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We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce new metrics (coverage, class diversity, round-trip accuracy and Jensen-Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is constructed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and academic exams. Overall, the frameworks has a very good performance with few weaknesses due to the bias induced during the training process. The use of the newly introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks through focusing on the performance of the single-step model only.

Deep neural networks achieve outstanding results in challenging image classification tasks. However, the design of network topologies is a complex task and the research community makes a constant effort in discovering top-accuracy topologies, either manually or employing expensive architecture searches. In this work, we propose a unique narrow-space architecture search that focuses on delivering low-cost and fast executing networks that respect strict memory and time requirements typical of Internet-of-Things (IoT) near-sensor computing platforms. Our approach provides solutions with classification latencies below 10ms running on a $35 device with 1GB RAM and 5.6GFLOPS peak performance. The narrow-space search of floating-point models improves the accuracy on CIFAR10 of an established IoT model from 70.64% to 74.87% respecting the same memory constraints. We further improve the accuracy to 82.07% by including 16-bit half types and we obtain the best accuracy of 83.45% by extending the search with model optimized IEEE 754 reduced types. To the best of our knowledge, we are the first that empirically demonstrate on over 3000 trained models that running with reduced precision pushes the Pareto optimal front by a wide margin. Under a given memory constraint, accuracy is improved by over 7% points for half and over 1% points further for running with the best model individual format.

Information extraction and data mining in biochemical literature is a daunting task that demands resource-intensive computation and appropriate means to scale knowledge ingestion. Being able to leverage this immense source of technical information helps to drastically reduce costs and time to solution in multiple application fields from food safety to pharmaceutics. We present a scalable document ingestion system that integrates data from databases and publications (in PDF format) in a biochemistry knowledge graph (BCKG). The BCKG is a comprehensive source of knowledge that can be queried to retrieve known biochemical facts and to generate novel insights. After describing the knowledge ingestion framework, we showcase an application of our system in the field of carbohydrate enzymes. The BCKG represents a way to scale knowledge ingestion and automatically exploit prior knowledge to accelerate discovery in biochemical sciences., Comment: 4 pages, 1 figure, Workshop on Applied Data Science for Healthcare at KDD, Anchorage, AK, 2019

Application of neural networks to a vast variety of practical applications is transforming the way AI is applied in practice. Pre-trained neural network models available through APIs or capability to custom train pre-built neural network architectures with customer data has made the consumption of AI by developers much simpler and resulted in broad adoption of these complex AI models. While prebuilt network models exist for certain scenarios, to try and meet the constraints that are unique to each application, AI teams need to think about developing custom neural network architectures that can meet the tradeoff between accuracy and memory footprint to achieve the tight constraints of their unique use-cases. However, only a small proportion of data science teams have the skills and experience needed to create a neural network from scratch, and the demand far exceeds the supply. In this paper, we present NeuNetS : An automated Neural Network Synthesis engine for custom neural network design that is available as part of IBM's AI OpenScale's product. NeuNetS is available for both Text and Image domains and can build neural networks for specific tasks in a fraction of the time it takes today with human effort, and with accuracy similar to that of human-designed AI models., Comment: 14 pages, 12 figures. arXiv admin note: text overlap with arXiv:1806.00250

Organic synthesis is one of the key stumbling blocks in medicinal chemistry. A necessary yet unsolved step in planning synthesis is solving the forward problem: given reactants and reagents, predict the products. Similar to other work, we treat reaction prediction as a machine translation problem between SMILES strings of reactants-reagents and the products. We show that a multi-head attention Molecular Transformer model outperforms all algorithms in the literature, achieving a top-1 accuracy above 90% on a common benchmark dataset. Our algorithm requires no handcrafted rules, and accurately predicts subtle chemical transformations. Crucially, our model can accurately estimate its own uncertainty, with an uncertainty score that is 89% accurate in terms of classifying whether a prediction is correct. Furthermore, we show that the model is able to handle inputs without reactant-reagent split and including stereochemistry, which makes our method universally applicable., Comment: Machine Learning for Molecules and Materials workshop, NeurIPS 2018 / Platform: https://rxn.res.ibm.com