Jun Kong

George Teodoro, Tony Pan, Tahsin M. Kurc et al.

We propose, implement, and experimentally evaluate a runtime middleware to support high-throughput execution on hybrid cluster machines of large-scale analysis applications. A hybrid cluster machine consists of computation nodes which have multiple CPUs and general purpose graphics processing units (GPUs). Our work targets scientific analysis applications in which datasets are processed in application-specific data chunks, and the processing of a data chunk is expressed as a hierarchical pipeline of operations. The proposed middleware system combines a bag-of-tasks style execution with coarse-grain dataflow execution. Data chunks and associated data processing pipelines are scheduled across cluster nodes using a demand driven approach, while within a node operations in a given pipeline instance are scheduled across CPUs and GPUs. The runtime system implements several optimizations, including performance aware task scheduling, architecture aware process placement, data locality conscious task assignment, and data prefetching and asynchronous data copy, to maximize utilization of the aggregate computing power of CPUs and GPUs and minimize data copy overheads. The application and performance benefits of the runtime middleware are demonstrated using an image analysis application, which is employed in a brain cancer study, on a state-of-the-art hybrid cluster in which each node has two 6-core CPUs and three GPUs. Our results show that implementing and scheduling application data processing as a set of fine-grain operations provide more opportunities for runtime optimizations and attain better performance than a coarser-grain, monolithic implementation. The proposed runtime system can achieve high-throughput processing of large datasets - we were able to process an image dataset consisting of 36,848 4Kx4K-pixel image tiles at about 150 tiles/second rate on 100 nodes.

Yanni Zhang, Qiang Li, Miao Qi et al.

Image deblurring aims to restore the detailed texture information or structures from blurry images, which has become an indispensable step in many computer vision tasks. Although various methods have been proposed to deal with the image deblurring problem, most of them treated the blurry image as a whole and neglected the characteristics of different image frequencies. In this paper, we present a new method called multi-scale frequency separation network (MSFS-Net) for image deblurring. MSFS-Net introduces the frequency separation module (FSM) into an encoder-decoder network architecture to capture the low- and high-frequency information of image at multiple scales. Then, a cycle-consistency strategy and a contrastive learning module (CLM) are respectively designed to retain the low-frequency information and recover the high-frequency information during deblurring. At last, the features of different scales are fused by a cross-scale feature fusion module (CSFFM). Extensive experiments on benchmark datasets show that the proposed network achieves state-of-the-art performance.

Dongpo Xu, Jinlan Liu, Yinghua Lu et al.

The stochastic momentum method is a commonly used acceleration technique for solving large-scale stochastic optimization problems in artificial neural networks. Current convergence results of stochastic momentum methods under non-convex stochastic settings mostly discuss convergence in terms of the random output and minimum output. To this end, we address the convergence of the last iterate output (called last-iterate convergence) of the stochastic momentum methods for non-convex stochastic optimization problems, in a way conformal with traditional optimization theory. We prove the last-iterate convergence of the stochastic momentum methods under a unified framework, covering both stochastic heavy ball momentum and stochastic Nesterov accelerated gradient momentum. The momentum factors can be fixed to be constant, rather than time-varying coefficients in existing analyses. Finally, the last-iterate convergence of the stochastic momentum methods is verified on the benchmark MNIST and CIFAR-10 datasets.

Xiaoyuan Guo, Fusheng Wang, George Teodorou et al.

Liver steatosis is known as the abnormal accumulation of lipids within cells. An accurate quantification of steatosis area within the liver histopathological microscopy images plays an important role in liver disease diagnosis and trans-plantation assessment. Such a quantification analysis often requires a precise steatosis segmentation that is challenging due to abundant presence of highly overlapped steatosis droplets. In this paper, a deep learning model Mask-RCNN is used to segment the steatosis droplets in clumps. Extended from Faster R-CNN, Mask-RCNN can predict object masks in addition to bounding box detection. With transfer learning, the resulting model is able to segment overlapped steatosis regions at 75.87% by Average Precision, 60.66% by Recall,65.88% by F1-score, and 76.97% by Jaccard index, promising to support liver disease diagnosis and allograft rejection prediction in future clinical practice.

Xiaoyuan Guo, Hanyi Yu, Blair Rossetti et al.

Highly clumped nuclei clusters captured in fluorescence in situ hybridization microscopy images are common histology entities under investigations in a wide spectrum of tissue-related biomedical investigations. Due to their large scale in presence, computer based image analysis is used to facilitate such analysis with improved analysis efficiency and reproducibility. To ensure the quality of downstream biomedical analyses, it is essential to segment clustered nuclei with high quality. However, this presents a technical challenge commonly encountered in a large number of biomedical research, as nuclei are often overlapped due to a high cell density. In this paper, we propose an segmentation algorithm that identifies point pair connection candidates and evaluates adjacent point connections with a formulated ellipse fitting quality indicator. After connection relationships are determined, we recover the resulting dividing paths by following points with specific eigenvalues from Hessian in a constrained searching space. We validate our algorithm with 560 image patches from two classes of tumor regions of seven brain tumor patients. Both qualitative and quantitative experimental results suggest that our algorithm is promising for dividing overlapped nuclei in fluorescence in situ hybridization microscopy images widely used in various biomedical research.

Mousumi Roy, Fusheng Wang, George Teodoro et al.

Cellular phenotypic features derived from histopathology images are the basis of pathologic diagnosis and are thought to be related to underlying molecular profiles. Due to overwhelming cell numbers and population heterogeneity, it remains challenging to quantitatively compute and compare features of cells with distinct molecular signatures. In this study, we propose a self-reliant and efficient analysis framework that supports quantitative analysis of cellular phenotypic difference across distinct molecular groups. To demonstrate efficacy, we quantitatively analyze astrocytomas that are molecularly characterized as either Isocitrate Dehydrogenase (IDH) mutant (MUT) or wildtype (WT) using imaging data from The Cancer Genome Atlas database. Representative cell instances that are phenotypically different between these two groups are retrieved after segmentation, feature computation, data pruning, dimensionality reduction, and unsupervised clustering. Our analysis is generic and can be applied to a wide set of cell-based biomedical research.

Mousumi Roy, Fusheng Wang, George Teodoro et al.

An accurate steatosis quantification with pathology tissue samples is of high clinical importance. However, such pathology measurement is manually made in most clinical practices, subject to severe reader variability due to large sampling bias and poor reproducibility. Although some computerized automated methods are developed to quantify the steatosis regions, they present limited analysis capacity for high resolution whole-slide microscopy images and accurate overlapped steatosis division. In this paper, we propose a method that extracts an individual whole tissue piece at high resolution with minimum background area by estimating tissue bounding box and rotation angle. This is followed by the segmentation and segregation of steatosis regions with high curvature point detection and an ellipse fitting quality assessment method. We validate our method with isolated and overlapped steatosis regions in liver tissue images of 11 patients. The experimental results suggest that our method is promising for enhanced support of steatosis quantization during the pathology review for liver disease treatment.