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1. Weakly Supervised Deep Nuclei Segmentation using Points Annotation in Histopathology Images

   Qu, H ; Wu, P. ; Huang, Q. ; Yi, J. ; Riedlinger, G. M. ; De, S. ; Metaxas, D. ( July 2019 , Proceedings of Machine Learning Research)

   Nuclei segmentation is a fundamental task in histopathological image analysis. Typically, such segmentation tasks require significant effort to manually generate pixel-wise annotations for fully supervised training. To alleviate the manual effort, in this paper we propose a novel approach using points only annotation. Two types of coarse labels with complementary information are derived from the points annotation, and are then utilized to train a deep neural network. The fully- connected conditional random field loss is utilized to further refine the model without introducing extra computational complexity during inference. Experimental results on two nuclei segmentation datasets reveal that the proposed methodmore »is able to achieve competitive performance compared to the fully supervised counterpart and the state-of-the-art methods while requiring significantly less annotation effort. Our code is publicly available.« less
2. Self-supervised Feature Learning by Cross-modality and Cross-view Correspondences

   Jing, L ; Zhang, L ; Tian, Y ( June 2021 , The 4th Multimodal Learning and Applications (MULA) Workshop in conjunction with CVPR 2021)

   The success of supervised learning requires large-scale ground truth labels which are very expensive, time- consuming, or may need special skills to annotate. To address this issue, many self- or un-supervised methods are developed. Unlike most existing self-supervised methods to learn only 2D image features or only 3D point cloud features, this paper presents a novel and effective self-supervised learning approach to jointly learn both 2D image features and 3D point cloud features by exploiting cross-modality and cross-view correspondences without using any human annotated labels. Specifically, 2D image features of rendered images from different views are extracted by a 2Dmore »convolutional neural network, and 3D point cloud features are extracted by a graph convolution neural network. Two types of features are fed into a two-layer fully connected neural network to estimate the cross-modality correspondence. The three networks are jointly trained (i.e. cross-modality) by verifying whether two sampled data of different modalities belong to the same object, meanwhile, the 2D convolutional neural network is additionally optimized through minimizing intra-object distance while maximizing inter-object distance of rendered images in different views (i.e. cross-view). The effectiveness of the learned 2D and 3D features is evaluated by transferring them on five different tasks including multi-view 2D shape recognition, 3D shape recognition, multi-view 2D shape retrieval, 3D shape retrieval, and 3D part-segmentation. Extensive evaluations on all the five different tasks across different datasets demonstrate strong generalization and effectiveness of the learned 2D and 3D features by the proposed self-supervised method.« less
3. Narrow Band Active Contour Attention Model for Medical Segmentation

   https://doi.org/10.3390/diagnostics11081393  

   Le, Ngan ; Bui, Toan ; Vo-Ho, Viet-Khoa ; Yamazaki, Kashu ; Luu, Khoa ( August 2021 , Diagnostics)

   Medical image segmentation is one of the most challenging tasks in medical image analysis and widely developed for many clinical applications. While deep learning-based approaches have achieved impressive performance in semantic segmentation, they are limited to pixel-wise settings with imbalanced-class data problems and weak boundary object segmentation in medical images. In this paper, we tackle those limitations by developing a new two-branch deep network architecture which takes both higher level features and lower level features into account. The first branch extracts higher level feature as region information by a common encoder-decoder network structure such as Unet and FCN, whereas themore »second branch focuses on lower level features as support information around the boundary and processes in parallel to the first branch. Our key contribution is the second branch named Narrow Band Active Contour (NB-AC) attention model which treats the object contour as a hyperplane and all data inside a narrow band as support information that influences the position and orientation of the hyperplane. Our proposed NB-AC attention model incorporates the contour length with the region energy involving a fixed-width band around the curve or surface. The proposed network loss contains two fitting terms: (i) a high level feature (i.e., region) fitting term from the first branch; (ii) a lower level feature (i.e., contour) fitting term from the second branch including the (ii1) length of the object contour and (ii2) regional energy functional formed by the homogeneity criterion of both the inner band and outer band neighboring the evolving curve or surface. The proposed NB-AC loss can be incorporated into both 2D and 3D deep network architectures. The proposed network has been evaluated on different challenging medical image datasets, including DRIVE, iSeg17, MRBrainS18 and Brats18. The experimental results have shown that the proposed NB-AC loss outperforms other mainstream loss functions: Cross Entropy, Dice, Focal on two common segmentation frameworks Unet and FCN. Our 3D network which is built upon the proposed NB-AC loss and 3DUnet framework achieved state-of-the-art results on multiple volumetric datasets.« less
4. A Functional Approach to Rotation Equivariant Non-Linearities for Tensor Field Networks

   Poulenard, Adrien ; Guibas, Leonidas ( January 2021 , Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition)

   Learning pose invariant representation is a fundamental problem in shape analysis. Most existing deep learning algorithms for 3D shape analysis are not robust to rotations and are often trained on synthetic datasets consisting of pre-aligned shapes, yielding poor generalization to unseen poses. This observation motivates a growing interest in rotation invariant and equivariant methods. The field of rotation equivariant deep learning is developing in recent years thanks to a well established theory of Lie group representations and convolutions. A fundamental problem in equivariant deep learning is to design activation functions which are both informative and preserve equivariance. The recently introducedmore »Tensor Field Network (TFN) framework provides a rotation equivariant network design for point cloud analysis. TFN features undergo a rotation in feature space given a rotation of the input pointcloud. TFN and similar designs consider nonlinearities which operate only over rotation invariant features such as the norm of equivariant features to preserve equivariance, making them unable to capture the directional information. In a recent work entitled "Gauge Equivariant Mesh CNNs: Anisotropic Convolutions on Geometric Graphs" Hann et al. interpret 2D rotation equivariant features as Fourier coefficients of functions on the circle. In this work we transpose the idea of Hann et al. to 3D by interpreting TFN features as spherical harmonics coefficients of functions on the sphere. We introduce a new equivariant nonlinearity and pooling for TFN. We show improvments over the original TFN design and other equivariant nonlinearities in classification and segmentation tasks. Furthermore our method is competitive with state of the art rotation invariant methods in some instances.« less
5. EDLT: Enabling Deep Learning for Generic Data Classification

   https://doi.org/10.1109/ICDM.2018.00030  

   Han, Huimei ; Zhu, Xingquan ; Li, Ying ( November 2018 , Proc. of the 18th IEEE International Conference on Data Mining (ICDM- 2018))

   This paper proposes to enable deep learning for generic machine learning tasks. Our goal is to allow deep learning to be applied to data which are already represented in instance feature tabular format for a better classification accuracy. Because deep learning relies on spatial/temporal correlation to learn new feature representation, our theme is to convert each instance of the original dataset into a synthetic matrix format to take the full advantage of the feature learning power of deep learning methods. To maximize the correlation of the matrix , we use 0/1 optimization to reorder features such that the ones withmore »strong correlations are adjacent to each other. By using a two dimensional feature reordering, we are able to create a synthetic matrix, as an image, to represent each instance. Because the synthetic image preserves the original feature values and data correlation, existing deep learning algorithms, such as convolutional neural networks (CNN), can be applied to learn effective features for classification. Our experiments on 20 generic datasets, using CNN as the deep learning classifier, confirm that enabling deep learning to generic datasets has clear performance gain, compared to generic machine learning methods. In addition, the proposed method consistently outperforms simple baselines of using CNN for generic dataset. As a result, our research allows deep learning to be broadly applied to generic datasets for learning and classification« less