How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

• URL: http://arxiv.org/abs/2409.11654v2
• Date: Mon, 14 Oct 2024 08:18:07 GMT
• Title: How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities
• Authors: Charlotte Bunne, Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicholas J. Sofroniew, Fabian Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake,
• Abstract summary: We propose a vision of leveraging advances in AI to construct virtual cells. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration.
• Score: 46.671834972945874
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

Related papers

• Empowering Biomedical Discovery with AI Agents [15.125735219811268]
  We envision "AI scientists" as systems capable of skeptical learning and reasoning. Biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies.
  arXiv  Detail & Related papers  (2024-04-03T16:08:01Z)
• ProBio: A Protocol-guided Multimodal Dataset for Molecular Biology Lab [67.24684071577211]
  The challenge of replicating research results has posed a significant impediment to the field of molecular biology. We first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings.
  arXiv  Detail & Related papers  (2023-11-01T14:44:01Z)
• Causal machine learning for single-cell genomics [94.28105176231739]
  We discuss the application of machine learning techniques to single-cell genomics and their challenges. We first present the model that underlies most of current causal approaches to single-cell biology. We then identify open problems in the application of causal approaches to single-cell data.
  arXiv  Detail & Related papers  (2023-10-23T13:35:24Z)
• The Future of Fundamental Science Led by Generative Closed-Loop Artificial Intelligence [67.70415658080121]
  Recent advances in machine learning and AI are disrupting technological innovation, product development, and society as a whole. AI has contributed less to fundamental science in part because large data sets of high-quality data for scientific practice and model discovery are more difficult to access. Here we explore and investigate aspects of an AI-driven, automated, closed-loop approach to scientific discovery.
  arXiv  Detail & Related papers  (2023-07-09T21:16:56Z)
• Zyxin is all you need: machine learning adherent cell mechanics [0.0]
  We develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. We next develop two approaches - one explicitly constrained by physics, the other more continuum - that help construct data-driven models of cellular forces.
  arXiv  Detail & Related papers  (2023-03-01T02:08:40Z)
• Application of Machine Learning in understanding plant virus pathogenesis: Trends and perspectives on emergence, diagnosis, host-virus interplay and management [1.949912057689623]
  Deep learning algorithms further promote the application of machine learning in several field of biology including plant virology. Considering a significant progress in the application of machine learning in understanding plant virology, this review highlights an introductory note on machine learning.
  arXiv  Detail & Related papers  (2021-12-03T16:25:26Z)
• Learning from learning machines: a new generation of AI technology to meet the needs of science [59.261050918992325]
  We outline emerging opportunities and challenges to enhance the utility of AI for scientific discovery. The distinct goals of AI for industry versus the goals of AI for science create tension between identifying patterns in data versus discovering patterns in the world from data.
  arXiv  Detail & Related papers  (2021-11-27T00:55:21Z)
• Towards an Automatic Analysis of CHO-K1 Suspension Growth in Microfluidic Single-cell Cultivation [63.94623495501023]
  We propose a novel Machine Learning architecture, which allows us to infuse a neural deep network with human-powered abstraction on the level of data. Specifically, we train a generative model simultaneously on natural and synthetic data, so that it learns a shared representation, from which a target variable, such as the cell count, can be reliably estimated.
  arXiv  Detail & Related papers  (2020-10-20T08:36:51Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.