Related papers: Molecular Sets (MOSES): A Benchmarking Platform fo…

Generative models aim to learn the probability distributions underlying data, enabling the generation of new, realistic samples. Quantum inspired generative models, such as Born machines based on the matrix product state framework, have…

Deep generative models have been applied with increasing success to the generation of two dimensional molecules as SMILES strings and molecular graphs. In this work we describe for the first time a deep generative model that can generate 3D…

Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…

Image classification methods are usually trained to perform predictions taking into account a predefined group of known classes. Real-world problems, however, may not allow for a full knowledge of the input and label spaces, making failures…

The machine learning community has mainly relied on real data to benchmark algorithms as it provides compelling evidence of model applicability. Evaluation on synthetic datasets can be a powerful tool to provide a better understanding of a…

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…

We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…

Motion generation, the task of synthesizing realistic motion sequences from various conditioning inputs, has become a central problem in computer vision, computer graphics, and robotics, with applications ranging from animation and virtual…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

One challenging and essential task in biochemistry is the generation of novel molecules with desired properties. Novel molecule generation remains a challenge since the molecule space is difficult to navigate through, and the generated…

Score-based Generative Models (SGMs) is one leading method in generative modeling, renowned for their ability to generate high-quality samples from complex, high-dimensional data distributions. The method enjoys empirical success and is…

Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment…

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…

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…

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the…

Deep generative models are effective methods of modeling data. However, it is not easy for a single generative model to faithfully capture the distributions of complex data such as images. In this paper, we propose an approach for boosting…

Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible…

De novo 3D molecule generation is a pivotal task in drug discovery. However, many recent geometric generative models struggle to produce high-quality 3D structures, even if they maintain 2D validity and topological stability. To tackle this…

It is common practice for chemists to search chemical databases based on substructures of compounds for finding molecules with desired properties. The purpose of de novo molecular generation is to generate instead of search. Existing…

Synthesizability in small molecule generative design remains a bottleneck. Existing works that do consider synthesizability can output predicted synthesis routes for generated molecules. However, there has been minimal attention in…