This generates two (possibly invalid) child molecules. If valid molecules exist, the we choose one of them randomly. Details of seven different ways of modifying a molecule are as follows. The atom_addition connects a new atom to a single atom. The atom_insertion puts an atom between two atoms.

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.

Scientific progress is tightly coupled to the emergence of new research tools. Today, machine learning (ML)-especially deep learning (DL)-has become a transformative instrument for quantum science and technology. Owing to the intrinsic complexity of quantum systems, DL enables efficient exploration of large parameter spaces, extraction of patterns from experimental data, and data-driven guidance for research directions. These capabilities already support tasks such as refining quantum control protocols and accelerating the discovery of materials with targeted quantum properties, making ML/DL literacy an essential skill for the next generation of quantum scientists. At the same time, DL's power brings risks: models can overfit noisy data, obscure causal structure, and yield results with limited physical interpretability. Recognizing these limitations and deploying mitigation strategies is crucial for scientific rigor. These lecture notes provide a comprehensive, graduate-level introduction to DL for quantum applications, combining conceptual exposition with hands-on examples. Organized as a progressive sequence, they aim to equip readers to decide when and how to apply DL effectively, to understand its practical constraints, and to adapt AI methods responsibly to problems across quantum physics, chemistry, and engineering.

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.

Building modern deep learning systems that are not just effective but also efficient requires rethinking established paradigms for model training and neural architecture design. Instead of adapting highly overparameterized networks and subsequently applying model compression techniques to reduce resource consumption, a new class of high-performing networks skips the need for expensive parameter updates, while requiring only a fraction of parameters, making them highly scalable. The Strong Lottery Ticket Hypothesis posits that within randomly initialized, sufficiently overparameterized neural networks, there exist subnetworks that can match the accuracy of the trained original model--without any training. This work explores the usage of genetic algorithms for identifying these strong lottery ticket subnetworks. We find that for instances of binary and multi-class classification tasks, our approach achieves better accuracies and sparsity levels than the current state-of-the-art without requiring any gradient information. In addition, we provide justification for the need for appropriate evaluation metrics when scaling to more complex network architectures and learning tasks. Keywords: Strong Lottery Ticket Hypothesis Evolutionary Optimization Neu-roevolution Neural Architecture Search Loss Landscape Analysis Pruning.An earlier version of this work was presented at the International Conference on Neural Computation Theory and Applications (NCT A 2024) [1]. This article extends our conference paper with updates to the method to improve multi-class classification, an expanded experimental setup, and a multi-class performance anaylsis with visual and analytical justifications.

Generative machine learning has emerged as a powerful tool for design representation and exploration. However, its application is often constrained by the need for large datasets of existing designs and the lack of interpretability about what features drive optimality. To address these challenges, we introduce a systematic framework for constructing training datasets tailored to generative models and demonstrate how these models can be leveraged for interpretable design. The novelty of this work is twofold: (i) we present a systematic framework for generating archetypes with internally homogeneous but mutually heterogeneous inputs that can be used to generate a training dataset, and (ii) we show how integrating generative models with Bayesian optimization can enhance the interpretability of the latent space of admissible designs. These findings are validated by using the framework to design a flow battery manifold, demonstrating that it effectively captures the space of feasible designs, including novel configurations while enabling efficient exploration. This work broadens the applicability of generative machine-learning models in system designs by enhancing quality and reliability.

Evolutionary approaches have previously been shown to be effective learning methods for a diverse set of domains. However, the domain of game-playing poses a particular challenge for evolutionary methods due to the inherently large state space of video games. As the size of the input state expands, the size of the policy must also increase in order to effectively learn the temporal patterns in the game space. Consequently, a larger policy must contain more trainable parameters, exponentially increasing the size of the search space. Any increase in search space is highly problematic for evolutionary methods, as increasing the number of trainable parameters is inversely correlated with convergence speed. To reduce the size of the input space while maintaining a meaningful representation of the original space, we introduce Sparse Cosine Optimized Policy Evolution (SCOPE). SCOPE utilizes the Discrete Cosine Transform (DCT) as a pseudo attention mechanism, transforming an input state into a coefficient matrix. By truncating and applying sparsification to this matrix, we reduce the dimensionality of the input space while retaining the highest energy features of the original input. We demonstrate the effectiveness of SCOPE as the policy for the Atari game Space Invaders. In this task, SCOPE with CMA-ES outperforms evolutionary methods that consider an unmodified input state, such as OpenAI-ES and HyperNEAT. SCOPE also outperforms simple reinforcement learning methods, such as DQN and A3C. SCOPE achieves this result through reducing the input size by 53% from 33,600 to 15,625 then using a bilinear affine mapping of sparse DCT coefficients to policy actions learned by the CMA-ES algorithm.

Many real-world applications require decision-makers to assess the quality of solutions while considering multiple conflicting objectives. Obtaining good approximation sets for highly constrained many-objective problems is often a difficult task even for modern multiobjective algorithms. In some cases, multiple instances of the problem scenario present similarities in their fitness landscapes. That is, there are recurring features in the fitness landscapes when searching for solutions to different problem instances. We propose a methodology to exploit this characteristic by solving one instance of a given problem scenario using computationally expensive multiobjective algorithms to obtain a good approximation set and then using Goal Programming with efficient single-objective algorithms to solve other instances of the same problem scenario. We use three goal-based objective functions and show that on benchmark instances of the multiobjective vehicle routing problem with time windows, the methodology is able to produce good results in short computation time. The methodology allows to combine the effectiveness of state-of-the-art multiobjective algorithms with the efficiency of goal programming to find good compromise solutions in problem scenarios where instances have similar fitness landscapes.