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Topological data analysis is an emerging field that applies the study of topological invariants to data. Perhaps the simplest of these invariants is the number of connected components or clusters. In this work, we explore a topological framework for cluster analysis and show how it can be used as a basis for explainability in unsupervised data analysis. Our main object of study will be hierarchical data structures referred to as Topological Hierarchical Decompositions (THDs). We give a number of examples of how traditional clustering algorithms can be topologized, and provide preliminary results on the THDs associated with Reeb graphs and the mapper algorithm. In particular, we give a generalized construction of the mapper functor as a pixelization of a cosheaf in order to generalize multiscale mapper.

Topological semantics for modal logic based on the Cantor derivative operator gives rise to derivative logics, also referred to as $d$-logics. Unlike logics based on the topological closure operator, $d$-logics have not previously been studied in the framework of dynamical systems, which are pairs $(X,f)$ consisting of a topological space $X$ equipped with a continuous function $f\colon X\to X$. We introduce the logics $\bf{wK4C}$, $\bf{K4C}$ and $\bf{GLC}$ and show that they all have the finite Kripke model property and are sound and complete with respect to the $d$-semantics in this dynamical setting. In particular, we prove that $\bf{wK4C}$ is the $d$-logic of all dynamic topological systems, $\bf{K4C}$ is the $d$-logic of all $T_D$ dynamic topological systems, and $\bf{GLC}$ is the $d$-logic of all dynamic topological systems based on a scattered space. We also prove a general result for the case where $f$ is a homeomorphism, which in particular yields soundness and completeness for the corresponding systems $\bf{wK4H}$, $\bf{K4H}$ and $\bf{GLH}$. The main contribution of this work is the foundation of a general proof method for finite model property and completeness of dynamic topological $d$-logics. Furthermore, our result for $\bf{GLC}$ constitutes the first step towards a proof of completeness for the trimodal topo-temporal language with respect to a finite axiomatisation -- something known to be impossible over the class of all 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.

The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.

Self-supervised learning has been widely used to obtain transferrable representations from unlabeled images. Especially, recent contrastive learning methods have shown impressive performances on downstream image classification tasks. While these contrastive methods mainly focus on generating invariant global representations at the image-level under semantic-preserving transformations, they are prone to overlook spatial consistency of local representations and therefore have a limitation in pretraining for localization tasks such as object detection and instance segmentation. Moreover, aggressively cropped views used in existing contrastive methods can minimize representation distances between the semantically different regions of a single image. In this paper, we propose a spatially consistent representation learning algorithm (SCRL) for multi-object and location-specific tasks. In particular, we devise a novel self-supervised objective that tries to produce coherent spatial representations of a randomly cropped local region according to geometric translations and zooming operations. On various downstream localization tasks with benchmark datasets, the proposed SCRL shows significant performance improvements over the image-level supervised pretraining as well as the state-of-the-art self-supervised learning methods.

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn node representations on the fixed and homogeneous graphs. The limitations especially become problematic when learning representations on a misspecified graph or a heterogeneous graph that consists of various types of nodes and edges. In this paper, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which involve identifying useful connections between unconnected nodes on the original graph, while learning effective node representation on the new graphs in an end-to-end fashion. Graph Transformer layer, a core layer of GTNs, learns a soft selection of edge types and composite relations for generating useful multi-hop connections so-called meta-paths. Our experiments show that GTNs learn new graph structures, based on data and tasks without domain knowledge, and yield powerful node representation via convolution on the new graphs. Without domain-specific graph preprocessing, GTNs achieved the best performance in all three benchmark node classification tasks against the state-of-the-art methods that require pre-defined meta-paths from domain knowledge.

There is a recent large and growing interest in generative adversarial networks (GANs), which offer powerful features for generative modeling, density estimation, and energy function learning. GANs are difficult to train and evaluate but are capable of creating amazingly realistic, though synthetic, image data. Ideas stemming from GANs such as adversarial losses are creating research opportunities for other challenges such as domain adaptation. In this paper, we look at the field of GANs with emphasis on these areas of emerging research. To provide background for adversarial techniques, we survey the field of GANs, looking at the original formulation, training variants, evaluation methods, and extensions. Then we survey recent work on transfer learning, focusing on comparing different adversarial domain adaptation methods. Finally, we take a look forward to identify open research directions for GANs and domain adaptation, including some promising applications such as sensor-based human behavior modeling.

Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.

Attention networks in multimodal learning provide an efficient way to utilize given visual information selectively. However, the computational cost to learn attention distributions for every pair of multimodal input channels is prohibitively expensive. To solve this problem, co-attention builds two separate attention distributions for each modality neglecting the interaction between multimodal inputs. In this paper, we propose bilinear attention networks (BAN) that find bilinear attention distributions to utilize given vision-language information seamlessly. BAN considers bilinear interactions among two groups of input channels, while low-rank bilinear pooling extracts the joint representations for each pair of channels. Furthermore, we propose a variant of multimodal residual networks to exploit eight-attention maps of the BAN efficiently. We quantitatively and qualitatively evaluate our model on visual question answering (VQA 2.0) and Flickr30k Entities datasets, showing that BAN significantly outperforms previous methods and achieves new state-of-the-arts on both datasets.

This paper proposes a method to modify traditional convolutional neural networks (CNNs) into interpretable CNNs, in order to clarify knowledge representations in high conv-layers of CNNs. In an interpretable CNN, each filter in a high conv-layer represents a certain object part. We do not need any annotations of object parts or textures to supervise the learning process. Instead, the interpretable CNN automatically assigns each filter in a high conv-layer with an object part during the learning process. Our method can be applied to different types of CNNs with different structures. The clear knowledge representation in an interpretable CNN can help people understand the logics inside a CNN, i.e., based on which patterns the CNN makes the decision. Experiments showed that filters in an interpretable CNN were more semantically meaningful than those in traditional CNNs.