Chemical data is increasingly openly available in databases such as PubChem, which contains approximately 110 million compound entries as of February 2021. With the availability of data at such scale, the burden has shifted to organisation, analysis and interpretation. Chemical ontologies provide structured classifications of chemical entities that can be used for navigation and filtering of the large chemical space. ChEBI is a prominent example of a chemical ontology, widely used in life science contexts. However, ChEBI is manually maintained and as such cannot easily scale to the full scope of public chemical data. There is a need for tools that are able to automatically classify chemical data into chemical ontologies, which can be framed as a hierarchical multi-class classification problem. In this paper we evaluate machine learning approaches for this task, comparing different learning frameworks including logistic regression, decision trees and long short-term memory artificial neural networks, and different encoding approaches for the chemical structures, including cheminformatics fingerprints and character-based encoding from chemical line notation representations. We find that classical learning approaches such as logistic regression perform well with sets of relatively specific, disjoint chemical classes, while the neural network is able to handle larger sets of overlapping classes but needs more examples per class to learn from, and is not able to make a class prediction for every molecule. Future work will explore hybrid and ensemble approaches, as well as alternative network architectures including neuro-symbolic approaches.
Chemical data is increasingly openly available in databases such as PubChem, which contains more than 110 million compound entries as of October 2020. With the availability of data at such scale, the burden has shifted to organisation, analysis and interpretation. Chemical ontologies provide structured classifications of chemical entities that can be used for navigation and filtering of the large chemical space. ChEBI is a prominent example of a chemical ontology, widely used in life science contexts. However, ChEBI is manually maintained and as such cannot easily scale to the full scope of public chemical data. There is a need for tools that are able to automatically classify chemical data into chemical ontologies, which can be framed as a hierarchical multi-class classification problem. In this paper we evaluate machine learning approaches for this task, comparing different learning frameworks including logistic regression, decision trees and long short-term memory articial neural networks, and different encoding approaches for the chemical structures, including cheminformatics fingerprints and character-based encoding from chemical line notation representations. We nd that classical learning approaches such as logistic regression perform well with sets of relatively specific, disjoint chemical classes, while the neural network is able to handle larger sets of overlapping classes but needs more examples per class to learn from, and is not able to make a class prediction for every molecule. Future work will explore hybrid and ensemble approaches, as well as alternative network architectures including neuro-symbolic approaches.
Ontologies represent human domain expertise symbolically in a way that is accessible to human experts and suitable for a variety of applications. As a result, they are widely used in scientific research. A challenge for the neuro-symbolic field is how to use the knowledge encoded in ontologies together with sub-symbolic learning approaches. In this chapter we describe a general neuro-symbolic architecture for using knowledge from ontologies to improve the generalisability and accuracy of predictions of a deep neural network applied to chemical data. The architecture consists of a multi-layer network with a multi-step training process: first, the network is given a self-supervised pre-training step with a masked language step in order to learn the input representation. Second, the network is given an ontology pre-training step in which the network learns to predict membership in the classes of the ontology as a way to learn organising knowledge from the ontology. Finally, we show that visualisation of the attention weights of the ontology-trained network allows some form of interpretability of network predictions. In general, we propose a three-layered architecture for neuro-symbolic integration, with layers for 1) encoding, 2) ontological classification, and 3) ontology-driven logical loss.
Reference ontologies provide a shared vocabulary and knowledge resource for their domain. Manual construction enables them to maintain a high quality, allowing them to be widely accepted across their community. However, the manual development process does not scale for large domains. We present a new methodology for automatic ontology extension and apply it to the ChEBI ontology, a prominent reference ontology for life sciences chemistry. We trained a Transformer-based deep learning model on the leaf node structures from the ChEBI ontology and the classes to which they belong. The model is then capable of automatically classifying previously unseen chemical structures. The proposed model achieved an overall F1 score of 0.80, an improvement of 6 percentage points over our previous results on the same dataset. Additionally, we demonstrate how visualizing the model's attention weights can help to explain the results by providing insight into how the model made its decisions.
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