NeotomaDB · tieandrews · Jun 28, 2023 · Jun 26, 2023 · Jun 26, 2023 · Jun 26, 2023
diff --git a/notebooks/2.2-NER-model-comparison.ipynb b/notebooks/2.2-NER-model-comparison.ipynb
diff --git a/reports/final/assets/data_review.png → reports/final_mds/assets/data_review.png b/reports/final/assets/data_review.png → reports/final_mds/assets/data_review.png
diff --git a/...s/finding-fossils-logo-symbol_highres.png → ...s/finding-fossils-logo-symbol_highres.png b/...s/finding-fossils-logo-symbol_highres.png → ...s/finding-fossils-logo-symbol_highres.png
diff --git a/reports/final_mds/assets/references.bib b/reports/final_mds/assets/references.bib
@@ -0,0 +1,179 @@
+@article{Goring,
+author = {Goring, Simon and Marsicek, Jeremiah and Ye, Shan and Williams, John and Meyers, Stephen and Peters, Shanan and Quinn, Daven and Schaen, Allen and Singer, Brad and Marcott, Shaun},
+year = {2021},
+month = {07},
+pages = {},
+title = {A Model Workflow for GeoDeepDive: Locating Pliocene and Pleistocene Ice-Rafted Debris},
+doi = {10.31223/X54312}
+}
+
+@article{NeotomaDB,
+author={Williams, J.W. and Grimm, E.G. and Blois, J. and Charles, D.F. and Davis, E. and Goring, S.J. and Graham, R. and Smith, A.J. and Anderson, M. and Arroyo-Cabrales, J. and Ashworth, A.C. and Betancourt, J.L. and Bills, B.W. and Booth, R.K. and Buckland, P. and Curry, B. and Giesecke, T. and Hausmann, S. and Jackson, S.T. and Latorre, C. and Nichols, J. and Purdum, T. and Roth, R.E. and Stryker, M. and Takahara, H.},
+year={2018},
+title={The Neotoma Paleoecology Database: A multi-proxy, international community-curated data resource},
+journal={Quaternary Research},
+volume={89},
+pages={156-177}
+}
+
+@misc{geodeepdive,
+  title = {xDD API},
+  author = {{Peters, S.E., I.A. Ross, T. Rekatsinas, M. Livny}},
+  year = {2021},
+  note = {Retrieved on May 9, 2023 from https://xdd.wisc.edu},
+  howpublished = {JSON},
+  license = {Apache License, Version 2.0},
+  url = {geodeepdive.org}
+}
+
+@misc{crossref,
+  title = {Crossref REST API},
+  author = {{Crossref}},
+  year = {2023},
+  url = {https://www.crossref.org/services/metadata-delivery/rest-api/},
+  note = {[Accessed May 9, 2023]},
+}
+
+@misc{alex2022raft,
+      title={RAFT: A Real-World Few-Shot Text Classification Benchmark},
+      author={Neel Alex and Eli Lifland and Lewis Tunstall and Abhishek Thakur and Pegah Maham and C. Jess Riedel and Emmie Hine and Carolyn Ashurst and Paul Sedille and Alexis Carlier and Michael Noetel and Andreas Stuhlmüller},
+      year={2022},
+      eprint={2109.14076},
+      archivePrefix={arXiv},
+      primaryClass={cs.CL}
+}
+
+@software{spacy,
+  publisher={Explosion},
+  title = {spaCy NER},
+  url = {https://spacy.io/api/entityrecognizer},
+  version = {3.5},
+  date = {2023-05-09}
+
+}
+
+@software{huggingface,
+  title = {HuggingFace},
+  url = {https://huggingface.co/},
+  date = {2023-05-09},
+  version = {4.29.1}
+}
+
+@misc{conneau2020unsupervised,
+      title={Unsupervised Cross-lingual Representation Learning at Scale}, 
+      author={Alexis Conneau and Kartikay Khandelwal and Naman Goyal and Vishrav Chaudhary and Guillaume Wenzek and Francisco Guzmán and Edouard Grave and Myle Ott and Luke Zettlemoyer and Veselin Stoyanov},
+      year={2020},
+      eprint={1911.02116},
+      archivePrefix={arXiv},
+      primaryClass={cs.CL}
+}
+
+@misc{ontonotes,
+  author={Ralph Weischedel, Martha Palmer, Mitchell Marcus, Eduard Hovy, Sameer Pradhan, Lance Ramshaw, Nianwen Xue, Ann Taylor, Jeff Kaufman, Michelle Franchini, Mohammed El-Bachouti, Robert Belvin, Ann Houston},
+  title={OntoNotes Release 5.0},
+  doi={	https://doi.org/10.35111/xmhb-2b84},
+  year={2013},
+  url={https://catalog.ldc.upenn.edu/LDC2013T19}
+}
+
+@software{LabelStudio,
+    title = {{Label Studio}: Data labeling software},
+    url = {https://github.com/heartexlabs/label-studio},
+    version = {1.7.3},
+    note={Open source software available from https://github.com/heartexlabs/label-studio},
+    date = {2023-05-09}
+}
+
+@article{inproceedings,
+  author = {Tran Thanh, Dien and Loc, Bui and Thai-Nghe, Nguyen},
+  year = {2019},
+  month = {11},
+  pages = {78-84},
+  title = {Article Classification using Natural Language Processing and Machine Learning},
+  doi = {10.1109/ACOMP.2019.00019}
+}
+
+@article{S-LSTM,
+  author  = {Guillaume Lample, Miguel Ballesteros, Sandeep Subramanian, Kazuya Kawakami, Chris Dyer},
+  title   = {Neural Architectures for Named Entity Recognition},
+  journal = {Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies},
+  year    = {2016},
+  month   = {3},
+  doi     = {http://dx.doi.org/10.18653/v1/N16-1030},
+}
+
+@article{unsupervised,
+    author = {Weber, Tobias and Kranzlmüller, Dieter and Fromm, Michael and de Sousa, Nelson Tavares},
+    title = "{Using supervised learning to classify metadata of research data by field of study}",
+    journal = {Quantitative Science Studies},
+    volume = {1},
+    number = {2},
+    pages = {525-550},
+    year = {2020},
+    month = {06},
+    issn = {2641-3337},
+    doi = {10.1162/qss_a_00049},
+    url = {https://doi.org/10.1162/qss\_a\_00049},
+    eprint = {https://direct.mit.edu/qss/article-pdf/1/2/525/1885831/qss\_a\_00049.pdf},
+}
+@inproceedings{chinchor-sundheim-1993-muc,
+    title = "{MUC}-5 Evaluation Metrics",
+    author = "Chinchor, Nancy  and
+      Sundheim, Beth",
+    booktitle = "Fifth Message Understanding Conference ({MUC}-5): Proceedings of a Conference Held in Baltimore, {M}aryland, August 25-27, 1993",
+    year = "1993",
+    url = "https://aclanthology.org/M93-1007",
+}
+
+@software{dash,
+  publisher={Plotly},
+  title = {Dash},
+  url = {https://dash.plotly.com},
+  version = {2.10.0},
+  date = {2023-05-25}
+
+}
+@Manual{shiny,
+  title = {shiny: Web Application Framework for R},
+  author = {Winston Chang and Joe Cheng and JJ Allaire and Carson Sievert and Barret Schloerke and Yihui Xie and Jeff Allen and Jonathan McPherson and Alan Dipert and Barbara Borges},
+  year = {2023},
+  note = {R package version 1.7.4.9002},
+  url = {https://shiny.rstudio.com/},
+}
+
+@misc{borealisai2023tutorial,
+  title = {Tutorial 17: Transformers III - Training},
+  author = {Borealis AI},
+  howpublished = {\url{https://www.borealisai.com/research-blogs/tutorial-17-transformers-iii-training/}},
+  year = {2023}
+}
+@misc{crossref,
+  title = {Crossref REST API},
+  author = {{Crossref}},
+  year = {2023},
+  url = {https://www.crossref.org/services/metadata-delivery/rest-api/},
+  note = {[Accessed May 9, 2023]},
+}
+
+@article{transformer-train-tips,
+  author       = {Martin Popel and
+                  Ondrej Bojar},
+  title        = {Training Tips for the Transformer Model},
+  journal      = {CoRR},
+  volume       = {abs/1804.00247},
+  year         = {2018},
+  url          = {http://arxiv.org/abs/1804.00247},
+  eprinttype    = {arXiv},
+  eprint       = {1804.00247},
+  timestamp    = {Mon, 13 Aug 2018 16:47:13 +0200},
+  biburl       = {https://dblp.org/rec/journals/corr/abs-1804-00247.bib},
+  bibsource    = {dblp computer science bibliography, https://dblp.org}
+}
+@article{roberta-ner-wang,
+    title={Application of Pre-training Models in Named Entity Recognition},
+    author={Yu Wang},
+    journal={2020 12th International Conference on Intelligent Human-Machine Systems and Cybernetics (IHMSC)},
+    year={2020},
+    volume={},
+    doi={10.1109/IHMSC49165.2020.00013}
+}
diff --git a/...nal/assets/relevance-model-comparison.png → ...mds/assets/relevance-model-comparison.png b/...nal/assets/relevance-model-comparison.png → ...mds/assets/relevance-model-comparison.png
diff --git a/reports/final/finding-fossils-final.pdf → ...s/final_mds/finding-fossils-final-mds.pdf b/reports/final/finding-fossils-final.pdf → ...s/final_mds/finding-fossils-final-mds.pdf