Manisha Verma

Liangzhi Li, Manisha Verma, Bowen Wang et al.

The status of retinal arteriovenous crossing is of great significance for clinical evaluation of arteriolosclerosis and systemic hypertension. As an ophthalmology diagnostic criteria, Scheie's classification has been used to grade the severity of arteriolosclerosis. In this paper, we propose a deep learning approach to support the diagnosis process, which, to the best of our knowledge, is one of the earliest attempts in medical imaging. The proposed pipeline is three-fold. First, we adopt segmentation and classification models to automatically obtain vessels in a retinal image with the corresponding artery/vein labels and find candidate arteriovenous crossing points. Second, we use a classification model to validate the true crossing point. At last, the grade of severity for the vessel crossings is classified. To better address the problem of label ambiguity and imbalanced label distribution, we propose a new model, named multi-diagnosis team network (MDTNet), in which the sub-models with different structures or different loss functions provide different decisions. MDTNet unifies these diverse theories to give the final decision with high accuracy. Our severity grading method was able to validate crossing points with precision and recall of 96.3% and 96.3%, respectively. Among correctly detected crossing points, the kappa value for the agreement between the grading by a retina specialist and the estimated score was 0.85, with an accuracy of 0.92. The numerical results demonstrate that our method can achieve a good performance in both arteriovenous crossing validation and severity grading tasks. By the proposed models, we could build a pipeline reproducing retina specialist's subjective grading without feature extractions. The code is available for reproducibility.

Liangzhi Li, Manisha Verma, Yuta Nakashima et al.

Retinal vessel segmentation is of great interest for diagnosis of retinal vascular diseases. To further improve the performance of vessel segmentation, we propose IterNet, a new model based on UNet, with the ability to find obscured details of the vessel from the segmented vessel image itself, rather than the raw input image. IterNet consists of multiple iterations of a mini-UNet, which can be 4$\times$ deeper than the common UNet. IterNet also adopts the weight-sharing and skip-connection features to facilitate training; therefore, even with such a large architecture, IterNet can still learn from merely 10$\sim$20 labeled images, without pre-training or any prior knowledge. IterNet achieves AUCs of 0.9816, 0.9851, and 0.9881 on three mainstream datasets, namely DRIVE, CHASE-DB1, and STARE, respectively, which currently are the best scores in the literature. The source code is available.

Sudhakar Kumawat, Manisha Verma, Yuta Nakashima et al.

Conventional 3D convolutional neural networks (CNNs) are computationally expensive, memory intensive, prone to overfitting, and most importantly, there is a need to improve their feature learning capabilities. To address these issues, we propose spatio-temporal short term Fourier transform (STFT) blocks, a new class of convolutional blocks that can serve as an alternative to the 3D convolutional layer and its variants in 3D CNNs. An STFT block consists of non-trainable convolution layers that capture spatially and/or temporally local Fourier information using a STFT kernel at multiple low frequency points, followed by a set of trainable linear weights for learning channel correlations. The STFT blocks significantly reduce the space-time complexity in 3D CNNs. In general, they use 3.5 to 4.5 times less parameters and 1.5 to 1.8 times less computational costs when compared to the state-of-the-art methods. Furthermore, their feature learning capabilities are significantly better than the conventional 3D convolutional layer and its variants. Our extensive evaluation on seven action recognition datasets, including Something-something v1 and v2, Jester, Diving-48, Kinetics-400, UCF 101, and HMDB 51, demonstrate that STFT blocks based 3D CNNs achieve on par or even better performance compared to the state-of-the-art methods.

Liangzhi Li, Manisha Verma, Yuta Nakashima et al.

Retinal imaging serves as a valuable tool for diagnosis of various diseases. However, reading retinal images is a difficult and time-consuming task even for experienced specialists. The fundamental step towards automated retinal image analysis is vessel segmentation and artery/vein classification, which provide various information on potential disorders. To improve the performance of the existing automated methods for retinal image analysis, we propose a two-step vessel classification. We adopt a UNet-based model, SeqNet, to accurately segment vessels from the background and make prediction on the vessel type. Our model does segmentation and classification sequentially, which alleviates the problem of label distribution bias and facilitates training. To further refine classification results, we post-process them considering the structural information among vessels to propagate highly confident prediction to surrounding vessels. Our experiments show that our method improves AUC to 0.98 for segmentation and the accuracy to 0.92 in classification over DRIVE dataset.

Manisha Verma, Sudhakar Kumawat, Yuta Nakashima et al.

Human pose estimation is a well-known problem in computer vision to locate joint positions. Existing datasets for the learning of poses are observed to be not challenging enough in terms of pose diversity, object occlusion, and viewpoints. This makes the pose annotation process relatively simple and restricts the application of the models that have been trained on them. To handle more variety in human poses, we propose the concept of fine-grained hierarchical pose classification, in which we formulate the pose estimation as a classification task, and propose a dataset, Yoga-82, for large-scale yoga pose recognition with 82 classes. Yoga-82 consists of complex poses where fine annotations may not be possible. To resolve this, we provide hierarchical labels for yoga poses based on the body configuration of the pose. The dataset contains a three-level hierarchy including body positions, variations in body positions, and the actual pose names. We present the classification accuracy of the state-of-the-art convolutional neural network architectures on Yoga-82. We also present several hierarchical variants of DenseNet in order to utilize the hierarchical labels.

Marc-Andre Schulz, Matt Chapman-Rounds, Manisha Verma et al.

Identification of disease subtypes and corresponding biomarkers can substantially improve clinical diagnosis and treatment selection. Discovering these subtypes in noisy, high dimensional biomedical data is often impossible for humans and challenging for machines. We introduce a new approach to facilitate the discovery of disease subtypes: Instead of analyzing the original data, we train a diagnostic classifier (healthy vs. diseased) and extract instance-wise explanations for the classifier's decisions. The distribution of instances in the explanation space of our diagnostic classifier amplifies the different reasons for belonging to the same class - resulting in a representation that is uniquely useful for discovering latent subtypes. We compare our ability to recover subtypes via cluster analysis on model explanations to classical cluster analysis on the original data. In multiple datasets with known ground-truth subclasses, most compellingly on UK Biobank brain imaging data and transcriptome data from the Cancer Genome Atlas, we show that cluster analysis on model explanations substantially outperforms the classical approach. While we believe clustering in explanation space to be particularly valuable for inferring disease subtypes, the method is more general and applicable to any kind of sub-type identification.

Sudhakar Kumawat, Manisha Verma, Shanmuganathan Raman

Recognizing facial expressions is one of the central problems in computer vision. Temporal image sequences have useful spatio-temporal features for recognizing expressions. In this paper, we propose a new 3D Convolution Neural Network (CNN) that can be trained end-to-end for facial expression recognition on temporal image sequences without using facial landmarks. More specifically, a novel 3D convolutional layer that we call Local Binary Volume (LBV) layer is proposed. The LBV layer, when used with our newly proposed LBVCNN network, achieve comparable results compared to state-of-the-art landmark-based or without landmark-based models on image sequences from CK+, Oulu-CASIA, and UNBC McMaster shoulder pain datasets. Furthermore, our LBV layer reduces the number of trainable parameters by a significant amount when compared to a conventional 3D convolutional layer. As a matter of fact, when compared to a 3x3x3 conventional 3D convolutional layer, the LBV layer uses 27 times less trainable parameters.