The challenge of discovering new molecules with desired properties is crucial in domains like drug discovery and material design. Recent advances in deep learning-based generative methods have shown promise but face the issue of sample efficiency due to the computational expense of evaluating the reward function. This paper proposes a novel algorithm for sample-efficient molecular optimization by distilling a powerful genetic algorithm into deep generative policy using GFlowNets training, the off-policy method for amortized inference. This approach enables the deep generative policy to learn from domain knowledge, which has been explicitly integrated into the genetic algorithm. Our method achieves state-of-theart performance in the official molecular optimization benchmark, significantly outperforming previous methods. It also demonstrates effectiveness in designing inhibitors against SARS-CoV-2 with substantially fewer reward calls.

This article develops a Bayesian optimization (BO) method which acts directly over raw strings, proposing the first uses of string kernels and genetic algorithms within BO loops. Recent applications of BO over strings have been hindered by the need to map inputs into a smooth and unconstrained latent space. Learning this projection is computationally and data-intensive. Our approach instead builds a powerful Gaussian process surrogate model based on string kernels, naturally supporting variable length inputs, and performs efficient acquisition function maximization for spaces with syntactical constraints. Experiments demonstrate considerably improved optimization over existing approaches across a broad range of constraints, including the popular setting where syntax is governed by a context-free grammar.

Distinguishing the automorphic equivalence of nodes in a graph plays an essential role in many scientific domains, e.g., computational biologist and social network analysis. However, existing graph neural networks (GNNs) fail to capture such an important property. To make GNN aware of automorphic equivalence, we first introduce a localized variant of this concept -- ego-centered automorphic equivalence (Ego-AE). Then, we design a novel variant of GNN, i.e., GRAPE, that uses learnable AE-aware aggregators to explicitly differentiate the Ego-AE of each node's neighbors with the aids of various subgraph templates. While the design of subgraph templates can be hard, we further propose a genetic algorithm to automatically search them from graph data. Moreover, we theoretically prove that GRAPE is expressive in terms of generating distinct representations for nodes with different Ego-AE features, which fills in a fundamental gap of existing GNN variants. Finally, we empirically validate our model on eight real-world graph data, including social network, e-commerce co-purchase network, and citation network, and show that it consistently outperforms existing GNNs.

This paper proposes the RePAIR dataset that represents a challenging benchmark to test modern computational and data driven methods for puzzle-solving and reassembly tasks. Our dataset has unique properties that are uncommon to current benchmarks for 2D and 3D puzzle solving. The fragments and fractures are realistic, caused by a collapse of a fresco during a World War II bombing at the Pompeii archaeological park. The fragments are also eroded and have missing pieces with irregular shapes and different dimensions, challenging further the reassembly algorithms. The dataset is multi-modal providing high resolution images with characteristic pictorial elements, detailed 3D scans of the fragments and metadata annotated by the archaeologists. Ground truth has been generated through several years of unceasing eldwork, including the excavation and cleaning of each fragment, followed by manual puzzle solving by archaeologists of a subset of approx.

Deep reinforcement learning (DRL) algorithms and evolution strategies (ES) have been applied to various tasks, showing excellent performances. These have the opposite properties, with DRL having good sample efficiency and poor stability, while ES being vice versa. Recently, there have been attempts to combine these algorithms, but these methods fully rely on synchronous update scheme, making it not ideal to maximize the benefits of the parallelism in ES. To solve this challenge, asynchronous update scheme was introduced, which is capable of good time-efficiency and diverse policy exploration. In this paper, we introduce an Asynchronous Evolution Strategy-Reinforcement Learning (AES-RL) that maximizes the parallel efficiency of ES and integrates it with policy gradient methods. Specifically, we propose 1) a novel framework to merge ES and DRL asynchronously and 2) various asynchronous update methods that can take all advantages of asynchronism, ES, and DRL, which are exploration and time efficiency, stability, and sample efficiency, respectively. The proposed framework and update methods are evaluated in continuous control benchmark work, showing superior performance as well as time efficiency compared to the previous methods.