Mehta, Pankaj, Bukov, Marin, Wang, Ching-Hao, Day, Alexandre G. R., Richardson, Clint, Fisher, Charles K., Schwab, David J.

Machine Learning (ML) is one of the most exciting and dynamic areas of modern research and application. The purpose of this review is to provide an introduction to the core concepts and tools of machine learning in a manner easily understood and intuitive to physicists. The review begins by covering fundamental concepts in ML and modern statistics such as the bias-variance tradeoff, overfitting, regularization, and generalization before moving on to more advanced topics in both supervised and unsupervised learning. Topics covered in the review include ensemble models, deep learning and neural networks, clustering and data visualization, energy-based models (including MaxEnt models and Restricted Boltzmann Machines), and variational methods. Throughout, we emphasize the many natural connections between ML and statistical physics. A notable aspect of the review is the use of Python notebooks to introduce modern ML/statistical packages to readers using physics-inspired datasets (the Ising Model and Monte-Carlo simulations of supersymmetric decays of proton-proton collisions). We conclude with an extended outlook discussing possible uses of machine learning for furthering our understanding of the physical world as well as open problems in ML where physicists maybe able to contribute. (Notebooks are available at https://physics.bu.edu/~pankajm/MLnotebooks.html )

Martin, M. P., Orton, T. G., Lacarce, E., Meersmans, J., Saby, N. P. A., Paroissien, J. B., Jolivet, C., Boulonne, L., Arrouays, D.

Soil organic carbon (SOC) plays a major role in the global carbon budget. It can act as a source or a sink of atmospheric carbon, thereby possibly influencing the course of climate change. Improving the tools that model the spatial distributions of SOC stocks at national scales is a priority, both for monitoring changes in SOC and as an input for global carbon cycles studies. In this paper, we compare and evaluate two recent and promising modelling approaches. First, we considered several increasingly complex boosted regression trees (BRT), a convenient and efficient multiple regression model from the statistical learning field. Further, we considered a robust geostatistical approach coupled to the BRT models. Testing the different approaches was performed on the dataset from the French Soil Monitoring Network, with a consistent cross-validation procedure. We showed that when a limited number of predictors were included in the BRT model, the standalone BRT predictions were significantly improved by robust geostatistical modelling of the residuals. However, when data for several SOC drivers were included, the standalone BRT model predictions were not significantly improved by geostatistical modelling. Therefore, in this latter situation, the BRT predictions might be considered adequate without the need for geostatistical modelling, provided that i) care is exercised in model fitting and validating, and ii) the dataset does not allow for modelling of local spatial autocorrelations, as is the case for many national systematic sampling schemes.

Feinberg, Evan N., Sheridan, Robert, Joshi, Elizabeth, Pande, Vijay S., Cheng, Alan C.

The Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of drug candidates are estimated to account for up to 50% of all clinical trial failures. Predicting ADMET properties has therefore been of great interest to the cheminformatics and medicinal chemistry communities in recent decades. Traditional cheminformatics approaches, whether the learner is a random forest or a deep neural network, leverage fixed fingerprint feature representations of molecules. In contrast, in this paper, we learn the features most relevant to each chemical task at hand by representing each molecule explicitly as a graph, where each node is an atom and each edge is a bond. By applying graph convolutions to this explicit molecular representation, we achieve, to our knowledge, unprecedented accuracy in prediction of ADMET properties. By challenging our methodology with rigorous cross-validation procedures and prospective analyses, we show that deep featurization better enables molecular predictors to not only interpolate but also extrapolate to new regions of chemical space.

Schwarzer, Max, Rogan, Bryce, Ruan, Yadong, Song, Zhengming, Lee, Diana, Percus, Allon G., Chau, Viet T., Moore, Bryan A., Rougier, Esteban, Viswanathan, Hari S., Srinivasan, Gowri

Understanding dynamic fracture propagation is essential to predicting how brittle materials fail. Various mathematical models and computational applications have been developed to predict fracture evolution and coalescence, including finite-discrete element methods such as the Hybrid Optimization Software Suite (HOSS). While such methods achieve high fidelity results, they can be computationally prohibitive: a single simulation takes hours to run, and thousands of simulations are required for a statistically meaningful ensemble. We propose a machine learning approach that, once trained on data from HOSS simulations, can predict fracture growth statistics within seconds. Our method uses deep learning, exploiting the capabilities of a graph convolutional network to recognize features of the fracturing material, along with a recurrent neural network to model the evolution of these features. In this way, we simultaneously generate predictions for qualitatively distinct material properties. Our prediction for total damage in a coalesced fracture, at the final simulation time step, is within 3% of its actual value, and our prediction for total length of a coalesced fracture is within 2%. We also develop a novel form of data augmentation that compensates for the modest size of our training data, and an ensemble learning approach that enables us to predict when the material fails, with a mean absolute error of approximately 15%.

Akita, Hirotaka, Nakago, Kosuke, Komatsu, Tomoki, Sugawara, Yohei, Maeda, Shin-ichi, Baba, Yukino, Kashima, Hisashi

Recent advances in graph convolutional networks have significantly improved the performance of chemical predictions, raising a new research question: "how do we explain the predictions of graph convolutional networks?" A possible approach to answer this question is to visualize evidence substructures responsible for the predictions. For chemical property prediction tasks, the sample size of the training data is often small and/or a label imbalance problem occurs, where a few samples belong to a single class and the majority of samples belong to the other classes. This can lead to uncertainty related to the learned parameters of the machine learning model. To address this uncertainty, we propose BayesGrad, utilizing the Bayesian predictive distribution, to define the importance of each node in an input graph, which is computed efficiently using the dropout technique. We demonstrate that BayesGrad successfully visualizes the substructures responsible for the label prediction in the artificial experiment, even when the sample size is small. Furthermore, we use a real dataset to evaluate the effectiveness of the visualization. The basic idea of BayesGrad is not limited to graph-structured data and can be applied to other data types.