Paper Citation Record · LEDGER

OTMol: Robust Molecular Structure Comparison via Optimal Transport

As of 8 August 2026, this Paper Citation Record lists 47 of 47 outbound references and 0 inbound Pith citation observations for arXiv:2509.01550.

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

pith.paper-citation-record.v1
2509.01550 v1

Coverage vector

measured 47 of 47 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-05T12:34:44.469146Z

measured 47 of 47 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-08T06:32:00.761636+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

47 of 47 outbound references displayed

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External citation measurements

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Outbound references

Observation c8add58a-9c51-4b88-9451-a871c4de45e2 · outbound

This paper cites Johnson, Gerald M.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Johnson, Gerald M

Reference 1

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Observation 059a15f8-5766-48a5-9c43-373b495b8924 · outbound

This paper cites Algorithm for efficient superposition and clustering of molecular assem- blies using the branch-and-bound method.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Algorithm for efficient superposition and clustering of molecular assem- blies using the branch-and-bound method

Reference 2

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Observation 1b8de66e-aea0-4749-bd17-eccb9adef772 · outbound

This paper cites Accurate structure prediction of biomolecular interactions with Al- phaFold3.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Accurate structure prediction of biomolecular interactions with Al- phaFold3

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.963388Z

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Observation 048b7627-00b4-42c9-89f3-de3bb94e84a6 · outbound

This paper cites Miller III, and Animashree Anandkumar.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Miller III, and Animashree Anandkumar

Reference 4

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Observation fa93f466-dd6f-4d62-8f1a-4180c41b67cd · outbound

This paper cites Boltz-1: Democratizing biomolecular interaction modeling with open-source foundation mod- els.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Boltz-1: Democratizing biomolecular interaction modeling with open-source foundation mod- els

Reference 5

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Observation 496c1a1d-294c-4546-8fe4-234e9bd180c3 · outbound

This paper cites Boltz-2: A biomolecular foundation model for structure and binding affinity prediction, 2025.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Boltz-2: A biomolecular foundation model for structure and binding affinity prediction, 2025

Reference 6

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Observation 4dbb3a55-cf59-4039-ad44-ece1450a4fd2 · outbound

This paper cites State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences.

OTMol: Robust Molecular Structure Comparison via Optimal Transport State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences

Reference 7

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Observation e505fca2-4160-4d8d-b9ac-481ed65ac0d4 · outbound

This paper cites Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.923759Z

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Observation 958f3e63-81d7-416d-ada0-dea493455794 · outbound

This paper cites Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.913757Z

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Observation 1494eb32-e6b6-412d-a059-e73b31546ff4 · outbound

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OTMol: Robust Molecular Structure Comparison via Optimal Transport Unresolved cited work

Reference 10

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Source-reported events for the cited work

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Observation 6d379463-b2ba-493f-a5aa-cee4d2a90f09 · outbound

This paper cites Temelso, K.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Temelso, K

Reference 11

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Observation 3f08d6a1-fced-4d56-ba7a-f3b567b71df5 · outbound

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OTMol: Robust Molecular Structure Comparison via Optimal Transport Unresolved cited work

Reference 12

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OTMol: Robust Molecular Structure Comparison via Optimal Transport Unresolved cited work

Reference 13

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Observation c423c70c-3774-4485-b3e6-3895b720bc17 · outbound

This paper cites Xiang, W.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Xiang, W

Reference 14

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Observation 919fb4e6-617e-4499-a992-8ec0f53b8f9c · outbound

This paper cites Xiang, L.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Xiang, L

Reference 15

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Observation 10ac9f97-f9fc-43e5-9eec-95b0e217ca75 · outbound

This paper cites ArbAlign: a tool for optimal alignment of arbitrarily ordered isomers using the Kuhn–Munkres algorithm.

OTMol: Robust Molecular Structure Comparison via Optimal Transport ArbAlign: a tool for optimal alignment of arbitrarily ordered isomers using the Kuhn–Munkres algorithm

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.843469Z

Source-reported events for the cited work

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Observation 134e780e-18c7-43bc-8386-d6382133b28c · outbound

This paper cites A solution for the best rotation to relate two sets of vectors.

OTMol: Robust Molecular Structure Comparison via Optimal Transport A solution for the best rotation to relate two sets of vectors

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.832709Z

Source-reported events for the cited work

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Observation 56995384-69d5-41e1-a7ec-6b697aa394a2 · outbound

This paper cites Using quaternions to calculate RMSD.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Using quaternions to calculate RMSD

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.822808Z

Source-reported events for the cited work

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Observation 63ce7eb5-80b4-4b58-9408-055abed09ed3 · outbound

This paper cites Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.812290Z

Source-reported events for the cited work

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Observation 7a244316-c35f-4ecb-b8b5-2b51702683ad · outbound

This paper cites Similarity recognition of molecular structures by op- timal atomic matching and rotational superposition.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Similarity recognition of molecular structures by op- timal atomic matching and rotational superposition

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.801746Z

Source-reported events for the cited work

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Observation ca7d03ca-2c6c-4919-81b8-622749d603ae · outbound

This paper cites How differ- ent are two chemical structures? Journal of Chemical information and Modeling, 50(12):2129– 2140, 2010.

OTMol: Robust Molecular Structure Comparison via Optimal Transport How differ- ent are two chemical structures? Journal of Chemical information and Modeling, 50(12):2129– 2140, 2010

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.791668Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 6eba600a-02df-48e5-b4a6-a3d050340f80 · outbound

This paper cites Alignment of three-dimensional molecules using an image recognition algorithm.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Alignment of three-dimensional molecules using an image recognition algorithm

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.781785Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 3dcabe42-f3d0-4318-a44b-1c4cd437ce52 · outbound

This paper cites Metrics for measuring distances in configuration spaces.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Metrics for measuring distances in configuration spaces

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.770056Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 76a8ffbe-b821-41c0-a3c6-48a7248889db · outbound

This paper cites The discovery of unexpected isomers in sodium heptamers by Born–Oppenheimer molecular dynamics.

OTMol: Robust Molecular Structure Comparison via Optimal Transport The discovery of unexpected isomers in sodium heptamers by Born–Oppenheimer molecular dynamics

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.759553Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 40e8be4c-e7d0-4218-acc4-ba3a1fd78472 · outbound

This paper cites aRMSD: a comprehensive tool for structural analysis.

OTMol: Robust Molecular Structure Comparison via Optimal Transport aRMSD: a comprehensive tool for structural analysis

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.749252Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 473a2be8-6a40-4517-bf94-3d084befcf58 · outbound

This paper cites Linear assignment problems and extensions.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Linear assignment problems and extensions

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.739014Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 614c646e-76d7-4c99-9691-33d7a9b0daa6 · outbound

This paper cites The Hungarian method for the assignment problem.

OTMol: Robust Molecular Structure Comparison via Optimal Transport The Hungarian method for the assignment problem

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.728803Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 9698b8ef-4307-4af0-a62d-a666df58af5b · outbound

This paper cites Algorithms for the assignment and transportation problems.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Algorithms for the assignment and transportation problems

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.719300Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 322e3bfb-45b9-4876-8b48-0c567b8ed949 · outbound

This paper cites A shortest augmenting path algorithm for dense and sparse linear assignment problems.

OTMol: Robust Molecular Structure Comparison via Optimal Transport A shortest augmenting path algorithm for dense and sparse linear assignment problems

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.709490Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 76c09f73-2855-46de-a7ee-143d597fba0e · outbound

This paper cites Gromov–Wasserstein distances and the metric approach to object matching.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Gromov–Wasserstein distances and the metric approach to object matching

Reference 30

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.699361Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 7d8ad632-da18-4d5f-98da-217f3099d839 · outbound

This paper cites Gromov-wasserstein averaging of kernel and distance matrices.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Gromov-wasserstein averaging of kernel and distance matrices

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.689455Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 951eb383-8b2a-4129-abee-9f2fb45bc396 · outbound

This paper cites Supervised optimal transport.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Supervised optimal transport

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.678869Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation b4d17ff4-d621-45ba-ae66-2f397b25083a · outbound

This paper cites Supervised Gromov–Wasserstein Optimal Trans- port with Metric-Preserving Constraints.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Supervised Gromov–Wasserstein Optimal Trans- port with Metric-Preserving Constraints

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.668946Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation cf0333ca-d989-42d6-a766-7173ab3a96ec · outbound

This paper cites Computational optimal transport: With applications to data science.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Computational optimal transport: With applications to data science

Reference 34

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.658995Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 3d50ddf7-0570-48b2-9dee-bf5c97c4aee4 · outbound

This paper cites Optimal transport for structured data with application on graphs.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Optimal transport for structured data with application on graphs

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.649038Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 6d62a5d5-680c-421d-aaa6-3f58ac223cfc · outbound

This paper cites A purely algebraic justification of the Kabsch-Umeyama algorithm.

OTMol: Robust Molecular Structure Comparison via Optimal Transport A purely algebraic justification of the Kabsch-Umeyama algorithm

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.639394Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 71fd7cc5-0093-491e-8343-2f18a4517464 · outbound

This paper cites Least-squares estimation of transformation parameters between two point patterns.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Least-squares estimation of transformation parameters between two point patterns

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.629580Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation ebe8b600-921a-40d3-9a0d-39dd82095721 · outbound

This paper cites Displacement interpolation using Lagrangian mass transport.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Displacement interpolation using Lagrangian mass transport

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.618951Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 111f94eb-e0c1-4e5a-a004-e5439bead6fc · outbound

This paper cites Atlas of putative minima and low-lying energy networks of water clusters n= 3–25.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Atlas of putative minima and low-lying energy networks of water clusters n= 3–25

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.607584Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 04d93e69-d421-4f4a-b42c-47d16345f0ca · outbound

This paper cites Alaya, Aur´ elie Boisbunon, Stanislas Chambon, Laetitia Chapel, Adrien Corenflos, Kilian Fatras, Nemo Fournier, L´ eo Gautheron, Nathalie T.H.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Alaya, Aur´ elie Boisbunon, Stanislas Chambon, Laetitia Chapel, Adrien Corenflos, Kilian Fatras, Nemo Fournier, L´ eo Gautheron, Nathalie T.H

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.597592Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation fbebe137-8c8a-40c8-9ef9-13148d44733c · outbound

This paper cites POT Python Optimal Transport (version 0.9.5), 2024.

OTMol: Robust Molecular Structure Comparison via Optimal Transport POT Python Optimal Transport (version 0.9.5), 2024

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.587431Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 0b31f3e0-bdff-4961-9353-9ddd24b5dd17 · outbound

This paper cites Hara and Akihiko Kondo.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Hara and Akihiko Kondo

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.576989Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation d33a2121-0e63-4762-a641-053f8b528246 · outbound

This paper cites Distinct Conformation of ATP Molecule in Solution and on Protein.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Distinct Conformation of ATP Molecule in Solution and on Protein

Reference 43

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.564886Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation b96fe6a4-44bd-4953-bb88-222f086f5bc2 · outbound

This paper cites an unresolved cited work.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Unresolved cited work

Reference 44

Resolution: unresolved; raw_fallback, observed 2026-08-05T12:34:44.554198Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 31e5a02e-4321-4403-81f4-2bca1b0c7032 · outbound

This paper cites Imatinib: A Breakthrough of Targeted Therapy in Cancer.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Imatinib: A Breakthrough of Targeted Therapy in Cancer

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.543271Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation 9f03dfc2-cac6-4585-9a4d-3cd8caa8fc07 · outbound

This paper cites Important Roles of Water Clusters Confined in a Nanospace as Revealed by a Synchrotron X-ray Diffraction Study.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Important Roles of Water Clusters Confined in a Nanospace as Revealed by a Synchrotron X-ray Diffraction Study

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.531936Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Observation aaee4def-5633-4e42-b30e-fe7206ad3288 · outbound

This paper cites Pouliquen.

OTMol: Robust Molecular Structure Comparison via Optimal Transport Pouliquen

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T12:34:44.519612Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

Pith citing papers

No inbound Pith citation observations are available.