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Bayesian Optimization (BO) is a powerful method for optimizing black-box functions by combining prior knowledge with ongoing function evaluations. BO constructs a probabilistic surrogate model of the objective function given the covariates, which is in turn used to inform the selection of future evaluation points through an acquisition function. For smooth continuous search spaces, Gaussian Processes (GPs) are commonly used as the surrogate model as they offer analytical access to posterior predictive distributions, thus facilitating the computation and optimization of acquisition functions. However, in complex scenarios involving optimizations over categorical or mixed covariate spaces, GPs may not be ideal. This paper introduces Simulation Based Bayesian Optimization (SBBO) as a novel approach to optimizing acquisition functions that only requires \emph{sampling-based} access to posterior predictive distributions. SBBO allows the use of surrogate probabilistic models tailored for combinatorial spaces with discrete variables. Any Bayesian model in which posterior inference is carried out through Markov chain Monte Carlo can be selected as the surrogate model in SBBO. In applications involving combinatorial optimization, we demonstrate empirically the effectiveness of SBBO method using various choices of surrogate models.

In temporal extensions of Answer Set Programming (ASP) based on linear-time, the behavior of dynamic systems is captured by sequences of states. While this representation reflects their relative order, it abstracts away the specific times associated with each state. In many applications, however, timing constraints are important like, for instance, when planning and scheduling go hand in hand. We address this by developing a metric extension of linear-time Dynamic Equilibrium Logic, in which dynamic operators are constrained by intervals over integers. The resulting Metric Dynamic Equilibrium Logic provides the foundation of an ASP-based approach for specifying qualitative and quantitative dynamic constraints. As such, it constitutes the most general among a whole spectrum of temporal extensions of Equilibrium Logic. In detail, we show that it encompasses Temporal, Dynamic, Metric, and regular Equilibrium Logic, as well as its classic counterparts once the law of the excluded middle is added.

The principal benefit of unsupervised graph representation learning is that a pre-trained model can be fine-tuned where data or labels are scarce. Existing approaches are domain specific, maintaining consistent node and edge attributes across the pre-training and target datasets. This precludes transfer to other domains. A model capable of positive transfer on arbitrary tasks and domains would represent the first foundation graph model. In this work we use adversarial contrastive learning to present FoToM, a graph pre-training method based on node and edge feature exclusion. We use FoToM to pre-train models over multiple graph domains, producing the first foundation graph models. We demonstrate positive transfer on evaluation datasets from multiple domains, including domains not present in pre-training data. On all datasets performance is at worst on-par and on 76% significantly better than a supervised baseline ($P \leq 0.01$), with an 8 to 40% reduction in error at 95% confidence. Contrary to other research, pre-training on a dataset with the target domain excluded leads us to better performance than pre-training on a dataset from only the target domain. The multi-domain model at worst, matches, and on 56% of tasks, significantly outperforms single-domain ($P \leq 0.01$). These results include when node labels are used in evaluation, where performance is consistently superior to single-domain or non-pre-trained models. Notably, FoToM benefits scenarios in both large or scarce data regimes for the target domains.

As machine learning becomes increasingly prevalent in impactful decisions, recognizing when inference data is outside the model's expected input distribution is paramount for giving context to predictions. Out-of-distribution (OOD) detection methods have been created for this task. Such methods can be split into representation-based or logit-based methods from whether they respectively utilize the model's embeddings or predictions for OOD detection. In contrast to most papers which solely focus on one such group, we address both. We employ dimensionality reduction on feature embeddings in representation-based methods for both time speedups and improved performance. Additionally, we propose DICE-COL, a modification of the popular logit-based method Directed Sparsification (DICE) that resolves an unnoticed flaw. We demonstrate the effectiveness of our methods on the OpenOODv1.5 benchmark framework, where they significantly improve performance and set state-of-the-art results.

Loss function learning is a new meta-learning paradigm that aims to automate the essential task of designing a loss function for a machine learning model. Existing techniques for loss function learning have shown promising results, often improving a model's training dynamics and final inference performance. However, a significant limitation of these techniques is that the loss functions are meta-learned in an offline fashion, where the meta-objective only considers the very first few steps of training, which is a significantly shorter time horizon than the one typically used for training deep neural networks. This causes significant bias towards loss functions that perform well at the very start of training but perform poorly at the end of training. To address this issue we propose a new loss function learning technique for adaptively updating the loss function online after each update to the base model parameters. The experimental results show that our proposed method consistently outperforms the cross-entropy loss and offline loss function learning techniques on a diverse range of neural network architectures and datasets.

Many machine learning approaches for decision making, such as reinforcement learning, rely on simulators or predictive models to forecast the time-evolution of quantities of interest, e.g., the state of an agent or the reward of a policy. Forecasts of such complex phenomena are commonly described by highly nonlinear dynamical systems, making their use in optimization-based decision-making challenging. Koopman operator theory offers a beneficial paradigm for addressing this problem by characterizing forecasts via linear time-invariant (LTI) ODEs, turning multi-step forecasts into sparse matrix multiplication. Though there exists a variety of learning approaches, they usually lack crucial learning-theoretic guarantees, making the behavior of the obtained models with increasing data and dimensionality unclear. We address the aforementioned by deriving a universal Koopman-invariant reproducing kernel Hilbert space (RKHS) that solely spans transformations into LTI dynamical systems. The resulting Koopman Kernel Regression (KKR) framework enables the use of statistical learning tools from function approximation for novel convergence results and generalization error bounds under weaker assumptions than existing work. Our experiments demonstrate superior forecasting performance compared to Koopman operator and sequential data predictors in RKHS.

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.

Contrastive learning models have achieved great success in unsupervised visual representation learning, which maximize the similarities between feature representations of different views of the same image, while minimize the similarities between feature representations of views of different images. In text summarization, the output summary is a shorter form of the input document and they have similar meanings. In this paper, we propose a contrastive learning model for supervised abstractive text summarization, where we view a document, its gold summary and its model generated summaries as different views of the same mean representation and maximize the similarities between them during training. We improve over a strong sequence-to-sequence text generation model (i.e., BART) on three different summarization datasets. Human evaluation also shows that our model achieves better faithfulness ratings compared to its counterpart without contrastive objectives.

We investigate a lattice-structured LSTM model for Chinese NER, which encodes a sequence of input characters as well as all potential words that match a lexicon. Compared with character-based methods, our model explicitly leverages word and word sequence information. Compared with word-based methods, lattice LSTM does not suffer from segmentation errors. Gated recurrent cells allow our model to choose the most relevant characters and words from a sentence for better NER results. Experiments on various datasets show that lattice LSTM outperforms both word-based and character-based LSTM baselines, achieving the best results.