Correcting systematic errors in diffraction data with modern scaling algorithms.
Luis A AldamaKevin M DaltonDoeke R HekstraPublished in: Acta crystallographica. Section D, Structural biology (2023)
X-ray diffraction enables the routine determination of the atomic structure of materials. Key to its success are data-processing algorithms that allow experimenters to determine the electron density of a sample from its diffraction pattern. Scaling, the estimation and correction of systematic errors in diffraction intensities, is an essential step in this process. These errors arise from sample heterogeneity, radiation damage, instrument limitations and other aspects of the experiment. New X-ray sources and sample-delivery methods, along with new experiments focused on changes in structure as a function of perturbations, have led to new demands on scaling algorithms. Classically, scaling algorithms use least-squares optimization to fit a model of common error sources to the observed diffraction intensities to force these intensities onto the same empirical scale. Recently, an alternative approach has been demonstrated which uses a Bayesian optimization method, variational inference, to simultaneously infer merged data along with corrections, or scale factors, for the systematic errors. Owing to its flexibility, this approach proves to be advantageous in certain scenarios. This perspective briefly reviews the history of scaling algorithms and contrasts them with variational inference. Finally, appropriate use cases are identified for the first such algorithm, Careless, guidance is offered on its use and some speculations are made about future variational scaling methods.
Keyphrases
- machine learning
- electron microscopy
- deep learning
- big data
- electronic health record
- patient safety
- crystal structure
- artificial intelligence
- adverse drug
- single cell
- high resolution
- drinking water
- climate change
- oxidative stress
- emergency department
- magnetic resonance imaging
- radiation therapy
- clinical practice
- solid phase extraction