Raoul Wolf

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Extrapolation of adverse biological (toxic) effects of chemicals is an important contribution to expand available hazard data in (eco)toxicology without the use of animals in laboratory experiments. In this work, we extrapolate effects based on a knowledge graph (KG) consisting of the most relevant effect data as domain-specific background knowledge. An effect prediction model, with and without background knowledge, was used to predict mean adverse biological effect concentration of chemicals as a prototypical type of stressors. The background knowledge improves the model prediction performance by up to 40\% in terms of $R^2$ (\ie coefficient of determination). We use the KG and KG embeddings to provide quantitative and qualitative insights into the predictions. These insights are expected to improve the confidence in effect prediction. Larger scale implementation of such extrapolation models should be expected to support hazard and risk assessment, by simplifying and reducing testing needs.

Erik B. Myklebust, Ernesto Jiménez-Ruiz, Jiaoyan Chen et al.

We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture that adapts the knowledge graph embeddings to the effect prediction task and leads to better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance.

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Ecological risk assessment requires large amounts of chemical effect data from laboratory experiments. Due to experimental effort and animal welfare concerns it is desired to extrapolate data from existing sources. To cover the required chemical effect data several data sources need to be integrated to enable their interoperability. In this paper we introduce the Toxicological Effect and Risk Assessment (TERA) knowledge graph, which aims at providing such integrated view, and the data preparation and steps followed to construct this knowledge graph. We also present the applications of TERA for chemical effect prediction and the potential applications within the Semantic Web community.

Erik Bryhn Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen et al.

Exploring the effects a chemical compound has on a species takes a considerable experimental effort. Appropriate methods for estimating and suggesting new effects can dramatically reduce the work needed to be done by a laboratory. In this paper we explore the suitability of using a knowledge graph embedding approach for ecotoxicological effect prediction. A knowledge graph has been constructed from publicly available data sets, including a species taxonomy and chemical classification and similarity. The publicly available effect data is integrated to the knowledge graph using ontology alignment techniques. Our experimental results show that the knowledge graph based approach improves the selected baselines.