# CCS Explorer: Relevance Prediction, Extractive Summarization, and Named Entity Recognition from Clinical Cohort Studies

arXiv: https://arxiv.org/abs/2211.00201 · HTML: https://mlsanity.com/paper/2211.00201/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 65 references that are in the map.
- First posted on arXiv 1 Nov 2022.

## Builds on (most cited first, 18 of 18)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [PEGASUS: Pre-training with Extracted Gap-sentences for Abstractive Summarization](https://mlsanity.com/paper/1912.08777/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [On Faithfulness and Factuality in Abstractive Summarization](https://mlsanity.com/paper/2005.00661/) (2020)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [Extractive Summarization as Text Matching](https://mlsanity.com/paper/2004.08795/) (2020)
- [Bottom-Up Abstractive Summarization](https://mlsanity.com/paper/1808.10792/) (2018)
- [Fine-tune BERT for Extractive Summarization](https://mlsanity.com/paper/1903.10318/) (2019)
- [A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature](https://mlsanity.com/paper/1806.04185/) (2018)
- [Inferring Which Medical Treatments Work from Reports of Clinical Trials](https://mlsanity.com/paper/1904.01606/) (2019)
- [Evidence Inference 2.0: More Data, Better Models](https://mlsanity.com/paper/2005.04177/) (2020)
- [Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations](https://mlsanity.com/paper/2010.03550/) (2020)

## Built on by (most cited first, 2 of 2)

- [Measuring Risk of Bias in Biomedical Reports: The RoBBR Benchmark](https://mlsanity.com/paper/2411.18831/) (2024)
- [Faithful by Design: Evaluating and Improving LLM-Generated Clinical Trial Summaries for Multi-Stakeholder Audiences](https://mlsanity.com/paper/2607.09932/) (2026)

## Abstract (arXiv)

Clinical Cohort Studies (CCS), such as randomized clinical trials, are a great source of documented clinical research. Ideally, a clinical expert inspects these articles for exploratory analysis ranging from drug discovery for evaluating the efficacy of existing drugs in tackling emerging diseases to the first test of newly developed drugs. However, more than 100 articles are published daily on a single prevalent disease like COVID-19 in PubMed. As a result, it can take days for a physician to find articles and extract relevant information. Can we develop a system to sift through the long list of these articles faster and document the crucial takeaways from each of these articles? In this work, we propose CCS Explorer, an end-to-end system for relevance prediction of sentences, extractive summarization, and patient, outcome, and intervention entity detection from CCS. CCS Explorer is packaged in a web-based graphical user interface where the user can provide any disease name. CCS Explorer then extracts and aggregates all relevant information from articles on PubMed based on the results of an automatically generated query produced on the back-end. For each task, CCS Explorer fine-tunes pre-trained language representation models based on transformers with additional layers. The models are evaluated using two publicly available datasets. CCS Explorer obtains a recall of 80.2%, AUC-ROC of 0.843, and an accuracy of 88.3% on sentence relevance prediction using BioBERT and achieves an average Micro F1-Score of 77.8% on Patient, Intervention, Outcome detection (PIO) using PubMedBERT. Thus, CCS Explorer can reliably extract relevant information to summarize articles, saving time by ~ 660×.