We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy barriers separating the states, these transition paths are unlikely to be sampled with standard Molecular Dynamics (MD) simulation. Traditional methods to augment MD with a bias potential to increase the probability of the transition rely on a dimensionality reduction step based on Collective Variables (CVs). Unfortunately, selecting appropriate CVs requires chemical intuition and traditional methods are therefore not always applicable to larger systems. Additionally, when incorrect CVs are used, the bias potential might not be minimal and bias the system along dimensions irrelevant to the transition. Showing a formal relation between the problem of sampling molecular transition paths, the Schr\"odinger bridge problem and stochastic optimal control with neural network policies, we propose a machine learning method for sampling said transitions. Unlike previous non-machine learning approaches our method, named PIPS, does not depend on CVs. We show that our method successful generates low energy transitions for Alanine Dipeptide as well as the larger Polyproline and Chignolin proteins.

We focus on the problem of efficient sampling and learning of probability densities by incorporating symmetries in probabilistic models. We first introduce Equivariant Stein Variational Gradient Descent algorithm -- an equivariant sampling method based on Stein's identity for sampling from densities with symmetries. Equivariant SVGD explicitly incorporates symmetry information in a density through equivariant kernels which makes the resultant sampler efficient both in terms of sample complexity and the quality of generated samples. Subsequently, we define equivariant energy based models to model invariant densities that are learned using contrastive divergence. By utilizing our equivariant SVGD for training equivariant EBMs, we propose new ways of improving and scaling up training of energy based models. We apply these equivariant energy models for modelling joint densities in regression and classification tasks for image datasets, many-body particle systems and molecular structure generation.

Neural networks are state-of-the-art classification approaches but are generally difficult to interpret. This issue can be partly alleviated by constructing a precise decision process within the neural network. In this work, a network architecture, denoted as Classification-By-Components network (CBC), is proposed. It is restricted to follow an intuitive reasoning based decision process inspired by Biederman's recognition-by-components theory from cognitive psychology. The network is trained to learn and detect generic components that characterize objects.

Adversarial attacks and the development of (deep) neural networks robust against them are currently two widely researched topics. The robustness of Learning Vector Quantization (LVQ) models against adversarial attacks has however not yet been studied to the same extend. We therefore present an extensive evaluation of three LVQ models: Generalized LVQ, Generalized Matrix LVQ and Generalized Tangent LVQ. The evaluation suggests that both Generalized LVQ and Generalized Tangent LVQ have a high base robustness, on par with the current state-of-the-art in robust neural network methods. In contrast to this, Generalized Matrix LVQ shows a high susceptibility to adversarial attacks, scoring consistently behind all other models. Additionally, our numerical evaluation indicates that increasing the number of prototypes per class improves the robustness of the models.

Neural networks currently dominate the machine learning community and they do so for good reasons. Their accuracy on complex tasks such as image classification is unrivaled at the moment and with recent improvements they are reasonably easy to train. Nevertheless, neural networks are lacking robustness and interpretability. Prototype-based vector quantization methods on the other hand are known for being robust and interpretable. For this reason, we propose techniques and strategies to merge both approaches. This contribution will particularly highlight the similarities between them and outline how to construct a prototype-based classification layer for multilayer networks. Additionally, we provide an alternative, prototype-based, approach to the classical convolution operation. Numerical results are not part of this report, instead the focus lays on establishing a strong theoretical framework. By publishing our framework and the respective theoretical considerations and justifications before finalizing our numerical experiments we hope to jump-start the incorporation of prototype-based learning in neural networks and vice versa.