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Researcher profile

Stephan Günnemann

Stephan Günnemann contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial Intelligencephysics.comp-phphysics.chem-phSocial and Information NetworksSoftware EngineeringComputation and LanguageComputer Visionmath.NANumerical AnalysisQuantitative MethodsApplicationsBiomoleculesCryptography and SecurityData Structures and AlgorithmsGenomics

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Published work

34 published item(s)

preprint2026arXiv

Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models

In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular systems. However, while classical diffusion sampling usually recovers the training distribution, the corresponding energy-based interpretation of the learned score is often inconsistent with this distribution, even for low-dimensional toy systems. We trace this inconsistency to inaccuracies of the learned score at very small diffusion timesteps, where the model must capture the correct evolution of the data distribution. In this regime, diffusion models fail to satisfy the Fokker-Planck equation, which governs the evolution of the score. We interpret this deviation as one source of the observed inconsistencies and propose an energy-based diffusion model with a Fokker-Planck-derived regularization term to enforce consistency. We demonstrate our approach by sampling and simulating multiple biomolecular systems, including fast-folding proteins, and by introducing a state-of-the-art transferable Boltzmann emulator for dipeptides that supports simulation and achieves improved consistency and efficient sampling. Our code, model weights, and self-contained JAX and PyTorch notebooks are available at https://github.com/noegroup/ScoreMD.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Task-Aware Calibration: Provably Optimal Decoding in LLMs

LLM decoding often relies on the model's predictive distribution to generate an output. Consequently, misalignment with respect to the true generating distribution leads to suboptimal decisions in practice. While a natural solution is to calibrate the model's output distribution, for LLMs, this is ill-posed at the combinatorially vast level of free-form language. We address this by building on the insight that in many tasks, these free-form outputs can be interpreted in a semantically meaningful latent structure, for example, discrete class labels, integers, or sets. We introduce task calibration as a paradigm to calibrate the model's predictive distribution in the task-induced latent space. We apply a decision-theoretic result to show that Minimum Bayes Risk (MBR) decoding on the task-calibrated latent distribution is the optimal decoding strategy on latent model beliefs. Empirically, it consistently improves generation quality across different tasks and baselines. We also introduce Task Calibration Error (TCE), an application-aware calibration metric that quantifies the excess loss due to miscalibration. Our work demonstrates that task calibration enables more reliable model decisions across various tasks and applications.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Graph Data Augmentation for Graph Machine Learning: A Survey

Data augmentation has recently seen increased interest in graph machine learning given its demonstrated ability to improve model performance and generalization by added training data. Despite this recent surge, the area is still relatively under-explored, due to the challenges brought by complex, non-Euclidean structure of graph data, which limits the direct analogizing of traditional augmentation operations on other types of image, video or text data. Our work aims to give a necessary and timely overview of existing graph data augmentation methods; notably, we present a comprehensive and systematic survey of graph data augmentation approaches, summarizing the literature in a structured manner. We first introduce three different taxonomies for categorizing graph data augmentation methods from the data, task, and learning perspectives, respectively. Next, we introduce recent advances in graph data augmentation, differentiated by their methodologies and applications. We conclude by outlining currently unsolved challenges and directions for future research. Overall, our work aims to clarify the landscape of existing literature in graph data augmentation and motivates additional work in this area, providing a helpful resource for researchers and practitioners in the broader graph machine learning domain. Additionally, we provide a continuously updated reading list at https://github.com/zhao-tong/graph-data-augmentation-papers.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Invariance-Aware Randomized Smoothing Certificates

Building models that comply with the invariances inherent to different domains, such as invariance under translation or rotation, is a key aspect of applying machine learning to real world problems like molecular property prediction, medical imaging, protein folding or LiDAR classification. For the first time, we study how the invariances of a model can be leveraged to provably guarantee the robustness of its predictions. We propose a gray-box approach, enhancing the powerful black-box randomized smoothing technique with white-box knowledge about invariances. First, we develop gray-box certificates based on group orbits, which can be applied to arbitrary models with invariance under permutation and Euclidean isometries. Then, we derive provably tight gray-box certificates. We experimentally demonstrate that the provably tight certificates can offer much stronger guarantees, but that in practical scenarios the orbit-based method is a good approximation.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

torchode: A Parallel ODE Solver for PyTorch

We introduce an ODE solver for the PyTorch ecosystem that can solve multiple ODEs in parallel independently from each other while achieving significant performance gains. Our implementation tracks each ODE's progress separately and is carefully optimized for GPUs and compatibility with PyTorch's JIT compiler. Its design lets researchers easily augment any aspect of the solver and collect and analyze internal solver statistics. In our experiments, our implementation is up to 4.3 times faster per step than other ODE solvers and it is robust against within-batch interactions that lead other solvers to take up to 4 times as many steps. Code available at https://github.com/martenlienen/torchode

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Training Differentially Private Graph Neural Networks with Random Walk Sampling

Deep learning models are known to put the privacy of their training data at risk, which poses challenges for their safe and ethical release to the public. Differentially private stochastic gradient descent is the de facto standard for training neural networks without leaking sensitive information about the training data. However, applying it to models for graph-structured data poses a novel challenge: unlike with i.i.d. data, sensitive information about a node in a graph cannot only leak through its gradients, but also through the gradients of all nodes within a larger neighborhood. In practice, this limits privacy-preserving deep learning on graphs to very shallow graph neural networks. We propose to solve this issue by training graph neural networks on disjoint subgraphs of a given training graph. We develop three random-walk-based methods for generating such disjoint subgraphs and perform a careful analysis of the data-generating distributions to provide strong privacy guarantees. Through extensive experiments, we show that our method greatly outperforms the state-of-the-art baseline on three large graphs, and matches or outperforms it on four smaller ones.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

3D Infomax improves GNNs for Molecular Property Prediction

Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks. However, this information is infeasible to compute at the scale required by several real-world applications. We propose pre-training a model to reason about the geometry of molecules given only their 2D molecular graphs. Using methods from self-supervised learning, we maximize the mutual information between 3D summary vectors and the representations of a Graph Neural Network (GNN) such that they contain latent 3D information. During fine-tuning on molecules with unknown geometry, the GNN still generates implicit 3D information and can use it to improve downstream tasks. We show that 3D pre-training provides significant improvements for a wide range of properties, such as a 22% average MAE reduction on eight quantum mechanical properties. Moreover, the learned representations can be effectively transferred between datasets in different molecular spaces.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Disentangling Epistemic and Aleatoric Uncertainty in Reinforcement Learning

Characterizing aleatoric and epistemic uncertainty on the predicted rewards can help in building reliable reinforcement learning (RL) systems. Aleatoric uncertainty results from the irreducible environment stochasticity leading to inherently risky states and actions. Epistemic uncertainty results from the limited information accumulated during learning to make informed decisions. Characterizing aleatoric and epistemic uncertainty can be used to speed up learning in a training environment, improve generalization to similar testing environments, and flag unfamiliar behavior in anomalous testing environments. In this work, we introduce a framework for disentangling aleatoric and epistemic uncertainty in RL. (1) We first define four desiderata that capture the desired behavior for aleatoric and epistemic uncertainty estimation in RL at both training and testing time. (2) We then present four RL models inspired by supervised learning (i.e. Monte Carlo dropout, ensemble, deep kernel learning models, and evidential networks) to instantiate aleatoric and epistemic uncertainty. Finally, (3) we propose a practical evaluation method to evaluate uncertainty estimation in model-free RL based on detection of out-of-distribution environments and generalization to perturbed environments. We present theoretical and experimental evidence to validate that carefully equipping model-free RL agents with supervised learning uncertainty methods can fulfill our desiderata.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

On the Robustness and Anomaly Detection of Sparse Neural Networks

The robustness and anomaly detection capability of neural networks are crucial topics for their safe adoption in the real-world. Moreover, the over-parameterization of recent networks comes with high computational costs and raises questions about its influence on robustness and anomaly detection. In this work, we show that sparsity can make networks more robust and better anomaly detectors. To motivate this even further, we show that a pre-trained neural network contains, within its parameter space, sparse subnetworks that are better at these tasks without any further training. We also show that structured sparsity greatly helps in reducing the complexity of expensive robustness and detection methods, while maintaining or even improving their results on these tasks. Finally, we introduce a new method, SensNorm, which uses the sensitivity of weights derived from an appropriate pruning method to detect anomalous samples in the input.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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 .

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Winning the Lottery Ahead of Time: Efficient Early Network Pruning

Pruning, the task of sparsifying deep neural networks, received increasing attention recently. Although state-of-the-art pruning methods extract highly sparse models, they neglect two main challenges: (1) the process of finding these sparse models is often very expensive; (2) unstructured pruning does not provide benefits in terms of GPU memory, training time, or carbon emissions. We propose Early Compression via Gradient Flow Preservation (EarlyCroP), which efficiently extracts state-of-the-art sparse models before or early in training addressing challenge (1), and can be applied in a structured manner addressing challenge (2). This enables us to train sparse networks on commodity GPUs whose dense versions would be too large, thereby saving costs and reducing hardware requirements. We empirically show that EarlyCroP outperforms a rich set of baselines for many tasks (incl. classification, regression) and domains (incl. computer vision, natural language processing, and reinforcment learning). EarlyCroP leads to accuracy comparable to dense training while outperforming pruning baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

A Model-Driven Approach to Machine Learning and Software Modeling for the IoT

Models are used in both Software Engineering (SE) and Artificial Intelligence (AI). SE models may specify the architecture at different levels of abstraction and for addressing different concerns at various stages of the software development life-cycle, from early conceptualization and design, to verification, implementation, testing and evolution. However, AI models may provide smart capabilities, such as prediction and decision-making support. For instance, in Machine Learning (ML), which is currently the most popular sub-discipline of AI, mathematical models may learn useful patterns in the observed data and can become capable of making predictions. The goal of this work is to create synergy by bringing models in the said communities together and proposing a holistic approach to model-driven software development for intelligent systems that require ML. We illustrate how software models can become capable of creating and dealing with ML models in a seamless manner. The main focus is on the domain of the Internet of Things (IoT), where both ML and model-driven SE play a key role. In the context of the need to take a Cyber-Physical System-of-Systems perspective of the targeted architecture, an integrated design environment for both SE and ML sub-systems would best support the optimization and overall efficiency of the implementation of the resulting system. In particular, we implement the proposed approach, called ML-Quadrat, based on ThingML, and validate it using a case study from the IoT domain, as well as through an empirical user evaluation. It transpires that the proposed approach is not only feasible, but may also contribute to the performance leap of software development for smart Cyber-Physical Systems (CPS) which are connected to the IoT, as well as an enhanced user experience of the practitioners who use the proposed modeling solution.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Deep Representation Learning and Clustering of Traffic Scenarios

Determining the traffic scenario space is a major challenge for the homologation and coverage assessment of automated driving functions. In contrast to current approaches that are mainly scenario-based and rely on expert knowledge, we introduce two data driven autoencoding models that learn a latent representation of traffic scenes. First is a CNN based spatio-temporal model that autoencodes a grid of traffic participants' positions. Secondly, we develop a pure temporal RNN based model that auto-encodes a sequence of sets. To handle the unordered set data, we had to incorporate the permutation invariance property. Finally, we show how the latent scenario embeddings can be used for clustering traffic scenarios and similarity retrieval.

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preprint2020arXiv

Graph Hawkes Neural Network for Forecasting on Temporal Knowledge Graphs

The Hawkes process has become a standard method for modeling self-exciting event sequences with different event types. A recent work has generalized the Hawkes process to a neurally self-modulating multivariate point process, which enables the capturing of more complex and realistic impacts of past events on future events. However, this approach is limited by the number of possible event types, making it impossible to model the dynamics of evolving graph sequences, where each possible link between two nodes can be considered as an event type. The number of event types increases even further when links are directional and labeled. To address this issue, we propose the Graph Hawkes Neural Network that can capture the dynamics of evolving graph sequences and can predict the occurrence of a fact in a future time instance. Extensive experiments on large-scale temporal multi-relational databases, such as temporal knowledge graphs, demonstrate the effectiveness of our approach.

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preprint2020arXiv

Intensity-Free Learning of Temporal Point Processes

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.

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preprint2020arXiv

Scene Graph Reasoning for Visual Question Answering

Visual question answering is concerned with answering free-form questions about an image. Since it requires a deep linguistic understanding of the question and the ability to associate it with various objects that are present in the image, it is an ambitious task and requires techniques from both computer vision and natural language processing. We propose a novel method that approaches the task by performing context-driven, sequential reasoning based on the objects and their semantic and spatial relationships present in the scene. As a first step, we derive a scene graph which describes the objects in the image, as well as their attributes and their mutual relationships. A reinforcement agent then learns to autonomously navigate over the extracted scene graph to generate paths, which are then the basis for deriving answers. We conduct a first experimental study on the challenging GQA dataset with manually curated scene graphs, where our method almost reaches the level of human performance.

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preprint2020arXiv

Uncertainty on Asynchronous Time Event Prediction

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.

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