The black box problem in machine learning has led to the introduction of an ever-increasing set of explanation methods for complex models. These explanations have different properties, which in turn has led to the problem of method selection: which explanation method is most suitable for a given use case? In this work, we propose a unifying framework of attribution-based explanation methods, which provides a step towards a rigorous study of the similarities and differences of explanations. We first introduce removal-based attribution methods (RBAMs), and show that an extensively broad selection of existing methods can be viewed as such RBAMs. We then introduce the canonical additive decomposition (CAD). This is a general construction for additively decomposing any function based on the central idea of removing (groups of) features. We proceed to show that indeed every valid additive decomposition is an instance of the CAD, and that any removal-based attribution method is associated with a specific CAD. Next, we show that any removal-based attribution method can be completely defined as a game-theoretic value or interaction index for a specific (possibly constant-shifted) cooperative game, which is defined using the corresponding CAD of the method. We then use this intrinsic connection to define formal descriptions of specific behaviours of explanation methods, which we also call functional axioms, and identify sufficient conditions on the corresponding CAD and game-theoretic value or interaction index of an attribution method under which the attribution method is guaranteed to adhere to these functional axioms. Finally, we show how this unifying framework can be used to develop new, efficient approximations for existing explanation methods.

This paper presents TRACE, a tool to analyze the quality of 2D embeddings generated through dimensionality reduction techniques. Dimensionality reduction methods often prioritize preserving either local neighborhoods or global distances, but insights from visual structures can be misleading if the objective has not been achieved uniformly. TRACE addresses this challenge by providing a scalable and extensible pipeline for computing both local and global quality measures. The interactive browser-based interface allows users to explore various embeddings while visually assessing the pointwise embedding quality. The interface also facilitates in-depth analysis by highlighting high-dimensional nearest neighbors for any group of points and displaying high-dimensional distances between points. TRACE enables analysts to make informed decisions regarding the most suitable dimensionality reduction method for their specific use case, by showing the degree and location where structure is preserved in the reduced space.

Unsupervised representation learning methods are widely used for gaining insight into high-dimensional, unstructured, or structured data. In some cases, users may have prior topological knowledge about the data, such as a known cluster structure or the fact that the data is known to lie along a tree- or graph-structured topology. However, generic methods to ensure such structure is salient in the low-dimensional representations are lacking. This negatively impacts the interpretability of low-dimensional embeddings, and plausibly downstream learning tasks. To address this issue, we introduce topological regularization: a generic approach based on algebraic topology to incorporate topological prior knowledge into low-dimensional embeddings. We introduce a class of topological loss functions, and show that jointly optimizing an embedding loss with such a topological loss function as a regularizer yields embeddings that reflect not only local proximities but also the desired topological structure. We include a self-contained overview of the required foundational concepts in algebraic topology, and provide intuitive guidance on how to design topological loss functions for a variety of shapes, such as clusters, cycles, and bifurcations. We empirically evaluate the proposed approach on computational efficiency, robustness, and versatility in combination with linear and non-linear dimensionality reduction and graph embedding methods.

Recent advances in dimensionality reduction have achieved more accurate lower-dimensional embeddings of high-dimensional data. In addition to visualisation purposes, these embeddings can be used for downstream processing, including batch effect normalisation, clustering, community detection or trajectory inference. We use the notion of structure preservation at both local and global levels to create a deep learning model, based on a variational autoencoder (VAE) and the stochastic quartet loss from the SQuadMDS algorithm. Our encoder model, called GroupEnc, uses a 'group loss' function to create embeddings with less global structure distortion than VAEs do, while keeping the model parametric and the architecture flexible. We validate our approach using publicly available biological single-cell transcriptomic datasets, employing RNX curves for evaluation.

Unsupervised feature learning often finds low-dimensional embeddings that capture the structure of complex data. For tasks for which expert prior topological knowledge is available, incorporating this into the learned representation may lead to higher quality embeddings. For example, this may help one to embed the data into a given number of clusters, or to accommodate for noise that prevents one from deriving the distribution of the data over the model directly, which can then be learned more effectively. However, a general tool for integrating different prior topological knowledge into embeddings is lacking. Although differentiable topology layers have been recently developed that can (re)shape embeddings into prespecified topological models, they have two important limitations for representation learning, which we address in this paper. First, the currently suggested topological losses fail to represent simple models such as clusters and flares in a natural manner. Second, these losses neglect all original structural (such as neighborhood) information in the data that is useful for learning. We overcome these limitations by introducing a new set of topological losses, and proposing their usage as a way for topologically regularizing data embeddings to naturally represent a prespecified model. We include thorough experiments on synthetic and real data that highlight the usefulness and versatility of this approach, with applications ranging from modeling high-dimensional single cell data, to graph embedding.

Distances between data points are widely used in point cloud representation learning. Yet, it is no secret that under the effect of noise, these distances-and thus the models based upon them-may lose their usefulness in high dimensions. Indeed, the small marginal effects of the noise may then accumulate quickly, shifting empirical closest and furthest neighbors away from the ground truth. In this paper, we characterize such effects in high-dimensional data using an asymptotic probabilistic expression. Furthermore, while it has been previously argued that neighborhood queries become meaningless and unstable when there is a poor relative discrimination between the furthest and closest point, we conclude that this is not necessarily the case when explicitly separating the ground truth data from the noise. More specifically, we derive that under particular conditions, empirical neighborhood relations affected by noise are still likely to be true even when we observe this discrimination to be poor. We include thorough empirical verification of our results, as well as experiments that interestingly show our derived phase shift where neighbors become random or not is identical to the phase shift where common dimensionality reduction methods perform poorly or well for finding low-dimensional representations of high-dimensional data with dense noise.

Regional adversarial attacks often rely on complicated methods for generating adversarial perturbations, making it hard to compare their efficacy against well-known attacks. In this study, we show that effective regional perturbations can be generated without resorting to complex methods. We develop a very simple regional adversarial perturbation attack method using cross-entropy sign, one of the most commonly used losses in adversarial machine learning. Our experiments on ImageNet with multiple models reveal that, on average, $76\%$ of the generated adversarial examples maintain model-to-model transferability when the perturbation is applied to local image regions. Depending on the selected region, these localized adversarial examples require significantly less $L_p$ norm distortion (for $p \in \{0, 2, \infty\}$) compared to their non-local counterparts. These localized attacks therefore have the potential to undermine defenses that claim robustness under the aforementioned norms.

The input-output mappings learned by state-of-the-art neural networks are significantly discontinuous.It is possible to cause a neural network used for image recognition to misclassify its input by applying very specific, hardly perceptible perturbations to the input, called adversarial perturbations. Many hypotheses have been proposed to explain the existence of these peculiar samples as well as several methods to mitigate them, but a proven explanation remains elusive. In this work, we take steps towards a formal characterization of adversarial perturbations by deriving lower bounds on the magnitudes of perturbations necessary to change the classification of neural networks. The proposed bounds can be computed efficiently, requiring time at most linear in the number of parameters and hyperparameters of the model for any given sample. This makes them suitable for use in model selection, when one wishes to find out which of several proposed classifiers is most robust to adversarial perturbations. They may also be used as a basis for developing techniques to increase the robustness of classifiers, since they enjoy the theoretical guarantee that no adversarial perturbation could possibly be any smaller than the quantities provided by the bounds. We experimentally verify the bounds on the MNIST and CIFAR-10 data sets and find no violations. Additionally, the experimental results suggest that very small adversarial perturbations may occur with nonzero probability on natural samples.