Stochastic-gradient MCMC methods enable scalable Bayesian posterior sampling but often suffer from sensitivity to minibatch size and gradient noise. To address this, we propose Stochastic Gradient Lattice Random Walk (SGLRW), an extension of the Lattice Random Walk discretization. Unlike conventional Stochastic Gradient Langevin Dynamics (SGLD), SGLRW introduces stochastic noise only through the off-diagonal elements of the update covariance; this yields greater robustness to minibatch size while retaining asymptotic correctness. Furthermore, as comparison we analyze a natural analogue of SGLD utilizing gradient clipping. Experimental validation on Bayesian regression and classification demonstrates that SGLRW remains stable in regimes where SGLD fails, including in the presence of heavy-tailed gradient noise, and matches or improves predictive performance.

Originating from lectures delivered at the African Institute of Mathematical Sciences, this book presents a unifying perspective on traditional and modern methods in generative AI and stochastic thermodynamics. By relating the core topics in machine learning to the notion of (variational) free-energy, a bridge is built between methods such as latent variable models, variational auto-encoders, optimal control, optimal transport, normalizing flows and diffusion models and concepts such as entropy production and fluctuation theorems in stochastic thermodynamics. Structured into three main parts, the book commences by setting up the required mathematical and statistical physics preliminaries needed to make it broadly accessible. The largest part of the book then focuses on building intuition of major advances in generative AI by considering discrete time processes and their relationship to topics in stochastic thermodynamics. Finally, the authors take a short excursion to the continuous time domain for the more advanced learner.

Estimating relative free energy differences between multiple thermodynamic states lies at the core of numerous problems in computational biochemistry. Traditional estimators, such as Free Energy Perturbation and its non-equilibrium counterpart based on the Jarzynski equality, rely on defining a switching protocol between thermodynamic states and computing the free energy difference from the work performed during this process. In this work, we present a method for learning such switching protocols within the class of escorted protocols that combine deterministic and stochastic steps. For this purpose, we use Conditional Flow Matching, and introduce Conditional Density Matching (CDM) for the purpose of estimating the change in Free-Energy. We further reduce the variance in the multistate setting by coupling multiple flows between thermodynamic states into a Flow Graph, enforcing estimator consistency across different transition paths.

We consider the problem of Sampling Transition Paths: Given two metastable conformational states of a molecular system, \eg\ a folded and unfolded protein, we aim to sample the most likely transition path between the two states. Sampling such a transition path is computationally expensive due to the existence of high free energy barriers between the two states. To circumvent this, previous work has focused on simplifying the trajectories to occur along specific molecular descriptors called Collective Variables (CVs). However, finding CVs is non trivial and requires chemical intuition. For larger molecules, where intuition is not sufficient, using these CV-based methods biases the transition along possibly irrelevant dimensions. In this work, we propose a method for sampling transition paths that considers the entire geometry of the molecules. We achieve this by relating the problem to recent works on the Schr\"odinger bridge problem and stochastic optimal control. Using this relation, we construct a path integral method that incorporates important characteristics of molecular systems such as second-order dynamics and invariance to rotations and translations. We demonstrate our method on commonly studied protein structures like Alanine Dipeptide, and also consider larger proteins such as Polyproline and Chignolin.

We consider the problem of sampling transition paths between two given metastable states of a molecular system, eg. 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 Schrodinger 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.

A Classification-by-Components network (CBC) operates under the assumption that every input image can be classified based on its decomposition into a set of components. An important characteristic of these components is that they can be used in the decomposition of images from different classes. The components are class independent. In this work, we discuss the latent class structure encoded in the sharing of components between classes. We propose to visualize this structure using a Shared Component Graph (SCG). Consecutively we discuss the insight into the decision making process of a CBC the visualization can provide.

Methods for adversarial robustness certification aim to provide an upper bound on the test error of a classifier under adversarial manipulation of its input. Current certification methods are computationally expensive and limited to attacks that optimize the manipulation with respect to a norm. We overcome these limitations by investigating the robustness properties of Nearest Prototype Classifiers (NPCs) like learning vector quantization and large margin nearest neighbor. For this purpose, we study the hypothesis margin. We prove that if NPCs use a dissimilarity measure induced by a seminorm, the hypothesis margin is a tight lower bound on the size of adversarial attacks and can be calculated in constant time—this provides the first adversarial robustness certificate calculable in reasonable time. Finally, we show that each NPC trained by a triplet loss maximizes the hypothesis margin and is therefore optimized for adversarial robustness. In the presented evaluation, we demonstrate that NPCs optimized for adversarial robustness are competitive with state-of-the-art methods and set a new benchmark with respect to computational complexity for robustness certification.

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 extent. 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 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. In parallel, a class-wise reasoning strategy based on these components is learned to solve the classification problem. In contrast to other work on reasoning, we propose three different types of reasoning: positive, negative, and indefinite. These three types together form a probability space to provide a probabilistic classifier. The decomposition of objects into generic components combined with the probabilistic reasoning provides by design a clear interpretation of the classification decision process. The evaluation of the approach on MNIST shows that CBCs are viable classifiers. Additionally, we demonstrate that the inherent interpretability offers a profound understanding of the classification behavior such that we can explain the success of an adversarial attack. The method's scalability is successfully tested using the IMAGENET dataset.

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.