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Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

There is increasing appetite for analysing populations of network data due to the fast-growing body of applications demanding such methods. While methods exist to provide readily interpretable summaries of heterogeneous network populations, these are often descriptive or ad hoc, lacking any formal justification. In contrast, principled analysis methods often provide results difficult to relate back to the applied problem of interest. Motivated by two complementary applied examples, we develop a Bayesian framework to appropriately model complex heterogeneous network populations, whilst also allowing analysts to gain insights from the data, and make inferences most relevant to their needs. The first application involves a study in Computer Science measuring human movements across a University. The second analyses data from Neuroscience investigating relationships between different regions of the brain. While both applications entail analysis of a heterogeneous population of networks, network sizes vary considerably. We focus on the problem of clustering the elements of a network population, where each cluster is characterised by a network representative. We take advantage of the Bayesian machinery to simultaneously infer the cluster membership, the representatives, and the community structure of the representatives, thus allowing intuitive inferences to be made. The implementation of our method on the human movement study reveals interesting movement patterns of individuals in clusters, readily characterised by their network representative. For the brain networks application, our model reveals a cluster of individuals with different network properties of particular interest in Neuroscience. The performance of our method is additionally validated in extensive simulation studies.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

In multivariate time series analysis, the coherence measures the linear dependency between two-time series at different frequencies. However, real data applications often exhibit nonlinear dependency in the frequency domain. Conventional coherence analysis fails to capture such dependency. The quantile coherence, on the other hand, characterizes nonlinear dependency by defining the coherence at a set of quantile levels based on trigonometric quantile regression. Although quantile coherence is a more powerful tool, its estimation remains challenging due to the high level of noise. This paper introduces a new estimation technique for quantile coherence. The proposed method is semi-parametric, which uses the parametric form of the spectrum of the vector autoregressive (VAR) model as an approximation to the quantile spectral matrix, along with nonparametric smoothing across quantiles. For each fixed quantile level, we obtain the VAR parameters from the quantile periodograms, then, using the Durbin-Levinson algorithm, we calculate the preliminary estimate of quantile coherence using the VAR parameters. Finally, we smooth the preliminary estimate of quantile coherence across quantiles using a nonparametric smoother. Numerical results show that the proposed estimation method outperforms nonparametric methods. We show that quantile coherence-based bivariate time series clustering has advantages over the ordinary VAR coherence. For applications, the identified clusters of financial stocks by quantile coherence with a market benchmark are shown to have an intriguing and more accurate structure of diversified investment portfolios that may be used by investors to make better decisions.

AIFV (almost instantaneous fixed-to-variable length) codes are noiseless source codes that can attain a shorter average codeword length than Huffman codes by allowing a time-variant encoder with two code tables and a decoding delay of at most 2 bits. First, we consider a general class of noiseless source codes, called k-bit delay decodable codes, in which one allows a finite number of code tables and a decoding delay of at most k bits for k >= 0. Then we prove that AIFV codes achieve the optimal average codeword length in the 2-bit delay decodable codes class.

Object detection is an important topic in computer vision, with post-processing, an essential part of the typical object detection pipeline, posing a significant bottleneck affecting the performance of traditional object detection models. The detection transformer (DETR), as the first end-to-end target detection model, discards the requirement of manual components like the anchor and non-maximum suppression (NMS), significantly simplifying the target detection process. However, compared with most traditional object detection models, DETR converges very slowly, and a query's meaning is obscure. Thus, inspired by the Step-by-Step concept, this paper proposes a new two-stage object detection model, named DETR with YOLO (DEYO), which relies on a progressive inference to solve the above problems. DEYO is a two-stage architecture comprising a classic target detection model and a DETR-like model as the first and second stages, respectively. Specifically, the first stage provides high-quality query and anchor feeding into the second stage, improving the performance and efficiency of the second stage compared to the original DETR model. Meanwhile, the second stage compensates for the performance degradation caused by the first stage detector's limitations. Extensive experiments demonstrate that DEYO attains 50.6 AP and 52.1 AP in 12 and 36 epochs, respectively, while utilizing ResNet-50 as the backbone and multi-scale features on the COCO dataset. Compared with DINO, an optimal DETR-like model, the developed DEYO model affords a significant performance improvement of 1.6 AP and 1.2 AP in two epoch settings.

Knowledge graphs represent factual knowledge about the world as relationships between concepts and are critical for intelligent decision making in enterprise applications. New knowledge is inferred from the existing facts in the knowledge graphs by encoding the concepts and relations into low-dimensional feature vector representations. The most effective representations for this task, called Knowledge Graph Embeddings (KGE), are learned through neural network architectures. Due to their impressive predictive performance, they are increasingly used in high-impact domains like healthcare, finance and education. However, are the black-box KGE models adversarially robust for use in domains with high stakes? This thesis argues that state-of-the-art KGE models are vulnerable to data poisoning attacks, that is, their predictive performance can be degraded by systematically crafted perturbations to the training knowledge graph. To support this argument, two novel data poisoning attacks are proposed that craft input deletions or additions at training time to subvert the learned model's performance at inference time. These adversarial attacks target the task of predicting the missing facts in knowledge graphs using KGE models, and the evaluation shows that the simpler attacks are competitive with or outperform the computationally expensive ones. The thesis contributions not only highlight and provide an opportunity to fix the security vulnerabilities of KGE models, but also help to understand the black-box predictive behaviour of KGE models.

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.

This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.

Image captioning is a challenging task that combines the field of computer vision and natural language processing. A variety of approaches have been proposed to achieve the goal of automatically describing an image, and recurrent neural network (RNN) or long-short term memory (LSTM) based models dominate this field. However, RNNs or LSTMs cannot be calculated in parallel and ignore the underlying hierarchical structure of a sentence. In this paper, we propose a framework that only employs convolutional neural networks (CNNs) to generate captions. Owing to parallel computing, our basic model is around 3 times faster than NIC (an LSTM-based model) during training time, while also providing better results. We conduct extensive experiments on MSCOCO and investigate the influence of the model width and depth. Compared with LSTM-based models that apply similar attention mechanisms, our proposed models achieves comparable scores of BLEU-1,2,3,4 and METEOR, and higher scores of CIDEr. We also test our model on the paragraph annotation dataset, and get higher CIDEr score compared with hierarchical LSTMs