15 papers · ranked by Valyu relevance
Derek van Tilborg, Helena Brinkmann, Emanuele Criscuolo, Luke Rossen + 2 more
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to protein structure prediction and synthesis planning. However, it is often challenged by the small data regimes typical of certain drug discovery tasks. In such scenarios, deep learning approaches – which are notoriously…
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The rapid progress in Artificial Intelligence (AI) has led to extraordinary achievements across various domains, significantly impacting every aspect of daily life. This advancement is also revolutionizing research in numerous scientific areas, particularly within bioinformatics, chemistry, pharmaceuticals, and…
Nathan Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi + 3 more
Massive scale, both in terms of data availability and computation, enables significant breakthroughs in key application areas of deep learning such as natural language processing (NLP) and computer vision. There is emerging evidence that scale may be a key ingredient in scientific deep learning, but the importance of…
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In recent years, generative deep learning has emerged as a transformative approach in drug design, promising to explore the vast chemical space and generate novel molecules with desired biological properties. This perspective examines the challenges and opportunities of applying generative models to drug discovery…
Derek van Tilborg, Francesca Grisoni
Deep learning is accelerating drug discovery. However, current approaches are often affected by limitations in the available data, e.g., in terms of size or molecular diversity. Active deep learning has an untapped potential for low-data drug discovery, as it allows to improve a model iteratively during the screening…
Wout Bittremieux, Varun Ananth, William E. Fondrie, Carlo Melendez + 5 more
Protein tandem mass spectrometry data is most often interpreted by matching observed mass spectra to a protein database derived from the reference genome of the sample being analyzed. In many application domains, however, a relevant protein database is unavailable or incomplete, and in such settings de novo sequencing…
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Real-world datasets in chemical engineering and bioengineering processes--such as those from catalytic reactors, multiphase flows, polymerization reactors, bioreactors, and clinical trials--can often be unlabelled or disorganized, rendering the training of existing supervised learning models ineffective at learning the…
Zachary Humphreys, Xenophon Evangelopoulos, Stavros Gerolymatos, Edward O. Pyzer-Knapp + 1 more
Graph neural networks have recently met huge success in various inference tasks including materials property prediction amongst many others. Nevertheless, having an inherently locally-based representation capacity as they do, global representation of materials' structures can only only be achieved by expanding the…
Andrew McNutt, Yanjing Li, Paul Francoeur, David Koes
Knowledge of the bound protein-ligand structure is critical to many drug discovery tasks. One tool for in silico bound structure elucidation is molecular docking, which samples and scores ligand binding conformations. Recent work has demonstrated that convolutional neural networks (CNNs) for protein-ligand pose scoring…
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X-ray diffraction (XRD) is an immediate and powerful characterization technique that provides detailed information on the lattice structure and long-range order in crystalline materials. In recent decades, the quality and quantity of available crystal structure data has exploded, in large part due to the advent of…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
David Buterez, Jon Paul Janet, Steven J. Kiddle, Dino Oglic + 1 more
Atom-centred neural networks represent the state-of-the-art for approximating the quantum chemical properties of molecules, such as internal energies. While the design of machine learning architectures that respect chemical principles has continued to advance, the final atom pooling operation that is necessary to…
Haotong Sun, Yinghui Jiang, Minhao Wang, Xianglu Xiao + 5 more
Rapid and accurate prediction of molecular properties is a fundamental task in drug discovery. In recent years, deep learning-based molecular property prediction methods have received much attention and recent successes have shown that learning the representations of molecular structures by applying graph neural…
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Machine olfaction—the artificial replication of the sense of smell—faces significant challenges due to the absence of large, standardized training datasets. Unlike vision, language, and audio models, which benefit from extensive corpora such as ImageNet, GLUE, and AudioSet, olfaction lacks scaled equivalents and…
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Olfaction arises from the interaction of odorants with olfactory receptors, a process shaped by molecular geometry, electron distribution, and conformational preference. We present ConfDENSE, a Set2Set enhanced PointNet model that learns directly from Hirshfeld promolecule electron-density point clouds, preserving full…