Tag Archives: Chemistry

Developing industrial use cases for physical simulation on future error-corrected quantum computers

Posted by Nicholas Rubin, Senior Research Scientist, and Ryan Babbush, Head of Quantum Algorithms, Quantum AI Team

If you’ve paid attention to the quantum computing space, you’ve heard the claim that in the future, quantum computers will solve certain problems exponentially more efficiently than classical computers can. They have the potential to transform many industries, from pharmaceuticals to energy.

For the most part, these claims have rested on arguments about the asymptotic scaling of algorithms as the problem size approaches infinity, but this tells us very little about the practical performance of quantum computers for finite-sized problems. We want to be more concrete: Exactly which problems are quantum computers more suited to tackle than their classical counterparts, and exactly what quantum algorithms could we run to solve these problems? Once we’ve designed an algorithm, we can go beyond analysis based on asymptotic scaling — we can determine the actual resources required to compile and run the algorithm on a quantum computer, and how that compares to a classical computation.

Over the last few years, Google Quantum AI has collaborated with industry and academic partners to assess the prospects for quantum simulation to revolutionize specific technologies and perform concrete analyses of the resource requirements. In 2022, we developed quantum algorithms to analyze the chemistry of an important enzyme family called cytochrome P450. Then, in our paper released this fall, we demonstrated how to use a quantum computer to study sustainable alternatives to cobalt for use in lithium ion batteries. And most recently, as we report in a preprint titled “Quantum computation of stopping power for inertial fusion target design,” we’ve found a new application in modeling the properties of materials in inertial confinement fusion experiments, such as those at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory, which recently made headlines for a breakthrough in nuclear fusion.

Below, we describe these three industrially relevant applications for simulations with quantum computers. While running the algorithms will require an error-corrected quantum computer, which is still years away, working on this now will ensure that we are ready with efficient quantum algorithms when such a quantum computer is built. Already, our work has reduced the cost of compiling and running the algorithms significantly, as we have reported in the past. Our work is essential for demonstrating the potential of quantum computing, but it also provides our hardware team with target specifications for the number of qubits and time needed to run useful quantum algorithms in the future.


Application 1: The CYP450 mechanism

The pharmaceutical industry is often touted as a field ripe for discovery using quantum computers. But concrete examples of such potential applications are few and far between. Working with collaborators at the pharmaceutical company Boehringer Ingelheim, our partners at the startup QSimulate, and academic colleagues at Columbia University, we explored one example in the 2022 PNAS article, “Reliably assessing the electronic structure of cytochrome P450 on today’s classical computers and tomorrow’s quantum computers”.

Cytochrome P450 is an enzyme family naturally found in humans that helps us metabolize drugs. It excels at its job: more than 70% of all drug metabolism is performed by enzymes of the P450 family. The enzymes work by oxidizing the drug — a process that depends on complex correlations between electrons. The details of the interactions are too complicated for scientists to know a priori how effective the enzyme will be on a particular drug.

In the paper, we showed how a quantum computer could approach this problem. The CYP450 metabolic process is a complex chain of reactions with many intermediate changes in the electronic structure of the enzymes throughout. We first use state-of-the-art classical methods to determine the resources required to simulate this problem on a classical computer. Then we imagine implementing a phase-estimation algorithm — which is needed to compute the ground-state energies of the relevant electronic configurations throughout the reaction chain — on a surface-code error-corrected quantum computer.

With a quantum computer, we could follow the chain of changing electronic structure with greater accuracy and fewer resources. In fact, we find that the higher accuracy offered by a quantum computer is needed to correctly resolve the chemistry in this system, so not only will a quantum computer be better, it will be necessary. And as the system size gets bigger, i.e., the more quantum energy levels we include in the simulation, the more the quantum computer wins over the classical computer. Ultimately, we show that a few million physical qubits would be required to reach quantum advantage for this problem.

Left: Example of an electron orbital (red and blue) of a CYP enzyme. More than 60 such orbitals are required to model the CYP system. Right: Comparison of actual runtime (CPU) of various classical techniques (blue) to hypothetical runtime (QPU) of a quantum algorithm (green). The lower slope of the quantum algorithm demonstrates the favorable asymptotic scaling over classical methods. Already at about 20-30 orbitals, we see a crossover to the regime where a quantum algorithm would be more efficient than classical methods.

Application 2: Lithium-ion batteries

Lithium-ion batteries rely on the electrochemical potential difference between two lithium containing materials. One material used today for the cathodes of Li-ion batteries is LiCoO2. Unfortunately, it has drawbacks from a manufacturing perspective. Cobalt mining is expensive, destructive to the environment, and often utilizes unsafe or abusive labor practices. Consequently, many in the field are interested in alternatives to cobalt for lithium-ion cathodes.

In the 1990’s, researchers discovered that nickel could replace cobalt to form LiNiO2 (called “lithium nickel oxide” or “LNO”) for cathodes. While pure LNO was found to be unstable in production, many cathode materials used in the automotive industry today use a high fraction of nickel and hence, resemble LNO. Despite its applications to industry, however, not all of the chemical properties of LNO are understood — even the properties of its ground state remains a subject of debate.

In our recent paper, “Fault tolerant quantum simulation of materials using Bloch orbitals,” we worked with the chemical company, BASF, the molecular modeling startup, QSimulate, and collaborators at Macquarie University in Australia to develop techniques to perform quantum simulations on systems with periodic, regularly spaced atomic structure, such as LNO. We then applied these techniques to design algorithms to study the relative energies of a few different candidate structures of LNO. With classical computers, high accuracy simulations of the quantum wavefunction are considered too expensive to perform. In our work, we found that a quantum computer would need tens of millions of physical qubits to calculate the energies of each of the four candidate ground-state LNO structures. This is out of reach of the first error-corrected quantum computers, but we expect this number to come down with future algorithmic improvements.

Four candidate structures of LNO. In the paper, we consider the resources required to compare the energies of these structures in order to find the ground state of LNO.

Application 3: Fusion reactor dynamics

In our third and most recent example, we collaborated with theorists at Sandia National Laboratories and our Macquarie University collaborators to put our hypothetical quantum computer to the task of simulating dynamics of charged particles in the extreme conditions typical of inertial confinement fusion (ICF) experiments, like those at the National Ignition Facility. In those experiments, high-intensity lasers are focused into a metallic cavity (hohlraum) that holds a target capsule consisting of an ablator surrounding deuterium–tritium fuel. When the lasers heat the inside of the hohlraum, its walls radiate x-rays that compress the capsule, heating the deuterium and tritium inside to 10s of millions of Kelvin. This allows the nucleons in the fuel to overcome their mutual electrostatic repulsion and start fusing into helium nuclei, also called alpha particles.

Simulations of these experiments are computationally demanding and rely on models of material properties that are themselves uncertain. Even testing these models, using methods similar to those in quantum chemistry, is extremely computationally expensive. In some cases, such test calculations have consumed >100 million CPU hours. One of the most expensive and least accurate aspects of the simulation is the dynamics of the plasma prior to the sustained fusion stage (>10s of millions of Kelvin), when parts of the capsule and fuel are a more balmy 100k Kelvin. In this “warm dense matter” regime, quantum correlations play a larger role in the behavior of the system than in the “hot dense matter” regime when sustained fusion takes place.

In our new preprint, “Quantum computation of stopping power for inertial fusion target design”, we present a quantum algorithm to compute the so-called “stopping power” of the warm dense matter in a nuclear fusion experiment. The stopping power is the rate at which a high energy alpha particle slows down due to Coulomb interactions with the surrounding plasma. Understanding the stopping power of the system is vital for optimizing the efficiency of the reactor. As the alpha particle is slowed by the plasma around it, it transfers its energy to the plasma, heating it up. This self-heating process is the mechanism by which fusion reactions sustain the burning plasma. Detailed modeling of this process will help inform future reactor designs.

We estimate that the quantum algorithm needed to calculate the stopping power would require resources somewhere between the P450 application and the battery application. But since this is the first case study on first-principles dynamics (or any application at finite temperature), such estimates are just a starting point and we again expect to find algorithmic improvements to bring this cost down in the future. Despite this uncertainty, it is still certainly better than the classical alternative, for which the only tractable approaches for these simulations are mean-field methods. While these methods incur unknown systematic errors when describing the physics of these systems, they are currently the only meaningful means of performing such simulations.

Left: A projectile (red) passing through a medium (blue) with initial velocity vproj. Right: To calculate the stopping power, we monitor the energy transfer between the projectile and the medium (blue solid line) and determine its average slope (red dashed line).

Discussion and conclusion

The examples described above are just three of a large and growing body of concrete applications for a future error-corrected quantum computer in simulating physical systems. This line of research helps us understand the classes of problems that will most benefit from the power of quantum computing. In particular, the last example is distinct from the other two in that it is simulating a dynamical system. In contrast to the other problems, which focus on finding the lowest energy, static ground state of a quantum system, quantum dynamics is concerned with how a quantum system changes over time. Since quantum computers are inherently dynamic — the qubit states evolve and change as each operation is performed — they are particularly well suited to solving these kinds of problems. Together with collaborators at Columbia, Harvard, Sandia National Laboratories and Macquarie University in Australia we recently published a paper in Nature Communications demonstrating that quantum algorithms for simulating electron dynamics can be more efficient even than approximate, “mean-field” classical calculations, while simultaneously offering much higher accuracy.

Developing and improving algorithms today prepares us to take full advantage of them when an error-corrected quantum computer is eventually realized. Just as in the classical computing case, we expect improvements at every level of the quantum computing stack to further lower the resource requirements. But this first step helps separate hyperbole from genuine applications amenable to quantum computational speedups.


Acknowledgements

We would like to thank Katie McCormick, our Quantum Science Communicator, for helping to write this blog post.

Source: Google AI Blog


Digitizing Smell: Using Molecular Maps to Understand Odor

Posted by Richard C. Gerkin, Google Research, and Alexander B. Wiltschko, Google

Did you ever try to measure a smell? …Until you can measure their likenesses and differences you can have no science of odor. If you are ambitious to found a new science, measure a smell.
— Alexander Graham Bell, 1914.

How can we measure a smell? Smells are produced by molecules that waft through the air, enter our noses, and bind to sensory receptors. Potentially billions of molecules can produce a smell, so figuring out which ones produce which smells is difficult to catalog or predict. Sensory maps can help us solve this problem. Color vision has the most familiar examples of these maps, from the color wheel we each learn in primary school to more sophisticated variants used to perform color correction in video production. While these maps have existed for centuries, useful maps for smell have been missing, because smell is a harder problem to crack: molecules vary in many more ways than photons do; data collection requires physical proximity between the smeller and smell (we don’t have good smell “cameras” and smell “monitors”); and the human eye only has three sensory receptors for color while the human nose has > 300 for odor. As a result, previous efforts to produce odor maps have failed to gain traction.

In 2019, we developed a graph neural network (GNN) model that began to explore thousands of examples of distinct molecules paired with the smell labels that they evoke, e.g., “beefy”, “floral”, or “minty”, to learn the relationship between a molecule’s structure and the probability that such a molecule would have each smell label. The embedding space of this model contains a representation of each molecule as a fixed-length vector describing that molecule in terms of its odor, much as the RGB value of a visual stimulus describes its color.

Left: An example of a color map (CIE 1931) in which coordinates can be directly translated into values for hue and saturation. Similar colors lie near each other, and specific wavelengths of light (and combinations thereof) can be identified with positions on the map. Right: Odors in the Principal Odor Map operate similarly. Individual molecules correspond to points (grey), and the locations of these points reflect predictions of their odor character.

Today we introduce the “Principal Odor Map” (POM), which identifies the vector representation of each odorous molecule in the model’s embedding space as a single point in a high-dimensional space. The POM has the properties of a sensory map: first, pairs of perceptually similar odors correspond to two nearby points in the POM (by analogy, red is nearer to orange than to green on the color wheel). Second, the POM enables us to predict and discover new odors and the molecules that produce them. In a series of papers, we demonstrate that the map can be used to prospectively predict the odor properties of molecules, understand these properties in terms of fundamental biology, and tackle pressing global health problems. We discuss each of these promising applications of the POM and how we test them below.

Test 1: Challenging the Model with Molecules Never Smelled Before
First, we asked if the underlying model could correctly predict the odors of new molecules that no one had ever smelled before and that were very different from molecules used during model development. This is an important test — many models perform well on data that looks similar to what the model has seen before, but break down when tested on novel cases.

To test this, we collected the largest ever dataset of odor descriptions for novel molecules. Our partners at the Monell Center trained panelists to rate the smell of each of 400 molecules using 55 distinct labels (e.g., “minty”) that were selected to cover the space of possible smells while being neither redundant nor too sparse. Unsurprisingly, we found that different people had different characterizations of the same molecule. This is why sensory research typically uses panels of dozens or hundreds of people and highlights why smell is a hard problem to solve. Rather than see if the model could match any one person, we asked how close it was to the consensus: the average across all of the panelists. We found that the predictions of the model were closer to the consensus than the average panelist was. In other words, the model demonstrated an exceptional ability to predict odor from a molecule’s structure.

Predictions made by two models, our GNN model (orange) and a baseline chemoinformatic random forest (RF) model (blue), compared with the mean ratings given by trained panelists (green) for the molecule 2,3-dihydrobenzofuran-5-carboxaldehyde. Each bar corresponds to one odor character label (with only the top 17 of 55 shown for clarity). The top five are indicated in color; our model correctly identifies four of the top five, with high confidence, vs. only three of five, with low confidence, for the RF model. The correlation (R) to the full set of 55 labels is also higher in our model.
Unlike alternative benchmark models (RF and nearest-neighbor models trained on various sets of chemoinformatic features), our GNN model outperforms the median human panelist at predicting the panel mean rating. In other words, our GNN model better reflects the panel consensus than the typical panelist.

The POM also exhibited state-of-the-art performance on alternative human olfaction tasks like detecting the strength of a smell or the similarity of different smells. Thus, with the POM, it should be possible to predict the odor qualities of any of billions of as-yet-unknown odorous molecules, with broad applications to flavor and fragrance.

Test 2: Linking Odor Quality Back to Fundamental Biology
Because the Principal Odor Map was useful in predicting human odor perception, we asked whether it could also predict odor perception in animals, and the brain activity that underlies it. We found that the map could successfully predict the activity of sensory receptors, neurons, and behavior in most animals that olfactory neuroscientists have studied, including mice and insects.

What common feature of the natural world makes this map applicable to species separated by hundreds of millions of years of evolution? We realized that the common purpose of the ability to smell might be to detect and discriminate between metabolic states, i.e., to sense when something is ripe vs. rotten, nutritious vs. inert, or healthy vs. sick. We gathered data about metabolic reactions in dozens of species across the kingdoms of life and found that the map corresponds closely to metabolism itself. When two molecules are far apart in odor, according to the map, a long series of metabolic reactions is required to convert one to the other; by contrast, similarly smelling molecules are separated by just one or a few reactions. Even long reaction pathways containing many steps trace smooth paths through the map. And molecules that co-occur in the same natural substances (e.g., an orange) are often very tightly clustered on the map. The POM shows that olfaction is linked to our natural world through the structure of metabolism and, perhaps surprisingly, captures fundamental principles of biology.

Left: We aggregated metabolic reactions found in 17 species across 4 kingdoms to construct a metabolic graph. In this illustration, each circle is a distinct metabolite molecule and an arrow indicates that there is a metabolic reaction that converts one molecule to another. Some metabolites have an odor (color) and others do not (gray), and the metabolic distance between two odorous metabolites is the minimum number of reactions necessary to convert one into the other. In the path shown in bold, the distance is 3. Right: Metabolic distance was highly correlated with distance in the POM, an estimate of perceived odor dissimilarity.

Test 3: Extending the Model to Tackle a Global Health Challenge
A map of odor that is tightly connected to perception and biology across the animal kingdom opens new doors. Mosquitos and other insect pests are drawn to humans in part by their odor perception. Since the POM can be used to predict animal olfaction generally, we retrained it to tackle one of humanity’s biggest problems, the scourge of diseases transmitted by mosquitoes and ticks, which kill hundreds of thousands of people each year.

For this purpose, we improved our original model with two new sources of data: (1) a long-forgotten set of experiments conducted by the USDA on human volunteers beginning 80 years ago and recently made discoverable by Google Books, which we subsequently made machine-readable; and (2) a new dataset collected by our partners at TropIQ, using their high-throughput laboratory mosquito assay. Both datasets measure how well a given molecule keeps mosquitos away. Together, the resulting model can predict the mosquito repellency of nearly any molecule, enabling a virtual screen over huge swaths of molecular space. We validated this screen experimentally using entirely new molecules and found over a dozen of them with repellency at least as high as DEET, the active ingredient in most insect repellents. Less expensive, longer lasting, and safer repellents can reduce the worldwide incidence of diseases like malaria, potentially saving countless lives.

We digitized USDA mosquito repellency data for thousands of molecules previously scanned by Google Books, and used it to refine the learned representation (the map) at the heart of the model. We added additional layers, specifically to predict repellency in a mosquito feeder assay, and iteratively trained the model to improve assay predictions while running computational screens for candidate repellents.
Many molecules showing mosquito repellency in the laboratory assay also showed repellency when applied to humans. Several showed repellency greater than the most common repellents used today (DEET and picaridin).

The Road Ahead
We discovered that our modeling approach to smell prediction could be used to draw a Principal Odor Map for tackling odor-related problems more generally. This map was the key to measuring smell: it answered a range of questions about novel smells and the molecules that produce them, it connected smells back to their origins in evolution and the natural world, and it is helping us tackle important human-health challenges that affect millions of people. Going forward, we hope that this approach can be used to find new solutions to problems in food and fragrance formulation, environmental quality monitoring, and the detection of human and animal diseases.

Acknowledgements
This work was performed by the ML olfaction research team, including Benjamin Sanchez-Lengeling, Brian K. Lee, Jennifer N. Wei, Wesley W. Qian, and Jake Yasonik (the latter two were partly supported by the Google Student Researcher program) and our external partners including Emily Mayhew and Joel D. Mainland from the Monell Center, and Koen Dechering and Marnix Vlot from TropIQ. The Google Books team brought the USDA dataset online. Richard C. Gerkin was supported by the Google Visiting Faculty Researcher program and is also an Associate Research Professor at Arizona State University.

Source: Google AI Blog


Scaling Up Fundamental Quantum Chemistry Simulations on Quantum Hardware

Posted by Nicholas Rubin and Charles Neill, Research Scientists, Google AI Quantum

Accurate computational prediction of chemical processes from the quantum mechanical laws that govern them is a tool that can unlock new frontiers in chemistry, improving a wide variety of industries. Unfortunately, the exact solution of quantum chemical equations for all but the smallest systems remains out of reach for modern classical computers, due to the exponential scaling in the number and statistics of quantum variables. However, by using a quantum computer, which by its very nature takes advantage of unique quantum mechanical properties to handle calculations intractable to its classical counterpart, simulations of complex chemical processes can be achieved. While today’s quantum computers are powerful enough for a clear computational advantage at some tasks, it is an open question whether such devices can be used to accelerate our current quantum chemistry simulation techniques.

In “Hartree-Fock on a Superconducting Qubit Quantum Computer”, appearing today in Science, the Google AI Quantum team explores this complex question by performing the largest chemical simulation performed on a quantum computer to date. In our experiment, we used a noise-robust variational quantum eigensolver (VQE) to directly simulate a chemical mechanism via a quantum algorithm. Though the calculation focused on the Hartree-Fock approximation of a real chemical system, it was twice as large as previous chemistry calculations on a quantum computer, and contained ten times as many quantum gate operations. Importantly, we validate that algorithms being developed for currently available quantum computers can achieve the precision required for experimental predictions, revealing pathways towards realistic simulations of quantum chemical systems. Furthermore, we have released the code for the experiment, which uses OpenFermion, our open source repository for quantum computations of chemistry.

Google’s Sycamore processor mounted in a cryostat, recently used to demonstrate quantum supremacy and the largest quantum chemistry simulation on a quantum computer. Photo Credit: Rocco Ceselin

Developing an Error Robust Quantum Algorithm for Chemistry
There are a number of ways to use a quantum computer to simulate the ground state energy of a molecular system. In this work we focused on a quantum algorithm “building block”, or circuit primitive, and perfect its performance through a VQE (more on that later). In the classical setting this circuit primitive is equivalent to the Hartree-Fock model and is an important circuit component of an algorithm we previously developed for optimal chemistry simulations. This allows us to focus on scaling up without incurring exponential simulation costs to validate our device. Therefore, robust error mitigation on this component is crucial for accurate simulations when scaling to the “beyond classical” regime.

Errors in quantum computation emerge from interactions of the quantum circuitry with the environment, causing erroneous logic operations — even minor temperature fluctuations can cause qubit errors. Algorithms for simulating chemistry on near-term quantum devices must account for these errors with low overhead, both in terms of the number of qubits or additional quantum resources, such as implementing a quantum error correcting code. The most popular method to account for errors (and why we used it for our experiment) is to use a VQE. For our experiment, we selected the VQE we developed a few years ago, which treats the quantum processor like an neural network and attempts to optimize a quantum circuit’s parameters to account for noisy quantum logic by minimizing a cost function. Just like how classical neural networks can tolerate imperfections in data by optimization, a VQE dynamically adjusts quantum circuit parameters to account for errors that occur during the quantum computation.

Enabling High Accuracy with Sycamore
The experiment was run on the Sycamore processor that was recently used to demonstrate quantum supremacy. Though our experiment required fewer qubits, even higher quantum gate fidelity was needed to resolve chemical bonding. This led to the development of new, targeted calibration techniques that optimally amplify errors so they can be diagnosed and corrected.

Energy predictions of molecular geometries by the Hartree-Fock model simulated on 10 qubits of the Sycamore processor.

Errors in the quantum computation can originate from a variety of sources in the quantum hardware stack. Sycamore has 54-qubits and consists of over 140 individually tunable elements, each controlled with high-speed, analog electrical pulses. Achieving precise control over the whole device requires fine tuning more than 2,000 control parameters, and even small errors in these parameters can quickly add up to large errors in the total computation.

To accurately control the device, we use an automated framework that maps the control problem onto a graph with thousands of nodes, each of which represent a physics experiment to determine a single unknown parameter. Traversing this graph takes us from basic priors about the device to a high fidelity quantum processor, and can be done in less than a day. Ultimately, these techniques along with the algorithmic error mitigation enabled orders of magnitude reduction in the errors.

Left: The energy of a linear chain of Hydrogen atoms as the bond distance between each atom is increased. The solid line is the Hartree-Fock simulation with a classical computer while the points are computed with the Sycamore processor. Right: Two accuracy metrics (infidelity and mean absolute error) for each point computed with Sycamore. “Raw” is the non-error-mitigated data from Sycamore. “+PS” is data from a type of error mitigation correcting the number of electrons. “+Purification” is a type of error mitigation correcting for the right kind of state. “+VQE” is the combination of all the error mitigation along with variational relaxation of the circuit parameters. Experiments on H8, H10, and H12 show similar performance improvements upon error mitigation.

Pathways Forward
We hope that this experiment serves as a blueprint for how to run chemistry calculations on quantum processors, and as a jumping off point on the path to physical simulation advantage. One exciting prospect is that it is known how to modify the quantum circuits used in this experiment in a simple way such that they are no longer efficiently simulable, which would determine new directions for improved quantum algorithms and applications. We hope that the results from this experiment can be used to explore this regime by the broader research community. To run these experiments, you can find the code here.

Source: Google AI Blog


Unlocking the "Chemome" with DNA-Encoded Chemistry and Machine Learning

Posted by Patrick Riley, Principal Engineer, Accelerated Science Team, Google Research

Much of the development of therapeutics for human disease is built around understanding and modulating the function of proteins, which are the main workhorses of many biological activities. Small molecule drugs such as ibuprofen often work by inhibiting or promoting the function of proteins or their interactions with other biomolecules. Developing useful “virtual screening” methods where potential small molecules can be evaluated computationally rather than in a lab, has long been an area of research. However, the persistent challenge is to build a method that works well enough across a wide range of chemical space to be useful for finding small molecules with physically verified useful interaction with a protein of interest, i.e., “hits”.

In “Machine learning on DNA-encoded libraries: A new paradigm for hit-finding”, recently published in the Journal of Medicinal Chemistry, we worked in collaboration with X-Chem Pharmaceuticals to demonstrate an effective new method for finding biologically active molecules using a combination of physical screening with DNA-encoded small molecule libraries and virtual screening using a graph convolutional neural network (GCNN). This research has led to the creation of the Chemome initiative, a cooperative project between our Accelerated Science team and ZebiAI that will enable the discovery of many more small molecule chemical probes for biological research.

Background on Chemical Probes
Making sense of the biological networks that support life and produce disease is an immensely complex task. One approach to study these processes is using chemical probes, small molecules that aren’t necessarily useful as drugs, but that selectively inhibit or promote the function of specific proteins. When you have a biological system to study (such as cancer cells growing in a dish), you can add the chemical probe at a specific time and observe how the biological system responds differently when the targeted protein has increased or decreased activity. But, despite how useful chemical probes are for this kind of basic biomedical research, only 4% of human proteins have a known chemical probe available.

The process of finding chemical probes begins similarly to the earliest stages of small molecule drug discovery. Given a protein target of interest, the space of small molecules is scanned to find “hit” molecules that can be further tested. Robotic assisted high throughput screening where up to hundred of thousands or millions of molecules are physically tested is a cornerstone of modern drug research. However, the number of small molecules you can easily purchase (1.2x109) is much larger than that, which in turn is much smaller than the number of small drug like molecules (estimates from 1020 to 1060). “Virtual screening” could possibly quickly and efficiently search this vast space of potentially synthesizable molecules and greatly speed up the discovery of therapeutic compounds.

DNA-Encoded Small Molecule Library Screening
The physical part of the screening process uses DNA-encoded small molecule libraries (DELs), which contain many distinct small molecules in one pool, each of which is attached to a fragment of DNA serving as a unique barcode for that molecule. While this basic technique has been around for several decades, the quality of the library and screening process is key to producing meaningful results.

DELs are a very clever idea to solve a biochemical challenge, which is how to collect small molecules into one place with an easy way to identify each. The key is to use DNA as a barcode to identify each molecule, similar to Nobel Prize winning phage display technology. First, one generates many chemical fragments, each with a unique DNA barcode attached, along with a common chemical handle (the NH2 in this case). The results are then pooled and split into separate reactions where a set of distinct chemical fragments with another common chemical handle (e.g., OH) are added. The chemical fragments from the two steps react and fuse together at the common chemical handles. The DNA fragments are also connected to build one continuous barcode for each molecule. The net result is that by performing 2N operations, one gets N2 unique molecules, each of which is identified by its own unique DNA barcode. By using more fragments or more cycles, it’s relatively easy to make libraries with millions or even billions of distinct molecules.
An overview of the process of creating a DNA encoded small molecule library. First, DNA “barcodes” (represented here with numbered helices) are attached to small chemical fragments (the blue shapes) which expose a common chemical “handle” (e.g. the NH2 shown here). When mixed with other chemical fragments (the orange shapes) each of which has another exposed chemical “handle” (the OH) with attached DNA fragments, reactions merge the sets of chemical and DNA fragments, resulting in a voluminous library of small molecules of interest, each with a unique DNA “barcode”.
Once the library has been generated, it can be used to find the small molecules that bind to the protein of interest by mixing the DEL together with the protein and washing away the small molecules that do not attach. Sequencing the remaining DNA barcodes produces millions of individual reads of DNA fragments, which can then be carefully processed to estimate which of the billions of molecules in the original DEL interact with the protein.

Machine Learning on DEL Data
Given the physical screening data returned for a particular protein, we build an ML model to predict whether an arbitrarily chosen small molecule will bind to that protein. The physical screening with the DEL provides positive and negative examples for an ML classifier. To simplify slightly, the small molecules that remain at the end of the screening process are positive examples and everything else are negative examples. We use a graph convolutional neural network, which is a type of neural network specially designed for small graph-like inputs, such as the small molecules in which we are interested.

Results
We physically screened three diverse proteins using DEL libraries: sEH (a hydrolase), ERα (a nuclear receptor), and c-KIT (a kinase). Using the DEL-trained models, we virtually screened large make-on-demand libraries from Mcule and an internal molecule library at X-Chem to identify a diverse set of molecules predicted to show affinity with each target. We compared the results of the GCNN models to a random forest (RF) model, a common method for virtual screening that uses standard chemical fingerprints, which we use as baseline. We find that the GCNN model significantly outperforms the RF model in discovering more potent candidates.
Fraction of molecules (“hit rates”) from those tested showing various levels of activity, comparing predictions from two different machine learned models (a GCNN and random forests, RF) on three distinct protein targets. The color scale on the right uses a common metric IC50 for representing the potency of a molecule. nM means “nanomolar” and µM means “micromolar”. Smaller values / darker colors are generally better molecules. Note that typical virtual screening approaches not built with DEL data normally only reach a few percent on this scale.
Importantly, unlike many other uses of virtual screening, the process to select the molecules to test was automated or easily automatable given the results of the model, and we did not rely on review and selection of the most promising molecules by a trained chemist. In addition, we tested almost 2000 molecules across the three targets, the largest published prospective study of virtual screening of which we are aware. While providing high confidence on the hit rates above, this also allows one to carefully examine the diversity of hits and the usefulness of the model for molecules near and far from the training set.

The Chemome Initiative
ZebiAI Therapeutics was founded based on the results of this research and has partnered with our team and X-Chem Pharmaceuticals to apply these techniques to efficiently deliver new chemical probes to the research community for human proteins of interest, an effort called the Chemome Initiative.

As part of the Chemome Initiative, ZebiAI will work with researchers to identify proteins of interest and source screening data, which our team will use to build machine learning models and make predictions on commercially available libraries of small molecules. ZebiAI will provide the predicted molecules to researchers for activity testing and will collaborate with researchers to advance some programs through discovery. Participation in the program requires that the validated hits be published within a reasonable time frame so that the whole community can benefit. While more validation must be done to make the hit molecules useful as chemical probes, especially for specifically targeting the protein of interest and the ability to function correctly in common assays, having potent hits is a big step forward in the process.

We’re excited to be a part of the Chemome Initiative enabled by the effective ML techniques described here and look forward to its discovery of many new chemical probes. We expect the Chemome will spur significant new biological discoveries and ultimately accelerate new therapeutic discovery for the world.

Acknowledgements
This work represents a multi-year effort between the Accelerated Science Team and X-Chem Pharmaceuticals with many people involved. This project would not have worked without the combined diverse skills of biologists, chemists, and ML researchers. We should especially acknowledge Eric Sigel (of X-Chem, now at ZebiAI) and Kevin McCloskey (of Google), the first authors on the paper and Steve Kearnes (of Google) for core modelling ideas and technical work.

Source: Google AI Blog


Learning to Smell: Using Deep Learning to Predict the Olfactory Properties of Molecules

Posted by Alexander B Wiltschko, Senior Research Scientist, Google Research

Smell is a sense shared by an incredible range of living organisms, and plays a critical role in how they analyze and react to the world. For humans, our sense of smell is tied to our ability to enjoy food and can also trigger vivid memories. Smell allows us to appreciate all of the fragrances that abound in our everyday lives, be they the proverbial roses, a batch of freshly baked cookies, or a favorite perfume. Yet despite its importance, smell has not received the same level of attention from machine learning researchers as have vision and hearing.

Odor perception in humans is the result of the activation of 400 different types of olfactory receptors (ORs), expressed in 1 million olfactory sensory neurons (OSNs), in a small patch of tissue called the olfactory epithelium. These OSNs send signals to the olfactory bulb, and then to further structures in the brain. Based on analogous advances in deep learning for sight and sound, it should be possible to directly predict the end sensory result of an input molecule, even without knowing the intricate details of all the systems involved. Solving the odor prediction problem would aid in discovering new synthetic odorants, thereby reducing the ecological impact of harvesting natural products. Inspection of the resulting olfactory models may even lead to new insights into the biology of smell.

Small odorant molecules are the most basic building blocks of flavors and fragrances, and therefore represent the simplest version of the odor prediction problem. Yet each molecule can have multiple odor descriptors. Vanillin, for example, has descriptors such as sweet, vanilla, creamy, and chocolate, with some notes being more apparent than others. So odor prediction is also a multi-label classification problem.

In “Machine Learning for Scent: Learning Generalizable Perceptual Representations of Small Molecules”, we leverage graph neural networks (GNNs), a kind of deep neural network designed to operate on graphs as input, to directly predict the odor descriptors for individual molecules, without using any handcrafted rules. We demonstrate that this approach yields significantly improved performance in odor prediction compared to current state-of-the-art and is a promising direction for future research.

Graph Neural Networks for Odor Prediction
Since molecules are analogous to graphs, with atoms forming the vertices and bonds forming the edges, GNNs are the natural model of choice for their understanding. But how does one translate the structure of a molecule into a graph representation? Initially, every node in the graph is represented as a vector, using any preferred featurization — atom identity, atom charge, etc. Then, in a series of message passing steps, every node broadcasts its current vector value to each of its neighbors. An update function then takes the collection of vectors sent to it, and generates an updated vector value. This process can be repeated many times, until finally all of the nodes in the graph are summarized into a single vector via summing or averaging. That single vector, representing the entire molecule, can then be passed into a fully connected network as a learned molecular featurization. This network outputs a prediction for odor descriptors, as provided by perfume experts.
Each node is represented as a vector, and each entry in the vector initially encodes some atomic-level information.
For each node we look at adjacent nodes and collect their information, which is then transformed with a neural network into new information for the centered node. This procedure is performed iteratively. Other variants of GNNs utilize edge and graph-level information.
Illustration of a GNN for odor prediction. We translate the structure of molecules into graphs that are fed into GNN layers to learn a better representation of the nodes. These nodes are reduced into a single vector and passed into a neural network that is used to predict multiple odor descriptors.
This representation doesn’t know anything about spatial positions of atoms, and so it can’t distinguish stereoisomers, molecules made of the same atoms but in slightly different configurations that can smell different, such as (R)- and (S)-carvone. Nevertheless, we have found that even without distinguishing stereoisomers, in practice it is still possible to predict odor quite well.

For odor prediction, GNNs consistently demonstrate improved performance compared to previous state-of-the-art methods, such as random forests, which do not directly encode graph structure. The magnitude of the improvement depends on which odor one tries to predict.
Example of the performance of a GNN on odor descriptors against a strong baseline, as measured by the AUROC score. Example odor descriptors are picked randomly. Closer to 1.0 means better. In the majority of cases GNNs outperform the field-standard baseline substantially, with similar performance seen against other metrics (e.g., AUPRC, recall, precision).
Learning from the Model, and Extending It to Other Tasks
In addition to predicting odor descriptors, GNNs can be applied to other olfaction tasks. For example, take the case of classifying new or refined odor descriptors using only limited data. For each molecule, we extract a learned representation from an intermediate layer of the model that is optimized for our odor descriptors, which we call an “odor embedding”. One can think of this as an olfaction version of a color space, like RGB or CMYK. To see if this odor embedding is useful for predicting related but different tasks, we designed experiments that test our learned embedding on related tasks for which it was not originally designed. We then compared the performance of our odor embedding representation to a common chemoinformatic representation that encodes structural information of a molecule, but is agnostic to odor and found that the odor embedding generalized to several challenging new tasks, even matching state-of-the-art on some.
2D snapshot of our embedding space with some example odors highlighted. Left: Each odor is clustered in its own space. Right: The hierarchical nature of the odor descriptor. Shaded and contoured areas are computed with a kernel-density estimate of the embeddings.
Future Work
Within the realm of machine learning, smell remains the most elusive of the senses, and we’re excited to continue doing a small part to shed light on it through further fundamental research. The possibilities for future research are numerous, and touch on everything from designing new olfactory molecules that are cheaper and more sustainably produced, to digitizing scent, or even one day giving those without a sense of smell access to roses (and, unfortunately, also rotten eggs). We hope to also bring this problem to the attention of more of the machine learning world through the eventual creation and sharing of high-quality, open datasets.

Acknowledgements
This early research is the result of the work and advisement of a team of talented researchers and engineers in Google Brain — Benjamin Sanchez-Lengeling, Jennifer Wei, Brian Lee, Emily Reif, Carey Radebaugh, Max Bileschi, Yoni Halpern, and D. Sculley. We are delighted to have collaborated on this work with Richard Gerkin at ASU and Alán Aspuru-Guzik at the University of Toronto. We are of course building on an enormous amount of prior work, and have benefitted particularly from work by Justin Gilmer, George Dahl and others on fundamental methodology in GNNs, among many other works in neuroscience, statistics and chemistry. We are also grateful to helpful comments from Steven Kearnes, David Belanger, Joel Mainland, and Emily Mayhew.

Source: Google AI Blog


Announcing Cirq: an open source framework for NISQ algorithms

Cross-posted from the Google AI Blog

Over the past few years, quantum computing has experienced a growth not only in the construction of quantum hardware, but also in the development of quantum algorithms. With the availability of Noisy Intermediate Scale Quantum (NISQ) computers (devices with ~50 - 100 qubits and high fidelity quantum gates), the development of algorithms to understand the power of these machines is of increasing importance. However, a common problem when designing a quantum algorithm on a NISQ processor is how to take full advantage of these limited quantum devices—using resources to solve the hardest part of the problem rather than on overheads from poor mappings between the algorithm and hardware. Furthermore some quantum processors have complex geometric constraints and other nuances, and ignoring these will either result in faulty quantum computation, or a computation that is modified and sub-optimal.*

Today at the First International Workshop on Quantum Software and Quantum Machine Learning (QSML), the Google AI Quantum team announced the public alpha of Cirq, an open source framework for NISQ computers. Cirq is focused on near-term questions and helping researchers understand whether NISQ quantum computers are capable of solving computational problems of practical importance. Cirq is licensed under Apache 2, and is free to be modified or embedded in any commercial or open source package.

Once installed, Cirq enables researchers to write quantum algorithms for specific quantum processors. Cirq gives users fine tuned control over quantum circuits, specifying gate behavior using native gates, placing these gates appropriately on the device, and scheduling the timing of these gates within the constraints of the quantum hardware. Data structures are optimized for writing and compiling these quantum circuits to allow users to get the most out of NISQ architectures. Cirq supports running these algorithms locally on a simulator, and is designed to easily integrate with future quantum hardware or larger simulators via the cloud.


We are also announcing the release of OpenFermion-Cirq, an example of a Cirq based application enabling near-term algorithms. OpenFermion is a platform for developing quantum algorithms for chemistry problems, and OpenFermion-Cirq is an open source library which compiles quantum simulation algorithms to Cirq. The new library uses the latest advances in building low depth quantum algorithms for quantum chemistry problems to enable users to go from the details of a chemical problem to highly optimized quantum circuits customized to run on particular hardware. For example, this library can be used to easily build quantum variational algorithms for simulating properties of molecules and complex materials.

Quantum computing will require strong cross-industry and academic collaborations if it is going to realize its full potential. In building Cirq, we worked with early testers to gain feedback and insight into algorithm design for NISQ computers. Below are some examples of Cirq work resulting from these early adopters:
To learn more about how Cirq is helping enable NISQ algorithms, please visit the links above where many of the adopters have provided example source code for their implementations.

Today, the Google AI Quantum team is using Cirq to create circuits that run on Google’s Bristlecone processor. In the future, we plan to make this processor available in the cloud, and Cirq will be the interface in which users write programs for this processor. In the meantime, we hope Cirq will improve the productivity of NISQ algorithm developers and researchers everywhere. Please check out the GitHub repositories for Cirq and OpenFermion-Cirq — pull requests welcome!

By Alan Ho, Product Lead and Dave Bacon, Software Lead, Google AI Quantum Team

Acknowledgements
We would like to thank Craig Gidney for leading the development of Cirq, Ryan Babbush and Kevin Sung for building OpenFermion-Cirq and a whole host of code contributors to both frameworks.


* An analogous situation is how early classical programmers needed to run complex programs in very small memory spaces by paying careful attention to the lowest level details of the hardware.↩

Automating Drug Discoveries Using Computer Vision

Vincent Vanhoucke, Principal Scientist, Google Brain Team

“Every time you miss a protein crystal, because they are so rare, you risk missing on an important biomedical discovery.”
- Patrick Charbonneau, Duke University Dept. of Chemistry and Lead Researcher, MARCO initiative.

Protein crystallization is a key step to biomedical research concerned with discovering the structure of complex biomolecules. Because that structure determines the molecule’s function, it helps scientists design new drugs that are specifically targeted to that function. However, protein crystals are rare and difficult to find. Hundreds of experiments are typically run for each protein, and while the setup and imaging are mostly automated, finding individual protein crystals remains largely performed through visual inspection and thus prone to human error. Critically, missing these structures can result in lost opportunity for important biomedical discoveries for advancing the state of medicine.

In collaboration with researchers from the MAchine Recognition of Crystallization Outcomes (MARCO) initiative, we have published “Classification of Crystallization Outcomes using Deep Convolutional Neural Networks” in PLOS One (ArXiv preprint), in which we discuss how we used some of the most recent architectures of deep convolutional networks and customized them to achieve an accuracy of more than 94% on the visual recognition task of identifying protein crystals. In order to spur further research in this area, we have made the data freely accessible, and open-sourced our model as part of the TensorFlow research model repository, and available to researchers as a Cloud ML Engine endpoint.
Image of protein crystal, courtesy of the MARCO repository (CC-BY-4.0 license)
The MARCO initiative is a joint project between several pharmaceutical companies and academic research centers to pool and host a large repository of curated crystallography images, and make them available to the community to help develop better image analysis tools. When a member of the initiative reached out to Google with a well-defined problem, and half a million labelled images, we embraced the challenge of trying to apply the recent advances in deep learning to the problem.

Due to the large variability between imaging technologies and data acquisition approaches, coming up with a single approach to the visual recognition problem may appear daunting. Crystals can be very small, which makes them rare structures in a large image containing otherwise undifferentiated visual clutter.
Samples from the MARCO repository, illustrating the degree of variability between data sources.
Fortunately, given sufficient training data, modern deep convolutional networks are well suited to handle extreme variability in visual appearance. We modified the basic Inception V3 model to handle larger images while still being able to be trained quickly. The model achieves a level of precision and recall that makes its use practical in automated assessment pipelines.

This work is a great example of the effectiveness of multi-institutional collaborations aimed at solving problems that require data in amounts and level of diversity that no single collaborator has access to. We invite researchers to take advantage of these resources that are the result of this work and share what they learn. This research was conducted as a personal 20% project by the author. To learn more about this work, please see our paper here and read the recent Duke Research Blog post.

Source: Google AI Blog


Reformulating Chemistry for More Efficient Quantum Computation

Posted by Ryan Babbush, Senior Research Scientist, Quantum AI Team

The first known classical “computer” was the Antikythera mechanism, an analog machine used to simulate the classical mechanics governing dynamics of celestial bodies on an astronomical scale. Similarly, a major ambition of quantum computers is to simulate the quantum mechanics governing dynamics of particles on the atomic scale. These simulations are often classically intractable due to the complex quantum mechanics at play. Of particular interest is the simulation of electrons forming chemical bonds, which give rise to the properties of essentially all molecules, materials and chemical reactions.
Left: The first known computing device, the Antikythera mechanism: a classical machine used to simulate classical mechanics. Right: Google’s 22 Xmon qubit “foxtail” chip arranged in a bilinear array on a wafer, the predecessor to Google’s new Bristlecone quantum processor with 72 qubits, a quantum machine we intend to use to simulate quantum mechanics, among other applications.
Since the launch of the Quantum AI team in 2013, we have been developing practical algorithms for quantum processors. In 2015, we conducted the first quantum chemistry experiment on a superconducting quantum computing device, published in Physical Review X. More recently, our quantum simulation effort experimentally simulated exotic phases of matter and released the first software package for quantum computing chemistry, OpenFermion. Earlier this month, our hardware team announced the new Bristlecone quantum processor with 72 qubits.

Today, we highlight two recent publications with theoretical advances that significantly reduce the cost of these quantum computations. Our results were presented at the Quantum Information Processing and IBM ThinkQ conferences.

The first of these works, “Low-Depth Quantum Simulation of Materials,” published this week in Physical Review X, was a collaboration between researchers at Google, the group of Professor Garnet Chan at Caltech and the QuArC group at Microsoft. Our fundamental advance was to realize that by changing how molecules are represented on quantum computers, we can greatly simplify the quantum circuits required to solve the problem. Specifically, we specially design basis sets so that the equations describing the system energies (i.e. the Hamiltonian) become more straightforward to express for quantum computation.

To do this, we focused on using basis sets related to functions (plane waves) used in classical electronic structure calculations to provide a periodic representation of the physical system. This enables one to go beyond the quantum simulation of single-molecules and instead use quantum computers to model realistic materials. For instance, instead of simulating a single lithium hydride molecule floating in free space, with our approach one can quantum simulate a crystal of lithium hydride, which is how the material appears in nature. With larger quantum computers one could study other important materials problems such as the degradation of battery cathodes, chemical reactions involving heterogeneous catalysts, or the unusual electrical properties of graphene and superconductors.

In “Quantum Simulation of Electronic Structure with Linear Depth and Connectivity,” published last week in Physical Review Letters with the same collaborators and a Google intern from the Aspuru-Guzik group at Harvard, we leverage the structure introduced in the work above to design algorithms for near-term quantum computers with qubits laid out in a linear array. Whereas past methods required such quantum computers to run for time scaling as the fifth power of the number of simulated electrons for each dynamic step, our improved algorithm runs for time scaling linearly with respect to the number of electrons. This reduction in computational cost makes it viable to perform quantum chemistry simulations on near-term devices with fewer gates in each quantum circuit, possibly avoiding the need for full error-correction.

Even with these improvements, it is no small task to deploy such new technology to outperform classical quantum chemistry algorithms and methods which have been refined in parallel with the development of classical computers for more than eighty years. However, at the current rate of advances in quantum algorithms and hardware, quantum technologies may provide chemists with an invaluable new tool. We look forward to sharing our research results as they develop.

Source: Google AI Blog


Reformulating Chemistry for More Efficient Quantum Computation

Posted by Ryan Babbush, Senior Research Scientist, Quantum AI Team

The first known classical “computer” was the Antikythera mechanism, an analog machine used to simulate the classical mechanics governing dynamics of celestial bodies on an astronomical scale. Similarly, a major ambition of quantum computers is to simulate the quantum mechanics governing dynamics of particles on the atomic scale. These simulations are often classically intractable due to the complex quantum mechanics at play. Of particular interest is the simulation of electrons forming chemical bonds, which give rise to the properties of essentially all molecules, materials and chemical reactions.
Left: The first known computing device, the Antikythera mechanism: a classical machine used to simulate classical mechanics. Right: Google’s 22 Xmon qubit “foxtail” chip arranged in a bilinear array on a wafer, the predecessor to Google’s new Bristlecone quantum processor with 72 qubits, a quantum machine we intend to use to simulate quantum mechanics, among other applications.
Since the launch of the Quantum AI team in 2013, we have been developing practical algorithms for quantum processors. In 2015, we conducted the first quantum chemistry experiment on a superconducting quantum computing device, published in Physical Review X. More recently, our quantum simulation effort experimentally simulated exotic phases of matter and released the first software package for quantum computing chemistry, OpenFermion. Earlier this month, our hardware team announced the new Bristlecone quantum processor with 72 qubits.

Today, we highlight two recent publications with theoretical advances that significantly reduce the cost of these quantum computations. Our results were presented at the Quantum Information Processing and IBM ThinkQ conferences.

The first of these works, “Low-Depth Quantum Simulation of Materials,” published this week in Physical Review X, was a collaboration between researchers at Google, the group of Professor Garnet Chan at Caltech and the QuArC group at Microsoft. Our fundamental advance was to realize that by changing how molecules are represented on quantum computers, we can greatly simplify the quantum circuits required to solve the problem. Specifically, we specially design basis sets so that the equations describing the system energies (i.e. the Hamiltonian) become more straightforward to express for quantum computation.

To do this, we focused on using basis sets related to functions (plane waves) used in classical electronic structure calculations to provide a periodic representation of the physical system. This enables one to go beyond the quantum simulation of single-molecules and instead use quantum computers to model realistic materials. For instance, instead of simulating a single lithium hydride molecule floating in free space, with our approach one can quantum simulate a crystal of lithium hydride, which is how the material appears in nature. With larger quantum computers one could study other important materials problems such as the degradation of battery cathodes, chemical reactions involving heterogeneous catalysts, or the unusual electrical properties of graphene and superconductors.

In “Quantum Simulation of Electronic Structure with Linear Depth and Connectivity,” published last week in Physical Review Letters with the same collaborators and a Google intern from the Aspuru-Guzik group at Harvard, we leverage the structure introduced in the work above to design algorithms for near-term quantum computers with qubits laid out in a linear array. Whereas past methods required such quantum computers to run for time scaling as the fifth power of the number of simulated electrons for each dynamic step, our improved algorithm runs for time scaling linearly with respect to the number of electrons. This reduction in computational cost makes it viable to perform quantum chemistry simulations on near-term devices with fewer gates in each quantum circuit, possibly avoiding the need for full error-correction.

Even with these improvements, it is no small task to deploy such new technology to outperform classical quantum chemistry algorithms and methods which have been refined in parallel with the development of classical computers for more than eighty years. However, at the current rate of advances in quantum algorithms and hardware, quantum technologies may provide chemists with an invaluable new tool. We look forward to sharing our research results as they develop.

Announcing OpenFermion: The Open Source Chemistry Package for Quantum Computers

Crossposted on the Google Research Blog

“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 College, 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! By Ryan Babbush and Jarrod McClean, Quantum Software Engineers, Quantum AI Team

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.↩