De novo molecular design attempts to search over the chemical space for molecules with the desired property. Recently, deep learning has gained considerable attention as a promising approach to solve the problem. In this paper, we propose genetic expert-guided learning (GEGL), a simple yet novel framework for training a deep neural network (DNN) to generate highly-rewarding molecules. Our main idea is to design a "genetic expert improvement" procedure, which generates high-quality targets for imitation learning of the DNN. Extensive experiments show that GEGL significantly improves over state-of-the-art methods. For example, GEGL manages to solve the penalized octanol-water partition coefficient optimization with a score of 31.40, while the best-known score in the literature is 27.22. Besides, for the GuacaMol benchmark with 20 tasks, our method achieves the highest score for 19 tasks, in comparison with state-of-the-art methods, and newly obtains the perfect score for three tasks. Our training code is available at https://github.com/

We sincerely thank all reviewers for their valuable efforts and insightful comments. We thank R1 for the helpful comment. Following R1's insightful suggestion, we compared GEGL with an additional "ablation" We thank R1 for the opportunity to make the following clarifications. We thank R2 and R3 for mentioning an important point. R2's comment: the current literature fails to search for a molecule that is high-scoring and realistic simultaneously.

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve the performance by leveraging the shared underlying physics of the binding processes.

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.

We present a novel method for symbolic regression (SR), the task of searching for compact programmatic hypotheses that best explain a dataset. The problem is commonly solved using genetic algorithms; we show that we can enhance such methods by inducing a library of abstract textual concepts.

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.

Quality diversity (QD) is a growing branch of stochastic optimization research that studies the problem of generating an archive of solutions that maximize a given objective function but are also diverse with respect to a set of specified measure functions. However, even when these functions are differentiable, QD algorithms treat them as "black boxes", ignoring gradient information. We present the differentiable quality diversity (DQD) problem, a special case of QD, where both the objective and measure functions are first order differentiable. We then present MAP-Elites via a Gradient Arborescence (MEGA), a DQD algorithm that leverages gradient information to efficiently explore the joint range of the objective and measure functions. Results in two QD benchmark domains and in searching the latent space of a StyleGAN show that MEGA significantly outperforms state-ofthe-art QD algorithms, highlighting DQD's promise for efficient quality diversity optimization when gradient information is available. Source code is available at https://github.com/icaros-usc/dqd.

When deploying machine learning estimators in science and engineering (SAE) domains, it is critical to avoid failed estimations that can have disastrous consequences, e.g., in aero engine design. This work focuses on detecting and correcting failed state estimations before adopting them in SAE inverse problems, by utilizing simulations and performance metrics guided by physical laws. We suggest to flag a machine learning estimation when its physical model error exceeds a feasible threshold, and propose a novel approach, GEESE, to correct it through optimization, aiming at delivering both low error and high efficiency. The key designs of GEESE include (1) a hybrid surrogate error model to provide fast error estimations to reduce simulation cost and to enable gradient based backpropagation of error feedback, and (2) two generative models to approximate the probability distributions of the candidate states for simulating the exploitation and exploration behaviours. All three models are constructed as neural networks. GEESE is tested on three real-world SAE inverse problems and compared to a number of state-of-the-art optimization/search approaches. Results show that it fails the least number of times in terms of finding a feasible state correction, and requires physical evaluations less frequently in general.

The nadir objective vector plays a key role in solving multi-objective optimization problems (MOPs), where it is often used to normalize the objective space and guide the search. The current methods for estimating the nadir objective vector perform effectively only on specific MOPs. This paper reveals the limitations of these methods: exact methods can only work on discrete MOPs, while heuristic methods cannot deal with the MOP with a complicated feasible objective region. To fill this gap, we propose a general and rigorous method, namely boundary decomposition for nadir objective vector estimation (BDNE).