arXiv subjects

Stephan Günnemann

Publications and source records attributed to Stephan Günnemann.

At least 163 records · Page 9Linked to original sources

arXiv2022

Predict then Propagate: Graph Neural Networks meet Personalized PageRank

Neural message passing algorithms for semi-supervised classification on graphs have recently achieved great success. However, for classifying a node these methods only consider nodes that are a few propagation steps away and the size of this utilized neighborhood is hard to extend. In this paper, we use the relationship between graph convolutional networks (GCN) and PageRank to derive an improved propagation scheme based on personalized PageRank. We utilize this propagation procedure to construct a simple model, personalized propagation of neural predictions (PPNP), and its fast approximation, APPNP. Our model's training time is on par or faster and its number of parameters on par or lower than previous models. It leverages a large, adjustable neighborhood for classification and can be easily combined with any neural network. We show that this model outperforms several recently proposed methods for semi-supervised classification in the most thorough study done so far for GCN-like models. Our implementation is available online.

cs.LG↗

arXiv2022

Diffusion Improves Graph Learning

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.

cs.SI↗

arXiv2022

Directional Message Passing for Molecular Graphs

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.

cs.LG↗

arXiv2022

Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules

Many important tasks in chemistry revolve around molecules during reactions. This requires predictions far from the equilibrium, while most recent work in machine learning for molecules has been focused on equilibrium or near-equilibrium states. In this paper we aim to extend this scope in three ways. First, we propose the DimeNet++ model, which is 8x faster and 10% more accurate than the original DimeNet on the QM9 benchmark of equilibrium molecules. Second, we validate DimeNet++ on highly reactive molecules by developing the challenging COLL dataset, which contains distorted configurations of small molecules during collisions. Finally, we investigate ensembling and mean-variance estimation for uncertainty quantification with the goal of accelerating the exploration of the vast space of non-equilibrium structures. Our DimeNet++ implementation as well as the COLL dataset are available online.

cs.LG↗

arXiv2022

Scalable Optimal Transport in High Dimensions for Graph Distances, Embedding Alignment, and More

The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for large sets of objects. In this work we propose two effective log-linear time approximations of the cost matrix: First, a sparse approximation based on locality-sensitive hashing (LSH) and, second, a Nyström approximation with LSH-based sparse corrections, which we call locally corrected Nyström (LCN). These approximations enable general log-linear time algorithms for entropy-regularized OT that perform well even for the complex, high-dimensional spaces common in deep learning. We analyse these approximations theoretically and evaluate them experimentally both directly and end-to-end as a component for real-world applications. Using our approximations for unsupervised word embedding alignment enables us to speed up a state-of-the-art method by a factor of 3 while also improving the accuracy by 3.1 percentage points without any additional model changes. For graph distance regression we propose the graph transport network (GTN), which combines graph neural networks (GNNs) with enhanced Sinkhorn. GTN outcompetes previous models by 48% and still scales log-linearly in the number of nodes.

cs.LG↗

arXiv2022

Directional Message Passing on Molecular Graphs via Synthetic Coordinates

Graph neural networks that leverage coordinates via directional message passing have recently set the state of the art on multiple molecular property prediction tasks. However, they rely on atom position information that is often unavailable, and obtaining it is usually prohibitively expensive or even impossible. In this paper we propose synthetic coordinates that enable the use of advanced GNNs without requiring the true molecular configuration. We propose two distances as synthetic coordinates: Distance bounds that specify the rough range of molecular configurations, and graph-based distances using a symmetric variant of personalized PageRank. To leverage both distance and angular information we propose a method of transforming normal graph neural networks into directional MPNNs. We show that with this transformation we can reduce the error of a normal graph neural network by 55% on the ZINC benchmark. We furthermore set the state of the art on ZINC and coordinate-free QM9 by incorporating synthetic coordinates in the SMP and DimeNet++ models. Our implementation is available online.

cs.LG↗

arXiv2022

Scaling Graph Neural Networks with Approximate PageRank

Graph neural networks (GNNs) have emerged as a powerful approach for solving many network mining tasks. However, learning on large graphs remains a challenge - many recently proposed scalable GNN approaches rely on an expensive message-passing procedure to propagate information through the graph. We present the PPRGo model which utilizes an efficient approximation of information diffusion in GNNs resulting in significant speed gains while maintaining state-of-the-art prediction performance. In addition to being faster, PPRGo is inherently scalable, and can be trivially parallelized for large datasets like those found in industry settings. We demonstrate that PPRGo outperforms baselines in both distributed and single-machine training environments on a number of commonly used academic graphs. To better analyze the scalability of large-scale graph learning methods, we introduce a novel benchmark graph with 12.4 million nodes, 173 million edges, and 2.8 million node features. We show that training PPRGo from scratch and predicting labels for all nodes in this graph takes under 2 minutes on a single machine, far outpacing other baselines on the same graph. We discuss the practical application of PPRGo to solve large-scale node classification problems at Google.

cs.LG↗

arXiv2022

Supporting AI Engineering on the IoT Edge through Model-Driven TinyML

Software engineering of network-centric Artificial Intelligence (AI) and Internet of Things (IoT) enabled Cyber-Physical Systems (CPS) and services, involves complex design and validation challenges. In this paper, we propose a novel approach, based on the model-driven software engineering paradigm, in particular the domain-specific modeling methodology. We focus on a sub-discipline of AI, namely Machine Learning (ML) and propose the delegation of data analytics and ML to the IoT edge. This way, we may increase the service quality of ML, for example, its availability and performance, regardless of the network conditions, as well as maintaining the privacy, security and sustainability. We let practitioners assign ML tasks to heterogeneous edge devices, including highly resource-constrained embedded microcontrollers with main memories in the order of Kilobytes, and energy consumption in the order of milliwatts. This is known as TinyML. Furthermore, we show how software models with different levels of abstraction, namely platform-independent and platform-specific models can be used in the software development process. Finally, we validate the proposed approach using a case study addressing the predictive maintenance of a hydraulics system with various networked sensors and actuators.

cs.SE↗

arXiv2022

Ab-Initio Potential Energy Surfaces by Pairing GNNs with Neural Wave Functions

Solving the Schrödinger equation is key to many quantum mechanical properties. However, an analytical solution is only tractable for single-electron systems. Recently, neural networks succeeded at modeling wave functions of many-electron systems. Together with the variational Monte-Carlo (VMC) framework, this led to solutions on par with the best known classical methods. Still, these neural methods require tremendous amounts of computational resources as one has to train a separate model for each molecular geometry. In this work, we combine a Graph Neural Network (GNN) with a neural wave function to simultaneously solve the Schrödinger equation for multiple geometries via VMC. This enables us to model continuous subsets of the potential energy surface with a single training pass. Compared to existing state-of-the-art networks, our Potential Energy Surface Network PESNet speeds up training for multiple geometries by up to 40 times while matching or surpassing their accuracy. This may open the path to accurate and orders of magnitude cheaper quantum mechanical calculations.

cs.LG↗

arXiv2022

Generalization of Neural Combinatorial Solvers Through the Lens of Adversarial Robustness

End-to-end (geometric) deep learning has seen first successes in approximating the solution of combinatorial optimization problems. However, generating data in the realm of NP-hard/-complete tasks brings practical and theoretical challenges, resulting in evaluation protocols that are too optimistic. Specifically, most datasets only capture a simpler subproblem and likely suffer from spurious features. We investigate these effects by studying adversarial robustness - a local generalization property - to reveal hard, model-specific instances and spurious features. For this purpose, we derive perturbation models for SAT and TSP. Unlike in other applications, where perturbation models are designed around subjective notions of imperceptibility, our perturbation models are efficient and sound, allowing us to determine the true label of perturbed samples without a solver. Surprisingly, with such perturbations, a sufficiently expressive neural solver does not suffer from the limitations of the accuracy-robustness trade-off common in supervised learning. Although such robust solvers exist, we show empirically that the assessed neural solvers do not generalize well w.r.t. small perturbations of the problem instance.

cs.LG↗

arXiv2022

Natural Posterior Network: Deep Bayesian Uncertainty for Exponential Family Distributions

Uncertainty awareness is crucial to develop reliable machine learning models. In this work, we propose the Natural Posterior Network (NatPN) for fast and high-quality uncertainty estimation for any task where the target distribution belongs to the exponential family. Thus, NatPN finds application for both classification and general regression settings. Unlike many previous approaches, NatPN does not require out-of-distribution (OOD) data at training time. Instead, it leverages Normalizing Flows to fit a single density on a learned low-dimensional and task-dependent latent space. For any input sample, NatPN uses the predicted likelihood to perform a Bayesian update over the target distribution. Theoretically, NatPN assigns high uncertainty far away from training data. Empirically, our extensive experiments on calibration and OOD detection show that NatPN delivers highly competitive performance for classification, regression and count prediction tasks.

cs.LG↗

arXiv2022

Differentiable DAG Sampling

We propose a new differentiable probabilistic model over DAGs (DP-DAG). DP-DAG allows fast and differentiable DAG sampling suited to continuous optimization. To this end, DP-DAG samples a DAG by successively (1) sampling a linear ordering of the node and (2) sampling edges consistent with the sampled linear ordering. We further propose VI-DP-DAG, a new method for DAG learning from observational data which combines DP-DAG with variational inference. Hence,VI-DP-DAG approximates the posterior probability over DAG edges given the observed data. VI-DP-DAG is guaranteed to output a valid DAG at any time during training and does not require any complex augmented Lagrangian optimization scheme in contrast to existing differentiable DAG learning approaches. In our extensive experiments, we compare VI-DP-DAG to other differentiable DAG learning baselines on synthetic and real datasets. VI-DP-DAG significantly improves DAG structure and causal mechanism learning while training faster than competitors.

cs.LG↗

arXiv2022

Is it all a cluster game? -- Exploring Out-of-Distribution Detection based on Clustering in the Embedding Space

It is essential for safety-critical applications of deep neural networks to determine when new inputs are significantly different from the training distribution. In this paper, we explore this out-of-distribution (OOD) detection problem for image classification using clusters of semantically similar embeddings of the training data and exploit the differences in distance relationships to these clusters between in- and out-of-distribution data. We study the structure and separation of clusters in the embedding space and find that supervised contrastive learning leads to well-separated clusters while its self-supervised counterpart fails to do so. In our extensive analysis of different training methods, clustering strategies, distance metrics, and thresholding approaches, we observe that there is no clear winner. The optimal approach depends on the model architecture and selected datasets for in- and out-of-distribution. While we could reproduce the outstanding results for contrastive training on CIFAR-10 as in-distribution data, we find standard cross-entropy paired with cosine similarity outperforms all contrastive training methods when training on CIFAR-100 instead. Cross-entropy provides competitive results as compared to expensive contrastive training methods.

cs.CV↗

arXiv2022

Learning the Dynamics of Physical Systems from Sparse Observations with Finite Element Networks

We propose a new method for spatio-temporal forecasting on arbitrarily distributed points. Assuming that the observed system follows an unknown partial differential equation, we derive a continuous-time model for the dynamics of the data via the finite element method. The resulting graph neural network estimates the instantaneous effects of the unknown dynamics on each cell in a meshing of the spatial domain. Our model can incorporate prior knowledge via assumptions on the form of the unknown PDE, which induce a structural bias towards learning specific processes. Through this mechanism, we derive a transport variant of our model from the convection equation and show that it improves the transfer performance to higher-resolution meshes on sea surface temperature and gas flow forecasting against baseline models representing a selection of spatio-temporal forecasting methods. A qualitative analysis shows that our model disentangles the data dynamics into their constituent parts, which makes it uniquely interpretable.

cs.LG↗

arXiv2022

Multi-Objective Model Selection for Time Series Forecasting

Research on time series forecasting has predominantly focused on developing methods that improve accuracy. However, other criteria such as training time or latency are critical in many real-world applications. We therefore address the question of how to choose an appropriate forecasting model for a given dataset among the plethora of available forecasting methods when accuracy is only one of many criteria. For this, our contributions are two-fold. First, we present a comprehensive benchmark, evaluating 7 classical and 6 deep learning forecasting methods on 44 heterogeneous, publicly available datasets. The benchmark code is open-sourced along with evaluations and forecasts for all methods. These evaluations enable us to answer open questions such as the amount of data required for deep learning models to outperform classical ones. Second, we leverage the benchmark evaluations to learn good defaults that consider multiple objectives such as accuracy and latency. By learning a mapping from forecasting models to performance metrics, we show that our method PARETOSELECT is able to accurately select models from the Pareto front -- alleviating the need to train or evaluate many forecasting models for model selection. To the best of our knowledge, PARETOSELECT constitutes the first method to learn default models in a multi-objective setting.

cs.LG↗

arXiv2022

ML-Quadrat & DriotData: A Model-Driven Engineering Tool and a Low-Code Platform for Smart IoT Services

In this paper, we present ML-Quadrat, an open-source research prototype that is based on the Eclipse Modeling Framework (EMF) and the state of the art in the literature of Model-Driven Software Engineering (MDSE) for smart Cyber-Physical Systems (CPS) and the Internet of Things (IoT). Its envisioned users are mostly software developers who might not have deep knowledge and skills in the heterogeneous IoT platforms and the diverse Artificial Intelligence (AI) technologies, specifically regarding Machine Learning (ML). ML-Quadrat is released under the terms of the Apache 2.0 license on Github. Additionally, we demonstrate an early tool prototype of DriotData, a web-based Low-Code platform targeting citizen data scientists and citizen/end-user software developers. DriotData exploits and adopts ML-Quadrat in the industry by offering an extended version of it as a subscription-based service to companies, mainly Small- and Medium-Sized Enterprises (SME). The current preliminary version of DriotData has three web-based model editors: text-based, tree-/form-based and diagram-based. The latter is designed for domain experts in the problem or use case domains (namely the IoT vertical domains) who might not have knowledge and skills in the field of IT. Finally, a short video demonstrating the tools is available on YouTube: https://youtu.be/VAuz25w0a5k

cs.SE↗

arXiv2022

Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph)

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

cs.LG↗

arXiv2021

Detecting Anomalous Event Sequences with Temporal Point Processes

Automatically detecting anomalies in event data can provide substantial value in domains such as healthcare, DevOps, and information security. In this paper, we frame the problem of detecting anomalous continuous-time event sequences as out-of-distribution (OoD) detection for temporal point processes (TPPs). First, we show how this problem can be approached using goodness-of-fit (GoF) tests. We then demonstrate the limitations of popular GoF statistics for TPPs and propose a new test that addresses these shortcomings. The proposed method can be combined with various TPP models, such as neural TPPs, and is easy to implement. In our experiments, we show that the proposed statistic excels at both traditional GoF testing, as well as at detecting anomalies in simulated and real-world data.

cs.LG↗