Evidence map›Paper›PMID 38164955›Full record

ArticleActa crystallographica. Section D, Structural biology2024

Deep residual networks for crystallography trained on synthetic data.

Derek Mendez, James M Holton, Artem Y Lyubimov, Sabine Hollatz, Irimpan I Mathews, Aleksander Cichosz, Vardan Martirosyan, Teo Zeng, Ryan Stofer, Ruobin Liu and 4 more

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026
    Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Derek MendezStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
James M HoltonStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Artem Y LyubimovStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Sabine HollatzStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Irimpan I MathewsStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.ORCID 0000-0001-6254-3519
Aleksander CichoszDepartment of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA.
Vardan MartirosyanDepartment of Mathematics, UC Santa Barbara, Santa Barbara, CA 93106, USA.
Teo ZengDepartment of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA.
Ryan StoferDepartment of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA.
Ruobin LiuDepartment of Statistics and Applied Probability, UC Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0003-1628-5226
Jinhu SongStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Scott McPhillipsStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Mike SoltisStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Aina E CohenStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.ORCID 0000-0003-2414-9427

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Ritimukta Sarangi · 2020 to 2026
$43.3M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
Eliminating Critical Systematic Errors In Structural Biology With Next-Generation SimulationR01GM124149 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HOLTON, JAMES M · 2017 to 2024
$2.5M
NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P30 GM133894NIGMS NIH HHS R01 GM124149
6 · The paper itself

Abstract

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

Indexed as

Artificial IntelligenceSynchrotronsAlgorithmsComputer SimulationCrystallography, X-Rayartificial intelligencerotation crystallographyserial crystallographysynchrotronsXFELs

Identifiers

PMID38164955
PMCPMC10833344

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.