Towards Graph Foundation Models: A Study on the Generalization of Positional and Structural Encodings

Recent advances in integrating positional and structural encodings (PSEs) into graph neural networks (GNNs) have significantly enhanced their performance across various graph learning tasks. However, the general applicability of these encodings and their potential to serve as foundational representations for graphs remain uncertain. This paper investigates the fine-tuning efficiency, scalability with sample size, and generalization capability of learnable PSEs across diverse graph datasets. Specifically, we evaluate their potential as universal pre-trained models that can be easily adapted to new tasks with minimal fine-tuning and limited data. Furthermore, we assess the expressivity of the learned representations, particularly, when used to augment downstream GNNs. We demonstrate through extensive benchmarking and empirical analysis that PSEs generally enhance downstream models. However, some datasets may require specific PSE-augmentations to achieve optimal performance. Nevertheless, our findings highlight their significant potential to become integral components of future graph foundation models. We provide new insights into the strengths and limitations of PSEs, contributing to the broader discourse on foundation models in graph learning.

Tethering Broken Themes: Aligning Neural Topic Models with Labels and Authors

Topic models are a popular approach for extracting semantic information from large document collections. However, recent studies suggest that the topics generated by these models often do not align well with human intentions. While metadata such as labels and authorship information is available, it has not yet been effectively incorporated into neural topic models. To address this gap, we introduce FANToM, a novel method for aligning neural topic models with both labels and authorship information. FANToM allows for the inclusion of this metadata when available, producing interpretable topics and author distributions for each topic. Our approach demonstrates greater expressiveness than conventional topic models by learning the alignment between labels, topics, and authors. Experimental results show that FANToM improves upon existing models in terms of both topic quality and alignment. Additionally, it identifies author interests and similarities.

SetPINNs: Set-based Physics-informed Neural Networks

Physics-Informed Neural Networks (PINNs) have emerged as a promising method for approximating solutions to partial differential equations (PDEs) using deep learning. However, PINNs, based on multilayer perceptrons (MLP), often employ point-wise predictions, overlooking the implicit dependencies within the physical system such as temporal or spatial dependencies. These dependencies can be captured using more complex network architectures, for example CNNs or Transformers. However, these architectures conventionally do not allow for incorporating physical constraints, as advancements in integrating such constraints within these frameworks are still lacking. Relying on point-wise predictions often results in trivial solutions. To address this limitation, we propose SetPINNs, a novel approach inspired by Finite Elements Methods from the field of Numerical Analysis. SetPINNs allow for incorporating the dependencies inherent in the physical system while at the same time allowing for incorporating the physical constraints. They accurately approximate PDE solutions of a region, thereby modeling the inherent dependencies between multiple neighboring points in that region. Our experiments show that SetPINNs demonstrate superior generalization performance and accuracy across diverse physical systems, showing that they mitigate failure modes and converge faster in comparison to existing approaches. Furthermore, we demonstrate the utility of SetPINNs on two real-world physical systems.

Comgra: A Tool for Analyzing and Debugging Neural Networks

Neural Networks are notoriously difficult to inspect. We introduce comgra, an open source python library for use with PyTorch. Comgra extracts data about the internal activations of a model and organizes it in a GUI (graphical user interface). It can show both summary statistics and individual data points, compare early and late stages of training, focus on individual samples of interest, and visualize the flow of the gradient through the network. This makes it possible to inspect the model's behavior from many different angles and save time by rapidly testing different hypotheses without having to rerun it. Comgra has applications for debugging, neural architecture design, and mechanistic interpretability. We publish our library through Python Package Index (PyPI) and provide code, documentation, and tutorials at https://github.com/FlorianDietz/comgra.

HANNA: Hard-constraint Neural Network for Consistent Activity Coefficient Prediction

We present the first hard-constraint neural network for predicting activity coefficients (HANNA), a thermodynamic mixture property that is the basis for many applications in science and engineering. Unlike traditional neural networks, which ignore physical laws and result in inconsistent predictions, our model is designed to strictly adhere to all thermodynamic consistency criteria. By leveraging deep-set neural networks, HANNA maintains symmetry under the permutation of the components. Furthermore, by hard-coding physical constraints in the network architecture, we ensure consistency with the Gibbs-Duhem equation and in modeling the pure components. The model was trained and evaluated on 317,421 data points for activity coefficients in binary mixtures from the Dortmund Data Bank, achieving significantly higher prediction accuracies than the current state-of-the-art model UNIFAC. Moreover, HANNA only requires the SMILES of the components as input, making it applicable to any binary mixture of interest. HANNA is fully open-source and available for free use.

On the Challenges and Opportunities in Generative AI

The field of deep generative modeling has grown rapidly and consistently over the years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models do not sufficiently address several fundamental issues that hinder their widespread adoption across domains. In this work, we aim to identify key unresolved challenges in modern generative AI paradigms that should be tackled to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with valuable insights for exploring fruitful research directions, thereby fostering the development of more robust and accessible generative AI solutions.

Reimagining Anomalies: What If Anomalies Were Normal?

Deep learning-based methods have achieved a breakthrough in image anomaly detection, but their complexity introduces a considerable challenge to understanding why an instance is predicted to be anomalous. We introduce a novel explanation method that generates multiple counterfactual examples for each anomaly, capturing diverse concepts of anomalousness. A counterfactual example is a modification of the anomaly that is perceived as normal by the anomaly detector. The method provides a high-level semantic explanation of the mechanism that triggered the anomaly detector, allowing users to explore "what-if scenarios." Qualitative and quantitative analyses across various image datasets show that the method applied to state-of-the-art anomaly detectors can achieve high-quality semantic explanations of detectors.

Evaluating Dynamic Topic Models

There is a lack of quantitative measures to evaluate the progression of topics through time in dynamic topic models (DTMs). Filling this gap, we propose a novel evaluation measure for DTMs that analyzes the changes in the quality of each topic over time. Additionally, we propose an extension combining topic quality with the model's temporal consistency. We demonstrate the utility of the proposed measure by applying it to synthetic data and data from existing DTMs. We also conducted a human evaluation, which indicates that the proposed measure correlates well with human judgment. Our findings may help in identifying changing topics, evaluating different DTMs, and guiding future research in this area.

Text Style Transfer Evaluation Using Large Language Models

Text Style Transfer (TST) is challenging to evaluate because the quality of the generated text manifests itself in multiple aspects, each of which is hard to measure individually: style transfer accuracy, content preservation, and overall fluency of the text. Human evaluation is the gold standard in TST evaluation; however, it is expensive, and the results are difficult to reproduce. Numerous automated metrics are employed to assess performance in these aspects, serving as substitutes for human evaluation. However, the correlation between many of these automated metrics and human evaluations remains unclear, raising doubts about their effectiveness as reliable benchmarks. Recent advancements in Large Language Models (LLMs) have demonstrated their ability to not only match but also surpass the average human performance across a wide range of unseen tasks. This suggests that LLMs have the potential to serve as a viable alternative to human evaluation and other automated metrics. We assess the performance of different LLMs on TST evaluation by employing multiple input prompts and comparing their results. Our findings indicate that (even zero-shot) prompting correlates strongly with human evaluation and often surpasses the performance of (other) automated metrics. Additionally, we propose the ensembling of prompts and show it increases the robustness of TST evaluation.This work contributes to the ongoing efforts in evaluating LLMs on diverse tasks, which includes a discussion of failure cases and limitations.

A Call for Standardization and Validation of Text Style Transfer Evaluation

Text Style Transfer (TST) evaluation is, in practice, inconsistent. Therefore, we conduct a meta-analysis on human and automated TST evaluation and experimentation that thoroughly examines existing literature in the field. The meta-analysis reveals a substantial standardization gap in human and automated evaluation. In addition, we also find a validation gap: only few automated metrics have been validated using human experiments. To this end, we thoroughly scrutinize both the standardization and validation gap and reveal the resulting pitfalls. This work also paves the way to close the standardization and validation gap in TST evaluation by calling out requirements to be met by future research.