Driven by steady progress in deep generative modeling, simulation-based inference (SBI) has emerged as the workhorse for inferring the parameters of stochastic simulators. However, recent work has demonstrated that model misspecification can harm SBI's reliability, preventing its adoption in important applications where only misspecified simulators are available. This work introduces robust posterior estimation (RoPE), a framework that overcomes model misspecification with a small real-world calibration set of ground truth parameter measurements. We formalize the misspecification gap as the solution of an optimal transport (OT) problem between learned representations of real-world and simulated observations, allowing RoPE to learn a model of the misspecification without placing additional assumptions on its nature. RoPE shows how the calibration set and OT together offer a controllable balance between calibrated uncertainty and informative inference even under severely misspecified simulators. Results on four synthetic tasks and two real-world problems with ground-truth labels demonstrate that RoPE outperforms baselines and consistently returns informative and calibrated credible intervals.

Invertible neural networks (INNs) have been used to design generative models, implement memory-saving gradient computation, and solve inverse problems. In this work, we show that commonly-used INN architectures suffer from exploding inverses and are thus prone to becoming numerically non-invertible. Across a wide range of INN use-cases, we reveal failures including the non-applicability of the change-of-variables formula on in- and out-of-distribution (OOD) data, incorrect gradients for memory-saving backprop, and the inability to sample from normalizing flow models. We further derive bi-Lipschitz properties of atomic building blocks of common architectures. These insights into the stability of INNs then provide ways forward to remedy these failures. For tasks where local invertibility is sufficient, like memory-saving backprop, we propose a flexible and efficient regularizer. For problems where global invertibility is necessary, such as applying normalizing flows on OOD data, we show the importance of designing stable INN building blocks.

Adversarial examples are malicious inputs crafted to induce misclassification. Commonly studied \emph{sensitivity-based} adversarial examples introduce semantically-small changes to an input that result in a different model prediction. This paper studies a complementary failure mode, \emph{invariance-based} adversarial examples, that introduce minimal semantic changes that modify an input’s true label yet preserve the model’s prediction. We demonstrate fundamental tradeoffs between these two types of adversarial examples. We show that defenses against sensitivity-based attacks actively harm a model’s accuracy on invariance-based attacks, and that new approaches are needed to resist both attack types. In particular, we break state-of-the-art adversarially-trained and \emph{certifiably-robust} models by generating small perturbations that the models are (provably) robust to, yet that change an input’s class according to human labelers. Finally, we formally show that the existence of excessively invariant classifiers arises from the presence of \emph{overly-robust} predictive features in standard datasets.

We show that standard ResNet architectures can be made invertible, allowing the same model to be used for classification, density estimation, and generation. Typically, enforcing invertibility requires partitioning dimensions or restricting network architectures. In contrast, our approach only requires adding a simple normalization step during training, already available in standard frameworks. Invertible ResNets define a generative model which can be trained by maximum likelihood on unlabeled data. To compute likelihoods, we introduce a tractable approximation to the Jacobian log-determinant of a residual block. Our empirical evaluation shows that invertible ResNets perform competitively with both state-of-the-art image classifiers and flow-based generative models, something that has not been previously achieved with a single architecture.

Flow-based generative models parameterize probability distributions through an invertible transformation and can be trained by maximum likelihood. Invertible residual networks provide a flexible family of transformations where only Lipschitz conditions rather than strict architectural constraints are needed for enforcing invertibility. However, prior work trained invertible residual networks for density estimation by relying on biased log-density estimates whose bias increased with the network's expressiveness. We give a tractable unbiased estimate of the log density, and reduce the memory required during training by a factor of ten. Furthermore, we improve invertible residual blocks by proposing the use of activation functions that avoid gradient saturation and generalizing the Lipschitz condition to induced mixed norms. The resulting approach, called Residual Flows, achieves state-of-the-art performance on density estimation amongst flow-based models, and outperforms networks that use coupling blocks at joint generative and discriminative modeling.

Motivation: Tumor classification using imaging mass spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are required to fully process the data. Since mass spectra exhibit certain structural similarities to image data, deep learning may offer a promising strategy for classification of IMS data as it has been successfully applied to image classification. Results: Methodologically, we propose an adapted architecture based on deep convolutional networks to handle the characteristics of mass spectrometry data, as well as a strategy to interpret the learned model in the spectral domain based on a sensitivity analysis. The proposed methods are evaluated on two algorithmically challenging tumor classification tasks and compared to a baseline approach. Competitiveness of the proposed methods is shown on both tasks by studying the performance via cross-validation. Moreover, the learned models are analyzed by the proposed sensitivity analysis revealing biologically plausible effects as well as confounding factors of the considered tasks. Thus, this study may serve as a starting point for further development of deep learning approaches in IMS classification tasks. Availability and implementation: https://gitlab.informatik.uni-bremen.de/digipath/Deep_Learning_for_Tumor_Classification_in_IMS. Contact: [email protected] or [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.