Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userCQ-VAE: Coordinate Quantized VAE for Uncertainty Estimation with Application to Disk Shape Analysis from Lumbar Spine MRI Images
155
0
0.0
(
0
)
Added by
Linchen Qian
Publication date
2020
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Ambiguity is inevitable in medical images, which often results in different image interpretations (e.g. object boundaries or segmentation maps) from different human experts. Thus, a model that learns the ambiguity and outputs a probability distribution of the target, would be valuable for medical applications to assess the uncertainty of diagnosis. In this paper, we propose a powerful generative model to learn a representation of ambiguity and to generate probabilistic outputs. Our model, named Coordinate Quantization Variational Autoencoder (CQ-VAE) employs a discrete latent space with an internal discrete probability distribution by quantizing the coordinates of a continuous latent space. As a result, the output distribution from CQ-VAE is discrete. During training, Gumbel-Softmax sampling is used to enable backpropagation through the discrete latent space. A matching algorithm is used to establish the correspondence between model-generated samples and ground-truth samples, which makes a trade-off between the ability to generate new samples and the ability to represent training samples. Besides these probabilistic components to generate possible outputs, our model has a deterministic path to output the best estimation. We demonstrated our method on a lumbar disk image dataset, and the results show that our CQ-VAE can learn lumbar disk shape variation and uncertainty.
rate research
Read More
Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work, we introduce a joint geometric-neural networks approach for comparing, deforming and generating 3D protein structures. Viewing protein structures as 3D open curves, we adopt the Square Root Velocity Function (SRVF) representation and leverage its suitable geometric properties along with Deep Residual Networks (ResNets) for a joint registration and comparison. Our ResNets handle better large protein deformations while being more computationally efficient. On top of the mathematical framework, we further design a Geometric Variational Auto-Encoder (G-VAE), that once trained, maps original, previously unseen structures, into a low-dimensional (latent) hyper-sphere. Motivated by the spherical structure of the pre-shape space, we naturally adopt the von Mises-Fisher (vMF) distribution to model our hidden variables. We test the effectiveness of our models by generating novel protein structures and predicting completions of corrupted protein structures. Experimental results show that our method is able to generate plausible structures, different from the structures in the training data.
Given an image dataset, we are often interested in finding data generative factors that encode semantic content independently from pose variables such as rotation and translation. However, current disentanglement approaches do not impose any specific structure on the learned latent representations. We propose a method for explicitly disentangling image rotation and translation from other unstructured latent factors in a variational autoencoder (VAE) framework. By formulating the generative model as a function of the spatial coordinate, we make the reconstruction error differentiable with respect to latent translation and rotation parameters. This formulation allows us to train a neural network to perform approximate inference on these latent variables while explicitly constraining them to only represent rotation and translation. We demonstrate that this framework, termed spatial-VAE, effectively learns latent representations that disentangle image rotation and translation from content and improves reconstruction over standard VAEs on several benchmark datasets, including applications to modeling continuous 2-D views of proteins from single particle electron microscopy and galaxies in astronomical images.
We consider the task of generating diverse and novel videos from a single video sample. Recently, new hierarchical patch-GAN based approaches were proposed for generating diverse images, given only a single sample at training time. Moving to videos, these approaches fail to generate diverse samples, and often collapse into generating samples similar to the training video. We introduce a novel patch-based variational autoencoder (VAE) which allows for a much greater diversity in generation. Using this tool, a new hierarchical video generation scheme is constructed: at coarse scales, our patch-VAE is employed, ensuring samples are of high diversity. Subsequently, at finer scales, a patch-GAN renders the fine details, resulting in high quality videos. Our experiments show that the proposed method produces diverse samples in both the image domain, and the more challenging video domain.
Recent studies show that advanced priors play a major role in deep generative models. Exemplar VAE, as a variant of VAE with an exemplar-based prior, has achieved impressive results. However, due to the nature of model design, an exemplar-based model usually requires vast amounts of data to participate in training, which leads to huge computational complexity. To address this issue, we propose Bayesian Pseudocoresets Exemplar VAE (ByPE-VAE), a new variant of VAE with a prior based on Bayesian pseudocoreset. The proposed prior is conditioned on a small-scale pseudocoreset rather than the whole dataset for reducing the computational cost and avoiding overfitting. Simultaneously, we obtain the optimal pseudocoreset via a stochastic optimization algorithm during VAE training aiming to minimize the Kullback-Leibler divergence between the prior based on the pseudocoreset and that based on the whole dataset. Experimental results show that ByPE-VAE can achieve competitive improvements over the state-of-the-art VAEs in the tasks of density estimation, representation learning, and generative data augmentation. Particularly, on a basic VAE architecture, ByPE-VAE is up to 3 times faster than Exemplar VAE while almost holding the performance. Code is available at our supplementary materials.
We explore the use of Vector Quantized Variational AutoEncoder (VQ-VAE) models for large scale image generation. To this end, we scale and enhance the autoregressive priors used in VQ-VAE to generate synthetic samples of much higher coherence and fidelity than possible before. We use simple feed-forward encoder and decoder networks, making our model an attractive candidate for applications where the encoding and/or decoding speed is critical. Additionally, VQ-VAE requires sampling an autoregressive model only in the compressed latent space, which is an order of magnitude faster than sampling in the pixel space, especially for large images. We demonstrate that a multi-scale hierarchical organization of VQ-VAE, augmented with powerful priors over the latent codes, is able to generate samples with quality that rivals that of state of the art Generative Adversarial Networks on multifaceted datasets such as ImageNet, while not suffering from GANs known shortcomings such as mode collapse and lack of diversity.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
