We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder–decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis.

Modern software systems are built to be used in dynamic environments using configuration capabilities to adapt to changes and external uncertainties. In a self-adaptation context, we are often interested in reasoning about the performance of the systems under different configurations. Usually, we learn a black-box model based on real measurements to predict the performance of the system given a specific configuration. However, as modern systems become more complex, there are many configuration parameters that may interact and we end up learning an exponentially large configuration space. Naturally, this does not scale when relying on real measurements in the actual changing environment. We propose a different solution: Instead of taking the measurements from the real system, we learn the model using samples from other sources, such as simulators that approximate performance of the real system at low cost. We define a cost model that transform the traditional view of model learning into a multi-objective problem that not only takes into account model accuracy but also measurements effort as well. We evaluate our cost-aware transfer learning solution using real-world configurable software including (i) a robotic system, (ii) 3 different stream processing applications, and (iii) a NoSQL database system. The experimental results demonstrate that our approach can achieve (a) a high prediction accuracy, as well as (b) a high model reliability.

Massively parallel reporter assays (MPRAs) are a method to probe the effects of short sequences on transcriptional regulation activity. In a MPRA, short sequences are extracted from suspected regulatory regions, inserted into reporter plasmids, transfected into cell-types of interest, and the transcriptional activity of each reporter is assayed. Recently, Ernst et al. presented MPRA data covering 15750 putative regulatory regions. We trained a multitask convolutional neural network architecture using these sequence expression readouts which predicts as output the expression level outputs across four combinations of cell types and promoters. The model allows for the assigning of importance scores to each base through in silico mutagenesis, and the resulting importance scores correlated well with regions enriched for conservation and transcription factor binding.

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