GitHub - Unusuala1l2e3x4/Extracting-ADEs-from-Medical-Forum-Posts: Identified ADEs and associated terms in an annotated corpus with Named Entity Recognition (NER) modeling with Flair and PyTorch. Fine-tuned pre-trained transformer models such as XLM-RoBERTa, SpanBERT, and Bio_ClinicalBERT. Achieved F1 scores of 0.73 and 0.77 for BIOES and BIO tagging models, respectively.

Project Report: project final report/SI630_Project_Final_Report.pdf

dataset info

original paper: https://www.sciencedirect.com/science/article/pii/S1532046415000532
1250 forum posts
2.5 MB when combined with metadata

Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
baseline_meddra_model_v2		baseline_meddra_model_v2
baseline_meddra_model_v3		baseline_meddra_model_v3
baseline_ner_model_v2		baseline_ner_model_v2
baseline_ner_model_v3		baseline_ner_model_v3
data_v1		data_v1
data_v2		data_v2
data_v3		data_v3
datasets/CADEC		datasets/CADEC
flair_ner_model_v1		flair_ner_model_v1
flair_ner_model_v2		flair_ner_model_v2
flair_ner_model_v2_Bio_ClinicalBERT		flair_ner_model_v2_Bio_ClinicalBERT
flair_ner_model_v2_finetune_glove		flair_ner_model_v2_finetune_glove
flair_ner_model_v2_no_rnn		flair_ner_model_v2_no_rnn
flair_ner_model_v2_spanbert-large-cased		flair_ner_model_v2_spanbert-large-cased
flair_ner_model_v2_xlm-roberta-large		flair_ner_model_v2_xlm-roberta-large
flair_ner_model_v3		flair_ner_model_v3
flair_ner_model_v3_Bio_ClinicalBERT		flair_ner_model_v3_Bio_ClinicalBERT
flair_ner_model_v3_finetune_glove		flair_ner_model_v3_finetune_glove
flair_ner_model_v3_no_rnn		flair_ner_model_v3_no_rnn
flair_ner_model_v3_spanbert-large-cased		flair_ner_model_v3_spanbert-large-cased
flair_ner_model_v3_xlm-roberta-large		flair_ner_model_v3_xlm-roberta-large
project final report		project final report
runs		runs
.gitattributes		.gitattributes
.gitignore		.gitignore
MedDRA_term_counts.csv		MedDRA_term_counts.csv
MedDRA_term_counts.xlsx		MedDRA_term_counts.xlsx
README.md		README.md
cadec_process_data_v1.ipynb		cadec_process_data_v1.ipynb
cadec_process_data_v2.ipynb		cadec_process_data_v2.ipynb
cadec_process_data_v3.ipynb		cadec_process_data_v3.ipynb
combine_reports.ipynb		combine_reports.ipynb
flair_cadec_v1.ipynb		flair_cadec_v1.ipynb
flair_cadec_v2.ipynb		flair_cadec_v2.ipynb
flair_cadec_v2_Bio_ClinicalBERT.ipynb		flair_cadec_v2_Bio_ClinicalBERT.ipynb
flair_cadec_v2_baseline.ipynb		flair_cadec_v2_baseline.ipynb
flair_cadec_v2_finetune_glove.ipynb		flair_cadec_v2_finetune_glove.ipynb
flair_cadec_v2_no_rnn.ipynb		flair_cadec_v2_no_rnn.ipynb
flair_cadec_v2_spanbert_large_cased.ipynb		flair_cadec_v2_spanbert_large_cased.ipynb
flair_cadec_v2_xlm-roberta-large.ipynb		flair_cadec_v2_xlm-roberta-large.ipynb
flair_cadec_v3.ipynb		flair_cadec_v3.ipynb
flair_cadec_v3_Bio_ClinicalBERT.ipynb		flair_cadec_v3_Bio_ClinicalBERT.ipynb
flair_cadec_v3_baseline.ipynb		flair_cadec_v3_baseline.ipynb
flair_cadec_v3_finetune_glove.ipynb		flair_cadec_v3_finetune_glove.ipynb
flair_cadec_v3_no_rnn.ipynb		flair_cadec_v3_no_rnn.ipynb
flair_cadec_v3_spanbert_large_cased.ipynb		flair_cadec_v3_spanbert_large_cased.ipynb
flair_cadec_v3_xlm_roberta_large.ipynb		flair_cadec_v3_xlm_roberta_large.ipynb
print_doc.ipynb		print_doc.ipynb

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