Methods for dimensionality reduction are showing significant contributions to knowledge generation in high-dimensional modeling scenarios throughout many disciplines. By achieving a lower dimensional representation (also called embedding), fewer computing resources are needed in downstream machine learning tasks, thus leading to a faster training time, lower complexity, and statistical flexibility. In this work, we investigate the utility of three prominent unsupervised embedding techniques (principal component analysis—PCA, uniform manifold approximation and projection—UMAP, and variational autoencoders—VAEs) for solving classification tasks in the domain of toxicology. To this end, we compare these embedding techniques against a set of molecular fingerprint-based models that do not utilize additional pre-preprocessing of features. Inspired by the success of transfer learning in several fields, we further study the performance of embedders when trained on an external dataset of chemical compounds. To gain a better understanding of their characteristics, we evaluate the embedders with different embedding dimensionalities, and with different sizes of the external dataset. Our findings show that the recently popularized UMAP approach can be utilized alongside known techniques such as PCA and VAE as a pre-compression technique in the toxicology domain. Nevertheless, the generative model of VAE shows an advantage in pre-compressing the data with respect to classification accuracy.

Graph Neural Networks (GNNs) are effective in many applications. Still, there is a limited understanding of the effect of common graph structures on the learning process of GNNs. To fill this gap, we study the impact of community structure and homophily on the performance of GNNs in semi-supervised node classification on graphs. Our methodology consists of systematically manipulating the structure of eight datasets, and measuring the performance of GNNs on the original graphs and the change in performance in the presence and the absence of community structure and/or homophily. Our results show the major impact of both homophily and communities on the classification accuracy of GNNs, and provide insights on their interplay. In particular, by analyzing community structure and its correlation with node labels, we are able to make informed predictions on the suitability of GNNs for classification on a given graph. Using an information-theoretic metric for community-label correlation, we devise a guideline for model selection based on graph structure. With our work, we provide insights on the abilities of GNNs and the impact of common network phenomena on their performance. Our work improves model selection for node classification in semi-supervised settings.

PyChemFlow is a Python library for automated and reproducible data pre-processing. Based on open-source code, PyChemFlow has simple requirements that rely on pandas, scikit-learn and joblib. The library's backbone is built up of transformer objects, which are fully constructed during the PyChemFlow fitting process using training data and can be conveniently stored using joblib. The user can run the library with a one-line command after splitting data into train and validation sets or while working with additional data. This is especially useful when reproducibility is critical. PyChemFlow also offers the ability to persistently store metadata, in addition to providing customizable and configurable data manipulation steps.

We propose the novel concept of anomaly-free regions (AFR) to improve anomaly detection. An AFR is a region in the data space for which it is known that there are no anomalies inside it, e.g., via domain knowledge. This region can contain any number of normal data points and can be anywhere in the data space. AFRs have the key advantage that they constrain the estimation of the distribution of non-anomalies: The estimated probability mass inside the AFR must be consistent with the number of normal data points inside the AFR. Based on this insight, we provide a solid theoretical foundation and a reference implementation of anomaly detection using AFRs. Our empirical results confirm that anomaly detection constrained via AFRs improves upon unconstrained anomaly detection. Specifically, we show that, when equipped with an estimated AFR, an efficient algorithm based on random guessing becomes a strong baseline that several widely-used methods struggle to overcome. On a dataset with a ground-truth AFR available, the current state of the art is outperformed.

We present evidence for the existence and effectiveness of adversarial attacks on graph neural networks (GNNs) that aim to degrade fairness. These attacks can disadvantage a particular subgroup of nodes in GNN-based node classification, where nodes of the underlying network have sensitive attributes, such as race or gender. We conduct qualitative and experimental analyses explaining how adversarial link injection impairs the fairness of GNN predictions. For example, an attacker can compromise the fairness of GNN-based node classification by injecting adversarial links between nodes belonging to opposite subgroups and opposite class labels. Our experiments on empirical datasets demonstrate that adversarial fairness attacks can significantly degrade the fairness of GNN predictions (attacks are effective) with a low perturbation rate (attacks are efficient) and without a significant drop in accuracy (attacks are deceptive). This work demonstrates the vulnerability of GNN models to adversarial fairness attacks. We hope our findings raise awareness about this issue in our community and lay a foundation for the future development of GNN models that are more robust to such attacks.

In this work, we study the utility of graph embeddings to generate latent user representations for trust-based collaborative filtering. In a cold-start setting, on three publicly available datasets, we evaluate approaches from four method families: (i) factorization-based, (ii) random walk-based, (iii) deep learning-based, and (iv) the Large-scale Information Network Embedding (LINE) approach. We find that across the four families, random-walk-based approaches consistently achieve the best accuracy. Besides, they result in highly novel and diverse recommendations. Furthermore, our results show that the use of graph embeddings in trust-based collaborative filtering significantly improves user coverage.