arXiv subjects

Justin S. Smith

Publications and source records attributed to Justin S. Smith.

23 records · Page 2Linked to original sources

arXiv2018

Transferable Molecular Charge Assignment Using Deep Neural Networks

We use HIP-NN, a neural network architecture that excels at predicting molecular energies, to predict atomic charges. The charge predictions are accurate over a wide range of molecules (both small and large) and for a diverse set of charge assignment schemes. To demonstrate the power of charge prediction on non-equilibrium geometries, we use HIP-NN to generate IR spectra from dynamical trajectories on a variety of molecules. The results are in good agreement with reference IR spectra produced by traditional theoretical methods. Critically, for this application, HIP-NN charge predictions are about 104 times faster than direct DFT charge calculations. Thus, ML provides a pathway to greatly increase the range of feasible simulations while retaining quantum-level accuracy. In summary, our results provide further evidence that machine learning can replicate high-level quantum calculations at a tiny fraction of the computational cost.

physics.chem-ph↗

arXiv2018

Learning to Navigate: Exploiting Deep Networks to Inform Sample-Based Planning During Vision-Based Navigation

Recent applications of deep learning to navigation have generated end-to-end navigation solutions whereby visual sensor input is mapped to control signals or to motion primitives. The resulting visual navigation strategies work very well at collision avoidance and have performance that matches traditional reactive navigation algorithms while operating in real-time. It is accepted that these solutions cannot provide the same level of performance as a global planner. However, it is less clear how such end-to-end systems should be integrated into a full navigation pipeline. We evaluate the typical end-to-end solution within a full navigation pipeline in order to expose its weaknesses. Doing so illuminates how to better integrate deep learning methods into the navigation pipeline. In particular, we show that they are an efficient means to provide informed samples for sample-based planners. Controlled simulations with comparison against traditional planners show that the number of samples can be reduced by an order of magnitude while preserving navigation performance. Implementation on a mobile robot matches the simulated performance outcomes.

cs.RO↗

arXiv2017

ANI-1: A data set of 20M off-equilibrium DFT calculations for organic molecules

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML), in particular neural networks, are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of 20M conformations for 57,454 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

physics.chem-ph↗

arXiv2017

Hierarchical modeling of molecular energies using a deep neural network

We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over hierarchical terms. These terms are generated from a neural network--a composition of many nonlinear transformations--acting on a representation of the molecule. HIP-NN achieves state-of-the-art performance on a dataset of 131k ground state organic molecules, and predicts energies with 0.26 kcal/mol mean absolute error. With minimal tuning, our model is also competitive on a dataset of molecular dynamics trajectories. In addition to enabling accurate energy predictions, the hierarchical structure of HIP-NN helps to identify regions of model uncertainty.

stat.ML↗

arXiv2017

ANI-1: An extensible neural network potential with DFT accuracy at force field computational cost

Deep learning is revolutionizing many areas of science and technology, especially image, text and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mechanical (QM) DFT calculations can learn an accurate and fully transferable potential for organic molecules. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Molecular Energies) or ANI in short. ANI is a new method and procedure for training neural network potentials that utilizes a highly modified version of the Behler and Parrinello symmetry functions to build single-atom atomic environment vectors as a molecular representation. We utilize ANI to build a potential called ANI-1, which was trained on a subset of the GDB databases with up to 8 heavy atoms to predict total energies for organic molecules containing four atom types: H, C, N, and O. To obtain an accelerated but physically relevant sampling of molecular potential surfaces, we also propose a Normal Mode Sampling (NMS) method for generating molecular configurations. Through a series of case studies, we show that ANI-1 is chemically accurate compared to reference DFT calculations on much larger molecular systems (up to 54 atoms) than those included in the training data set, with root mean square errors as low as 0.56 kcal/mol.

physics.chem-ph↗