The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

We suggest that there is a potential danger to the hydrological sciences community in not recognizing how transformative machine learning will be for the future of hydrological modeling. Given the recent success of machine learning applied to modeling problems, it is unclear what the role of hydrological theory might be in the future. We suggest that a central challenge in hydrology right now should be to clearly delineate where and when hydrological theory adds value to prediction systems. Lessons learned from the history of hydrological modeling motivate several clear next steps toward integrating machine learning into hydrological modeling workflows.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020WR028091

What Role Does Hydrological Science Play in the Age of Machine Learning

Artificial intelligence (AI) plays a growing role in remote sensing (RS). Applications of AI, particularly machine learning algorithms, range from initial image processing to high-level data understanding and knowledge discovery. AI techniques have emerged as a powerful strategy for analyzing RS data and led to remarkable breakthroughs in all RS fields. Given this period of breathtaking evolution, this work aims to provide a comprehensive review of the recent achievements of AI algorithms and applications in RS data analysis. The review includes more than 270 research papers, covering the following major aspects of AI innovation for RS: machine learning, computational intelligence, AI explicability, data mining, natural language processing (NLP), and AI security. We conclude this review by identifying promising directions for future research.

Artificial Intelligence for Remote Sensing Data Analysis: A review of challenges and opportunities

Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific disciplines. In this review, we examine how current quantum algorithms could revolutionize computational biology and bioinformatics. There are potential benefits across the entire field, from the ability to process vast amounts of information and run machine learning algorithms far more efficiently, to algorithms for quantum simulation that are poised to improve computational calculations in drug discovery, to quantum algorithms for optimization that may advance fields from protein structure prediction to network analysis. However, these exciting prospects are susceptible to "hype", and it is also important to recognize the caveats and challenges in this new technology. Our aim is to introduce the promise and limitations of emerging quantum computing technologies in the areas of computational molecular biology and bioinformatics.

The prospects of quantum computing in computational molecular biology

Recent breakthroughs in artificial intelligence (AI), and particularly in deep learning (DL), have created tremendous excitement and opportunities in the earth and environmental sciences communitie...

Deep Learning, Explained: Fundamentals, Explainability, and Bridgeability to Process-based Modelling

Although a wide variety of quantum computers are currently being developed, actual computational results have been largely restricted to contrived, artificial tasks. Finding ways to apply quantum computers to useful, real-world computational tasks remains an active research area. Here we describe our mapping of the protein design problem to the D-Wave quantum annealer. We present a system whereby Rosetta, a state-of-the-art protein design software suite, interfaces with the D-Wave quantum processing unit to find amino acid side chain identities and conformations to stabilize a fixed protein backbone. Our approach, which we call the QPacker, uses a large side-chain rotamer library and the full Rosetta energy function, and in no way reduces the design task to a simpler format. We demonstrate that quantum-annealer-based design can be applied to complex real-world design tasks, producing designed molecules comparable to those produced by widely adopted classical design approaches. We also show through large-scale classical folding simulations that the results produced on the quantum annealer can inform wet-lab experiments. For design tasks that scale exponentially on classical computers, the QPacker achieves nearly constant runtime performance, independent of the complexity of the task, up to the limits of the quantum computer’s size. This document is a preprint of a scientific manuscript, and the developments that it reports have not been subjected to peer review.

/pdf/designing-peptides-on-a-quantum-computer-5d1iyii44o.pdf

Designing Peptides on a Quantum Computer

A hybrid machine learning and process-based-modeling (PBM) approach is proposed and evaluated at a handful of AmeriFlux sites to simulate the top-layer soil moisture state. The Hybrid-PBM (HPBM) employed here uses the Noah land-surface model integrated with Gaussian Processes. It is designed to correct the model only in climatological situations similar to the training data else it reverts to the PBM. In this way, our approach avoids bad predictions in scenarios where similar training data is not available and incorporates our physical understanding of the system. Here we assume an autoregressive model and obtain out-of-sample results with upwards of a 3-fold reduction in the RMSE using a one-year leave-one-out cross-validation at each of the selected sites. A path is outlined for using hybrid modeling to build global land-surface models with the potential to significantly outperform the current state-of-the-art.

Combining Parametric Land Surface Models with Machine Learning.

Quantum Computing has been invigorated by the introduction of the first commercially available computers. Quantum Annealers (QAs) like the D-Wave are now housing ∼5000 quantum-bits, and quantum computing, a potentially disruptive technology, is closer to becoming a reality than ever. Here we investigate quantum-assisted approaches to image registration of MODIS images using QAs. We present two approaches: (1) a mapping of image matching to a quadratic-unconstrained-binary optimization problem and (2) a machine learning approach that employs generative models trained using quantum annealing statistics. Results are shown and discussed.

Craig Pelissier

Papers

What Role Does Hydrological Science Play in the Age of Machine Learning

Designing Peptides on a Quantum Computer

Combining Parametric Land Surface Models with Machine Learning.

Quantum Assisted Image Registration

Combining Parametric Land Surface Models with Machine Learning