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byAK and the research community

Mar 11

Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

H-DenseUNet: Hybrid Densely Connected UNet for Liver and Tumor Segmentation from CT Volumes

Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We formulate the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge and 3DIRCADb Dataset. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model.

An Energy and GPU-Computation Efficient Backbone Network for Real-Time Object Detection

As DenseNet conserves intermediate features with diverse receptive fields by aggregating them with dense connection, it shows good performance on the object detection task. Although feature reuse enables DenseNet to produce strong features with a small number of model parameters and FLOPs, the detector with DenseNet backbone shows rather slow speed and low energy efficiency. We find the linearly increasing input channel by dense connection leads to heavy memory access cost, which causes computation overhead and more energy consumption. To solve the inefficiency of DenseNet, we propose an energy and computation efficient architecture called VoVNet comprised of One-Shot Aggregation (OSA). The OSA not only adopts the strength of DenseNet that represents diversified features with multi receptive fields but also overcomes the inefficiency of dense connection by aggregating all features only once in the last feature maps. To validate the effectiveness of VoVNet as a backbone network, we design both lightweight and large-scale VoVNet and apply them to one-stage and two-stage object detectors. Our VoVNet based detectors outperform DenseNet based ones with 2x faster speed and the energy consumptions are reduced by 1.6x - 4.1x. In addition to DenseNet, VoVNet also outperforms widely used ResNet backbone with faster speed and better energy efficiency. In particular, the small object detection performance has been significantly improved over DenseNet and ResNet.