Tag Archives: Chemistry

Announcing OpenFermion: The Open Source Chemistry Package for Quantum Computers

Posted by Ryan Babbush and Jarrod McClean, Quantum Software Engineers, Quantum AI Team


“The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble.”
-Paul Dirac, Quantum Mechanics of Many-Electron Systems (1929)

In this passage, physicist Paul Dirac laments that while quantum mechanics accurately models all of chemistry, exactly simulating the associated equations appears intractably complicated. Not until 1982 would Richard Feynman suggest that instead of surrendering to the complexity of quantum mechanics, we might harness it as a computational resource. Hence, the original motivation for quantum computing: by operating a computer according to the laws of quantum mechanics, one could efficiently unravel exact simulations of nature. Such simulations could lead to breakthroughs in areas such as photovoltaics, batteries, new materials, pharmaceuticals and superconductivity. And while we do not yet have a quantum computer large enough to solve classically intractable problems in these areas, rapid progress is being made. Last year, Google published this paper detailing the first quantum computation of a molecule using a superconducting qubit quantum computer. Building on that work, the quantum computing group at IBM scaled the experiment to larger molecules, which made the cover of Nature last month.

Today, we announce the release of OpenFermion, the first open source platform for translating problems in chemistry and materials science into quantum circuits that can be executed on existing platforms. OpenFermion is a library for simulating the systems of interacting electrons (fermions) which give rise to the properties of matter. Prior to OpenFermion, quantum algorithm developers would need to learn a significant amount of chemistry and write a large amount of code hacking apart other codes to put together even the most basic quantum simulations. While the project began at Google, collaborators at ETH Zurich, Lawrence Berkeley National Labs, University of Michigan, Harvard University, Oxford University, Dartmouth University, Rigetti Computing and NASA all contributed to alpha releases. You can learn more details about this release in our paper, OpenFermion: The Electronic Structure Package for Quantum Computers.

One way to think of OpenFermion is as a tool for generating and compiling physics equations which describe chemical and material systems into representations which can be interpreted by a quantum computer1. The most effective quantum algorithms for these problems build upon and extend the power of classical quantum chemistry packages used and developed by research chemists across government, industry and academia. Accordingly, we are also releasing OpenFermion-Psi4 and OpenFermion-PySCF which are plugins for using OpenFermion in conjunction with the classical electronic structure packages Psi4 and PySCF.

The core OpenFermion library is designed in a quantum programming framework agnostic way to ensure compatibility with various platforms being developed by the community. This allows OpenFermion to support external packages which compile quantum assembly language specifications for diverse hardware platforms. We hope this decision will help establish OpenFermion as a community standard for putting quantum chemistry on quantum computers. To see how OpenFermion is used with diverse quantum programming frameworks, take a look at OpenFermion-ProjectQ and Forest-OpenFermion - plugins which link OpenFermion to the externally developed circuit simulation and compilation platforms known as ProjectQ and Forest.

The following workflow describes how a quantum chemist might use OpenFermion in order to simulate the energy surface of a molecule (for instance, by preparing the sort of quantum computation we described in our past blog post):
  1. The researcher initializes an OpenFermion calculation with specification of:
    • An input file specifying the coordinates of the nuclei in the molecule.
    • The basis set (e.g. cc-pVTZ) that should be used to discretize the molecule.
    • The charge and spin multiplicity (if known) of the system.
  1. The researcher uses the OpenFermion-Psi4 plugin or the OpenFermion-PySCF plugin to perform scalable classical computations which are used to optimally stage the quantum computation. For instance, one might perform a classical Hartree-Fock calculation to choose a good initial state for the quantum simulation.
  2. The researcher then specifies which electrons are most interesting to study on a quantum computer (known as an active space) and asks OpenFermion to map the equations for those electrons to a representation suitable for quantum bits, using one of the available procedures in OpenFermion, e.g. the Bravyi-Kitaev transformation.
  3. The researcher selects a quantum algorithm to solve for the properties of interest and uses a quantum compilation framework such as OpenFermion-ProjectQ to output the quantum circuit in assembly language which can be run on a quantum computer. If the researcher has access to a quantum computer, they then execute the experiment.
A few examples of what one might do with OpenFermion are demonstrated in ipython notebooks here, here and here. While quantum simulation is widely recognized as one of the most important applications of quantum computing in the near term, very few quantum computer scientists know quantum chemistry and even fewer chemists know quantum computing. Our hope is that OpenFermion will help to close the gap between these communities and bring the power of quantum computing to chemists and material scientists. If you’re interested, please checkout our GitHub repository - pull requests welcome!


1 If we may be allowed one sentence for the experts: the primary function of OpenFermion is to encode the electronic structure problem in second quantization defined by various basis sets and active spaces and then to transform those operators into spin Hamiltonians using various isomorphisms between qubit and fermion algebras.↩

Predicting Properties of Molecules with Machine Learning

Posted by George Dahl, Research Scientist, Google Brain Team

Recently there have been many exciting applications of machine learning (ML) to chemistry, particularly in chemical search problems, from drug discovery and battery design to finding better OLEDs and catalysts. Historically, chemists have used numerical approximations to Schrödinger’s equation, such as Density Functional Theory (DFT), in these sorts of chemical searches. However, the computational cost of these approximations limits the size of the search. In the hope of enabling larger searches, several research groups have created ML models to predict chemical properties using training data generated by DFT (e.g. Rupp et al. and Behler and Parrinello). Expanding upon this previous work, we have been applying various modern ML methods to the QM9 benchmark –a public collection of molecules paired with DFT-computed electronic, thermodynamic, and vibrational properties.

We have recently posted two papers describing our research in this area that grew out of a collaboration between the Google Brain Team, Google Accelerated Science, DeepMind, and the University of Basel. The first paper includes a new featurization of molecules and a systematic assessment of a multitude of machine learning methods on the QM9 benchmark. After trying many existing approaches on this benchmark, we worked on improving the most promising deep neural network models.

The resulting second paper, “Neural Message Passing for Quantum Chemistry,” describes a model family called Message Passing Neural Networks (MPNNs), which are defined abstractly enough to include many previous neural net models that are invariant to graph symmetries. We developed novel variations within the MPNN family which significantly outperform all baseline methods on the QM9 benchmark, with improvements of nearly a factor of four on some targets.

One reason molecular data is so interesting from a machine learning standpoint is that one natural representation of a molecule is as a graph with atoms as nodes and bonds as edges. Models that can leverage inherent symmetries in data will tend to generalize better — part of the success of convolutional neural networks on images is due to their ability to incorporate our prior knowledge about the invariances of image data (e.g. a picture of a dog shifted to the left is still a picture of a dog). Invariance to graph symmetries is a particularly desirable property for machine learning models that operate on graph data, and there has been a lot of interesting research in this area as well (e.g. Li et al., Duvenaud et al., Kearnes et al., Defferrard et al.). However, despite this progress, much work remains. We would like to find the best versions of these models for chemistry (and other) applications and map out the connections between different models proposed in the literature.

Our MPNNs set a new state of the art for predicting all 13 chemical properties in QM9. On this particular set of molecules, our model can predict 11 of these properties accurately enough to potentially be useful to chemists, but up to 300,000 times faster than it would take to simulate them using DFT. However, much work remains to be done before MPNNs can be of real practical use to chemists. In particular, MPNNs must be applied to a significantly more diverse set of molecules (e.g. larger or with a more varied set of heavy atoms) than exist in QM9. Of course, even with a realistic training set, generalization to very different molecules could still be poor. Overcoming both of these challenges will involve making progress on questions–such as generalization–that are at the heart of machine learning research.

Predicting the properties of molecules is a practically important problem that both benefits from advanced machine learning techniques and presents interesting fundamental research challenges for learning algorithms. Eventually, such predictions could aid the design of new medicines and materials that benefit humanity. At Google, we feel that it’s important to disseminate our research and to help train new researchers in machine learning. As such, we are delighted that the first and second authors of our MPNN paper are Google Brain residents.