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Deep Convolutional Neural Networks (DCNN) has shown excellent performance in a variety of machine learning tasks. This manuscript presents Deep Convolutional Neural Fields (DeepCNF), a combination of DCNN with Conditional Random Field (CRF), for sequence labeling with highly imbalanced label distribution. The widely-used training methods, such as maximum-likelihood and maximum labelwise accuracy, do not work well on highly imbalanced data. To handle this, we present a new training algorithm called maximum-AUC for DeepCNF. That is, we train DeepCNF by directly maximizing the empirical Area Under the ROC Curve (AUC), which is an unbiased measurement for imbalanced data. To fulfill this, we formulate AUC in a pairwise ranking framework, approximate it by a polynomial function and then apply a gradient-based procedure to optimize it. We then test our AUC-maximized DeepCNF on three very different protein sequence labeling tasks: solvent accessibility prediction, 8-state secondary structure prediction, and disorder prediction. Our experimental results confirm that maximum-AUC greatly outperforms the other two training methods on 8-state secondary structure prediction and disorder prediction since their label distributions are highly imbalanced and also have similar performance as the other two training methods on the solvent accessibility prediction problem which has three equally-distributed labels. Furthermore, our experimental results also show that our AUC-trained DeepCNF models greatly outperform existing popular predictors of these three tasks.
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A convolutional sequence to sequence non-intrusive load monitoring model is proposed in this paper. Gated linear unit convolutional layers are used to extract information from the sequences of aggregate electricity consumption. Residual blocks are also introduced to refine the output of the neural network. The partially overlapped output sequences of the network are averaged to produce the final output of the model. We apply the proposed model to the REDD dataset and compare it with the convolutional sequence to point model in the literature. Results show that the proposed model is able to give satisfactory disaggregation performance for appliances with varied characteristics.
Discrete Fourier transforms provide a significant speedup in the computation of convolutions in deep learning. In this work, we demonstrate that, beyond its advantages for efficient computation, the spectral domain also provides a powerful representation in which to model and train convolutional neural networks (CNNs). We employ spectral representations to introduce a number of innovations to CNN design. First, we propose spectral pooling, which performs dimensionality reduction by truncating the representation in the frequency domain. This approach preserves considerably more information per parameter than other pooling strategies and enables flexibility in the choice of pooling output dimensionality. This representation also enables a new form of stochastic regularization by randomized modification of resolution. We show that these methods achieve competitive results on classification and approximation tasks, without using any dropout or max-pooling. Finally, we demonstrate the effectiveness of complex-coefficient spectral parameterization of convolutional filters. While this leaves the underlying model unchanged, it results in a representation that greatly facilitates optimization. We observe on a variety of popular CNN configurations that this leads to significantly faster convergence during training.
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.
This report examines the Pinned AUC metric introduced and highlights some of its limitations. Pinned AUC provides a threshold-agnostic measure of unintended bias in a classification model, inspired by the ROC-AUC metric. However, as we highlight in this report, there are ways that the metric can obscure different kinds of unintended biases when the underlying class distributions on which bias is being measured are not carefully controlled.
Stochastic Gradient Descent has been widely studied with classification accuracy as a performance measure. However, these stochastic algorithms cannot be directly used when non-decomposable pairwise performance measures are used such as Area under the ROC curve (AUC) which is a common performance metric when the classes are imbalanced. There have been several algorithms proposed for optimizing AUC as a performance metric, and one of the recent being a stochastic proximal gradient algorithm (SPAM). But the downside of the stochastic methods is that they suffer from high variance leading to slower convergence. To combat this issue, several variance reduced methods have been proposed with faster convergence guarantees than vanilla stochastic gradient descent. Again, these variance reduced methods are not directly applicable when non-decomposable performance measures are used. In this paper, we develop a Variance Reduced Stochastic Proximal algorithm for AUC Maximization (textsc{VRSPAM}) and perform a theoretical analysis as well as empirical analysis to show that our algorithm converges faster than SPAM which is the previous state-of-the-art for the AUC maximization problem.
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