Related papers: Population-based de novo molecule generation, usin…

Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…

The differential evolution (DE) algorithm suffers from high computational time due to slow nature of evaluation. In contrast, micro-DE (MDE) algorithms employ a very small population size, which can converge faster to a reasonable solution.…

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Generating a synthetic population that is both feasible and diverse is crucial for ensuring the validity of downstream activity schedule simulation in activity-based models (ABMs). While deep generative models (DGMs), such as variational…

Deep generative models of molecules have grown immensely in popularity, trained on relevant datasets, these models are used to search through chemical space. The downstream utility of generative models for the inverse design of novel…

Generating new molecules with specified chemical and biological properties via generative models has emerged as a promising direction for drug discovery. However, existing methods require extensive training/fine-tuning with a large dataset,…

This work introduces a novel probabilistic deep learning technique called deep Gaussian mixture ensembles (DGMEs), which enables accurate quantification of both epistemic and aleatoric uncertainty. By assuming the data generating process…

Generative models for molecules based on sequential line notation (e.g. SMILES) or graph representation have attracted an increasing interest in the field of structure-based drug design, but they struggle to capture important 3D spatial…

Molecular generation plays an important role in drug discovery and materials science, especially in data-scarce scenarios where traditional generative models often struggle to achieve satisfactory conditional generalization. To address this…

The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an…

Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…

A rational design of new therapeutic drugs aims to find a molecular structure with desired biological functionality, e.g., an ability to activate or suppress a specific protein via binding to it. Molecular docking is a common technique for…

While generative models have recently become ubiquitous in many scientific areas, less attention has been paid to their evaluation. For molecular generative models, the state-of-the-art examines their output in isolation or in relation to…

Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient…

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations…

Dialogue systems pretrained with large language models generate locally coherent responses, but lack the fine-grained control over responses necessary to achieve specific goals. A promising method to control response generation is…

Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through excluded volume effects. However the standard approach to…

Although real-coded differential evolution (DE) algorithms can perform well on continuous optimization problems (CoOPs), it is still a challenging task to design an efficient binary-coded DE algorithm. Inspired by the learning mechanism of…

In applications such as molecule design or drug discovery, it is desirable to have an algorithm which recommends new candidate molecules based on the results of past tests. These molecules first need to be synthesized and then tested for…

Text generation is a highly active area of research in the computational linguistic community. The evaluation of the generated text is a challenging task and multiple theories and metrics have been proposed over the years. Unfortunately,…