive breast cancer cases that can be downloaded for further downstream analyses.