Stefan Kuhn

Stefan Kuhn, Carlos Cobas, Agustin Barba et al.

This paper presents a proof-of-concept method for classifying chemical compounds directly from NMR data without doing structure elucidation. This can help to reduce time in finding good structure candidates, as in most cases matching must be done by a human engineer, or at the very least a process for matching must be meaningfully interpreted by one. Therefore, for a long time automation in the area of NMR has been actively sought. The method identified as suitable for the classification is a convolutional neural network (CNN). Other methods, including clustering and image registration, have not been found suitable for the task in a comparative analysis. The result shows that deep learning can offer solutions to automation problems in cheminformatics.

Herman Rull, Markus Fischer, Stefan Kuhn

Prediction of chemical shift in NMR using machine learning methods is typically done with the maximum amount of data available to achieve the best results. In some cases, such large amounts of data are not available, e.g. for heteronuclei. We demonstrate a novel machine learning model which is able to achieve good results with comparatively low amounts of data. We show this by predicting 19F and 13C NMR chemical shifts of small molecules in specific solvents.

Stefan Kuhn, Vandana Dwarka, Przemyslaw Karol Grenda et al.

We introduce a reversible deep learning model for 13C NMR that uses a single conditional invertible neural network for both directions between molecular structures and spectra. The network is built from i-RevNet style bijective blocks, so the forward map and its inverse are available by construction. We train the model to predict a 128-bit binned spectrum code from a graph-based structure encoding, while the remaining latent dimensions capture residual variability. At inference time, we invert the same trained network to generate structure candidates from a spectrum code, which explicitly represents the one-to-many nature of spectrum-to-structure inference. On a filtered subset, the model is numerically invertible on trained examples, achieves spectrum-code prediction above chance, and produces coarse but meaningful structural signals when inverted on validation spectra. These results demonstrate that invertible architectures can unify spectrum prediction and uncertainty-aware candidate generation within one end-to-end model.

Antonio Cau, Stefan Kuhn, James Hoey

In this paper the reversibility of executable Interval Temporal Logic (ITL) specifications is investigated. ITL allows for the reasoning about systems in terms of behaviours which are represented as non-empty sequences of states. It allows for the specification of systems at different levels of abstraction. At a high level this specification is in terms of properties, for instance safety and liveness properties. At concrete level one can specify a system in terms of programming constructs. One can execute these concrete specification, i.e., test and simulate the behaviour of the system. In this paper we will formalise this notion of executability of ITL specifications. ITL also has a reflection operator which allows for the reasoning about reversed behaviours. We will investigate the reversibility of executable ITL specifications, i.e., how one can use this reflection operator to reverse the concrete behaviour of a particular system.

Stefan Kuhn, Eda Tumer, Simon Colreavy-Donnelly et al.

This paper presents a method to identify substructures in NMR spectra of mixtures, specifically 2D spectra, using a bespoke image-based Convolutional Neural Network application. This is done using HSQC and HMBC spectra separately and in combination. The application can reliably detect substructures in pure compounds, using a simple network. It can work for mixtures when trained on pure compounds only. HMBC data and the combination of HMBC and HSQC show better results than HSQC alone.