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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).

Gaussian Process Networks (GPNs) are a class of directed graphical models which employ Gaussian processes as priors for the conditional expectation of each variable given its parents in the network. The model allows describing continuous joint distributions in a compact but flexible manner with minimal parametric assumptions on the dependencies between variables. Bayesian structure learning of GPNs requires computing the posterior over graphs of the network and is computationally infeasible even in low dimensions. This work implements Monte Carlo and Markov Chain Monte Carlo methods to sample from the posterior distribution of network structures. As such, the approach follows the Bayesian paradigm, comparing models via their marginal likelihood and computing the posterior probability of the GPN features. Simulation studies show that our method outperforms state-of-the-art algorithms in recovering the graphical structure of the network and provides an accurate approximation of its posterior distribution.

In extreme value theory and other related risk analysis fields, probability weighted moments (PWM) have been frequently used to estimate the parameters of classical extreme value distributions. This method-of-moment technique can be applied when second moments are finite, a reasonable assumption in many environmental domains like climatological and hydrological studies. Three advantages of PWM estimators can be put forward: their simple interpretations, their rapid numerical implementation and their close connection to the well-studied class of U-statistics. Concerning the later, this connection leads to precise asymptotic properties, but non asymptotic bounds have been lacking when off-the-shelf techniques (Chernoff method) cannot be applied, as exponential moment assumptions become unrealistic in many extreme value settings. In addition, large values analysis is not immune to the undesirable effect of outliers, for example, defective readings in satellite measurements or possible anomalies in climate model runs. Recently, the treatment of outliers has sparked some interest in extreme value theory, but results about finite sample bounds in a robust extreme value theory context are yet to be found, in particular for PWMs or tail index estimators. In this work, we propose a new class of robust PWM estimators, inspired by the median-of-means framework of Devroye et al. (2016). This class of robust estimators is shown to satisfy a sub-Gaussian inequality when the assumption of finite second moments holds. Such non asymptotic bounds are also derived under the general contamination model. Our main proposition confirms theoretically a trade-off between efficiency and robustness. Our simulation study indicates that, while classical estimators of PWMs can be highly sensitive to outliers.

By exploiting the theory of skew-symmetric distributions, we generalise existing results in sensitivity analysis by providing the analytic expression of the bias induced by marginalization over an unobserved continuous confounder in a logistic regression model. The expression is approximated and mimics Cochran's formula under some simplifying assumptions. Other link functions and error distributions are also considered. A simulation study is performed to assess its properties. The derivations can also be applied in causal mediation analysis, thereby enlarging the number of circumstances where simple parametric formulations can be used to evaluate causal direct and indirect effects. Standard errors of the causal effect estimators are provided via the first-order Delta method. Simulations show that our proposed estimators perform equally well as others based on numerical methods and that the additional interpretability of the explicit formulas does not compromise their precision. The new estimator has been applied to measure the effect of humidity on upper airways diseases mediated by the presence of common aeroallergens in the air.

Text Classification is the most essential and fundamental problem in Natural Language Processing. While numerous recent text classification models applied the sequential deep learning technique, graph neural network-based models can directly deal with complex structured text data and exploit global information. Many real text classification applications can be naturally cast into a graph, which captures words, documents, and corpus global features. In this survey, we bring the coverage of methods up to 2023, including corpus-level and document-level graph neural networks. We discuss each of these methods in detail, dealing with the graph construction mechanisms and the graph-based learning process. As well as the technological survey, we look at issues behind and future directions addressed in text classification using graph neural networks. We also cover datasets, evaluation metrics, and experiment design and present a summary of published performance on the publicly available benchmarks. Note that we present a comprehensive comparison between different techniques and identify the pros and cons of various evaluation metrics in this survey.

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.

Structural data well exists in Web applications, such as social networks in social media, citation networks in academic websites, and threads data in online forums. Due to the complex topology, it is difficult to process and make use of the rich information within such data. Graph Neural Networks (GNNs) have shown great advantages on learning representations for structural data. However, the non-transparency of the deep learning models makes it non-trivial to explain and interpret the predictions made by GNNs. Meanwhile, it is also a big challenge to evaluate the GNN explanations, since in many cases, the ground-truth explanations are unavailable. In this paper, we take insights of Counterfactual and Factual (CF^2) reasoning from causal inference theory, to solve both the learning and evaluation problems in explainable GNNs. For generating explanations, we propose a model-agnostic framework by formulating an optimization problem based on both of the two casual perspectives. This distinguishes CF^2 from previous explainable GNNs that only consider one of them. Another contribution of the work is the evaluation of GNN explanations. For quantitatively evaluating the generated explanations without the requirement of ground-truth, we design metrics based on Counterfactual and Factual reasoning to evaluate the necessity and sufficiency of the explanations. Experiments show that no matter ground-truth explanations are available or not, CF^2 generates better explanations than previous state-of-the-art methods on real-world datasets. Moreover, the statistic analysis justifies the correlation between the performance on ground-truth evaluation and our proposed metrics.

Causality can be described in terms of a structural causal model (SCM) that carries information on the variables of interest and their mechanistic relations. For most processes of interest the underlying SCM will only be partially observable, thus causal inference tries to leverage any exposed information. Graph neural networks (GNN) as universal approximators on structured input pose a viable candidate for causal learning, suggesting a tighter integration with SCM. To this effect we present a theoretical analysis from first principles that establishes a novel connection between GNN and SCM while providing an extended view on general neural-causal models. We then establish a new model class for GNN-based causal inference that is necessary and sufficient for causal effect identification. Our empirical illustration on simulations and standard benchmarks validate our theoretical proofs.

The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, if not better than, the original dense networks. Sparsity can reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.

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.