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Persistent homology is an important methodology from topological data analysis which adapts theory from algebraic topology to data settings and has been successfully implemented in many applications. It produces a statistical summary in the form of a persistence diagram, which captures the shape and size of the data. Despite its widespread use, persistent homology is simply impossible to implement when a dataset is very large. In this paper we address the problem of finding a representative persistence diagram for prohibitively large datasets. We adapt the classical statistical method of bootstrapping, namely, drawing and studying smaller multiple subsamples from the large dataset. We show that the mean of the persistence diagrams of subsamples -- taken as a mean persistence measure computed from the subsamples -- is a valid approximation of the true persistent homology of the larger dataset. We give the rate of convergence of the mean persistence diagram to the true persistence diagram in terms of the number of subsamples and size of each subsample. Given the complex algebraic and geometric nature of persistent homology, we adapt the convexity and stability properties in the space of persistence diagrams together with random set theory to achieve our theoretical results for the general setting of point cloud data. We demonstrate our approach on simulated and real data, including an application of shape clustering on complex large-scale point cloud data.

Recruitment in large organisations often involves interviewing a large number of candidates. The process is resource intensive and complex. Therefore, it is important to carry it out efficiently and effectively. Planning the selection process consists of several problems, each of which maps to one or the other well-known computing problem. Research that looks at each of these problems in isolation is rich and mature. However, research that takes an integrated view of the problem is not common. In this paper, we take two of the most important aspects of the application processing problem, namely review/interview panel creation and interview scheduling. We have implemented our approach as a prototype system and have used it to automatically plan the interview process of a real-life data set. Our system provides a distinctly better plan than the existing practice, which is predominantly manual. We have explored various algorithmic options and have customised them to solve these panel creation and interview scheduling problems. We have evaluated these design options experimentally on a real data set and have presented our observations. Our prototype and experimental process and results may be a very good starting point for a full-fledged development project for automating application processing process.

Despite the recent progress, the existing multi-view unsupervised feature selection methods mostly suffer from two limitations. First, they generally utilize either cluster structure or similarity structure to guide the feature selection, neglecting the possibility of a joint formulation with mutual benefits. Second, they often learn the similarity structure by either global structure learning or local structure learning, lacking the capability of graph learning with both global and local structural awareness. In light of this, this paper presents a joint multi-view unsupervised feature selection and graph learning (JMVFG) approach. Particularly, we formulate the multi-view feature selection with orthogonal decomposition, where each target matrix is decomposed into a view-specific basis matrix and a view-consistent cluster indicator. Cross-space locality preservation is incorporated to bridge the cluster structure learning in the projected space and the similarity learning (i.e., graph learning) in the original space. Further, a unified objective function is presented to enable the simultaneous learning of the cluster structure, the global and local similarity structures, and the multi-view consistency and inconsistency, upon which an alternating optimization algorithm is developed with theoretically proved convergence. Extensive experiments demonstrate the superiority of our approach for both multi-view feature selection and graph learning tasks.

A natural way of increasing our understanding of NP-complete graph problems is to restrict the input to a special graph class. Classes of $H$-free graphs, that is, graphs that do not contain some graph $H$ as an induced subgraph, have proven to be an ideal testbed for such a complexity study. However, if the forbidden graph $H$ contains a cycle or claw, then these problems often stay NP-complete. A recent complexity study on the $k$-Colouring problem shows that we may still obtain tractable results if we also bound the diameter of the $H$-free input graph. We continue this line of research by initiating a complexity study on the impact of bounding the diameter for a variety of classical vertex partitioning problems restricted to $H$-free graphs. We prove that bounding the diameter does not help for Independent Set, but leads to new tractable cases for problems closely related to 3-Colouring. That is, we show that Near-Bipartiteness, Independent Feedback Vertex Set, Independent Odd Cycle Transversal, Acyclic 3-Colouring and Star 3-Colouring are all polynomial-time solvable for chair-free graphs of bounded diameter. To obtain these results we exploit a new structural property of 3-colourable chair-free graphs.

In variable selection, a selection rule that prescribes the permissible sets of selected variables (called a "selection dictionary") is desirable due to the inherent structural constraints among the candidate variables. The methods that can incorporate such restrictions can improve model interpretability and prediction accuracy. Penalized regression can integrate selection rules by assigning the coefficients to different groups and then applying penalties to the groups. However, no general framework has been proposed to formalize selection rules and their applications. In this work, we establish a framework for structured variable selection that can incorporate universal structural constraints. We develop a mathematical language for constructing arbitrary selection rules, where the selection dictionary is formally defined. We show that all selection rules can be represented as a combination of operations on constructs, which can be used to identify the related selection dictionary. One may then apply some criteria to select the best model. We show that the theoretical framework can help to identify the grouping structure in existing penalized regression methods. In addition, we formulate structured variable selection into mixed-integer optimization problems which can be solved by existing software. Finally, we discuss the significance of the framework in the context of statistics.

Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

In the last decade or so, we have witnessed deep learning reinvigorating the machine learning field. It has solved many problems in the domains of computer vision, speech recognition, natural language processing, and various other tasks with state-of-the-art performance. The data is generally represented in the Euclidean space in these domains. Various other domains conform to non-Euclidean space, for which graph is an ideal representation. Graphs are suitable for representing the dependencies and interrelationships between various entities. Traditionally, handcrafted features for graphs are incapable of providing the necessary inference for various tasks from this complex data representation. Recently, there is an emergence of employing various advances in deep learning to graph data-based tasks. This article provides a comprehensive survey of graph neural networks (GNNs) in each learning setting: supervised, unsupervised, semi-supervised, and self-supervised learning. Taxonomy of each graph based learning setting is provided with logical divisions of methods falling in the given learning setting. The approaches for each learning task are analyzed from both theoretical as well as empirical standpoints. Further, we provide general architecture guidelines for building GNNs. Various applications and benchmark datasets are also provided, along with open challenges still plaguing the general applicability of GNNs.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.