Jonas Köhler

Lixue Cheng, P. Bernát Szabó, Zeno Schätzle et al. · microsoft-research

Variational ab-initio methods in quantum chemistry stand out among other methods in providing direct access to the wave function. This allows in principle straightforward extraction of any other observable of interest, besides the energy, but in practice this extraction is often technically difficult and computationally impractical. Here, we consider the electron density as a central observable in quantum chemistry and introduce a novel method to obtain accurate densities from real-space many-electron wave functions by representing the density with a neural network that captures known asymptotic properties and is trained from the wave function by score matching and noise-contrastive estimation. We use variational quantum Monte Carlo with deep-learning ansätze (deep QMC) to obtain highly accurate wave functions free of basis set errors, and from them, using our novel method, correspondingly accurate electron densities, which we demonstrate by calculating dipole moments, nuclear forces, contact densities, and other density-based properties.

Jonas Köhler, Yaoyi Chen, Andreas Krämer et al.

Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly relied on force-matching or relative entropy minimization, which require many samples from costly simulations with all-atom or CG resolutions, respectively. Here we present flow-matching, a new training method for CG force fields that combines the advantages of both methods by leveraging normalizing flows, a generative deep learning method. Flow-matching first trains a normalizing flow to represent the CG probability density, which is equivalent to minimizing the relative entropy without requiring iterative CG simulations. Subsequently, the flow generates samples and forces according to the learned distribution in order to train the desired CG free energy model via force matching. Even without requiring forces from the all-atom simulations, flow-matching outperforms classical force-matching by an order of magnitude in terms of data efficiency, and produces CG models that can capture the folding and unfolding transitions of small proteins.

Jonas Köhler, Michele Invernizzi, Pim de Haan et al.

Normalizing flows (NF) are a class of powerful generative models that have gained popularity in recent years due to their ability to model complex distributions with high flexibility and expressiveness. In this work, we introduce a new type of normalizing flow that is tailored for modeling positions and orientations of multiple objects in three-dimensional space, such as molecules in a crystal. Our approach is based on two key ideas: first, we define smooth and expressive flows on the group of unit quaternions, which allows us to capture the continuous rotational motion of rigid bodies; second, we use the double cover property of unit quaternions to define a proper density on the rotation group. This ensures that our model can be trained using standard likelihood-based methods or variational inference with respect to a thermodynamic target density. We evaluate the method by training Boltzmann generators for two molecular examples, namely the multi-modal density of a tetrahedral system in an external field and the ice XI phase in the TIP4P water model. Our flows can be combined with flows operating on the internal degrees of freedom of molecules and constitute an important step towards the modeling of distributions of many interacting molecules.

Adam Foster, Zeno Schätzle, P. Bernát Szabó et al. · microsoft-research

Reliable description of bond breaking remains a major challenge for quantum chemistry due to the multireferential character of the electronic structure in dissociating species. Multireferential methods in particular suffer from large computational cost, which under the normal paradigm has to be paid anew for each system at a full price, ignoring commonalities in electronic structure across molecules. Quantum Monte Carlo with deep neural networks (deep QMC) uniquely offers to exploit such commonalities by pretraining transferable wavefunction models, but all such attempts were so far limited in scope. Here, we bring this new paradigm to fruition with Orbformer, a novel transferable wavefunction model pretrained on 22,000 equilibrium and dissociating structures that can be fine-tuned on unseen molecules reaching an accuracy-cost ratio rivalling classical multireferential methods. On established benchmarks as well as more challenging bond dissociations and Diels-Alder reactions, Orbformer is the only method that consistently converges to chemical accuracy (1 kcal/mol). This work turns the idea of amortizing the cost of solving the Schrödinger equation over many molecules into a practical approach in quantum chemistry.

Jonas Köhler, Andreas Krämer, Frank Noé

Normalizing flows are a promising tool for modeling probability distributions in physical systems. While state-of-the-art flows accurately approximate distributions and energies, applications in physics additionally require smooth energies to compute forces and higher-order derivatives. Furthermore, such densities are often defined on non-trivial topologies. A recent example are Boltzmann Generators for generating 3D-structures of peptides and small proteins. These generative models leverage the space of internal coordinates (dihedrals, angles, and bonds), which is a product of hypertori and compact intervals. In this work, we introduce a class of smooth mixture transformations working on both compact intervals and hypertori. Mixture transformations employ root-finding methods to invert them in practice, which has so far prevented bi-directional flow training. To this end, we show that parameter gradients and forces of such inverses can be computed from forward evaluations via the inverse function theorem. We demonstrate two advantages of such smooth flows: they allow training by force matching to simulation data and can be used as potentials in molecular dynamics simulations.

Søren Ager Meldgaard, Jonas Köhler, Henrik Lund Mortensen et al.

Chemical space is routinely explored by machine learning methods to discover interesting molecules, before time-consuming experimental synthesizing is attempted. However, these methods often rely on a graph representation, ignoring 3D information necessary for determining the stability of the molecules. We propose a reinforcement learning approach for generating molecules in cartesian coordinates allowing for quantum chemical prediction of the stability. To improve sample-efficiency we learn basic chemical rules from imitation learning on the GDB-11 database to create an initial model applicable for all stoichiometries. We then deploy multiple copies of the model conditioned on a specific stoichiometry in a reinforcement learning setting. The models correctly identify low energy molecules in the database and produce novel isomers not found in the training set. Finally, we apply the model to larger molecules to show how reinforcement learning further refines the imitation learning model in domains far from the training data.

Andreas Krämer, Jonas Köhler, Frank Noé

Many types of neural network layers rely on matrix properties such as invertibility or orthogonality. Retaining such properties during optimization with gradient-based stochastic optimizers is a challenging task, which is usually addressed by either reparameterization of the affected parameters or by directly optimizing on the manifold. This work presents a novel approach for training invertible linear layers. In lieu of directly optimizing the network parameters, we train rank-one perturbations and add them to the actual weight matrices infrequently. This P$^{4}$Inv update allows keeping track of inverses and determinants without ever explicitly computing them. We show how such invertible blocks improve the mixing and thus the mode separation of the resulting normalizing flows. Furthermore, we outline how the P$^4$ concept can be utilized to retain properties other than invertibility.

Jonas Köhler, Leon Klein, Frank Noé

Normalizing flows are exact-likelihood generative neural networks which approximately transform samples from a simple prior distribution to samples of the probability distribution of interest. Recent work showed that such generative models can be utilized in statistical mechanics to sample equilibrium states of many-body systems in physics and chemistry. To scale and generalize these results, it is essential that the natural symmetries in the probability density -- in physics defined by the invariances of the target potential -- are built into the flow. We provide a theoretical sufficient criterion showing that the distribution generated by \textit{equivariant} normalizing flows is invariant with respect to these symmetries by design. Furthermore, we propose building blocks for flows which preserve symmetries which are usually found in physical/chemical many-body particle systems. Using benchmark systems motivated from molecular physics, we demonstrate that those symmetry preserving flows can provide better generalization capabilities and sampling efficiency.

Hao Wu, Jonas Köhler, Frank Noé

The sampling of probability distributions specified up to a normalization constant is an important problem in both machine learning and statistical mechanics. While classical stochastic sampling methods such as Markov Chain Monte Carlo (MCMC) or Langevin Dynamics (LD) can suffer from slow mixing times there is a growing interest in using normalizing flows in order to learn the transformation of a simple prior distribution to the given target distribution. Here we propose a generalized and combined approach to sample target densities: Stochastic Normalizing Flows (SNF) -- an arbitrary sequence of deterministic invertible functions and stochastic sampling blocks. We show that stochasticity overcomes expressivity limitations of normalizing flows resulting from the invertibility constraint, whereas trainable transformations between sampling steps improve efficiency of pure MCMC/LD along the flow. By invoking ideas from non-equilibrium statistical mechanics we derive an efficient training procedure by which both the sampler's and the flow's parameters can be optimized end-to-end, and by which we can compute exact importance weights without having to marginalize out the randomness of the stochastic blocks. We illustrate the representational power, sampling efficiency and asymptotic correctness of SNFs on several benchmarks including applications to sampling molecular systems in equilibrium.

Frederik Harder, Jonas Köhler, Max Welling et al.

Developing a differentially private deep learning algorithm is challenging, due to the difficulty in analyzing the sensitivity of objective functions that are typically used to train deep neural networks. Many existing methods resort to the stochastic gradient descent algorithm and apply a pre-defined sensitivity to the gradients for privatizing weights. However, their slow convergence typically yields a high cumulative privacy loss. Here, we take a different route by employing the method of auxiliary coordinates, which allows us to independently update the weights per layer by optimizing a per-layer objective function. This objective function can be well approximated by a low-order Taylor's expansion, in which sensitivity analysis becomes tractable. We perturb the coefficients of the expansion for privacy, which we optimize using more advanced optimization routines than SGD for faster convergence. We empirically show that our algorithm provides a decent trained model quality under a modest privacy budget.

Jonas Köhler, Leon Klein, Frank Noé

Flows are exact-likelihood generative neural networks that transform samples from a simple prior distribution to the samples of the probability distribution of interest. Boltzmann Generators (BG) combine flows and statistical mechanics to sample equilibrium states of strongly interacting many-body systems such as proteins with 1000 atoms. In order to scale and generalize these results, it is essential that the natural symmetries of the probability density - in physics defined by the invariances of the energy function - are built into the flow. Here we develop theoretical tools for constructing such equivariant flows and demonstrate that a BG that is equivariant with respect to rotations and particle permutations can generalize to sampling nontrivially new configurations where a nonequivariant BG cannot.

Frank Noé, Simon Olsson, Jonas Köhler et al.

Computing equilibrium states in condensed-matter many-body systems, such as solvated proteins, is a long-standing challenge. Lacking methods for generating statistically independent equilibrium samples in "one shot", vast computational effort is invested for simulating these system in small steps, e.g., using Molecular Dynamics. Combining deep learning and statistical mechanics, we here develop Boltzmann Generators, that are shown to generate unbiased one-shot equilibrium samples of representative condensed matter systems and proteins. Boltzmann Generators use neural networks to learn a coordinate transformation of the complex configurational equilibrium distribution to a distribution that can be easily sampled. Accurate computation of free energy differences and discovery of new configurations are demonstrated, providing a statistical mechanics tool that can avoid rare events during sampling without prior knowledge of reaction coordinates.

Taco Cohen, Mario Geiger, Jonas Köhler et al.

The success of convolutional networks in learning problems involving planar signals such as images is due to their ability to exploit the translation symmetry of the data distribution through weight sharing. Many areas of science and egineering deal with signals with other symmetries, such as rotation invariant data on the sphere. Examples include climate and weather science, astrophysics, and chemistry. In this paper we present spherical convolutional networks. These networks use convolutions on the sphere and rotation group, which results in rotational weight sharing and rotation equivariance. Using a synthetic spherical MNIST dataset, we show that spherical convolutional networks are very effective at dealing with rotationally invariant classification problems.