Research Group Stephan Günnemann

Recent advancements in generative modeling, particularly diffusion models, have opened new directions for time series modeling, achieving state-of-the-art performance in forecasting and synthesis. However, the reliance of diffusion-based models on a simple, fixed prior complicates the generative process since the data and prior distributions differ significantly. We introduce TSFlow, a conditional flow matching (CFM) model for time series combining Gaussian processes, optimal transport paths, and data-dependent prior distributions. By incorporating (conditional) Gaussian processes, TSFlow aligns the prior distribution more closely with the temporal structure of the data, enhancing both unconditional and conditional generation. Furthermore, we propose conditional prior sampling to enable probabilistic forecasting with an unconditionally trained model. In our experimental evaluation on eight real-world datasets, we demonstrate the generative capabilities of TSFlow, producing high-quality unconditional samples. Finally, we show that both conditionally and unconditionally trained models achieve competitive results across multiple forecasting benchmarks.

Neural network sparsification is a promising avenue to save computational time and memory costs, especially in an age where many successful AI models are becoming too large to naïvely deploy on consumer hardware. While much work has focused on different weight pruning criteria, the overall sparsifiability of the network, i.e., its capacity to be pruned without quality loss, has often been overlooked. We present Sparsifiability via the Marginal likelihood (SpaM), a pruning framework that highlights the effectiveness of using the Bayesian marginal likelihood in conjunction with sparsity-inducing priors for making neural networks more sparsifiable. Our approach implements an automatic Occam’s razor that selects the most sparsifiable model that still explains the data well, both for structured and unstructured sparsification. In addition, we demonstrate that the pre-computed posterior Hessian approximation used in the Laplace approximation can be re-used to define a cheap pruning criterion, which outperforms many existing (more expensive) approaches. We demonstrate the effectiveness of our framework, especially at high sparsity levels, across a range of different neural network architectures and datasets.

Hierarchical clustering has usually been addressed by discrete optimization using heuristics or continuous optimization of relaxed scores for hierarchies. In this work, we propose to optimize expected scores under a probabilistic model over hierarchies. (1) We show theoretically that the global optimal values of the expected Dasgupta cost and Tree-Sampling divergence (TSD), two unsupervised metrics for hierarchical clustering, are equal to the optimal values of their discrete counterparts contrary to some relaxed scores. (2) We propose Expected Probabilistic Hierarchies (EPH), a probabilistic model to learn hierarchies in data by optimizing expected scores. EPH uses differentiable hierarchy sampling enabling end-to-end gradient descent based optimization, and an unbiased subgraph sampling approach to scale to large datasets. (3) We evaluate EPH on synthetic and real-world datasets including vector and graph datasets. EPH outperforms all other approaches quantitatively and provides meaningful hierarchies in qualitative evaluations.

Machine learning models are highly vulnerable to label flipping, i.e., the adversarial modification (poisoning) of training labels to compromise performance. Thus, deriving robustness certificates is important to guarantee that test predictions remain unaffected and to understand worst-case robustness behavior. However, for Graph Neural Networks (GNNs), the problem of certifying label flipping has so far been unsolved. We change this by introducing an exact certification method, deriving both sample-wise and collective certificates. Our method leverages the Neural Tangent Kernel (NTK) to capture the training dynamics of wide networks enabling us to reformulate the bilevel optimization problem representing label flipping into a Mixed-Integer Linear Program (MILP). We apply our method to certify a broad range of GNN architectures in node classification tasks. Thereby, concerning the worst-case robustness to label flipping: (i) we establish hierarchies of GNNs on different benchmark graphs; (ii) quantify the effect of architectural choices such as activations, depth and skip-connections; and surprisingly, (iii) uncover a novel phenomenon of the robustness plateauing for intermediate perturbation budgets across all investigated datasets and architectures. While we focus on GNNs, our certificates are applicable to sufficiently wide NNs in general through their NTK. Thus, our work presents the first exact certificate to a poisoning attack ever derived for neural networks, which could be of independent interest.

Bayesian inference in deep neural networks is challenging due to the high-dimensional, strongly multi-modal parameter posterior density landscape. Markov chain Monte Carlo approaches asymptotically recover the true posterior but are considered prohibitively expensive for large modern architectures. Local methods, which have emerged as a popular alternative, focus on specific parameter regions that can be approximated by functions with tractable integrals. While these often yield satisfactory empirical results, they fail, by definition, to account for the multi-modality of the parameter posterior. In this work, we argue that the dilemma between exact-but-unaffordable and cheap-but-inexact approaches can be mitigated by exploiting symmetries in the posterior landscape. Such symmetries, induced by neuron interchangeability and certain activation functions, manifest in different parameter values leading to the same functional output value. We show theoretically that the posterior predictive density in Bayesian neural networks can be restricted to a symmetry-free parameter reference set. By further deriving an upper bound on the number of Monte Carlo chains required to capture the functional diversity, we propose a straightforward approach for feasible Bayesian inference. Our experiments suggest that efficient sampling is indeed possible, opening up a promising path to accurate uncertainty quantification in deep learning.

Bayesian inference in deep neural networks is challenging due to the high-dimensional, strongly multi-modal parameter posterior density landscape. Markov chain Monte Carlo approaches asymptotically recover the true posterior but are considered prohibitively expensive for large modern architectures. Local methods, which have emerged as a popular alternative, focus on specific parameter regions that can be approximated by functions with tractable integrals. While these often yield satisfactory empirical results, they fail, by definition, to account for the multi-modality of the parameter posterior. Such coarse approximations can be detrimental in practical applications, notably safety-critical ones. In this work, we argue that the dilemma between exact-but-unaffordable and cheap-but-inexact approaches can be mitigated by exploiting symmetries in the posterior landscape. These symmetries, induced by neuron interchangeability and certain activation functions, manifest in different parameter values leading to the same functional output value. We show theoretically that the posterior predictive density in Bayesian neural networks can be restricted to a symmetry-free parameter reference set. By further deriving an upper bound on the number of Monte Carlo chains required to capture the functional diversity, we propose a straightforward approach for feasible Bayesian inference. Our experiments suggest that efficient sampling is indeed possible, opening up a promising path to accurate uncertainty quantification in deep learning.

A powerful framework for studying graphs is to consider them as geometric graphs: nodes are randomly sampled from an underlying metric space, and any pair of nodes is connected if their distance is less than a specified neighborhood radius. Currently, the literature mostly focuses on uniform sampling and constant neighborhood radius. However, real-world graphs are likely to be better represented by a model in which the sampling density and the neighborhood radius can both vary over the latent space. For instance, in a social network communities can be modeled as densely sampled areas, and hubs as nodes with larger neighborhood radius. In this work, we first perform a rigorous mathematical analysis of this (more general) class of models, including derivations of the resulting graph shift operators. The key insight is that graph shift operators should be corrected in order to avoid potential distortions introduced by the non-uniform sampling. Then, we develop methods to estimate the unknown sampling density in a self-supervised fashion. Finally, we present exemplary applications in which the learnt density is used to 1) correct the graph shift operator and improve performance on a variety of tasks, 2) improve pooling, and 3) extract knowledge from networks. Our experimental findings support our theory and provide strong evidence for our model.

Temporal point processes (TPPs) provide a natural framework for modeling continuous-time event data such as earthquake catalogs in seismology or spike trains in neuroscience. Unlike conventional TPP models, neural TPPs are able to capture complex patterns present in real-world event data. The two main themes of this thesis are design of flexible, tractable and efficient neural TPP models, and their applications to real-world problems.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully.We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

Randomized smoothing is one of the most promising frameworks for certifying the adversarial robustness of machine learning models, including Graph Neural Networks (GNNs). Yet, existing randomized smoothing certificates for GNNs are overly pessimistic since they treat the model as a black box, ignoring the underlying architecture. To remedy this, we propose novel gray-box certificates that exploit the message-passing principle of GNNs: We randomly intercept messages and carefully analyze the probability that messages from adversarially controlled nodes reach their target nodes. Compared to existing certificates, we certify robustness to much stronger adversaries that control entire nodes in the graph and can arbitrarily manipulate node features. Our certificates provide stronger guarantees for attacks at larger distances, as messages from farther-away nodes are more likely to get intercepted. We demonstrate the effectiveness of our method on various models and datasets. Since our gray-box certificates consider the underlying graph structure, we can significantly improve certifiable robustness by applying graph sparsification.

In this thesis we look at graph neural networks (GNNs) from a perspective of adversarial robustness. We generalize the notion of adversarial attacks – small perturbations to the input data deliberately crafted to mislead a machine learning model – from traditional vector data such as images to graphs. We further propose robustness certification procedures for perturbations of the node attributes as well as the graph structure.

Modeling sets is an important problem in machine learning since this type of data can be found in many domains. A promising approach defines a family of permutation invariant densities with continuous normalizing flows. This allows us to maximize the likelihood directly and sample new realizations with ease. In this work, we demonstrate how calculating the trace, a crucial step in this method, raises issues that occur both during training and inference, limiting its practicality. We propose an alternative way of defining permutation equivariant transformations that give closed form trace. This leads not only to improvements while training, but also to better final performance. We demonstrate the benefits of our approach on point processes and general set modeling.

In tasks like node classification, image segmentation, and named-entity recognition we have a classifier that simultaneously outputs multiple predictions (a vector of labels) based on a single input, i.e. a single graph, image, or document respectively. Existing adversarial robustness certificates consider each prediction independently and are thus overly pessimistic for such tasks. They implicitly assume that an adversary can use different perturbed inputs to attack different predictions, ignoring the fact that we have a single shared input. We propose the first collective robustness certificate which computes the number of predictions that are simultaneously guaranteed to remain stable under perturbation, i.e. cannot be attacked. We focus on Graph Neural Networks and leverage their locality property - perturbations only affect the predictions in a close neighborhood - to fuse multiple single-node certificates into a drastically stronger collective certificate. For example, on the Citeseer dataset our collective certificate for node classification increases the average number of certifiable feature perturbations from 7 to 351.

Perturbations targeting the graph structure have proven to be extremely effective in reducing the performance of Graph Neural Networks (GNNs), and traditional defenses such as adversarial training do not seem to be able to improve robustness. This work is motivated by the observation that adversarially injected edges effectively can be viewed as additional samples to a node’s neighborhood aggregation function, which results in distorted aggregations accumulating over the layers. Conventional GNN aggregation functions, such as a sum or mean, can be distorted arbitrarily by a single outlier. We propose a robust aggregation function motivated by the field of robust statistics. Our approach exhibits the largest possible breakdown point of 0.5, which means that the bias of the aggregation is bounded as long as the fraction of adversarial edges of a node is less than 50%. Our novel aggregation function, Soft Medoid, is a fully differentiable generalization of the Medoid and therefore lends itself well for end-to-end deep learning. Equipping a GNN with our aggregation improves the robustness with respect to structure perturbations on Cora ML by a factor of 3 (and 5.5 on Citeseer) and by a factor of 8 for low-degree nodes.

Temporal point process (TPP) models combined with recurrent neural networks provide a powerful framework for modeling continuous-time event data. While such models are flexible, they are inherently sequential and therefore cannot benefit from the parallelism of modern hardware. By exploiting the recent developments in the field of normalizing flows, we design TriTPP - a new class of non-recurrent TPP models, where both sampling and likelihood computation can be done in parallel. TriTPP matches the flexibility of RNN-based methods but permits several orders of magnitude faster sampling. This enables us to use the new model for variational inference in continuous-time discrete-state systems. We demonstrate the advantages of the proposed framework on synthetic and real-world datasets.

Recent works show that message-passing neural networks (MPNNs) can be fooled by adversarial attacks on both the node attributes and the graph structure. Since MPNNs are currently being rapidly adopted in real-world applications, it is thus crucial to improve their reliablility and robustness. While there has been progress on robustness certification of MPNNs under perturbation of the node attributes, no existing method can handle structural perturbations. These perturbations are especially challenging because they alter the message passing scheme itself. In this work we close this gap and propose the first method to certify robustness of Graph Convolutional Networks (GCNs) under perturbations of the graph structure. We show how this problem can be expressed as a jointly constrained bilinear program - a challenging, yet well-studied class of problems - and propose a novel branch-and-bound algorithm to obtain lower bounds on the global optimum. These lower bounds are significantly tighter and can certify up to twice as many nodes compared to a standard linear relaxation.

Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.

Temporal point processes are the dominant paradigm for modeling sequences of events happening at irregular intervals. The standard way of learning in such models is by estimating the conditional intensity function. However, parameterizing the intensity function usually incurs several trade-offs. We show how to overcome the limitations of intensity-based approaches by directly modeling the conditional distribution of inter-event times. We draw on the literature on normalizing flows to design models that are flexible and efficient. We additionally propose a simple mixture model that matches the flexibility of flow-based models, but also permits sampling and computing moments in closed form. The proposed models achieve state-of-the-art performance in standard prediction tasks and are suitable for novel applications, such as learning sequence embeddings and imputing missing data.

Asynchronous event sequences are the basis of many applications throughout different industries. In this work, we tackle the task of predicting the next event (given a history), and how this prediction changes with the passage of time. Since at some time points (e.g. predictions far into the future) we might not be able to predict anything with confidence, capturing uncertainty in the predictions is crucial. We present two new architectures, WGP-LN and FD-Dir, modelling the evolution of the distribution on the probability simplex with time-dependent logistic normal and Dirichlet distributions. In both cases, the combination of RNNs with either Gaussian process or function decomposition allows to express rich temporal evolution of the distribution parameters, and naturally captures uncertainty. Experiments on class prediction, time prediction and anomaly detection demonstrate the high performances of our models on various datasets compared to other approaches.

Despite the exploding interest in graph neural networks there has been little effort to verify and improve their robustness. This is even more alarming given recent findings showing that they are extremely vulnerable to adversarial attacks on both the graph structure and the node attributes. We propose the first method for verifying certifiable (non-)robustness to graph perturbations for a general class of models that includes graph neural networks and label/feature propagation. By exploiting connections to PageRank and Markov decision processes our certificates can be efficiently (and under many threat models exactly) computed. Furthermore, we investigate robust training procedures that increase the number of certifiably robust nodes while maintaining or improving the clean predictive accuracy.

Graph convolution is the core of most Graph Neural Networks (GNNs) and usually approximated by message passing between direct (one-hop) neighbors. In this work, we remove the restriction of using only the direct neighbors by introducing a powerful, yet spatially localized graph convolution: Graph diffusion convolution (GDC). GDC leverages generalized graph diffusion, examples of which are the heat kernel and personalized PageRank. It alleviates the problem of noisy and often arbitrarily defined edges in real graphs. We show that GDC is closely related to spectral-based models and thus combines the strengths of both spatial (message passing) and spectral methods. We demonstrate that replacing message passing with graph diffusion convolution consistently leads to significant performance improvements across a wide range of models on both supervised and unsupervised tasks and a variety of datasets. Furthermore, GDC is not limited to GNNs but can trivially be combined with any graph-based model or algorithm (e.g. spectral clustering) without requiring any changes to the latter or affecting its computational complexity. Our implementation is available online.

The goal of network representation learning is to learn low-dimensional node embeddings that capture the graph structure and are useful for solving downstream tasks. However, despite the proliferation of such methods, there is currently no study of their robustness to adversarial attacks. We provide the first adversarial vulnerability analysis on the widely used family of methods based on random walks. We derive efficient adversarial perturbations that poison the network structure and have a negative effect on both the quality of the embeddings and the downstream tasks. We further show that our attacks are transferable since they generalize to many models and are successful even when the attacker is restricted.