Related papers: GraphXForm: Graph transformer for computer-aided m…
In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles in chemistry and pharmaceutical sciences have investigated chemical compounds, but in cases the details of the…
Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…
In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
Molecular property prediction with deep learning has gained much attention over the past years. Owing to the scarcity of labeled molecules, there has been growing interest in self-supervised learning methods that learn generalizable…
Recent advancements in computational chemistry have leveraged the power of trans-former-based language models, such as MoLFormer, pre-trained using a vast amount of simplified molecular-input line-entry system (SMILES) sequences, to…
Tandem mass spectra capture fragmentation patterns that provide key structural information about a molecule. Although mass spectrometry is applied in many areas, the vast majority of small molecules lack experimental reference spectra. For…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…
Tackling molecular optimization problems using conventional computational methods is challenging, because the determination of the optimized configuration is known to be an NP-hard problem. Recently, there has been increasing interest in…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
Today we have a good theoretical understanding of the representational power of Graph Neural Networks (GNNs). For example, their limitations have been characterized in relation to a hierarchy of Weisfeiler-Lehman (WL) isomorphism tests.…
Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…
Drug discovery is a complex, resource-intensive process requiring significant time and cost to bring new medicines to patients. Many generative models aim to accelerate drug discovery, but few produce synthetically accessible molecules.…
Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…
Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…
Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared…
Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a…
Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…