Typed Graph Network
Recently, the deep learning community has given growing attention to neural architectures engineered to learn problems in relational domains. Convolutional Neural Networks employ parameter sharing over the image domain, tying the weights of neural connections on a grid topology and thus enforcing the learning of a number of convolutional kernels. By instantiating trainable neural modules and assembling them in varied configurations (apart from grids), one can enforce parameter sharing over graphs, yielding models which can effectively be fed with relational data. In this context, vertices in a graph can be projected into a hyperdimensional real space and iteratively refined over many message-passing iterations in an end-to-end differentiable architecture. Architectures of this family have been referred to with several definitions in the literature, such as Graph Neural Networks, Message-passing Neural Networks, Relational Networks and Graph Networks. In this paper, we revisit the original Graph Neural Network model and show that it generalises many of the recent models, which in turn benefit from the insight of thinking about vertex \textbf{types}. To illustrate the generality of the original model, we present a Graph Neural Network formalisation, which partitions the vertices of a graph into a number of types. Each type represents an entity in the ontology of the problem one wants to learn. This allows – for instance – one to assign embeddings to edges, hyperedges, and any number of global attributes of the graph. As a companion to this paper we provide a Python/Tensorflow library to facilitate the development of such architectures, with which we instantiate the formalisation to reproduce a number of models proposed in the current literature. …

Fenchel Lifted Network
Despite the recent successes of deep neural networks, the corresponding training problem remains highly non-convex and difficult to optimize. Classes of models have been proposed that introduce greater structure to the objective function at the cost of lifting the dimension of the problem. However, these lifted methods sometimes perform poorly compared to traditional neural networks. In this paper, we introduce a new class of lifted models, Fenchel lifted networks, that enjoy the same benefits as previous lifted models, without suffering a degradation in performance over classical networks. Our model represents activation functions as equivalent biconvex constraints and uses Lagrange Multipliers to arrive at a rigorous lower bound of the traditional neural network training problem. This model is efficiently trained using block-coordinate descent and is parallelizable across data points and/or layers. We compare our model against standard fully connected and convolutional networks and show that we are able to match or beat their performance. …

Deep Complex U-Net
Most deep learning-based models for speech enhancement have mainly focused on estimating the magnitude of spectrogram while reusing the phase from noisy speech for reconstruction. This is due to the difficulty of estimating the phase of clean speech. To improve speech enhancement performance, we tackle the phase estimation problem in three ways. First, we propose Deep Complex U-Net, an advanced U-Net structured model incorporating well-defined complex-valued building blocks to deal with complex-valued spectrograms. Second, we propose a polar coordinate-wise complex-valued masking method to reflect the distribution of complex ideal ratio masks. Third, we define a novel loss function, weighted source-to-distortion ratio (wSDR) loss, which is designed to directly correlate with a quantitative evaluation measure. Our model was evaluated on a mixture of the Voice Bank corpus and DEMAND database, which has been widely used by many deep learning models for speech enhancement. Ablation experiments were conducted on the mixed dataset showing that all three proposed approaches are empirically valid. Experimental results show that the proposed method achieves state-of-the-art performance in all metrics, outperforming previous approaches by a large margin. …

Random Labeled Point Process (RLPP)
Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate the application of clustering algorithms, whose goals are to group points based on some similarity criterion. A common practice for dealing with missing values in the context of clustering is to first impute the missing values, and then apply the clustering algorithm on the completed data. We consider missing values in the context of optimal clustering, which finds an optimal clustering operator with reference to an underlying random labeled point process (RLPP). We show how the missing-value problem fits neatly into the overall framework of optimal clustering by incorporating the missing value mechanism into the random labeled point process and then marginalizing out the missing-value process. In particular, we demonstrate the proposed framework for the Gaussian model with arbitrary covariance structures. Comprehensive experimental studies on both synthetic and real-world RNA-seq data show the superior performance of the proposed optimal clustering with missing values when compared to various clustering approaches. Optimal clustering with missing values obviates the need for imputation-based pre-processing of the data, while at the same time possessing smaller clustering errors. …