Dongxia Wu

Peter Eckmann, Dongxia Wu, Germano Heinzelmann et al.

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

Peter Eckmann, Dongxia Wu, Germano Heinzelmann et al.

Current generative models for drug discovery primarily use molecular docking to evaluate the quality of generated compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. We propose a multi-fidelity approach, Multi-Fidelity Bind (MFBind), to achieve the optimal trade-off between accuracy and computational cost. MFBind integrates docking and binding free energy simulators to train a multi-fidelity deep surrogate model with active learning. Our deep surrogate model utilizes a pretraining technique and linear prediction heads to efficiently fit small amounts of high-fidelity data. We perform extensive experiments and show that MFBind (1) outperforms other state-of-the-art single and multi-fidelity baselines in surrogate modeling, and (2) boosts the performance of generative models with markedly higher quality compounds.

Dongxia Wu, Ruijia Niu, Matteo Chinazzi et al.

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs at the highest fidelity by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Deep learning-based methods often impose a hierarchical structure in hidden representations, which only supports passing information from low-fidelity to high-fidelity. These approaches can lead to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel framework called Disentangled Multi-fidelity Deep Bayesian Active Learning (D-MFDAL), which learns the surrogate models conditioned on the distribution of functions at multiple fidelities. On benchmark tasks of learning deep surrogates of partial differential equations including heat equation, Poisson's equation and fluid simulations, our approach significantly outperforms state-of-the-art in prediction accuracy and sample efficiency.

Dongxia Wu, Ruijia Niu, Matteo Chinazzi et al.

Stochastic simulations such as large-scale, spatiotemporal, age-structured epidemic models are computationally expensive at fine-grained resolution. While deep surrogate models can speed up the simulations, doing so for stochastic simulations and with active learning approaches is an underexplored area. We propose Interactive Neural Process (INP), a deep Bayesian active learning framework for learning deep surrogate models to accelerate stochastic simulations. INP consists of two components, a spatiotemporal surrogate model built upon Neural Process (NP) family and an acquisition function for active learning. For surrogate modeling, we develop Spatiotemporal Neural Process (STNP) to mimic the simulator dynamics. For active learning, we propose a novel acquisition function, Latent Information Gain (LIG), calculated in the latent space of NP based models. We perform a theoretical analysis and demonstrate that LIG reduces sample complexity compared with random sampling in high dimensions. We also conduct empirical studies on three complex spatiotemporal simulators for reaction diffusion, heat flow, and infectious disease. The results demonstrate that STNP outperforms the baselines in the offline learning setting and LIG achieves the state-of-the-art for Bayesian active learning.