Update README.md

README.md

@@ -71,11 +71,11 @@ Code: https://github.com/chufangao/ctod
 
 Descriptions:
 
-- human_labels contains the manually annotated subset. We follow the same rule-based termination of incomplete status and p-value < 0.05 as in the automated labeling step to remove the easy cases. The additional metadata is taken from studies.txt from CTTI.
-- linkage contains the weakly linked trials as predicted based on text similarity. E.g. if a similar trial is found in phase 3 from a trial in phase 2, then they are considered "linked". We use a reranking method after the initial text similarity retrieval to further refine relevance. "connected next phase" implies similar text similarity AND positive reranking. "weakly connected next phase" implies similar text similarity BUT negative reranking.
-- news contains the top 10 most similar (cosine text similarity) headlines to the trial, 0 being the most similar. "valid_sentiments" is a list of sentiments from a binary sentiment classifier, and "mode" is the most popular sentiment.
-- phase1_CTO_preds, phase2_CTO_preds, phase3_CTO_preds contain phase-specific CTO predictions. Note that each phase may have different columns due to the phase-specific thresholding of weak supervision sources. Some columns are duplicated (e.g. gpt1, gpt2) for dynamic programming purposes. Duplicated columns may be ignored in practice. The most relevant columns are ["nct_id", "pred", "pred_proba"], where "pred_proba" is the predicted probability of trial success.
-- pubmed_gpt contains linked GPT predictions on related trial publications
-- stocks_and_amendents contains scraped stock price Slope from a 5-day moving average. The Slope is calculated from: (trial completion date, trial completion date + 7 days). This file also contains the scraped number of amendments made to the trial on clinicaltrials.gov.
+- **human_labels** contains the manually annotated subset. We follow the same rule-based termination of incomplete status and p-value < 0.05 as in the automated labeling step to remove the easy cases. The additional metadata is taken from studies.txt from CTTI.
+- **linkage** contains the weakly linked trials as predicted based on text similarity. E.g. if a similar trial is found in phase 3 from a trial in phase 2, then they are considered "linked". We use a reranking method after the initial text similarity retrieval to further refine relevance. "connected next phase" implies similar text similarity AND positive reranking. "weakly connected next phase" implies similar text similarity BUT negative reranking.
+- **news** contains the top 10 most similar (cosine text similarity) headlines to the trial, 0 being the most similar. "valid_sentiments" is a list of sentiments from a binary sentiment classifier, and "mode" is the most popular sentiment.
+- **phase1_CTO_preds**, **phase2_CTO_preds**, **phase3_CTO_preds** contain phase-specific CTO predictions. Note that each phase may have different columns due to the phase-specific thresholding of weak supervision sources. Some columns are duplicated (e.g. gpt1, gpt2) for dynamic programming purposes. Duplicated columns may be ignored in practice. The most relevant columns are ["nct_id", "pred", "pred_proba"], where "pred_proba" is the predicted probability of trial success.
+- **pubmed_gpt** contains linked GPT predictions on related trial publications
+- **stocks_and_amendents** contains scraped stock price Slope from a 5-day moving average. The Slope is calculated from: (trial completion date, trial completion date + 7 days). This file also contains the scraped number of amendments made to the trial on clinicaltrials.gov.
 
 CTTI.zip is from: Aggregate Analysis of ClinicalTrials.gov (AACT) Database. Clinical Trials Transformation Initiative (CTTI). Available at: https://aact.ctti-clinicaltrials.org/ (Accessed: 10/2024).