A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

Semantic Autoencoder for Zero-Shot Learning

Existing zero-shot learning (ZSL) models typically learn a projection function from a feature space to a semantic embedding space (e.g.~attribute space). However, such a projection function is only concerned with predicting the training seen class semantic representation (e.g.~attribute prediction) or classification. When applied to test data, which in the context of ZSL contains different (unseen) classes without training data, a ZSL model typically suffers from the project domain shift problem. In this work, we present a novel solution to ZSL based on learning a Semantic AutoEncoder (SAE). Taking the encoder-decoder paradigm, an encoder aims to project a visual feature vector into the semantic space as in the existing ZSL models. However, the decoder exerts an additional constraint, that is, the projection/code must be able to reconstruct the original visual feature. We show that with this additional reconstruction constraint, the learned projection function from the seen classes is able to generalise better to the new unseen classes. Importantly, the encoder and decoder are linear and symmetric which enable us to develop an extremely efficient learning algorithm. Extensive experiments on six benchmark datasets demonstrate that the proposed SAE outperforms significantly the existing ZSL models with the additional benefit of lower computational cost. Furthermore, when the SAE is applied to supervised clustering problem, it also beats the state-of-the-art.Comment: accepted to CVPR201

Scalable and Interpretable One-class SVMs with Deep Learning and Random Fourier features

One-class support vector machine (OC-SVM) for a long time has been one of the most effective anomaly detection methods and extensively adopted in both research as well as industrial applications. The biggest issue for OC-SVM is yet the capability to operate with large and high-dimensional datasets due to optimization complexity. Those problems might be mitigated via dimensionality reduction techniques such as manifold learning or autoencoder. However, previous work often treats representation learning and anomaly prediction separately. In this paper, we propose autoencoder based one-class support vector machine (AE-1SVM) that brings OC-SVM, with the aid of random Fourier features to approximate the radial basis kernel, into deep learning context by combining it with a representation learning architecture and jointly exploit stochastic gradient descent to obtain end-to-end training. Interestingly, this also opens up the possible use of gradient-based attribution methods to explain the decision making for anomaly detection, which has ever been challenging as a result of the implicit mappings between the input space and the kernel space. To the best of our knowledge, this is the first work to study the interpretability of deep learning in anomaly detection. We evaluate our method on a wide range of unsupervised anomaly detection tasks in which our end-to-end training architecture achieves a performance significantly better than the previous work using separate training.Comment: Accepted at European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) 201