Högskolan i Skövde

We present a flexible deep convolutional neural network method for the analysis of arbitrary sized graph structures representing molecules. This method, which makes use of the Lipinski RDKit module, an open-source cheminformatics software, enables the incorporation of any global molecular (such as molecular charge and molecular weight) and local (such as atom hybridization and bond orders) information. In this paper, we show that this method significantly outperforms another recently proposed method based on deep convolutional neural networks on several datasets that are studied. Several best practices for training deep convolutional neural networks on chemical datasets are also highlighted within the article, such as how to select the information to be included in the model, how to prevent overfitting and how unbalanced classes in the data can be handled.

We present a flexible deep convolutional neural network method for the analyse of arbitrary sized graph structures representing molecules. The method makes use of RDKit, an open-source cheminformatics software, allowing the incorporation of any global molecular (such as molecular charge) and local (such as atom type) information. We evaluate the method on the Side Effect Resource (SIDER) v4.1 dataset and show that it significantly outperforms another recently proposed method based on deep convolutional neural networks. We also reflect on how different types of information and input data affect the predictive power of our model. This reflection highlights several open problems that should be solved to further improve the use of deep learning within cheminformatics.

The competitiveness in the manufacturing industry raises demands for using recent data analysis algorithms for manufacturing process development. Data-driven analysis enables extraction of novel knowledge from already existing sensors and data, which is necessary for advanced manufacturing process refinement involving aged machinery. Improved data analysis enables factories to stay competitive against newer factories, but without any hefty investment. In large manufacturing operations, the dependencies between data are highly complex and therefore very difficult to analyse manually. This paper applies a deep learning approach, using a recurrent neural network with long short term memory cells together with an attention mechanism to model the dependencies between the measured product shape, as measured before the most critical manufacturing operation, and the final product quality. Our approach predicts the ratio of flawed products already before the critical operation with an AUC-ROC score of 0.85, i.e., we can detect more than 80 % of all flawed products while having less than 25 % false positive predictions (false alarms). In contrast to previous deep learning approaches, our method shows how the recurrent neural network reasons about the input shape, using the attention mechanism to point out which parts of the product shape that have the highest influence on the predictions. Such information is crucial for both process developers, in order to understand and improve the process, and for process operators who can use the information to learn how to better trust the predictions and control the process.

In medicinal chemistry programs it is key to design and make compounds that are efficacious and safe. This is a long, complex, and difficult multiparameter optimization process, often including several properties with orthogonal trends. New methods for the automated design of compounds against profiles of multiple properties are thus of great value. Here we present a fragment-based reinforcement learning approach based on an actor-critic model, for the generation of novel molecules with optimal properties. The actor and the critic are both modeled with bidirectional long short-term memory (LSTM) networks. The AI method learns how to generate new compounds with desired properties by starting from an initial set of lead molecules and then improving these by replacing some of their fragments. A balanced binary tree based on the similarity of fragments is used in the generative process to bias the output toward structurally similar molecules. The method is demonstrated by a case study showing that 93% of the generated molecules are chemically valid and more than a third satisfy the targeted objectives, while there were none in the initial set.

Artificial intelligence (AI) is nowadays included into an increasing number of critical systems. Inclusion of AI in such systems may, however, pose a risk, since it is, still, infeasible to build AI systems that know how to function well in situations that differ greatly from what the AI has seen before. Therefore, it is crucial that future AI systems have the ability to not only function well in known domains, but also understand and show when they are uncertain when facing something unknown. In this paper, we evaluate four different methods that have been proposed to correctly quantifying uncertainty when the AI model is faced with new samples. We investigate the behaviour of these models when they are applied to samples far from what these models have seen before, and if they correctly attribute those samples with high uncertainty. We also examine if incorrectly classified samples are attributed with an higher uncertainty than correctly classified samples. The major finding from this simple experiment is, surprisingly, that the evaluated methods capture the uncertainty differently and the correlation between the quantified uncertainty of the models is low. This inconsistency is something that needs to be further understood and solved before AI can be used in critical applications in a trustworthy and safe manner. © 2020, Springer Nature Switzerland AG.

Basic oxygen steel making is a complex chemical and physical industrial process that reduces a mix of pig iron and recycled scrap into low-carbon steel. Good understanding of the process and the ability to predict how it will evolve requires long operator experience, but this can be augmented with process target prediction systems. Such systems may use machine learning to learn a model of the process based on a long process history, and have an advantage in that they can make useof vastly more process parameters than operators can comprehend. While it has become less of a challenge to build such prediction systems using machine learning algorithms, actual production implementations are rare. The hidden reasoning of complex prediction model and lack of transparency prevents operator trust, even for models that show high accuracy predictions. To express model behaviour and thereby increasing transparency we develop a reinforcement learning (RL) based agent approach, which task is to generate short polynomials that can explain the model of the process from what it has learnt from process data. The RL agent is rewarded on how well it generates polynomials that can predict the process from a smaller subset of the process parameters. Agent training is done with the REINFORCE algorithm, which enables the sampling of multiple concurrently plausible polynomials. Having multiple polynomials, process developers can evaluate several alternative and plausible explanations, as observed in the historic process data. The presented approach gives both a trained generative model and a set of polynomials that can explain the process. The performance of the polynomials is as good as or better than more complex and less interpretable models. Further, the relative simplicity of the resulting polynomials allows good generalisation to fit new instances of data. The best of the resulting polynomials in our evaluation achieves a better R 2 score on the test set in comparison to the other machine learning models evaluated.