Paper Citation Record · LEDGER

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use

As of 17 August 2026, this Paper Citation Record lists 41 of 41 outbound references and 2 inbound Pith citation observations for arXiv:2505.12650.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2505.12650 v2

Coverage vector

measured 41 of 41 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-15T20:34:12.852230Z

measured 43 of 43 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-16T06:30:59.297886+00:00

measured 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-06-30T17:13:18.594937Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: arxiv_reference, observed 2026-06-30T17:14:56.753818Z

Reference resolution

41 of 41 outbound references displayed

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verified fuzzy22
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation b24ca18e-e0cf-459e-a960-a2b58c7e50b6 · outbound

This paper cites MatterSim: A Deep Learning Atomistic Model Across Elements, Temperatures and Pressures.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use MatterSim: A Deep Learning Atomistic Model Across Elements, Temperatures and Pressures

Reference 1

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Observation 8be85826-30b3-43ac-a939-a0c905c8e8fa · outbound

This paper cites Elena, Dávid P.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Elena, Dávid P

Reference 2

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Observation 01b53e72-8f77-4dd6-ac27-87a7ac554eb9 · outbound

This paper cites Gemnet: Univer- sal directional graph neural networks for molecules.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Gemnet: Univer- sal directional graph neural networks for molecules

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.677240Z

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Observation 63135de8-e951-4254-a9e9-2e1358036c18 · outbound

This paper cites EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.666927Z

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Observation 968328f6-2f3c-4b75-ac02-fe55894694e2 · outbound

This paper cites Highly accurate quantum chemical property prediction with uni-mol+, 2023.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Highly accurate quantum chemical property prediction with uni-mol+, 2023

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.664383Z

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Observation e0bf7aa5-c054-46ba-9d2c-6693a83a4e67 · outbound

This paper cites Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.650593Z

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Observation c6d6701f-ef20-4c64-9e2e-6850a1f52c9a · outbound

This paper cites Three-dimensional inhomogeneity of zeolite structure and composition revealed by electron ptychography.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Three-dimensional inhomogeneity of zeolite structure and composition revealed by electron ptychography

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.636353Z

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Observation ff3ff1ea-0023-4d1a-8653-709c8dcc504a · outbound

This paper cites Electron microscopy studies of local structural modulations in zeolite crystals.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Electron microscopy studies of local structural modulations in zeolite crystals

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.623058Z

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Observation ea7a4ae3-8dd1-4c88-a6c8-26bd9482cd2c · outbound

This paper cites Direct imaging of single metal atoms and clusters in the pores of dealuminated hy zeolite.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Direct imaging of single metal atoms and clusters in the pores of dealuminated hy zeolite

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.608976Z

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Observation 89014666-23f0-4d0c-acc1-be1ab1072527 · outbound

This paper cites Machine learning in scanning transmission electron microscopy.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Machine learning in scanning transmission electron microscopy

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.594831Z

Source-reported events for the cited work

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Observation c42f7504-a62f-49b6-88c8-59beee722dbd · outbound

This paper cites Machine learning for automated experimentation in scanning transmission electron microscopy.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Machine learning for automated experimentation in scanning transmission electron microscopy

Reference 11

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Observation 2ff1c62c-0842-4ddd-9988-10665b6ee0d6 · outbound

This paper cites Deep learning-enabled stem imaging for precise single-molecule identification in zeo- lite structures.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Deep learning-enabled stem imaging for precise single-molecule identification in zeo- lite structures

Reference 12

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Observation e76a1ec7-8615-4757-b420-c7a7bfd0fc38 · outbound

This paper cites TEMImageNet Training Library and AtomSegNet Deep-Learning Models for High-Precision Atom Segmentation, Localization, Denoising, and Super-Resolution Processing of Atomic-Resolution Images.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use TEMImageNet Training Library and AtomSegNet Deep-Learning Models for High-Precision Atom Segmentation, Localization, Denoising, and Super-Resolution Processing of Atomic-Resolution Images

Reference 13

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Source-reported events for the cited work

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Observation 725a7e31-a4b3-4cef-8619-23ca4b18bd36 · outbound

This paper cites Temimagenet training library and atomsegnet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Temimagenet training library and atomsegnet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.567119Z

Source-reported events for the cited work

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Observation 79d715ab-d4fa-4a59-a238-c36517faa8a3 · outbound

This paper cites Noise2atom: unsupervised denoising for scanning transmission electron microscopy images.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Noise2atom: unsupervised denoising for scanning transmission electron microscopy images

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.551351Z

Source-reported events for the cited work

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Observation 6a4e6101-b40c-4179-acdb-b97d62ea7eaf · outbound

This paper cites Ziatdinov, O.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Ziatdinov, O

Reference 16

Resolution: verified exact; raw_fallback, observed 2026-08-15T20:34:13.258133Z

Source-reported events for the cited work

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Observation e9f1e0ae-c9dc-4b83-b30d-e18a0510acb1 · outbound

This paper cites Predicting column heights and elemental compo- sition in experimental transmission electron microscopy images of high-entropy oxides using deep learning.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Predicting column heights and elemental compo- sition in experimental transmission electron microscopy images of high-entropy oxides using deep learning

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.535102Z

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Observation bef8ef40-2eed-4ee3-93c8-bf9ff0a6f125 · outbound

This paper cites Localization and segmentation of atomic columns in supported nanoparticles for fast scanning transmission electron microscopy.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Localization and segmentation of atomic columns in supported nanoparticles for fast scanning transmission electron microscopy

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.521307Z

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Observation b23ed81d-31f1-4839-be92-a3a55cd0f241 · outbound

This paper cites Experimental reconstructions of 3d atomic structures from electron microscopy images using a bayesian genetic algorithm.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Experimental reconstructions of 3d atomic structures from electron microscopy images using a bayesian genetic algorithm

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.508678Z

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Observation 632beb71-abc1-4610-8ba4-cd2fa00dac8b · outbound

This paper cites Obtaining 3d atomic recon- structions from electron microscopy images using a bayesian genetic algorithm: Possibilities, insights, and limitations.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Obtaining 3d atomic recon- structions from electron microscopy images using a bayesian genetic algorithm: Possibilities, insights, and limitations

Reference 20

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Observation e29b7b98-b735-4d2c-9881-a36dccca8ffa · outbound

This paper cites Auto-resolving the atomic structure at van der waals interfaces using a generative model.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Auto-resolving the atomic structure at van der waals interfaces using a generative model

Reference 21

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Source-reported events for the cited work

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Observation 416397af-51b3-42d2-8917-c003deb37418 · outbound

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AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Unresolved cited work

Reference 22

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Observation 465f53d3-ea0d-4e16-b189-0a32269cecf7 · outbound

This paper cites Deep learning analysis of defect and phase evolution during electron beam-induced transformations in ws2.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Deep learning analysis of defect and phase evolution during electron beam-induced transformations in ws2

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.462902Z

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Observation f12ada5b-66e5-4058-b117-d0d3cfae644c · outbound

This paper cites Machine-learning approach for quantified resolvability enhancement of low-dose stem data.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Machine-learning approach for quantified resolvability enhancement of low-dose stem data

Reference 24

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Source-reported events for the cited work

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Observation 3dc86dab-f7a8-4b26-8116-92d6b613a76c · outbound

This paper cites Deep learning-based noise filtering toward millisecond order imaging by using scanning trans- mission electron microscopy.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Deep learning-based noise filtering toward millisecond order imaging by using scanning trans- mission electron microscopy

Reference 25

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Observation 511a43de-3d42-40a3-b6d7-97bcc94f1268 · outbound

This paper cites GPT-4 Technical Report.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use GPT-4 Technical Report

Reference 26

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Observation c39c5cd9-f2c5-4605-8c33-e46f3310dd2c · outbound

This paper cites Qwen2.5-VL Technical Report.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Qwen2.5-VL Technical Report

Reference 27

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Observation fe0a2f2f-b38f-41d9-ac63-6511bf0c9651 · outbound

This paper cites Atomai framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Atomai framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.429715Z

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Observation 392f237d-f276-4fba-8113-43cebe629047 · outbound

This paper cites The computational 2d materials database: high-throughput modeling and discovery of atomically thin crystals.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use The computational 2d materials database: high-throughput modeling and discovery of atomically thin crystals

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.415344Z

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Observation c71a8fe7-6003-4e18-bee4-39b325b0d831 · outbound

This paper cites Commentary: The materials project: A materials genome approach to accelerating materials innovation.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Commentary: The materials project: A materials genome approach to accelerating materials innovation

Reference 30

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Observation 7e8c1433-04b5-4115-a2f3-48359e83f793 · outbound

This paper cites Thiessen, Evan E.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Thiessen, Evan E

Reference 31

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Observation a938d572-bcac-47fb-8a92-0be9c0bc8dc7 · outbound

This paper cites abtem: Ab initio transmission electron microscopy image simulation.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use abtem: Ab initio transmission electron microscopy image simulation

Reference 32

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Observation fc8f0c22-65ba-48ca-ac16-d65149a83061 · outbound

This paper cites Chemvlm: Exploring the power of multimodal large language models in chemistry area.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Chemvlm: Exploring the power of multimodal large language models in chemistry area

Reference 33

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Observation 9453ce06-4fb5-4a4b-abd5-24cbaee96437 · outbound

This paper cites ChemCrow: Augmenting large-language models with chemistry tools.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use ChemCrow: Augmenting large-language models with chemistry tools

Reference 34

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Source-reported events for the cited work

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Observation 59e927d0-f44a-4657-ae6a-232210268dca · outbound

This paper cites ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning

Reference 35

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Observation 2fd1af60-ef59-40db-a8b1-43ce2a9c5d1e · outbound

This paper cites A universal graph deep learning interatomic potential for the periodic table.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use A universal graph deep learning interatomic potential for the periodic table

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.824939Z

Source-reported events for the cited work

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Observation 394d147a-d2cc-4025-975b-5e85562ad5f9 · outbound

This paper cites MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields

Reference 37

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.833801Z

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Observation 80f5f458-47cb-4cd5-a801-f03addd9e617 · outbound

This paper cites Viewrefer: Grasp the multi-view knowledge for 3d visual grounding.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Viewrefer: Grasp the multi-view knowledge for 3d visual grounding

Reference 38

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.841298Z

Source-reported events for the cited work

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Observation 0c33b0dc-006d-491f-963e-2871a87dea80 · outbound

This paper cites Any2point: Empowering any-modality large models for efficient 3d understanding.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Any2point: Empowering any-modality large models for efficient 3d understanding

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T20:34:13.344449Z

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Observation d2628135-3ace-4559-be10-35f9eef64f72 · outbound

This paper cites Exploring the potential of encoder-free architectures in 3d lmms.

AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use Exploring the potential of encoder-free architectures in 3d lmms

Reference 40

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.852230Z

Source-reported events for the cited work

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Observation d95544c0-fb8d-49d3-a6e0-0f10a137674e · outbound

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AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use A foundation model for atomistic materials chemistry

Reference 2024

Resolution: unresolved; no resolver link, observed 2026-08-15T20:34:12.656392Z

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Pith citing papers

Observation 43e7f381-84a1-49e8-a6b3-356bed84c0d7 · inbound

Semantic Granularity Navigation in Image Editing cites this paper.

Semantic Granularity Navigation in Image Editing AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use

Reference 20

Resolution: verified exact; arxiv_id, observed 2026-07-28T01:22:20.077855Z

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Observation 6edd8cd4-3de9-4aef-9638-a6d4374c1868 · inbound

Semantic Granularity Navigation in Image Editing cites this paper.

Semantic Granularity Navigation in Image Editing AutoMat: Enabling Automated Crystal Structure Reconstruction from Microscopy via Agentic Tool Use

Reference 20

Resolution: verified exact; arxiv_id, observed 2026-07-28T01:22:20.077855Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.