GroupEnc: encoder with group loss for global structure preservation

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.

Topologically Regularized Data Embeddings

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.

Distilling Deep RL Models Into Interpretable Neuro-Fuzzy Systems

Deep Reinforcement Learning uses a deep neural network to encode a policy, which achieves very good performance in a wide range of applications but is widely regarded as a black box model. A more interpretable alternative to deep networks is given by neuro-fuzzy controllers. Unfortunately, neuro-fuzzy controllers often need a large number of rules to solve relatively simple tasks, making them difficult to interpret. In this work, we present an algorithm to distill the policy from a deep Q-network into a compact neuro-fuzzy controller. This allows us to train compact neuro-fuzzy controllers through distillation to solve tasks that they are unable to solve directly, combining the flexibility of deep reinforcement learning and the interpretability of compact rule bases. We demonstrate the algorithm on three well-known environments from OpenAI Gym, where we nearly match the performance of a DQN agent using only 2 to 6 fuzzy rules.

PDD-SHAP: Fast Approximations for Shapley Values using Functional Decomposition

Because of their strong theoretical properties, Shapley values have become very popular as a way to explain predictions made by black box models. Unfortuately, most existing techniques to compute Shapley values are computationally very expensive. We propose PDD-SHAP, an algorithm that uses an ANOVA-based functional decomposition model to approximate the black-box model being explained. This allows us to calculate Shapley values orders of magnitude faster than existing methods for large datasets, significantly reducing the amortized cost of computing Shapley values when many predictions need to be explained.

Evaluating Feature Attribution Methods in the Image Domain

Feature attribution maps are a popular approach to highlight the most important pixels in an image for a given prediction of a model. Despite a recent growth in popularity and available methods, little attention is given to the objective evaluation of such attribution maps. Building on previous work in this domain, we investigate existing metrics and propose new variants of metrics for the evaluation of attribution maps. We confirm a recent finding that different attribution metrics seem to measure different underlying concepts of attribution maps, and extend this finding to a larger selection of attribution metrics. We also find that metric results on one dataset do not necessarily generalize to other datasets, and methods with desirable theoretical properties such as DeepSHAP do not necessarily outperform computationally cheaper alternatives. Based on these findings, we propose a general benchmarking approach to identify the ideal feature attribution method for a given use case. Implementations of attribution metrics and our experiments are available online.

The Curse Revisited: a Newly Quantified Concept of Meaningful Distances for Learning from High-Dimensional Noisy Data

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 Image Perturbation Reduces $L_p$ Norms of Adversarial Examples While Maintaining Model-to-model Transferability

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.

Cost-efficient segmentation of electron microscopy images using active learning

Over the last decade, electron microscopy has improved up to a point that generating high quality gigavoxel sized datasets only requires a few hours. Automated image analysis, particularly image segmentation, however, has not evolved at the same pace. Even though state-of-the-art methods such as U-Net and DeepLab have improved segmentation performance substantially, the required amount of labels remains too expensive. Active learning is the subfield in machine learning that aims to mitigate this burden by selecting the samples that require labeling in a smart way. Many techniques have been proposed, particularly for image classification, to increase the steepness of learning curves. In this work, we extend these techniques to deep CNN based image segmentation. Our experiments on three different electron microscopy datasets show that active learning can improve segmentation quality by 10 to 15% in terms of Jaccard score compared to standard randomized sampling.

Bayesian Deconvolution of Scanning Electron Microscopy Images Using Point-spread Function Estimation and Non-local Regularization

Microscopy is one of the most essential imaging techniques in life sciences. High-quality images are required in order to solve (potentially life-saving) biomedical research problems. Many microscopy techniques do not achieve sufficient resolution for these purposes, being limited by physical diffraction and hardware deficiencies. Electron microscopy addresses optical diffraction by measuring emitted or transmitted electrons instead of photons, yielding nanometer resolution. Despite pushing back the diffraction limit, blur should still be taken into account because of practical hardware imperfections and remaining electron diffraction. Deconvolution algorithms can remove some of the blur in post-processing but they depend on knowledge of the point-spread function (PSF) and should accurately regularize noise. Any errors in the estimated PSF or noise model will reduce their effectiveness. This paper proposes a new procedure to estimate the lateral component of the point spread function of a 3D scanning electron microscope more accurately. We also propose a Bayesian maximum a posteriori deconvolution algorithm with a non-local image prior which employs this PSF estimate and previously developed noise statistics. We demonstrate visual quality improvements and show that applying our method improves the quality of subsequent segmentation steps.