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Jan Eric Lenssen

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11 papers

2 author rows

ICLR Conference 2025 Conference Paper

ContextGNN: Beyond Two-Tower Recommendation Systems

Yiwen Yuan
Zecheng Zhang
Xinwei He
Akihiro Nitta
Weihua Hu
Manan Shah
Blaz Stojanovic
Shenyang Huang

Recommendation systems predominantly utilize two-tower architectures, which evaluate user-item rankings through the inner product of their respective embeddings. However, one key limitation of two-tower models is that they learn a pair-agnostic representation of users and items. In contrast, pair-wise representations either scale poorly due to their quadratic complexity or are too restrictive on the candidate pairs to rank. To address these issues, we introduce Context-based Graph Neural Networks (ContextGNNs), a novel deep learning architecture for link prediction in recommendation systems. The method employs a pair-wise representation technique for familiar items situated within a user's local subgraph, while leveraging two-tower representations to facilitate the recommendation of exploratory items. A final network then predicts how to fuse both pair-wise and two-tower recommendations into a single ranking of items. We demonstrate that ContextGNN is able to adapt to different data characteristics and outperforms existing methods, both traditional and GNN-based, on a diverse set of practical recommendation tasks, improving performance by 20\% on average.

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NeurIPS Conference 2025 Conference Paper

Solving Inverse Problems with FLAIR

Julius Erbach
Dominik Narnhofer
Andreas Dombos
Bernt Schiele
Jan Eric Lenssen
Konrad Schindler

Flow-based latent generative models such as Stable Diffusion 3 are able to generate images with remarkable quality, even enabling photorealistic text-to-image generation. Their impressive performance suggests that these models should also constitute powerful priors for inverse imaging problems, but that approach has not yet led to comparable fidelity. There are several key obstacles: (i) the data likelihood term is usually intractable; (ii) learned generative models cannot be directly conditioned on the distorted observations, leading to conflicting objectives between data likelihood and prior; and (iii) the reconstructions can deviate from the observed data. We present FLAIR, a novel, training-free variational framework that leverages flow-based generative models as prior for inverse problems. To that end, we introduce a variational objective for flow matching that is agnostic to the type of degradation, and combine it with deterministic trajectory adjustments to guide the prior towards regions which are more likely under the posterior. To enforce exact consistency with the observed data, we decouple the optimization of the data fidelity and regularization terms. Moreover, we introduce a time-dependent calibration scheme in which the strength of the regularization is modulated according to off-line accuracy estimates. Results on standard imaging benchmarks demonstrate that FLAIR consistently outperforms existing diffusion- and flow-based methods in terms of reconstruction quality and sample diversity. Source code is available at https: //inverseflair. github. io/.

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ICML Conference 2025 Conference Paper

Spatial Reasoning with Denoising Models

Christopher Wewer
Bartlomiej Pogodzinski
Bernt Schiele
Jan Eric Lenssen

We introduce Spatial Reasoning Models (SRMs), a framework to perform reasoning over sets of continuous variables via denoising generative models. SRMs infer continuous representations on a set of unobserved variables, given observations on observed variables. Current generative models on spatial domains, such as diffusion and flow matching models, often collapse to hallucination in case of complex distributions. To measure this, we introduce a set of benchmark tasks that test the quality of complex reasoning in generative models and can quantify hallucination. The SRM framework allows to report key findings about importance of sequentialization in generation, the associated order, as well as the sampling strategies during training. It demonstrates, for the first time, that order of generation can successfully be predicted by the denoising network itself. Using these findings, we can increase the accuracy of specific reasoning tasks from $ $50%. Our project website provides additional videos, code, and the benchmark datasets.

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ICLR Conference 2025 Conference Paper

TokenFormer: Rethinking Transformer Scaling with Tokenized Model Parameters

Haiyang Wang
Yue Fan
Muhammad Ferjad Naeem
Yongqin Xian
Jan Eric Lenssen
Liwei Wang 0001
Federico Tombari
Bernt Schiele

Transformers have become the predominant architecture in foundation models due to their excellent performance across various domains. However, the substantial cost of scaling these models remains a significant concern. This problem arises primarily from their dependence on a fixed number of parameters within linear projections. When architectural modifications (e.g., channel dimensions) are introduced, the entire model typically requires retraining from scratch. As model sizes continue growing, this strategy results in increasingly high computational costs and becomes unsustainable. To overcome this problem, we introduce Tokenformer, a natively scalable architecture that leverages the attention mechanism not only for computations among input tokens but also for interactions between tokens and model parameters, thereby enhancing architectural flexibility. By treating model parameters as tokens, we replace all the linear projections in Transformers with our token-parameter attention layer, where input tokens act as queries and model parameters as keys and values. This reformulation allows for progressive and efficient scaling without necessitating retraining from scratch. Our model scales from 124M to 1.4B parameters by incrementally adding new key-value parameter pairs, achieving performance comparable to Transformers trained from scratch while greatly reducing training costs. Code and models are available at {\color{red}\url{https://github.com/Haiyang-W/TokenFormer.git}}

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NeurIPS Conference 2024 Conference Paper

From Similarity to Superiority: Channel Clustering for Time Series Forecasting

Jialin Chen
Jan Eric Lenssen
Aosong Feng
Weihua Hu
Matthias Fey
Leandros Tassiulas
Jure Leskovec
Rex Ying

Time series forecasting has attracted significant attention in recent decades. Previous studies have demonstrated that the Channel-Independent (CI) strategy improves forecasting performance by treating different channels individually, while it leads to poor generalization on unseen instances and ignores potentially necessary interactions between channels. Conversely, the Channel-Dependent (CD) strategy mixes all channels with even irrelevant and indiscriminate information, which, however, results in oversmoothing issues and limits forecasting accuracy. There is a lack of channel strategy that effectively balances individual channel treatment for improved forecasting performance without overlooking essential interactions between channels. Motivated by our observation of a correlation between the time series model's performance boost against channel mixing and the intrinsic similarity on a pair of channels, we developed a novel and adaptable \textbf{C}hannel \textbf{C}lustering \textbf{M}odule (CCM). CCM dynamically groups channels characterized by intrinsic similarities and leverages cluster information instead of individual channel identities, combining the best of CD and CI worlds. Extensive experiments on real-world datasets demonstrate that CCM can (1) boost the performance of CI and CD models by an average margin of 2. 4% and 7. 2% on long-term and short-term forecasting, respectively; (2) enable zero-shot forecasting with mainstream time series forecasting models; (3) uncover intrinsic time series patterns among channels and improve interpretability of complex time series models.

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ICML Conference 2024 Conference Paper

Position: Relational Deep Learning - Graph Representation Learning on Relational Databases

Matthias Fey
Weihua Hu
Kexin Huang
Jan Eric Lenssen
Rishabh Ranjan
Joshua Robinson 0001
Rex Ying
Jiaxuan You

Much of the world’s most valued data is stored in relational databases and data warehouses, where the data is organized into tables connected by primary-foreign key relations. However, building machine learning models using this data is both challenging and time consuming because no ML algorithm can directly learn from multiple connected tables. Current approaches can only learn from a single table, so data must first be manually joined and aggregated into this format, the laborious process known as feature engineering. Feature engineering is slow, error prone and leads to suboptimal models. Here we introduce Relational Deep Learning (RDL), a blueprint for end-to-end learning on relational databases. The key is to represent relational databases as a temporal, heterogeneous graphs, with a node for each row in each table, and edges specified by primary-foreign key links. Graph Neural Networks then learn representations that leverage all input data, without any manual feature engineering. We also introduce RelBench, and benchmark and testing suite, demonstrating strong initial results. Overall, we define a new research area that generalizes graph machine learning and broadens its applicability.

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NeurIPS Conference 2024 Conference Paper

Scribbles for All: Benchmarking Scribble Supervised Segmentation Across Datasets

Wolfgang Boettcher
Lukas Hoyer
Ozan Unal
Jan Eric Lenssen
Bernt Schiele

In this work, we introduce Scribbles for All, a label and training data generation algorithm for semantic segmentation trained on scribble labels. Training or fine-tuning semantic segmentation models with weak supervision has become an important topic recently and was subject to significant advances in model quality. In this setting, scribbles are a promising label type to achieve high quality segmentation results while requiring a much lower annotation effort than usual pixel-wise dense semantic segmentation annotations. The main limitation of scribbles as source for weak supervision is the lack of challenging datasets for scribble segmentation, which hinders the development of novel methods and conclusive evaluations. To overcome this limitation, Scribbles for All provides scribble labels for several popular segmentation datasets and provides an algorithm to automatically generate scribble labels for any dataset with dense annotations, paving the way for new insights and model advancements in the field of weakly supervised segmentation. In addition to providing datasets and algorithm, we evaluate state-of-the-art segmentation models on our datasets and show that models trained with our synthetic labels perform competitively with respect to models trained on manual labels. Thus, our datasets enable state-of-the-art research into methods for scribble-labeled semantic segmentation. The datasets, scribble generation algorithm, and baselines are publicly available at https: //github. com/wbkit/Scribbles4All.

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ICML Conference 2021 Conference Paper

GNNAutoScale: Scalable and Expressive Graph Neural Networks via Historical Embeddings

Matthias Fey
Jan Eric Lenssen
Frank Weichert
Jure Leskovec

We present GNNAutoScale (GAS), a framework for scaling arbitrary message-passing GNNs to large graphs. GAS prunes entire sub-trees of the computation graph by utilizing historical embeddings from prior training iterations, leading to constant GPU memory consumption in respect to input node size without dropping any data. While existing solutions weaken the expressive power of message passing due to sub-sampling of edges or non-trainable propagations, our approach is provably able to maintain the expressive power of the original GNN. We achieve this by providing approximation error bounds of historical embeddings and show how to tighten them in practice. Empirically, we show that the practical realization of our framework, PyGAS, an easy-to-use extension for PyTorch Geometric, is both fast and memory-efficient, learns expressive node representations, closely resembles the performance of their non-scaling counterparts, and reaches state-of-the-art performance on large-scale graphs.

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ICLR Conference 2020 Conference Paper

Deep Graph Matching Consensus

Matthias Fey
Jan Eric Lenssen
Christopher Morris 0001
Jonathan Masci
Nils M. Kriege

This work presents a two-stage neural architecture for learning and refining structural correspondences between graphs. First, we use localized node embeddings computed by a graph neural network to obtain an initial ranking of soft correspondences between nodes. Secondly, we employ synchronous message passing networks to iteratively re-rank the soft correspondences to reach a matching consensus in local neighborhoods between graphs. We show, theoretically and empirically, that our message passing scheme computes a well-founded measure of consensus for corresponding neighborhoods, which is then used to guide the iterative re-ranking process. Our purely local and sparsity-aware architecture scales well to large, real-world inputs while still being able to recover global correspondences consistently. We demonstrate the practical effectiveness of our method on real-world tasks from the fields of computer vision and entity alignment between knowledge graphs, on which we improve upon the current state-of-the-art.

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AAAI Conference 2019 Conference Paper

Weisfeiler and Leman Go Neural: Higher-Order Graph Neural Networks

Christopher Morris
Martin Ritzert
Matthias Fey
William L. Hamilton
Jan Eric Lenssen
Gaurav Rattan
Martin Grohe

In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically—showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the 1-dimensional Weisfeiler-Leman graph isomorphism heuristic (1-WL). We show that GNNs have the same expressiveness as the 1-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcomings. Based on this, we propose a generalization of GNNs, so-called k-dimensional GNNs (k-GNNs), which can take higher-order graph structures at multiple scales into account. These higher-order structures play an essential role in the characterization of social networks and molecule graphs. Our experimental evaluation confirms our theoretical findings as well as confirms that higher-order information is useful in the task of graph classification and regression.

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NeurIPS Conference 2018 Conference Paper

Group Equivariant Capsule Networks

Jan Eric Lenssen
Matthias Fey
Pascal Libuschewski

We present group equivariant capsule networks, a framework to introduce guaranteed equivariance and invariance properties to the capsule network idea. Our work can be divided into two contributions. First, we present a generic routing by agreement algorithm defined on elements of a group and prove that equivariance of output pose vectors, as well as invariance of output activations, hold under certain conditions. Second, we connect the resulting equivariant capsule networks with work from the field of group convolutional networks. Through this connection, we provide intuitions of how both methods relate and are able to combine the strengths of both approaches in one deep neural network architecture. The resulting framework allows sparse evaluation of the group convolution operator, provides control over specific equivariance and invariance properties, and can use routing by agreement instead of pooling operations. In addition, it is able to provide interpretable and equivariant representation vectors as output capsules, which disentangle evidence of object existence from its pose.

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