Paper Citation Record · LEDGER

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly

As of 18 August 2026, this Paper Citation Record lists 40 of 40 outbound references and 0 inbound Pith citation observations for arXiv:2505.21833.

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

pith.paper-citation-record.v1
2505.21833 v1

Coverage vector

measured 40 of 40 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T13:26:25.871437Z

measured 40 of 40 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-18T06:34:40.430872+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

40 of 40 outbound references displayed

verified exact2
verified fuzzy22
unresolved15
parse uncertain0
malformed identifier0
metadata mismatch1

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 7299dd6d-0d52-484b-aa17-19c844c2ba78 · outbound

This paper cites Rational design of ligands with optimized residence time.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Rational design of ligands with optimized residence time

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:31.170236Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation d1c7baf9-9313-427c-b989-980a74d177e6 · outbound

This paper cites Chaudhri, Naren Chittar, and Michael Genesereth.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Chaudhri, Naren Chittar, and Michael Genesereth

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.967837Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f67d8e02-5f2f-4421-b3d8-f1da4c42f35f · outbound

This paper cites Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:22.495580Z

Source-reported events for the cited work

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Observation 5104569f-b6d6-432f-b090-73275eeea5e4 · outbound

This paper cites Functional connectomics reveals general wiring rule in mouse visual cortex.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Functional connectomics reveals general wiring rule in mouse visual cortex

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.791958Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation db52ef4f-6df3-4d22-aaca-400aa1181590 · outbound

This paper cites Uncertainty modeling in wireless sensor networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Uncertainty modeling in wireless sensor networks

Reference 5

Resolution: metadata mismatch; raw_fallback, observed 2026-08-07T13:26:26.616210Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation a712d483-e098-4cd8-971e-88f04e68bf09 · outbound

This paper cites Machine learning-aided generative molecular design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Machine learning-aided generative molecular design

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.606174Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation e010bb1b-6d51-4ea8-84a4-5eb1d1d3de98 · outbound

This paper cites 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:22.776874Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e30c4c22-f37c-4710-982c-462b7e108550 · outbound

This paper cites DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:22.838722Z

Source-reported events for the cited work

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Observation ce3feb06-fd92-424a-93d6-d75ca552332a · outbound

This paper cites Denoising Diffusion Probabilistic Models.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Denoising Diffusion Probabilistic Models

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:22.869934Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 66a038cf-89aa-40ac-8272-035abc704dd8 · outbound

This paper cites Equivariant Diffusion for Molecule Generation in 3D.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Equivariant Diffusion for Molecule Generation in 3D

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:22.931304Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 406e3856-85f1-4c24-a6ef-2fef245e100d · outbound

This paper cites 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design

Reference 11

Resolution: verified exact; local_arxiv, observed 2026-08-07T13:26:26.262539Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 10270f1e-acea-4b9d-aa15-40ed89010d8f · outbound

This paper cites Equivariant 3d-conditional diffusion model for molecular linker design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Equivariant 3d-conditional diffusion model for molecular linker design

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.396555Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation c19de015-01db-49fc-b966-980fa24e3562 · outbound

This paper cites Deep generative models for 3d linker design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Deep generative models for 3d linker design

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.216464Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5a0adfb8-8c8b-4ea2-971a-f591d55a2d5b · outbound

This paper cites Node deployment under position uncertainty for network localization.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Node deployment under position uncertainty for network localization

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:30.007465Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation bf2b9673-8939-44d6-9c56-c4def3ab82a1 · outbound

This paper cites Semi-Supervised Classification with Graph Convolutional Networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Semi-Supervised Classification with Graph Convolutional Networks

Reference 15

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 947ff8e3-a3e2-474e-8774-0edb544b4b6f · outbound

This paper cites Sgrec3d: Self-supervised 3d scene graph learning via object-level scene reconstruction.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Sgrec3d: Self-supervised 3d scene graph learning via object-level scene reconstruction

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:29.704127Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 6226cfbc-cbea-4b7d-a862-d65edd70aad7 · outbound

This paper cites Current perspectives in fragment-based lead discovery (fbld).

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Current perspectives in fragment-based lead discovery (fbld)

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:29.497166Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 318943d0-14df-483f-ada9-55e6efdfc890 · outbound

This paper cites Rdkit documentation.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Rdkit documentation

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:23.607042Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 94dca429-5eb5-4d50-9d93-ea333573aaef · outbound

This paper cites A purely algebraic justification of the kabsch-umeyama algorithm.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly A purely algebraic justification of the kabsch-umeyama algorithm

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:29.276198Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 387bbba8-d647-48f8-b03c-7df36fd3e0d1 · outbound

This paper cites Degiacomi, and Chris G.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Degiacomi, and Chris G

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:29.103290Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 947f65dd-cc23-4943-a564-21a8eac3a2d4 · outbound

This paper cites Evaluating graph neural networks for link prediction: Current pitfalls and new benchmarking.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Evaluating graph neural networks for link prediction: Current pitfalls and new benchmarking

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:28.912758Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 93de7207-2447-43ef-8b90-ab87426f7e8b · outbound

This paper cites Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:23.935393Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 0c0d180d-7fae-4114-88f6-459f1c20a505 · outbound

This paper cites Revisiting Link Prediction: A Data Perspective.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Revisiting Link Prediction: A Data Perspective

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:24.057032Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 9c69bba5-9d6e-4942-a7f6-32e57c34ef5e · outbound

This paper cites Retinal connectomics: towards complete, accurate networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Retinal connectomics: towards complete, accurate networks

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:28.677067Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4ef8d557-22e0-4a5d-95d9-f9a2f01d2d1a · outbound

This paper cites Geometry-complete diffusion for 3d molecule generation and optimization.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Geometry-complete diffusion for 3d molecule generation and optimization

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:28.402638Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 71018f5c-9a6f-4bf0-a2b4-b4d71b113591 · outbound

This paper cites Bronstein, Philippe Schwaller, and Bruno Correia.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Bronstein, Philippe Schwaller, and Bruno Correia

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:28.212395Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4f846d87-6841-4cc8-9beb-0d220ef15038 · outbound

This paper cites Clustering and preferential attachment in growing networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Clustering and preferential attachment in growing networks

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:28.030399Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f45e2aac-e042-4206-a6c0-8f91202ee182 · outbound

This paper cites Open babel: An open chemical toolbox.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Open babel: An open chemical toolbox

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:24.592588Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1c187079-3e98-48c4-a241-bd96610f30e4 · outbound

This paper cites Geometric deep learning for structure-based ligand design.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Geometric deep learning for structure-based ligand design

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:27.815467Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 51fa5280-ee2b-415b-995c-f6321123c474 · outbound

This paper cites MedSAGE : Bridging Generative AI and Medicinal Chemistry for Structure - Based Design of Small Molecule Drugs.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly MedSAGE : Bridging Generative AI and Medicinal Chemistry for Structure - Based Design of Small Molecule Drugs

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:24.755688Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 195e1a46-327c-4802-b242-65842193e356 · outbound

This paper cites Extended-connectivity fingerprints.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Extended-connectivity fingerprints

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:27.661337Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 6fc292e0-027e-4b9b-a0dc-cc2fed471040 · outbound

This paper cites E(n) Equivariant Graph Neural Networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly E(n) Equivariant Graph Neural Networks

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:24.963128Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 73cff2a2-79ee-4c02-8805-f1d15bf2ce1a · outbound

This paper cites an unresolved cited work.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Unresolved cited work

Reference 33

Resolution: unresolved; raw_fallback, observed 2026-08-07T13:26:27.487426Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2aeeca7e-a363-4855-b062-b4dfc8eb01fb · outbound

This paper cites Structure-based drug design with equivariant diffusion models.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Structure-based drug design with equivariant diffusion models

Reference 34

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:27.337686Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 67d9ed09-9be4-445f-ba22-1a6d868c9cb8 · outbound

This paper cites Dobbelstein, Thomas Castiglione, Michael M.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Dobbelstein, Thomas Castiglione, Michael M

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:27.181717Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4f4381be-e242-48a3-99f8-d5ed2e245547 · outbound

This paper cites Fragment informatics and computational fragment-based drug design: an overview and update.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Fragment informatics and computational fragment-based drug design: an overview and update

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:26.963795Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5bf4cc50-961c-42a9-a045-f3275a23586b · outbound

This paper cites Computational ligand-based rational design: role of conformational sampling and force fields in model development.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Computational ligand-based rational design: role of conformational sampling and force fields in model development

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:26:26.797304Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation e6abd636-f73f-4029-8ac0-42eba2c24cfc · outbound

This paper cites Deep unsupervised learning using nonequilibrium thermodynamics.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Deep unsupervised learning using nonequilibrium thermodynamics

Reference 38

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:25.652715Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f405336f-8d0d-4a13-b288-47d9b3c4f681 · outbound

This paper cites Graph Attention Networks.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly Graph Attention Networks

Reference 39

Resolution: unresolved; no resolver link, observed 2026-08-07T13:26:25.787084Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 26bbfab5-ae6b-4a1e-b4bf-6dc23770bfd3 · outbound

This paper cites A review of knowledge graph completion.

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly A review of knowledge graph completion

Reference 40

Resolution: verified exact; doi, observed 2026-08-07T13:26:26.038162Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Pith citing papers

No inbound Pith citation observations are available.