Upload pairwise dataset in parquet form
Browse files- README.md +113 -95
- pairs/test-00000-of-00004.parquet +3 -0
- pairs/test-00001-of-00004.parquet +3 -0
- pairs/test-00002-of-00004.parquet +3 -0
- pairs/test-00003-of-00004.parquet +3 -0
- pairs/train-00000-of-00003.parquet +3 -0
- pairs/train-00001-of-00003.parquet +3 -0
- pairs/train-00002-of-00003.parquet +3 -0
README.md
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@@ -5,105 +5,123 @@ pretty_name: CF/MS Homo sapiens Elution Profile PPI Dataset
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tags:
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- biology
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- chemistry
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dataset_summary:
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-
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spectrometry (CF/MS) experiments, as well as positive/negative protein-protein
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interaction (PPI) labels for each pair. Collated, maintained by the Drew Lab at
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University of Illinois at Chicago.
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citation_bibtex:
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{
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and
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and
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Foster, Leonard J. and Bader, Gary D. and Cayabyab, Francisco S. and Babu,
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Mohan}, year = {2019}, month = sep, pages = {1114–1132}}
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- >-
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@article{Wan2015, title = {Panorama of ancient metazoan macromolecular
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complexes}, volume = {525}, ISSN = {1476-4687}, url =
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{http://dx.doi.org/10.1038/nature14877}, DOI = {10.1038/nature14877}, number =
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{7569}, journal = {Nature}, publisher = {Springer Science and Business Media
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LLC}, author = {Wan, Cuihong and Borgeson, Blake and Phanse, Sadhna and
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-
Tu, Fan and Drew, Kevin and Clark, Greg and Xiong, Xuejian and Kagan,
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-
Olga and Kwan, Julian and Bezginov, Alexandr and Chessman, Kyle and Pal,
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Swati and Cromar, Graham and Papoulas, Ophelia and Ni, Zuyao and Boutz,
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Daniel R. and Stoilova, Snejana and Havugimana, Pierre C. and Guo, Xinghua
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and Malty, Ramy H. and Sarov, Mihail and Greenblatt, Jack and Babu, Mohan
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and Derry, W. Brent and R. Tillier, Elisabeth and Wallingford, John B. and
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Parkinson, John and Marcotte, Edward M. and Emili, Andrew}, year = {2015},
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month = sep, pages = {339–344}}
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citation_apa:
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---
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tags:
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- biology
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- chemistry
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+
dataset_summary: Processed data from several *Homo sapiens* protein co-fractionation
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+
mass spectrometry (CF/MS) experiments, as well as positive/negative protein-protein
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| 10 |
interaction (PPI) labels for each pair. Collated, maintained by the Drew Lab at
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University of Illinois at Chicago.
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| 12 |
citation_bibtex:
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+
- '@article{Connelly2018, title = {Analysis of Human Nuclear Protein Complexes by
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+
Quantitative Mass Spectrometry Profiling}, volume = {18}, ISSN = {1615-9861}, url
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= {http://dx.doi.org/10.1002/pmic.201700427}, DOI = {10.1002/pmic.201700427}, number
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= {11}, journal = {PROTEOMICS}, publisher = {Wiley}, author = {Connelly, Katelyn
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E. and Hedrick, Victoria and Paschoal Sobreira, Tiago Jose and Dykhuizen, Emily
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C. and Aryal, Uma K.}, year = {2018}, month = may}'
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- '@article{Kirkwood2013, title = {Characterization of Native Protein Complexes and
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Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics},
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volume = {12}, ISSN = {1535-9476}, url = {http://dx.doi.org/10.1074/mcp.M113.032367},
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DOI = {10.1074/mcp.m113.032367}, number = {12}, journal = {Molecular & Cellular
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Proteomics}, publisher = {Elsevier BV}, author = {Kirkwood, Kathryn J. and Ahmad, Yasmeen
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and Larance, Mark and Lamond, Angus I.}, year = {2013}, month = dec, pages = {3851–3873}}'
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- '@article{Larance2016, title = {Global Membrane Protein Interactome Analysis using
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In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling},
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volume = {15}, ISSN = {1535-9476}, url = {http://dx.doi.org/10.1074/mcp.O115.055467},
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+
DOI = {10.1074/mcp.o115.055467}, number = {7}, journal = {Molecular & Cellular
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Proteomics}, publisher = {Elsevier BV}, author = {Larance, Mark and Kirkwood, Kathryn
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J. and Tinti, Michele and Brenes Murillo, Alejandro and Ferguson, Michael A.J.
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and Lamond, Angus I.}, year = {2016}, month = jul, pages = {2476–2490}}'
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+
- '@article{Mallam2019, title = {Systematic Discovery of Endogenous Human Ribonucleoprotein
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+
Complexes}, volume = {29}, ISSN = {2211-1247}, url = {http://dx.doi.org/10.1016/j.celrep.2019.09.060},
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+
DOI = {10.1016/j.celrep.2019.09.060}, number = {5}, journal = {Cell Reports}, publisher
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= {Elsevier BV}, author = {Mallam, Anna L. and Sae-Lee, Wisath and Schaub, Jeffrey
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+
M. and Tu, Fan and Battenhouse, Anna and Jang, Yu Jin and Kim, Jonghwan and
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Wallingford, John B. and Finkelstein, Ilya J. and Marcotte, Edward M. and Drew, Kevin},
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year = {2019}, month = oct, pages = {1351--1368.e5}}'
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- '@article{Moutaoufik2019, title = {Rewiring of the Human Mitochondrial Interactome
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during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis},
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volume = {19}, ISSN = {2589-0042}, url = {http://dx.doi.org/10.1016/j.isci.2019.08.057},
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DOI = {10.1016/j.isci.2019.08.057}, journal = {iScience}, publisher = {Elsevier
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BV}, author = {Moutaoufik, Mohamed Taha and Malty, Ramy and Amin, Shahreen and
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Zhang, Qingzhou and Phanse, Sadhna and Gagarinova, Alla and Zilocchi, Mara and
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Hoell, Larissa and Minic, Zoran and Gagarinova, Maria and Aoki, Hiroyuki and
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Stockwell, Jocelyn and Jessulat, Matthew and Goebels, Florian and Broderick, Kirsten
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and Scott, Nichollas E. and Vlasblom, James and Musso, Gabriel and Prasad, Bhanu
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and Lamantea, Eleonora and Garavaglia, Barbara and Rajput, Alex and Murayama, Kei
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| 49 |
+
and Okazaki, Yasushi and Foster, Leonard J. and Bader, Gary D. and Cayabyab, Francisco
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| 50 |
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S. and Babu, Mohan}, year = {2019}, month = sep, pages = {1114–1132}}'
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| 51 |
+
- '@article{Wan2015, title = {Panorama of ancient metazoan macromolecular complexes},
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| 52 |
+
volume = {525}, ISSN = {1476-4687}, url = {http://dx.doi.org/10.1038/nature14877},
|
| 53 |
+
DOI = {10.1038/nature14877}, number = {7569}, journal = {Nature}, publisher = {Springer
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| 54 |
+
Science and Business Media LLC}, author = {Wan, Cuihong and Borgeson, Blake and
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+
Phanse, Sadhna and Tu, Fan and Drew, Kevin and Clark, Greg and Xiong, Xuejian
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| 56 |
+
and Kagan, Olga and Kwan, Julian and Bezginov, Alexandr and Chessman, Kyle and
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| 57 |
+
Pal, Swati and Cromar, Graham and Papoulas, Ophelia and Ni, Zuyao and Boutz, Daniel
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| 58 |
+
R. and Stoilova, Snejana and Havugimana, Pierre C. and Guo, Xinghua and Malty, Ramy
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| 59 |
+
H. and Sarov, Mihail and Greenblatt, Jack and Babu, Mohan and Derry, W. Brent
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| 60 |
+
and R. Tillier, Elisabeth and Wallingford, John B. and Parkinson, John and Marcotte, Edward
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M. and Emili, Andrew}, year = {2015}, month = sep, pages = {339–344}}'
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citation_apa:
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+
- Connelly, K. E., Hedrick, V., Paschoal Sobreira, T. J., Dykhuizen, E. C., & Aryal,
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| 64 |
+
U. K. (2018). Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry
|
| 65 |
+
Profiling. Proteomics, 18(11), e1700427. https://doi.org/10.1002/pmic.201700427
|
| 66 |
+
- ? Kirkwood, K. J., Ahmad, Y., Larance, M., & Lamond, A. I. (2013). Characterization
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| 67 |
+
of native protein complexes and protein isoform variation using size-fractionation-based
|
| 68 |
+
quantitative proteomics. Molecular & cellular proteomics
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| 69 |
+
: MCP, 12(12), 3851–3873. https://doi.org/10.1074/mcp.M113.032367
|
| 70 |
+
- ? Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. A.,
|
| 71 |
+
& Lamond, A. I. (2016). Global Membrane Protein Interactome Analysis using In
|
| 72 |
+
vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Molecular
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| 73 |
+
& cellular proteomics
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| 74 |
+
: MCP, 15(7), 2476–2490. https://doi.org/10.1074/mcp.O115.055467
|
| 75 |
+
- Mallam, A. L., Sae-Lee, W., Schaub, J. M., Tu, F., Battenhouse, A., Jang, Y. J.,
|
| 76 |
+
Kim, J., Wallingford, J. B., Finkelstein, I. J., Marcotte, E. M., & Drew, K. (2019).
|
| 77 |
+
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell reports,
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| 78 |
+
29(5), 1351–1368.e5. https://doi.org/10.1016/j.celrep.2019.09.060
|
| 79 |
+
- Moutaoufik, M. T., Malty, R., Amin, S., Zhang, Q., Phanse, S., Gagarinova, A., Zilocchi,
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| 80 |
+
M., Hoell, L., Minic, Z., Gagarinova, M., Aoki, H., Stockwell, J., Jessulat, M.,
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| 81 |
+
Goebels, F., Broderick, K., Scott, N. E., Vlasblom, J., Musso, G., Prasad, B., Lamantea,
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| 82 |
+
E., … Babu, M. (2019). Rewiring of the Human Mitochondrial Interactome during Neuronal
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| 83 |
+
Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. iScience,
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| 84 |
+
19, 1114–1132. https://doi.org/10.1016/j.isci.2019.08.057
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| 85 |
+
- Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan,
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| 86 |
+
O., Kwan, J., Bezginov, A., Chessman, K., Pal, S., Cromar, G., Papoulas, O., Ni,
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| 87 |
+
Z., Boutz, D. R., Stoilova, S., Havugimana, P. C., Guo, X., Malty, R. H., … Emili,
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| 88 |
+
A. (2015). Panorama of ancient metazoan macromolecular complexes. Nature, 525(7569),
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| 89 |
+
339–344. https://doi.org/10.1038/nature14877
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+
dataset_info:
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config_name: pairs
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features:
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- name: experiment_id
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dtype: string
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- name: uniprot_id1
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dtype: string
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- name: uniprot_id2
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dtype: string
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- name: elut_trace1
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sequence: int32
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- name: elut_trace2
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sequence: int32
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- name: label
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dtype:
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class_label:
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names:
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'0': neg
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'1': pos
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splits:
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- name: train
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num_bytes: 1412437731
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num_examples: 2496144
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- name: test
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num_bytes: 1531716983
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num_examples: 2769931
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download_size: 262731062
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dataset_size: 2944154714
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configs:
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- config_name: pairs
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data_files:
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- split: train
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path: pairs/train-*
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- split: test
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path: pairs/test-*
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---
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pairs/test-00000-of-00004.parquet
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pairs/test-00001-of-00004.parquet
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pairs/test-00002-of-00004.parquet
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pairs/test-00003-of-00004.parquet
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pairs/train-00000-of-00003.parquet
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pairs/train-00001-of-00003.parquet
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pairs/train-00002-of-00003.parquet
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