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).

A.1 Multiple data matrices A combinatorial optimization problem can be presented with multiple (f) relationship features between two groups of items. In FFSP, for example, a production cost could be different for each process that one has to take into account for scheduling in addition to the processing time for each pair of the job and the machine. "Trainable element-wise function" block in Figure A.1 is now an MLP with f + 1 input nodes and 1 output node. A.2 Alternative encoding sequences Equation (2) in the main text describes the application of F The bold line indicates the change from the original. A.3 Alternatives to one-hot initial node embeddings For initial node representations of nodes in group B, one only needs mutually distinct-enough N We have chosen to present our model with onehot vectors because it is the simplest to implement this way.

In the natural world, life has found innumerable ways to survive and often thrive. Between and even within species, each individual is in some manner unique, and this diversity lends adaptability and robustness to life. In this work, we aim to learn a space of diverse and high-reward policies in a given environment. To this end, we introduce a generative model of policies for reinforcement learning, which maps a low-dimensional latent space to an agent policy space. Our method enables learning an entire population of agent policies, without requiring the use of separate policy parameters. Just as real world populations can adapt and evolve via natural selection, our method is able to adapt to changes in our environment solely by selecting for policies in latent space. We test our generative model's capabilities in a variety of environments, including an open-ended grid-world and a two-player soccer environment.