We consider the problem of model selection in Gaussian Markov fields in the sample deficient scenario. In many cases, the underlying networks are embedded into Euclidean spaces which induces significant structure on them. Using this natural spatial structure, we introduce the notion of spatially stationary distributions over geometric graphs directly generalizing the notion of stationary time series to the multidimensional setup lacking time axis. We show that the idea of spatial stationarity leads to a dramatic decrease in the sample complexity of the model selection compared to abstract graphs with the same level of sparsity. For geometric graphs on randomly spread vertices and edges of bounded length, we develop tight information-theoretic bounds on the sample complexity and show that a finite number of independent samples is sufficient for a consistent recovery. Finally, we develop an efficient technique capable of reliably and consistently reconstructing graphs with a bounded number of measurements. Markov random fields, or undirected probabilistic graphical models, provide a structured representation of the joint distributions of families of random variables.

The vast majority of network datasets contains errors and omissions, although this is rarely incorporated in traditional network analysis. Recently, an increasing effort has been made to fill this methodological gap by developing network reconstruction approaches based on Bayesian inference. These approaches, however, rely on assumptions of uniform error rates and on direct estimations of the existence of each edge via repeated measurements, something that is currently unavailable for the majority of network data. Here we develop a Bayesian reconstruction approach that lifts these limitations by not only allowing for heterogeneous errors, but also for individual edge measurements without direct error estimates. Our approach works by coupling the inference approach with structured generative network models, which enable the correlations between edges to be used as reliable error estimates. Although our approach is general, we focus on the stochastic block model as the basic generative process, from which efficient nonparametric inference can be performed, and yields a principled method to infer hierarchical community structure from noisy data. We demonstrate the efficacy of our approach with a variety of empirical and artificial networks.

Future predictions on sequence data (e.g., videos or audios) require the algorithms to capture non-Markovian and compositional properties of high-level semantics. Context-free grammars are natural choices to capture such properties, but traditional grammar parsers (e.g., Earley parser) only take symbolic sentences as inputs. In this paper, we generalize the Earley parser to parse sequence data which is neither segmented nor labeled. This generalized Earley parser integrates a grammar parser with a classifier to find the optimal segmentation and labels, and makes top-down future predictions. Experiments show that our method significantly outperforms other approaches for future human activity prediction.

With the world moving towards being increasingly dependent on computers and automation, one of the main challenges in the current decade has been to build secure applications, systems and networks. Alongside these challenges, the number of threats is rising exponentially due to the attack surface increasing through numerous interfaces offered for each service. To alleviate the impact of these threats, researchers have proposed numerous solutions; however, current tools often fail to adapt to ever-changing architectures, associated threats and 0-days. This manuscript aims to provide researchers with a taxonomy and survey of current dataset composition and current Intrusion Detection Systems (IDS) capabilities and assets. These taxonomies and surveys aim to improve both the efficiency of IDS and the creation of datasets to build the next generation IDS as well as to reflect networks threats more accurately in future datasets. To this end, this manuscript also provides a taxonomy and survey or network threats and associated tools. The manuscript highlights that current IDS only cover 25% of our threat taxonomy, while current datasets demonstrate clear lack of real-network threats and attack representation, but rather include a large number of deprecated threats, hence limiting the accuracy of current machine learning IDS. Moreover, the taxonomies are open-sourced to allow public contributions through a Github repository.

A simple framework Probabilistic Multi-view Graph Embedding (PMvGE) is proposed for multi-view feature learning with many-to-many associations so that it generalizes various existing multi-view methods. PMvGE is a probabilistic model for predicting new associations via graph embedding of the nodes of data vectors with links of their associations. Multi-view data vectors with many-to-many associations are transformed by neural networks to feature vectors in a shared space, and the probability of new association between two data vectors is modeled by the inner product of their feature vectors. While existing multi-view feature learning techniques can treat only either of many-to-many association or non-linear transformation, PMvGE can treat both simultaneously. By combining Mercer's theorem and the universal approximation theorem, we prove that PMvGE learns a wide class of similarity measures across views. Our likelihood-based estimator enables efficient computation of non-linear transformations of data vectors in large-scale datasets by minibatch SGD, and numerical experiments illustrate that PMvGE outperforms existing multi-view methods.

We develop nested automatic differentiation (AD) algorithms for exact inference and learning in integer latent variable models. Recently, Winner, Sujono, and Sheldon showed how to reduce marginalization in a class of integer latent variable models to evaluating a probability generating function which contains many levels of nested high-order derivatives. We contribute faster and more stable AD algorithms for this challenging problem and a novel algorithm to compute exact gradients for learning. These contributions lead to significantly faster and more accurate learning algorithms, and are the first AD algorithms whose running time is polynomial in the number of levels of nesting.

Key to structured prediction is exploiting the problem structure to simplify the learning process. A major challenge arises when data exhibit a local structure (e.g., are made by "parts") that can be leveraged to better approximate the relation between (parts of) the input and (parts of) the output. Recent literature on signal processing, and in particular computer vision, has shown that capturing these aspects is indeed essential to achieve state-of-the-art performance. While such algorithms are typically derived on a case-by-case basis, in this work we propose the first theoretical framework to deal with part-based data from a general perspective. We derive a novel approach to deal with these problems and study its generalization properties within the setting of statistical learning theory. Our analysis is novel in that it explicitly quantifies the benefits of leveraging the part-based structure of the problem with respect to the learning rates of the proposed estimator.

The latest techniques from Neural Networks and Support Vector Machines (SVM) are used to investigate geometric properties of Complete Intersection Calabi-Yau (CICY) threefolds, a class of manifolds that facilitate string model building. An advanced neural network classifier and SVM are employed to (1) learn Hodge numbers and report a remarkable improvement over previous efforts, (2) query for favourability, and (3) predict discrete symmetries, a highly imbalanced problem to which the Synthetic Minority Oversampling Technique (SMOTE) is applied to boost performance. In each case study, we employ a genetic algorithm to optimise the hyperparameters of the neural network. We demonstrate that our approach provides quick diagnostic tools capable of shortlisting quasi-realistic string models based on compactification over smooth CICYs and further supports the paradigm that classes of problems in algebraic geometry can be machine learned.

Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.

Despite the recent successes of probabilistic programming languages (PPLs) in AI applications, PPLs offer only limited support for random variables whose distributions combine discrete and continuous elements. We develop the notion of measure-theoretic Bayesian networks (MTBNs) and use it to provide more general semantics for PPLs with arbitrarily many random variables defined over arbitrary measure spaces. We develop two new general sampling algorithms that are provably correct under the MTBN framework: the lexicographic likelihood weighting (LLW) for general MTBNs and the lexicographic particle filter (LPF), a specialized algorithm for state-space models. We further integrate MTBNs into a widely used PPL system, BLOG, and verify the effectiveness of the new inference algorithms through representative examples.