DALSA: Domain Adaptation for Supervised Learning From Sparsely Annotated MR Images

We propose a new method that employs transfer learning techniques to effectively correct sampling selection errors introduced by sparse annotations during supervised learning for automated tumor segmentation. The practicality of current learning-based automated tissue classification approaches is severely impeded by their dependency on manually segmented training databases that need to be recreated for each scenario of application, site, or acquisition setup. The comprehensive annotation of reference datasets can be highly labor-intensive, complex, and error-prone. The proposed method derives high-quality classifiers for the different tissue classes from sparse and unambiguous annotations and employs domain adaptation techniques for effectively correcting sampling selection errors introduced by the sparse sampling. The new approach is validated on labeled, multi-modal MR images of 19 patients with malignant gliomas and by comparative analysis on the BraTS 2013 challenge data sets. Compared to training on fully labeled data, we reduced the time for labeling and training by a factor greater than 70 and 180 respectively without sacrificing accuracy. This dramatically eases the establishment and constant extension of large annotated databases in various scenarios and imaging setups and thus represents an important step towards practical applicability of learning-based approaches in tissue classification.

On the Universality of Coupling-based Normalizing Flows

We present a novel theoretical framework for understanding the expressive power of coupling-based normalizing flows such as RealNVP. Despite their prevalence in scientific applications, a comprehensive understanding of coupling flows remains elusive due to their restricted architectures. Existing theorems fall short as they require the use of arbitrarily ill-conditioned neural networks, limiting practical applicability. Additionally, we demonstrate that these constructions inherently lead to volume-preserving flows, a property which we show to be a fundamental constraint for expressivity. We propose a new distributional universality theorem for coupling-based normalizing flows, which overcomes several limitations of prior work. Our results support the general wisdom that the coupling architecture is expressive and provide a nuanced view for choosing the expressivity of coupling functions, bridging a gap between empirical results and theoretical understanding.

Learning Distributions on Manifolds with Free-form Flows

Many real world data, particularly in the natural sciences and computer vision, lie on known Riemannian manifolds such as spheres, tori or the group of rotation matrices. The predominant approaches to learning a distribution on such a manifold require solving a differential equation in order to sample from the model and evaluate densities. The resulting sampling times are slowed down by a high number of function evaluations. In this work, we propose an alternative approach which only requires a single function evaluation followed by a projection to the manifold. Training is achieved by an adaptation of the recently proposed free-form flow framework to Riemannian manifolds. The central idea is to estimate the gradient of the negative log-likelihood via a trace evaluated in the tangent space. We evaluate our method on various manifolds, and find significantly faster inference at competitive performance compared to previous work. We make our code public at https://github.com/vislearn/FFF.

Towards Context-Aware Domain Generalization: Representing Environments with Permutation-Invariant Networks

In this work, we show that information about the context of an input $X$ can improve the predictions of deep learning models when applied in new domains or production environments. We formalize the notion of context as a permutation-invariant representation of a set of data points that originate from the same environment/domain as the input itself. These representations are jointly learned with a standard supervised learning objective, providing incremental information about the unknown outcome. Furthermore, we offer a theoretical analysis of the conditions under which our approach can, in principle, yield benefits, and formulate two necessary criteria that can be easily verified in practice. Additionally, we contribute insights into the kind of distribution shifts for which our approach promises robustness. Our empirical evaluation demonstrates the effectiveness of our approach for both low-dimensional and high-dimensional data sets. Finally, we demonstrate that we can reliably detect scenarios where a model is tasked with unwarranted extrapolation in out-of-distribution (OOD) domains, identifying potential failure cases. Consequently, we showcase a method to select between the most predictive and the most robust model, circumventing the well-known trade-off between predictive performance and robustness.

Consistency Models for Scalable and Fast Simulation-Based Inference

Simulation-based inference (SBI) is constantly in search of more expressive algorithms for accurately inferring the parameters of complex models from noisy data. We present consistency models for neural posterior estimation (CMPE), a new free-form conditional sampler for scalable, fast, and amortized SBI with generative neural networks. CMPE combines the advantages of normalizing flows and flow matching methods into a single generative architecture: It essentially distills a continuous probability flow and enables rapid few-shot inference with an unconstrained architecture that can be tailored to the structure of the estimation problem. Our empirical evaluation demonstrates that CMPE not only outperforms current state-of-the-art algorithms on three hard low-dimensional problems, but also achieves competitive performance in a high-dimensional Bayesian denoising experiment and in estimating a computationally demanding multi-scale model of tumor spheroid growth.

Free-form Flows: Make Any Architecture a Normalizing Flow

Normalizing Flows are generative models that directly maximize the likelihood. Previously, the design of normalizing flows was largely constrained by the need for analytical invertibility. We overcome this constraint by a training procedure that uses an efficient estimator for the gradient of the change of variables formula. This enables any dimension-preserving neural network to serve as a generative model through maximum likelihood training. Our approach allows placing the emphasis on tailoring inductive biases precisely to the task at hand. Specifically, we achieve excellent results in molecule generation benchmarks utilizing $E(n)$-equivariant networks. Moreover, our method is competitive in an inverse problem benchmark, while employing off-the-shelf ResNet architectures.

Sensitivity-Aware Amortized Bayesian Inference

Bayesian inference is a powerful framework for making probabilistic inferences and decisions under uncertainty. Fundamental choices in modern Bayesian workflows concern the specification of the likelihood function and prior distributions, the posterior approximator, and the data. Each choice can significantly influence model-based inference and subsequent decisions, thereby necessitating sensitivity analysis. In this work, we propose a multifaceted approach to integrate sensitivity analyses into amortized Bayesian inference (ABI, i.e., simulation-based inference with neural networks). First, we utilize weight sharing to encode the structural similarities between alternative likelihood and prior specifications in the training process with minimal computational overhead. Second, we leverage the rapid inference of neural networks to assess sensitivity to various data perturbations or pre-processing procedures. In contrast to most other Bayesian approaches, both steps circumvent the costly bottleneck of refitting the model(s) for each choice of likelihood, prior, or dataset. Finally, we propose to use neural network ensembles to evaluate variation in results induced by unreliable approximation on unseen data. We demonstrate the effectiveness of our method in applied modeling problems, ranging from the estimation of disease outbreak dynamics and global warming thresholds to the comparison of human decision-making models. Our experiments showcase how our approach enables practitioners to effectively unveil hidden relationships between modeling choices and inferential conclusions.

Leveraging Self-Consistency for Data-Efficient Amortized Bayesian Inference

We propose a method to improve the efficiency and accuracy of amortized Bayesian inference (ABI) by leveraging universal symmetries in the probabilistic joint model $p(\theta, y)$ of parameters $\theta$ and data $y$. In a nutshell, we invert Bayes' theorem and estimate the marginal likelihood based on approximate representations of the joint model. Upon perfect approximation, the marginal likelihood is constant across all parameter values by definition. However, approximation error leads to undesirable variance in the marginal likelihood estimates across different parameter values. We formulate violations of this symmetry as a loss function to accelerate the learning dynamics of conditional neural density estimators. We apply our method to a bimodal toy problem with an explicit likelihood (likelihood-based) and a realistic model with an implicit likelihood (simulation-based).