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Raman spectral analysis of mixtures with one-dimensional convolutional neural network

arXiv.org Artificial Intelligence

Recently, the combination of robust one-dimensional convolutional neural networks (1-D CNNs) and Raman spectroscopy has shown great promise in rapid identification of unknown substances with good accuracy. Using this technique, researchers can recognize a pure compound and distinguish it from unknown substances in a mixture. The novelty of this approach is that the trained neural network operates automatically without any pre- or post-processing of data. Some studies have attempted to extend this technique to the classification of pure compounds in an unknown mixture. However, the application of 1-D CNNs has typically been restricted to binary classifications of pure compounds. Here we will highlight a new approach in spectral recognition and quantification of chemical components in a multicomponent mixture. Two 1-D CNN models, RaMixNet I and II, have been developed for this purpose. The former is for rapid classification of components in a mixture while the latter is for quantitative determination of those constituents. In the proposed method, there is no limit to the number of compounds in a mixture. A data augmentation method is also introduced by adding random baselines to the Raman spectra. The experimental results revealed that the classification accuracy of RaMixNet I and II is 100% for analysis of unknown test mixtures; at the same time, the RaMixNet II model may achieve a regression accuracy of 88% for the quantification of each component.


Scientific intuition inspired by machine learning generated hypotheses

arXiv.org Artificial Intelligence

Machine learning with application to questions in the physical sciences has become a widely used tool, successfully applied to classification, regression and optimization tasks in many areas. Research focus mostly lies in improving the accuracy of the machine learning models in numerical predictions, while scientific understanding is still almost exclusively generated by human researchers analysing numerical results and drawing conclusions. In this work, we shift the focus on the insights and the knowledge obtained by the machine learning models themselves. In particular, we study how it can be extracted and used to inspire human scientists to increase their intuitions and understanding of natural systems. We apply gradient boosting in decision trees to extract human interpretable insights from big data sets from chemistry and physics. In chemistry, we not only rediscover widely know rules of thumb but also find new interesting motifs that tell us how to control solubility and energy levels of organic molecules. At the same time, in quantum physics, we gain new understanding on experiments for quantum entanglement. The ability to go beyond numerics and to enter the realm of scientific insight and hypothesis generation opens the door to use machine learning to accelerate the discovery of conceptual understanding in some of the most challenging domains of science.


Machine Learning Force Fields

arXiv.org Machine Learning

In recent years, the use of Machine Learning (ML) in computational chemistry has enabled numerous advances previously out of reach due to the computational complexity of traditional electronic-structure methods. One of the most promising applications is the construction of ML-based force fields (FFs), with the aim to narrow the gap between the accuracy of ab initio methods and the efficiency of classical FFs. The key idea is to learn the statistical relation between chemical structure and potential energy without relying on a preconceived notion of fixed chemical bonds or knowledge about the relevant interactions. Such universal ML approximations are in principle only limited by the quality and quantity of the reference data used to train them. This review gives an overview of applications of ML-FFs and the chemical insights that can be obtained from them. The core concepts underlying ML-FFs are described in detail and a step-by-step guide for constructing and testing them from scratch is given. The text concludes with a discussion of the challenges that remain to be overcome by the next generation of ML-FFs.


Artificial intelligence sheds light on membrane performance

#artificialintelligence

Membrane separations have long been recognized as energy-efficient processes with a rapidly growing market. In particular, organic solvent nanofiltration (OSN) technology has shown considerable potential when applied to various industries, such as petrochemicals, pharmaceuticals and natural products. The energy consumed by these industries accounts for 10 to 15 percent of the world's entire energy consumption. Nevertheless, difficulties in predicting the separation performance of OSN membranes have hindered smooth transition from lab discovery to industry implementation. Predicting the performance of membranes is a challenging task because of the complex nature of solvent, solute and membrane interactions.


Machine learning for electronically excited states of molecules

arXiv.org Machine Learning

Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on how machine learning is employed not only to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods, approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.


Predicting retrosynthetic pathways using a combined linguistic model and hyper-graph exploration strategy

arXiv.org Machine Learning

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.


Bioplastics to social robots, new tech to bring inclusivity - Express Computer

#artificialintelligence

From biodegradable plastics to humanoid robots, a new wave of emerging technologies is on the horizon that have the potential to provide major benefits to societies and economies in the years to come, a new World Economic Forum (WEF) report said. An international Steering Committee of leading technology experts identified this year's "Top 10 Emerging Technologies" -- humanoid (and animaloid) robots designed to socialize with people; a system for pinpointing the source of a food-poisoning outbreak in seconds and minuscule lenses that will pave the way for diminutive cameras and other devices, among others. "Technologies that are emerging today will soon be shaping the world tomorrow and well into the future – with impacts to economies and to society at large," said Mariette DiChristina, Editor-in-Chief of Scientific American, and chair of the Emerging Technologies Steering Committee. Bioplastics are advanced solvents and enzymes that are transforming woody wastes into better biodegradable plastics. Like standard plastics derived from petrochemicals, biodegradable versions consist of polymers (long-chain molecules) that can be moulded while in their fluid state into a variety of forms.


Are Learned Molecular Representations Ready For Prime Time?

arXiv.org Machine Learning

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 15 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.


Prediction of amino acid side chain conformation using a deep neural network

arXiv.org Machine Learning

A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate side chain conformation. Here, using a deep neural network architecture without physics-based assumptions, we have demonstrated that side chain conformation prediction accuracy can be improved by more than 25%, especially for aromatic residues compared with current standard methods. More strikingly, the prediction method presented here is robust enough to identify individual conformational outliers from high resolution structures in a protein data bank without providing its structural factors. We envisage that our amino acid side chain predictor could be used as a quality check step for future protein structure model validation and many other potential applications such as side chain assignment in Cryo-electron microscopy, crystallography model auto-building, protein folding and small molecule ligand docking.