Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of “separation” in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

This work proposes a solution for the problem of training physics-informed networks under partial integro-differential equations. These equations require an infinite or a large number of neural evaluations to construct a single residual for training. As a result, accurate evaluation may be impractical, and we show that naive approximations at replacing these integrals with unbiased estimates lead to biased loss functions and solutions. To overcome this bias, we investigate three types of potential solutions: the deterministic sampling approaches, the double-sampling trick, and the delayed target method. We consider three classes of PDEs for benchmarking; one defining Poisson problems with singular charges and weak solutions of up to 10 dimensions, another involving weak solutions on electro-magnetic fields and a Maxwell equation, and a third one defining a Smoluchowski coagulation problem. Our numerical results confirm the existence of the aforementioned bias in practice and also show that our proposed delayed target approach can lead to accurate solutions with comparable quality to ones estimated with a large sample size integral. Our implementation is open-source and available at https://github.com/ehsansaleh/btspinn.

In this paper, we present a policy gradient method that avoids exploratory noise injection and performs policy search over the deterministic landscape, with the goal of improving learning with long horizons and non-local rewards. By avoiding noise injection all sources of estimation variance can be eliminated in systems with deterministic dynamics (up to the initial state distribution). Since deterministic policy regularization is impossible using traditional non-metric measures such as the KL divergence, we derive a Wasserstein-based quadratic model for our purposes. We state conditions on the system model under which it is possible to establish a monotonic policy improvement guarantee, propose a surrogate function for policy gradient estimation, and show that it is possible to compute exact advantage estimates if both the state transition model and the policy are deterministic. Finally, we describe two novel robotic control environments---one with non-local rewards in the frequency domain and the other with a long horizon (8000 time-steps)---for which our policy gradient method (TDPO) significantly outperforms existing methods (PPO, TRPO, DDPG, and TD3). Our implementation with all the experimental settings and a video of the physical hardware test is available at https://github.com/ehsansaleh/tdpo .