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Tabular biomedical data is often high-dimensional but with a very small number of samples. Although recent work showed that well-regularised simple neural networks could outperform more sophisticated architectures on tabular data, they are still prone to overfitting on tiny datasets with many potentially irrelevant features. To combat these issues, we propose Weight Predictor Network with Feature Selection (WPFS) for learning neural networks from high-dimensional and small sample data by reducing the number of learnable parameters and simultaneously performing feature selection. In addition to the classification network, WPFS uses two small auxiliary networks that together output the weights of the first layer of the classification model. We evaluate on nine real-world biomedical datasets and demonstrate that WPFS outperforms other standard as well as more recent methods typically applied to tabular data. Furthermore, we investigate the proposed feature selection mechanism and show that it improves performance while providing useful insights into the learning task.

Reliable application of machine learning-based decision systems in the wild is one of the major challenges currently investigated by the field. A large portion of established approaches aims to detect erroneous predictions by means of assigning confidence scores. This confidence may be obtained by either quantifying the model's predictive uncertainty, learning explicit scoring functions, or assessing whether the input is in line with the training distribution. Curiously, while these approaches all state to address the same eventual goal of detecting failures of a classifier upon real-life application, they currently constitute largely separated research fields with individual evaluation protocols, which either exclude a substantial part of relevant methods or ignore large parts of relevant failure sources. In this work, we systematically reveal current pitfalls caused by these inconsistencies and derive requirements for a holistic and realistic evaluation of failure detection. To demonstrate the relevance of this unified perspective, we present a large-scale empirical study for the first time enabling benchmarking confidence scoring functions w.r.t all relevant methods and failure sources. The revelation of a simple softmax response baseline as the overall best performing method underlines the drastic shortcomings of current evaluation in the abundance of publicized research on confidence scoring. Code and trained models are at //github.com/IML-DKFZ/fd-shifts.

Neural networks with random weights appear in a variety of machine learning applications, most prominently as the initialization of many deep learning algorithms and as a computationally cheap alternative to fully learned neural networks. In the present article, we enhance the theoretical understanding of random neural networks by addressing the following data separation problem: under what conditions can a random neural network make two classes $\mathcal{X}^-, \mathcal{X}^+ \subset \mathbb{R}^d$ (with positive distance) linearly separable? We show that a sufficiently large two-layer ReLU-network with standard Gaussian weights and uniformly distributed biases can solve this problem with high probability. Crucially, the number of required neurons is explicitly linked to geometric properties of the underlying sets $\mathcal{X}^-, \mathcal{X}^+$ and their mutual arrangement. This instance-specific viewpoint allows us to overcome the usual curse of dimensionality (exponential width of the layers) in non-pathological situations where the data carries low-complexity structure. We quantify the relevant structure of the data in terms of a novel notion of mutual complexity (based on a localized version of Gaussian mean width), which leads to sound and informative separation guarantees. We connect our result with related lines of work on approximation, memorization, and generalization.

Graph neural networks (GNNs) have been widely used under semi-supervised settings. Prior studies have mainly focused on finding appropriate graph filters (e.g., aggregation schemes) to generalize well for both homophilic and heterophilic graphs. Even though these approaches are essential and effective, they still suffer from the sparsity in initial node features inherent in the bag-of-words representation. Common in semi-supervised learning where the training samples often fail to cover the entire dimensions of graph filters (hyperplanes), this can precipitate over-fitting of specific dimensions in the first projection matrix. To deal with this problem, we suggest a simple and novel strategy; create additional space by flipping the initial features and hyperplane simultaneously. Training in both the original and in the flip space can provide precise updates of learnable parameters. To the best of our knowledge, this is the first attempt that effectively moderates the overfitting problem in GNN. Extensive experiments on real-world datasets demonstrate that the proposed technique improves the node classification accuracy up to 40.2 %

The syntactic structure of a sentence can be represented as a graph where vertices are words and edges indicate syntactic dependencies between them. In this setting, the distance between two syntactically linked words can be defined as the difference between their positions. Here we want to contribute to the characterization of the actual distribution of syntactic dependency distances, and unveil its relationship with short-term memory limitations. We propose a new double-exponential model in which decay in probability is allowed to change after a break-point. This transition could mirror the transition from the processing of words chunks to higher-level structures. We find that a two-regime model -- where the first regime follows either an exponential or a power-law decay -- is the most likely one in all 20 languages we considered, independently of sentence length and annotation style. Moreover, the break-point is fairly stable across languages and averages values of 4-5 words, suggesting that the amount of words that can be simultaneously processed abstracts from the specific language to a high degree. Finally, we give an account of the relation between the best estimated model and the closeness of syntactic dependencies, as measured by a recently introduced optimality score.

Bayesian inference can quantify uncertainty in the predictions of neural networks using posterior distributions for model parameters and network output. By looking at these posterior distributions, one can separate the origin of uncertainty into aleatoric and epistemic. We use the joint distribution of predictive uncertainty and epistemic uncertainty to quantify how this interpretation of uncertainty depends upon model architecture, dataset complexity, and data distributional shifts in image classification tasks. We conclude that the origin of uncertainty is subjective to each neural network and that the quantification of the induced uncertainty from data distributional shifts depends on the complexity of the underlying dataset. Furthermore, we show that the joint distribution of predictive and epistemic uncertainty can be used to identify data domains where the model is most accurate. To arrive at these results, we use two common posterior approximation methods, Monte-Carlo dropout and deep ensembles, for fully-connected, convolutional and attention-based neural networks.

Moment methods are an important means of density estimation, but they are generally strongly dependent on the choice of feasible functions, which severely affects the performance. In this paper, which is a very preliminary version, we propose a non-classical parametrization for density estimation using the sample moments, which does not require the choice of such functions. The parametrization is induced by the squared Hellinger distance, and the solution of it, which is proved to exist and be unique subject to simple prior that does not depend on data, can be obtained by convex optimization. Simulation results show the performance of the proposed estimator in estimating multi-modal densities which are mixtures of different types of functions, with a comparison to the prevailing methods.

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.

Out-of-distribution (OOD) detection is critical to ensuring the reliability and safety of machine learning systems. For instance, in autonomous driving, we would like the driving system to issue an alert and hand over the control to humans when it detects unusual scenes or objects that it has never seen before and cannot make a safe decision. This problem first emerged in 2017 and since then has received increasing attention from the research community, leading to a plethora of methods developed, ranging from classification-based to density-based to distance-based ones. Meanwhile, several other problems are closely related to OOD detection in terms of motivation and methodology. These include anomaly detection (AD), novelty detection (ND), open set recognition (OSR), and outlier detection (OD). Despite having different definitions and problem settings, these problems often confuse readers and practitioners, and as a result, some existing studies misuse terms. In this survey, we first present a generic framework called generalized OOD detection, which encompasses the five aforementioned problems, i.e., AD, ND, OSR, OOD detection, and OD. Under our framework, these five problems can be seen as special cases or sub-tasks, and are easier to distinguish. Then, we conduct a thorough review of each of the five areas by summarizing their recent technical developments. We conclude this survey with open challenges and potential research directions.

In Multi-Label Text Classification (MLTC), one sample can belong to more than one class. It is observed that most MLTC tasks, there are dependencies or correlations among labels. Existing methods tend to ignore the relationship among labels. In this paper, a graph attention network-based model is proposed to capture the attentive dependency structure among the labels. The graph attention network uses a feature matrix and a correlation matrix to capture and explore the crucial dependencies between the labels and generate classifiers for the task. The generated classifiers are applied to sentence feature vectors obtained from the text feature extraction network (BiLSTM) to enable end-to-end training. Attention allows the system to assign different weights to neighbor nodes per label, thus allowing it to learn the dependencies among labels implicitly. The results of the proposed model are validated on five real-world MLTC datasets. The proposed model achieves similar or better performance compared to the previous state-of-the-art models.