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Register a new userFast Multiple Landmark Localisation Using a Patch-based Iterative Network
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Yuanwei Li
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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We propose a new Patch-based Iterative Network (PIN) for fast and accurate landmark localisation in 3D medical volumes. PIN utilises a Convolutional Neural Network (CNN) to learn the spatial relationship between an image patch and anatomical landmark positions. During inference, patches are repeatedly passed to the CNN until the estimated landmark position converges to the true landmark location. PIN is computationally efficient since the inference stage only selectively samples a small number of patches in an iterative fashion rather than a dense sampling at every location in the volume. Our approach adopts a multi-task learning framework that combines regression and classification to improve localisation accuracy. We extend PIN to localise multiple landmarks by using principal component analysis, which models the global anatomical relationships between landmarks. We have evaluated PIN using 72 3D ultrasound images from fetal screening examinations. PIN achieves quantitatively an average landmark localisation error of 5.59mm and a runtime of 0.44s to predict 10 landmarks per volume. Qualitatively, anatomical 2D standard scan planes derived from the predicted landmark locations are visually similar to the clinical ground truth. Source code is publicly available at https://github.com/yuanwei1989/landmark-detection.
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The detection of anatomical landmarks is a vital step for medical image analysis and applications for diagnosis, interpretation and guidance. Manual annotation of landmarks is a tedious process that requires domain-specific expertise and introduces inter-observer variability. This paper proposes a new detection approach for multiple landmarks based on multi-agent reinforcement learning. Our hypothesis is that the position of all anatomical landmarks is interdependent and non-random within the human anatomy, thus finding one landmark can help to deduce the location of others. Using a Deep Q-Network (DQN) architecture we construct an environment and agent with implicit inter-communication such that we can accommodate K agents acting and learning simultaneously, while they attempt to detect K different landmarks. During training the agents collaborate by sharing their accumulated knowledge for a collective gain. We compare our approach with state-of-the-art architectures and achieve significantly better accuracy by reducing the detection error by 50%, while requiring fewer computational resources and time to train compared to the naive approach of training K agents separately.
We present a new loss function, namely Wing loss, for robust facial landmark localisation with Convolutional Neural Networks (CNNs). We first compare and analyse different loss functions including L2, L1 and smooth L1. The analysis of these loss functions suggests that, for the training of a CNN-based localisation model, more attention should be paid to small and medium range errors. To this end, we design a piece-wise loss function. The new loss amplifies the impact of errors from the interval (-w, w) by switching from L1 loss to a modified logarithm function. To address the problem of under-representation of samples with large out-of-plane head rotations in the training set, we propose a simple but effective boosting strategy, referred to as pose-based data balancing. In particular, we deal with the data imbalance problem by duplicating the minority training samples and perturbing them by injecting random image rotation, bounding box translation and other data augmentation approaches. Last, the proposed approach is extended to create a two-stage framework for robust facial landmark localisation. The experimental results obtained on AFLW and 300W demonstrate the merits of the Wing loss function, and prove the superiority of the proposed method over the state-of-the-art approaches.
Modern digital cameras rely on the sequential execution of separate image processing steps to produce realistic images. The first two steps are usually related to denoising and demosaicking where the former aims to reduce noise from the sensor and the latter converts a series of light intensity readings to color images. Modern approaches try to jointly solve these problems, i.e. joint denoising-demosaicking which is an inherently ill-posed problem given that two-thirds of the intensity information is missing and the rest are perturbed by noise. While there are several machine learning systems that have been recently introduced to solve this problem, the majority of them relies on generic network architectures which do not explicitly take into account the physical image model. In this work we propose a novel algorithm which is inspired by powerful classical image regularization methods, large-scale optimization, and deep learning techniques. Consequently, our derived iterative optimization algorithm, which involves a trainable denoising network, has a transparent and clear interpretation compared to other black-box data driven approaches. Our extensive experimentation line demonstrates that our proposed method outperforms any previous approaches for both noisy and noise-free data across many different datasets. This improvement in reconstruction quality is attributed to the rigorous derivation of an iterative solution and the principled way we design our denoising network architecture, which as a result requires fewer trainable parameters than the current state-of-the-art solution and furthermore can be efficiently trained by using a significantly smaller number of training data than existing deep demosaicking networks. Code and results can be found at https://github.com/cig-skoltech/deep_demosaick
Tensor networks are efficient factorisations of high dimensional tensors into a network of lower order tensors. They have been most commonly used to model entanglement in quantum many-body systems and more recently are witnessing increased applications in supervised machine learning. In this work, we formulate image segmentation in a supervised setting with tensor networks. The key idea is to first lift the pixels in image patches to exponentially high dimensional feature spaces and using a linear decision hyper-plane to classify the input pixels into foreground and background classes. The high dimensional linear model itself is approximated using the matrix product state (MPS) tensor network. The MPS is weight-shared between the non-overlapping image patches resulting in our strided tensor network model. The performance of the proposed model is evaluated on three 2D- and one 3D- biomedical imaging datasets. The performance of the proposed tensor network segmentation model is compared with relevant baseline methods. In the 2D experiments, the tensor network model yeilds competitive performance compared to the baseline methods while being more resource efficient.
Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN.
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