Paper Citation Record · LEDGER

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval

As of 5 August 2026, this Paper Citation Record lists 40 of 40 outbound references and 0 inbound Pith citation observations for arXiv:2512.08508.

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

pith.paper-citation-record.v1
2512.08508 v2

Coverage vector

measured 40 of 40 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-03T17:44:13.891326Z

measured 40 of 40 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-05T06:32:48.257954+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 exact1
verified fuzzy0
unresolved38
parse uncertain0
malformed identifier1
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 7537f11e-f262-4ebd-b2a7-a12a1e114320 · outbound

This paper cites UniProt: the Universal protein knowledgebase in 2025.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval UniProt: the Universal protein knowledgebase in 2025

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:08.745376Z

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Observation 1c8c9dd2-c3a0-4710-a95f-7eacd7275b76 · outbound

This paper cites Enzyme function and evolution through the lens of bioinformatics.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Enzyme function and evolution through the lens of bioinformatics

Reference 2

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:08.855947Z

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Observation b3143348-9ff4-4b88-8eb4-467090179b54 · outbound

This paper cites Basic local alignment search tool.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Basic local alignment search tool

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:08.996235Z

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Observation ad34285e-aa61-4078-97bd-230541faec66 · outbound

This paper cites ModEnzA: accurate identification of metabolic enzymes using func- tion specific profile HMMs with optimised discrimination threshold and modified emission probabilities.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval ModEnzA: accurate identification of metabolic enzymes using func- tion specific profile HMMs with optimised discrimination threshold and modified emission probabilities

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.141329Z

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Observation 9891b769-e9d7-4a84-a669-ab74345044b8 · outbound

This paper cites Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.281255Z

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Observation 798c9f06-3378-4aa3-b139-2f96bd07a3ad · outbound

This paper cites Hidden Markov models in computational biology: Applications to protein modeling.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Hidden Markov models in computational biology: Applications to protein modeling

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.442034Z

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Observation 592835c1-6c38-48c1-a32a-7b6dfc24d4cc · outbound

This paper cites HH-suite3 for fast remote homology detection and deep protein annotation.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval HH-suite3 for fast remote homology detection and deep protein annotation

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.534118Z

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Observation e8edc757-3c72-429f-9c60-6e36150ebb03 · outbound

This paper cites COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.695766Z

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Observation 81d560b1-fa3b-4f98-b4b9-2bd650667f41 · outbound

This paper cites COFACTOR: improved protein func- tion prediction by combining structure, sequence and protein–protein interaction information.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval COFACTOR: improved protein func- tion prediction by combining structure, sequence and protein–protein interaction information

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:09.850081Z

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Observation 102dc776-3a64-4f5b-81fb-8d419c2abbd4 · outbound

This paper cites Enzyme function prediction using contrastive learning.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Enzyme function prediction using contrastive learning

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.001567Z

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Observation 1d084c43-ac21-4f4b-9262-4226f9140b4a · outbound

This paper cites CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.088853Z

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Observation 6884cd3e-d6dd-4aca-8321-ecb718cdea1e · outbound

This paper cites ReactZyme: A Benchmark for Enzyme-Reaction Prediction.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval ReactZyme: A Benchmark for Enzyme-Reaction Prediction

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.093818Z

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Observation 39c378a7-65e4-4d31-a80d-62113a864dcc · outbound

This paper cites Care: a benchmark suite for the classification and retrieval of enzymes.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Care: a benchmark suite for the classification and retrieval of enzymes

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.305858Z

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Observation a4430f63-cad0-4fbe-b5af-dbd69846a114 · outbound

This paper cites Learning transferable visual models from natural language supervision.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Learning transferable visual models from natural language supervision

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.401933Z

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Observation 5363147d-3a79-4559-a47e-8936bd0b1115 · outbound

This paper cites MLIP: Efficient Multi-Perspective Language-Image Pretraining with Exhaustive Data Utilization.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval MLIP: Efficient Multi-Perspective Language-Image Pretraining with Exhaustive Data Utilization

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.599812Z

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Observation 9badff33-d9b8-4a6e-a761-8379a7d97896 · outbound

This paper cites iclip: Bridging image classification and contrastive language-image pre- training for visual recognition.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval iclip: Bridging image classification and contrastive language-image pre- training for visual recognition

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.756294Z

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Observation 32fa8d34-dec0-4f17-bbe3-5daa83326802 · outbound

This paper cites Cross-Modal Retrieval Meets Inference:Improving Zero-Shot Classification with Cross-Modal Retrieval.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Cross-Modal Retrieval Meets Inference:Improving Zero-Shot Classification with Cross-Modal Retrieval

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.899336Z

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Observation c2d36ff7-715c-4c75-a866-8b457737b5f8 · outbound

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

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Gromov–Wasserstein distances and the metric approach to object matching

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:10.995435Z

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Observation b2525334-8f87-4163-8488-63c129f89f16 · outbound

This paper cites Linear-time gromov wasserstein distances using low rank couplings and costs.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Linear-time gromov wasserstein distances using low rank couplings and costs

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.096327Z

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Observation 237f59f9-41b4-4f54-bbdd-43cb4b9b5fe4 · outbound

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

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Optimal transport for structured data with application on graphs

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.173739Z

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Observation 82693e15-5b92-42b5-ac24-e130ac6f4c83 · outbound

This paper cites Fused gromov-wasserstein graph mixup for graph-level classifications.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Fused gromov-wasserstein graph mixup for graph-level classifications

Reference 21

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.227915Z

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Observation fbecaa53-d409-4af9-afc8-3f701f30e55d · outbound

This paper cites DeepEC: An error correction framework for dose prediction and organ segmentation using deep neural networks.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval DeepEC: An error correction framework for dose prediction and organ segmentation using deep neural networks

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.297563Z

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Observation 16e437eb-1c7f-40f4-b5c1-36d8c133b87b · outbound

This paper cites ProteInfer, deep neural networks for protein functional inference.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval ProteInfer, deep neural networks for protein functional inference

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.408972Z

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Observation 774eec46-3db3-463d-9186-ec2e866f8fbd · outbound

This paper cites Uni-Mol: A Universal 3D Molecular Representation Learning Frame- work.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Uni-Mol: A Universal 3D Molecular Representation Learning Frame- work

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.522078Z

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Observation fac96d6b-71c9-41df-aff7-8765715d4fd0 · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.592843Z

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Observation 7cdd7f34-d3c4-4c74-8bed-e0922e5b7ac9 · outbound

This paper cites Representation Learning with Contrastive Predictive Coding.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Representation Learning with Contrastive Predictive Coding

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.714872Z

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Observation 35c6c81f-9ef8-464f-8f3b-6504b18c24c9 · outbound

This paper cites Understanding and generalizing contrastive learning from the inverse optimal transport perspective.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Understanding and generalizing contrastive learning from the inverse optimal transport perspective

Reference 27

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.796761Z

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Observation d4985159-61e9-43cb-8b2f-de51a3c5acad · outbound

This paper cites S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:11.918054Z

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Observation 913adcab-bf72-4caa-ac5f-6bd2e4868377 · outbound

This paper cites EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions

Reference 29

Resolution: verified exact; doi, observed 2026-08-03T17:49:05.704797Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation a671f198-5444-4690-8be9-b57ccea944ba · outbound

This paper cites BRENDA, the ELIXIR core data resource in 2021: new developments and updates.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:12.242493Z

Source-reported events for the cited work

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Observation 82e74a31-6a7b-4ec2-b8a4-e6155a93e9f3 · outbound

This paper cites Enzyme function prediction using contrastive learning.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Enzyme function prediction using contrastive learning

Reference 31

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:12.446780Z

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Observation 83ac0c80-3c28-45aa-b346-049e8a1bb3bf · outbound

This paper cites Evaluating virtual screening methods: good and bad metrics for the “early recognition.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Evaluating virtual screening methods: good and bad metrics for the “early recognition

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:12.572688Z

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Observation 4bca1fba-8347-4463-8fe6-ba22ea23b305 · outbound

This paper cites Condensed graph of reaction: considering a chemical reaction as one single pseudo molecule.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Condensed graph of reaction: considering a chemical reaction as one single pseudo molecule

Reference 33

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:12.756729Z

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Observation dda33693-6d02-420b-a7f4-917f71b5e37a · outbound

This paper cites Frame Averaging for Invariant and Equivariant Network Design.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Frame Averaging for Invariant and Equivariant Network Design

Reference 34

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:12.956872Z

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Observation d1e6b979-3526-46a8-9eba-064e55a15a53 · outbound

This paper cites The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:13.138305Z

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Observation 885583e6-0379-4808-9884-1f565dcb4f48 · outbound

This paper cites Rhea, the reaction knowledgebase in 2022.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Rhea, the reaction knowledgebase in 2022

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:13.269653Z

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Observation bf08f859-fc95-4de7-9a42-90b64176ab5d · outbound

This paper cites A general model to predict small molecule substrates of enzymes based on machine and deep learning.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval A general model to predict small molecule substrates of enzymes based on machine and deep learning

Reference 37

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:13.338325Z

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Observation aeb02a4a-c263-4883-9971-05e180fd68a9 · outbound

This paper cites Molecule Attention Transformer.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval Molecule Attention Transformer

Reference 38

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:13.518295Z

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Observation f7d57153-67ce-4589-bbc6-7e11e1a0a8e9 · outbound

This paper cites SaProt: protein language modeling with structure-aware vocabulary.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval SaProt: protein language modeling with structure-aware vocabulary

Reference 39

Resolution: unresolved; no resolver link, observed 2026-08-03T17:44:13.696757Z

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Observation 43bf4a2f-a4bd-485a-b9cf-db883b705b24 · outbound

This paper cites For enzyme representations, ESM [25] and the structure- aware protein language model SaProt [39] are utilized.

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval For enzyme representations, ESM [25] and the structure- aware protein language model SaProt [39] are utilized

Reference 40

Resolution: malformed identifier; no resolver link, observed 2026-08-03T17:44:13.891326Z

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Pith citing papers

No inbound Pith citation observations are available.