Data Augmentation vs. Equivariant Networks: A Theory of Generalization on Dynamics Forecasting

Exploiting symmetry in dynamical systems is a powerful way to improve the generalization of deep learning. The model learns to be invariant to transformation and hence is more robust to distribution shift. Data augmentation and equivariant networks are two major approaches to injecting symmetry into learning. However, their exact role in improving generalization is not well understood. In this work, we derive the generalization bounds for data augmentation and equivariant networks, characterizing their effect on learning in a unified framework. Unlike most prior theories for the i.i.d. setting, we focus on non-stationary dynamics forecasting with complex temporal dependencies.

LIMO: Latent Inceptionism for Targeted Molecule Generation

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep generative models guided by Gaussian processes, which can be prohibitively slow when generating molecules with high binding affinity calculated by computationally-expensive physics-based methods. We present Latent Inceptionism on Molecules (LIMO), which significantly accelerates molecule generation with an inceptionism-like technique. LIMO employs a variational autoencoder-generated latent space and property prediction by two neural networks in sequence to enable faster gradient-based reverse-optimization of molecular properties. Comprehensive experiments show that LIMO performs competitively on benchmark tasks and markedly outperforms state-of-the-art techniques on the novel task of generating drug-like compounds with high binding affinity, reaching nanomolar range against two protein targets. We corroborate these docking-based results with more accurate molecular dynamics-based calculations of absolute binding free energy and show that one of our generated drug-like compounds has a predicted $K_D$ (a measure of binding affinity) of $6 \cdot 10^{-14}$ M against the human estrogen receptor, well beyond the affinities of typical early-stage drug candidates and most FDA-approved drugs to their respective targets. Code is available at https://github.com/Rose-STL-Lab/LIMO.

Multi-fidelity Hierarchical Neural Processes

Science and engineering fields use computer simulation extensively. These simulations are often run at multiple levels of sophistication to balance accuracy and efficiency. Multi-fidelity surrogate modeling reduces the computational cost by fusing different simulation outputs. Cheap data generated from low-fidelity simulators can be combined with limited high-quality data generated by an expensive high-fidelity simulator. Existing methods based on Gaussian processes rely on strong assumptions of the kernel functions and can hardly scale to high-dimensional settings. We propose Multi-fidelity Hierarchical Neural Processes (MF-HNP), a unified neural latent variable model for multi-fidelity surrogate modeling. MF-HNP inherits the flexibility and scalability of Neural Processes. The latent variables transform the correlations among different fidelity levels from observations to latent space. The predictions across fidelities are conditionally independent given the latent states. It helps alleviate the error propagation issue in existing methods. MF-HNP is flexible enough to handle non-nested high dimensional data at different fidelity levels with varying input and output dimensions. We evaluate MF-HNP on epidemiology and climate modeling tasks, achieving competitive performance in terms of accuracy and uncertainty estimation. In contrast to deep Gaussian Processes with only low-dimensional (< 10) tasks, our method shows great promise for speeding up high-dimensional complex simulations (over 7000 for epidemiology modeling and 45000 for climate modeling).

Faster Optimization on Sparse Graphs via Neural Reparametrization

In mathematical optimization, second-order Newton's methods generally converge faster than first-order methods, but they require the inverse of the Hessian, hence are computationally expensive. However, we discover that on sparse graphs, graph neural networks (GNN) can implement an efficient Quasi-Newton method that can speed up optimization by a factor of 10-100x. Our method, neural reparametrization, modifies the optimization parameters as the output of a GNN to reshape the optimization landscape. Using a precomputed Hessian as the propagation rule, the GNN can effectively utilize the second-order information, reaching a similar effect as adaptive gradient methods. As our method solves optimization through architecture design, it can be used in conjunction with any optimizers such as Adam and RMSProp. We show the application of our method on scientifically relevant problems including heat diffusion, synchronization and persistent homology.

Symmetry Teleportation for Accelerated Optimization

Existing gradient-based optimization methods update the parameters locally, in a direction that minimizes the loss function. We study a different approach, symmetry teleportation, that allows the parameters to travel a large distance on the loss level set, in order to improve the convergence speed in subsequent steps. Teleportation exploits parameter space symmetries of the optimization problem and transforms parameters while keeping the loss invariant. We derive the loss-invariant group actions for test functions and multi-layer neural networks, and prove a necessary condition of when teleportation improves convergence rate. We also show that our algorithm is closely related to second order methods. Experimentally, we show that teleportation improves the convergence speed of gradient descent and AdaGrad for several optimization problems including test functions, multi-layer regressions, and MNIST classification.

Probabilistic Symmetry for Improved Trajectory Forecasting

Trajectory prediction is a core AI problem with broad applications in robotics and autonomous driving. While most existing works focus on deterministic prediction, producing probabilistic forecasts to quantify prediction uncertainty is critical for downstream decision-making tasks such as risk assessment, motion planning, and safety guarantees. We introduce a new metric, mean regional score (MRS), to evaluate the quality of probabilistic trajectory forecasts. We propose a novel probabilistic trajectory prediction model, Probabilistic Equivariant Continuous COnvolution (PECCO) and show that leveraging symmetry, specifically rotation equivariance, can improve the predictions' accuracy as well as coverage. On both vehicle and pedestrian datasets, PECCO shows state-of-the-art prediction performance and improved calibration compared to baselines.

SELFIES and the future of molecular string representations

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings -- most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100\% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chemistry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.

Taming the Long Tail of Deep Probabilistic Forecasting

Deep probabilistic forecasting is gaining attention in numerous applications ranging from weather prognosis, through electricity consumption estimation, to autonomous vehicle trajectory prediction. However, existing approaches focus on improvements on the most common scenarios without addressing the performance on rare and difficult cases. In this work, we identify a long tail behavior in the performance of state-of-the-art deep learning methods on probabilistic forecasting. We present two moment-based tailedness measurement concepts to improve performance on the difficult tail examples: Pareto Loss and Kurtosis Loss. Kurtosis loss is a symmetric measurement as the fourth moment about the mean of the loss distribution. Pareto loss is asymmetric measuring right tailedness, modeling the loss using a generalized Pareto distribution (GPD). We demonstrate the performance of our approach on several real-world datasets including time series and spatiotemporal trajectories, achieving significant improvements on the tail examples.

Approximately Equivariant Networks for Imperfectly Symmetric Dynamics

Incorporating symmetry as an inductive bias into neural network architecture has led to improvements in generalization, data efficiency, and physical consistency in dynamics modeling. Methods such as CNN or equivariant neural networks use weight tying to enforce symmetries such as shift invariance or rotational equivariance. However, despite the fact that physical laws obey many symmetries, real-world dynamical data rarely conforms to strict mathematical symmetry either due to noisy or incomplete data or to symmetry breaking features in the underlying dynamical system. We explore approximately equivariant networks which are biased towards preserving symmetry but are not strictly constrained to do so. By relaxing equivariance constraints, we find that our models can outperform both baselines with no symmetry bias and baselines with overly strict symmetry in both simulated turbulence domains and real-world multi-stream jet flow.

AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We first unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Then, we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training, allowing us to limit the annotation imbalance and improve binding predictions for novel proteins and ligands. We illustrate the value of AI-Bind by predicting drugs and natural compounds with binding affinity to SARS-CoV-2 viral proteins and the associated human proteins. We also validate these predictions via auto-docking simulations and comparison with recent experimental evidence. Overall, AI-Bind offers a powerful high-throughput approach to identify drug-target combinations, with the potential of becoming a powerful tool in drug discovery.