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Presence-absence data is defined by vectors or matrices of zeroes and ones, where the ones usually indicate a "presence" in a certain place. Presence-absence data occur for example when investigating geographical species distributions, genetic information, or the occurrence of certain terms in texts. There are many applications for clustering such data; one example is to find so-called biotic elements, i.e., groups of species that tend to occur together geographically. Presence-absence data can be clustered in various ways, namely using a latent class mixture approach with local independence, distance-based hierarchical clustering with the Jaccard distance, or also using clustering methods for continuous data on a multidimensional scaling representation of the distances. These methods are conceptually very different and can therefore not easily be compared theoretically. We compare their performance with a comprehensive simulation study based on models for species distributions.

This paper surveys an important class of methods that combine iterative projection methods and variational regularization methods for large-scale inverse problems. Iterative methods such as Krylov subspace methods are invaluable in the numerical linear algebra community and have proved important in solving inverse problems due to their inherent regularizing properties and their ability to handle large-scale problems. Variational regularization describes a broad and important class of methods that are used to obtain reliable solutions to inverse problems, whereby one solves a modified problem that incorporates prior knowledge. Hybrid projection methods combine iterative projection methods with variational regularization techniques in a synergistic way, providing researchers with a powerful computational framework for solving very large inverse problems. Although the idea of a hybrid Krylov method for linear inverse problems goes back to the 1980s, several recent advances on new regularization frameworks and methodologies have made this field ripe for extensions, further analyses, and new applications. In this paper, we provide a practical and accessible introduction to hybrid projection methods in the context of solving large (linear) inverse problems.

Though inverse approach is computationally efficient in aerodynamic design as the desired target performance distribution is specified, it has some significant limitations that prevent full efficiency from being achieved. First, the iterative procedure should be repeated whenever the specified target distribution changes. Target distribution optimization can be performed to clarify the ambiguity in specifying this distribution, but several additional problems arise in this process such as loss of the representation capacity due to parameterization of the distribution, excessive constraints for a realistic distribution, inaccuracy of quantities of interest due to theoretical/empirical predictions, and the impossibility of explicitly imposing geometric constraints. To deal with these issues, a novel inverse design optimization framework with a two-step deep learning approach is proposed. A variational autoencoder and multi-layer perceptron are used to generate a realistic target distribution and predict the quantities of interest and shape parameters from the generated distribution, respectively. Then, target distribution optimization is performed as the inverse design optimization. The proposed framework applies active learning and transfer learning techniques to improve accuracy and efficiency. Finally, the framework is validated through aerodynamic shape optimizations of the airfoil of a wind turbine blade, where inverse design is actively being applied. The results of the optimizations show that this framework is sufficiently accurate, efficient, and flexible to be applied to other inverse design engineering applications.

Collaborative filtering (CF), as a fundamental approach for recommender systems, is usually built on the latent factor model with learnable parameters to predict users' preferences towards items. However, designing a proper CF model for a given data is not easy, since the properties of datasets are highly diverse. In this paper, motivated by the recent advances in automated machine learning (AutoML), we propose to design a data-specific CF model by AutoML techniques. The key here is a new framework that unifies state-of-the-art (SOTA) CF methods and splits them into disjoint stages of input encoding, embedding function, interaction function, and prediction function. We further develop an easy-to-use, robust, and efficient search strategy, which utilizes random search and a performance predictor for efficient searching within the above framework. In this way, we can combinatorially generalize data-specific CF models, which have not been visited in the literature, from SOTA ones. Extensive experiments on five real-world datasets demonstrate that our method can consistently outperform SOTA ones for various CF tasks. Further experiments verify the rationality of the proposed framework and the efficiency of the search strategy. The searched CF models can also provide insights for exploring more effective methods in the future

The area of Data Analytics on graphs promises a paradigm shift as we approach information processing of classes of data, which are typically acquired on irregular but structured domains (social networks, various ad-hoc sensor networks). Yet, despite its long history, current approaches mostly focus on the optimization of graphs themselves, rather than on directly inferring learning strategies, such as detection, estimation, statistical and probabilistic inference, clustering and separation from signals and data acquired on graphs. To fill this void, we first revisit graph topologies from a Data Analytics point of view, and establish a taxonomy of graph networks through a linear algebraic formalism of graph topology (vertices, connections, directivity). This serves as a basis for spectral analysis of graphs, whereby the eigenvalues and eigenvectors of graph Laplacian and adjacency matrices are shown to convey physical meaning related to both graph topology and higher-order graph properties, such as cuts, walks, paths, and neighborhoods. Next, to illustrate estimation strategies performed on graph signals, spectral analysis of graphs is introduced through eigenanalysis of mathematical descriptors of graphs and in a generic way. Finally, a framework for vertex clustering and graph segmentation is established based on graph spectral representation (eigenanalysis) which illustrates the power of graphs in various data association tasks. The supporting examples demonstrate the promise of Graph Data Analytics in modeling structural and functional/semantic inferences. At the same time, Part I serves as a basis for Part II and Part III which deal with theory, methods and applications of processing Data on Graphs and Graph Topology Learning from data.

We present a new clustering method in the form of a single clustering equation that is able to directly discover groupings in the data. The main proposition is that the first neighbor of each sample is all one needs to discover large chains and finding the groups in the data. In contrast to most existing clustering algorithms our method does not require any hyper-parameters, distance thresholds and/or the need to specify the number of clusters. The proposed algorithm belongs to the family of hierarchical agglomerative methods. The technique has a very low computational overhead, is easily scalable and applicable to large practical problems. Evaluation on well known datasets from different domains ranging between 1077 and 8.1 million samples shows substantial performance gains when compared to the existing clustering techniques.

In this paper, we propose an inverse reinforcement learning method for architecture search (IRLAS), which trains an agent to learn to search network structures that are topologically inspired by human-designed network. Most existing architecture search approaches totally neglect the topological characteristics of architectures, which results in complicated architecture with a high inference latency. Motivated by the fact that human-designed networks are elegant in topology with a fast inference speed, we propose a mirror stimuli function inspired by biological cognition theory to extract the abstract topological knowledge of an expert human-design network (ResNeXt). To avoid raising a too strong prior over the search space, we introduce inverse reinforcement learning to train the mirror stimuli function and exploit it as a heuristic guidance for architecture search, easily generalized to different architecture search algorithms. On CIFAR-10, the best architecture searched by our proposed IRLAS achieves 2.60% error rate. For ImageNet mobile setting, our model achieves a state-of-the-art top-1 accuracy 75.28%, while being 2~4x faster than most auto-generated architectures. A fast version of this model achieves 10% faster than MobileNetV2, while maintaining a higher accuracy.

Network embedding has attracted considerable research attention recently. However, the existing methods are incapable of handling billion-scale networks, because they are computationally expensive and, at the same time, difficult to be accelerated by distributed computing schemes. To address these problems, we propose RandNE, a novel and simple billion-scale network embedding method. Specifically, we propose a Gaussian random projection approach to map the network into a low-dimensional embedding space while preserving the high-order proximities between nodes. To reduce the time complexity, we design an iterative projection procedure to avoid the explicit calculation of the high-order proximities. Theoretical analysis shows that our method is extremely efficient, and friendly to distributed computing schemes without any communication cost in the calculation. We demonstrate the efficacy of RandNE over state-of-the-art methods in network reconstruction and link prediction tasks on multiple datasets with different scales, ranging from thousands to billions of nodes and edges.

We propose a flipped-Adversarial AutoEncoder (FAAE) that simultaneously trains a generative model G that maps an arbitrary latent code distribution to a data distribution and an encoder E that embodies an "inverse mapping" that encodes a data sample into a latent code vector. Unlike previous hybrid approaches that leverage adversarial training criterion in constructing autoencoders, FAAE minimizes re-encoding errors in the latent space and exploits adversarial criterion in the data space. Experimental evaluations demonstrate that the proposed framework produces sharper reconstructed images while at the same time enabling inference that captures rich semantic representation of data.

In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.