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Protocol

MassSpecGym · main (MassSpecGym Molecule retrieval)

MassSpecGym · main · Table 3. Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, main

5 evaluations · 20 metric rows

At a glance

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

How it works

Evaluation in this paper

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, main

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

MassSpecGym · main · Table 3

Hit rate @1 (percent) · Higher values are better for this metric.

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Evaluation protocol · MassSpecGym · main

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3: Hit rate @1, main
Values, uncertainty and evidence
Hit rate @1: original source values
Tested entityPrinted valueUncertaintyEvidence
Random (main) · Configuration0.37 (0.24-0.54) percenttype: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.24; upper: 0.54Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @1
DeepSets (main) · Configuration1.47 (1.18-1.77) percenttype: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.18; upper: 1.77Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @1
Fingerprint FFN (main) · Configuration2.54 (2.17-2.99) percenttype: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 2.17; upper: 2.99Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @1
DeepSets + Fourier features (main) · Configuration5.24 (4.71-5.83) percenttype: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 4.71; upper: 5.83Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @1
MIST (main) · Configuration14.64 (13.82-15.54) percenttype: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.82; upper: 15.54Author-reported evaluation · source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @1
Scope and limitations
  • Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.
  • Zero generation accuracy is a reported result, not missingness.
  • No checkpoint revision inferred from method name.
  • Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.
  • Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 5 evaluations · 20 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
Random (main): MassSpecGym · main

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Author-reported evaluation · Evaluation metadata: needs review

30.81 (30.40-31.21) MCES @1

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.40; upper: 31.21

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, MCES @1

Source checking is not independent reproduction.

2.01 (1.68-2.39)% Hit rate @5

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.68; upper: 2.39

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @5

Source checking is not independent reproduction.

0.37 (0.24-0.54)% Hit rate @1

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 0.24; upper: 0.54

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @1

Source checking is not independent reproduction.

8.22 (7.53-8.89)% Hit rate @20

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 7.53; upper: 8.89

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Random, Hit rate @20

Source checking is not independent reproduction.

DeepSets + Fourier features (main): MassSpecGym · main

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Author-reported evaluation · Evaluation metadata: needs review

22.13 (21.85-22.43) MCES @1

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.85; upper: 22.43

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, MCES @1

Source checking is not independent reproduction.

12.58 (11.80-13.42)% Hit rate @5

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 11.80; upper: 13.42

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @5

Source checking is not independent reproduction.

28.21 (27.10-29.36)% Hit rate @20

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 27.10; upper: 29.36

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @20

Source checking is not independent reproduction.

5.24 (4.71-5.83)% Hit rate @1

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 4.71; upper: 5.83

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets + Fourier features, Hit rate @1

Source checking is not independent reproduction.

Fingerprint FFN (main): MassSpecGym · main

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Author-reported evaluation · Evaluation metadata: needs review

20.00 (19.01-20.98)% Hit rate @20

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 19.01; upper: 20.98

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @20

Source checking is not independent reproduction.

7.59 (6.96-8.28)% Hit rate @5

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 6.96; upper: 8.28

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @5

Source checking is not independent reproduction.

24.66 (24.38-24.94) MCES @1

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 24.38; upper: 24.94

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, MCES @1

Source checking is not independent reproduction.

2.54 (2.17-2.99)% Hit rate @1

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 2.17; upper: 2.99

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, Fingerprint FFN, Hit rate @1

Source checking is not independent reproduction.

DeepSets (main): MassSpecGym · main

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Author-reported evaluation · Evaluation metadata: needs review

6.21 (5.64-6.82)% Hit rate @5

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 5.64; upper: 6.82

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @5

Source checking is not independent reproduction.

25.11 (24.84-25.39) MCES @1

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 24.84; upper: 25.39

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, MCES @1

Source checking is not independent reproduction.

1.47 (1.18-1.77)% Hit rate @1

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 1.18; upper: 1.77

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @1

Source checking is not independent reproduction.

19.23 (18.24-20.26)% Hit rate @20

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 18.24; upper: 20.26

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, DeepSets, Hit rate @20

Source checking is not independent reproduction.

MIST (main): MassSpecGym · main

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Author-reported evaluation · Evaluation metadata: needs review

59.15 (57.89-60.39)% Hit rate @20

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 57.89; upper: 60.39

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @20

Source checking is not independent reproduction.

15.37 (15.12-15.62) MCES @1

Unit: edge-edit distance · Direction: lower

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 15.12; upper: 15.62

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, MCES @1

Source checking is not independent reproduction.

14.64 (13.82-15.54)% Hit rate @1

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.82; upper: 15.54

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @1

Source checking is not independent reproduction.

34.87 (33.69-36.10)% Hit rate @5

Unit: percent · Direction: higher

Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 33.69; upper: 36.10

Scored: Not reported · Eligible: Not reported

source checkedMassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, main challenge, MIST, Hit rate @5

Source checking is not independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.

What is still missing

  • Independent batch review before import; preserve existing observation identities.
Search and extraction details

complete comparison tables extracted pending publication review

Searches

  • MassSpecGym 2410.23326 benchmark results Table 1 Table 2

Evidence locations

  • Table 3: Hit rate @1, main

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-protocol-a18b4bc79049513fb7

Evidence table

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

4 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statementOriginal source and locationReview and provenance
Evaluation in this paper

Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 3: Hit rate @1, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.sections.0.body

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Introduction

MassSpecGym · main · Table 3. Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 3: Hit rate @1, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.summary

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: evaluates task

discovery-benchmark-massspecgym-molecule-retrieval

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 3: Hit rate @1, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:evaluates_task:discovery-benchmark-massspecgym-molecule-retrieval

Claim: paper-claim-0a14393899ade8d2cb

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: part of

discovery-benchmark-massspecgym

Individual claims
MassSpecGym: A benchmark for the discovery and identification of molecules

Original source ↗

Table 3: Hit rate @1, main

Version: 2410.23326v1
Retrieved: 2026-09-17T07:56:11.146650+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:part_of:discovery-benchmark-massspecgym

Claim: paper-claim-6f79fb79df5f06d3ea

Source artifact SHA-256: 82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

Download this release
Technical metadata and extraction receipts

Stable ID: paper-protocol-a18b4bc79049513fb7

areas
metabolomics
entity level
protocol
protocol
Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
comparison panels
id: part2-massspecgym-table3-65ea68de77; title: MassSpecGym · main · Table 3; protocol id: paper-protocol-a18b4bc79049513fb7; dataset id: paper-dataset-43f783b5d7a7151aa9; metric: Hit rate @1; unit: percent; direction: higher; result ids: paper-result-9b0cc277a3cbc6c13d; paper-result-acf85ffa57a1906421; paper-result-a0d66c2c9d6bc8466d; paper-result-d73962270e10586574; paper-result-d5320e4453da6b09dd; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, main; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-dffdc0b0ef; title: MassSpecGym · main · Table 3; protocol id: paper-protocol-a18b4bc79049513fb7; dataset id: paper-dataset-43f783b5d7a7151aa9; metric: Hit rate @5; unit: percent; direction: higher; result ids: paper-result-35b54face42cd4df98; paper-result-3588b0e1eb7078ee40; paper-result-3bda21118a05d4e278; paper-result-46e2e44bcf768e94b2; paper-result-ed71048c3ebde971d5; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @5, main; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-629ab3b450; title: MassSpecGym · main · Table 3; protocol id: paper-protocol-a18b4bc79049513fb7; dataset id: paper-dataset-43f783b5d7a7151aa9; metric: Hit rate @20; unit: percent; direction: higher; result ids: paper-result-f871d7d35c275e848e; paper-result-e3dc19ea2e9e59e293; paper-result-29a4b30ef091c9e0e8; paper-result-cde595ad3523bf9f27; paper-result-6b9b0e247bfdc9c274; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @20, main; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17; id: part2-massspecgym-table3-b934e3725f; title: MassSpecGym · main · Table 3; protocol id: paper-protocol-a18b4bc79049513fb7; dataset id: paper-dataset-43f783b5d7a7151aa9; metric: MCES @1; unit: edge-edit distance; direction: lower; result ids: paper-result-002aa84a8224be7916; paper-result-3ff182c671377da6da; paper-result-57fd7d0cd8b73c56e2; paper-result-0dcae24f1e2c35b445; paper-result-80aa6ca411586dd8e5; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: MCES @1, main; context: Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split; caveats: Source metric equations define hit rates as fractions, while table values use percentage scale; recorded values are not rescaled.; Zero generation accuracy is a reported result, not missingness.; No checkpoint revision inferred from method name.; Bootstrap CIs reflect resampling of this test set; not independently reproduced and not seed standard deviations.; Full table retained, including weaker/random methods and unavailable formula-simulation similarity cells.; review: method: automated_source_review; date: 2026-09-17
benchmark research
review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-massspecgym-arxiv-v1; inspected locators: Table 3: Hit rate @1, main; searched queries: MassSpecGym 2410.23326 benchmark results Table 1 Table 2; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
legacy kinds
benchmark
entity classification
review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, main; ambiguities: None recorded
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