Extraction of Explicit and Implicit Cause-Effect Relationships in Patient-Reported Diabetes-Related Tweets From 2017 to 2021: Deep Learning Approach

Using Social Media as a Source of Real-World Data for Pharmaceutical Drug Development and Regulatory Decision Making

INTRODUCTION

While pharmaceutical companies aim to leverage real-world data (RWD) to bridge the gap between clinical drug development and real-world patient outcomes, extant research has mainly focused on the use of social media in a post-approval safety-surveillance setting. Recent regulatory and technological developments indicate that social media may serve as a rich source to expand the evidence base to pre-approval and drug development activities. However, use cases related to drug development have been largely omitted, thereby missing some of the benefits of RWD. In addition, an applied end-to-end understanding of RWD rooted in both industry and regulations is lacking.

OBJECTIVE

We aimed to investigate how social media can be used as a source of RWD to support regulatory decision making and drug development in the pharmaceutical industry. We aimed to specifically explore the data pipeline and examine how social-media derived RWD can align with regulatory guidance from the US Food and Drug Administration and industry needs.

METHODS

A machine learning pipeline was developed to extract patient insights related to anticoagulants from X (Twitter) data. These findings were then analysed from an industry perspective, and complemented by interviews with professionals from a pharmaceutical company.

RESULTS

The analysis reveals several use cases where RWD derived from social media can be beneficial, particularly in generating hypotheses around patient and therapeutic area needs. We also note certain limitations of social media data, particularly around inferring causality.

CONCLUSIONS

Social media display considerable potential as a source of RWD for guiding efforts in pharmaceutical drug development and pre-approval settings. Although further regulatory guidance on the use of social media for RWD is needed to encourage its use, regulatory and technological developments are suggested to warrant at least exploratory uses for drug development.

exKidneyBERT: a language model for kidney transplant pathology reports and the crucial role of extended vocabularies

Background

Pathology reports contain key information about the patient's diagnosis as well as important gross and microscopic findings. These information-rich clinical reports offer an invaluable resource for clinical studies, but data extraction and analysis from such unstructured texts is often manual and tedious. While neural information retrieval systems (typically implemented as deep learning methods for natural language processing) are automatic and flexible, they typically require a large domain-specific text corpus for training, making them infeasible for many medical subdomains. Thus, an automated data extraction method for pathology reports that does not require a large training corpus would be of significant value and utility.

Objective

To develop a language model-based neural information retrieval system that can be trained on small datasets and validate it by training it on renal transplant-pathology reports to extract relevant information for two predefined questions: (1) "What kind of rejection does the patient show?"; (2) "What is the grade of interstitial fibrosis and tubular atrophy (IFTA)?"

Methods

Kidney BERT was developed by pre-training Clinical BERT on 3.4K renal transplant pathology reports and 1.5M words. Then, exKidneyBERT was developed by extending Clinical BERT's tokenizer with six technical keywords and repeating the pre-training procedure. This extended the model's vocabulary. All three models were fine-tuned with information retrieval heads.

Results

The model with extended vocabulary, exKidneyBERT, outperformed Clinical BERT and Kidney BERT in both questions. For rejection, exKidneyBERT achieved an 83.3% overlap ratio for antibody-mediated rejection (ABMR) and 79.2% for T-cell mediated rejection (TCMR). For IFTA, exKidneyBERT had a 95.8% exact match rate.

Conclusion

ExKidneyBERT is a high-performing model for extracting information from renal pathology reports. Additional pre-training of BERT language models on specialized small domains does not necessarily improve performance. Extending the BERT tokenizer's vocabulary library is essential for specialized domains to improve performance, especially when pre-training on small corpora.

Building causal models for finding actual causes of unmanned aerial vehicle failures

Finding actual causes of unmanned aerial vehicle (UAV) failures can be split into two main tasks: building causal models and performing actual causality analysis (ACA) over them. While there are available solutions in the literature to perform ACA, building comprehensive causal models is still an open problem. The expensive and time-consuming process of building such models, typically performed manually by domain experts, has hindered the widespread application of causality-based diagnosis solutions in practice. This study proposes a methodology based on natural language processing for automating causal model generation for UAVs. After collecting textual data from online resources, causal keywords are identified in sentences. Next, cause-effect phrases are extracted from sentences based on predefined dependency rules between tokens. Finally, the extracted cause-effect pairs are merged to form a causal graph, which we then use for ACA. To demonstrate the applicability of our framework, we scrape online text resources of Ardupilot, an open-source UAV controller software. Our evaluations using real flight logs show that the generated graphs can successfully be used to find the actual causes of unwanted events. Moreover, our hybrid cause-effect extraction module performs better than a purely deep-learning based tool (i.e., CiRA) by 32% in precision and 25% in recall in our Ardupilot use case.

Year 2022 in Medical Natural Language Processing: Availability of Language Models as a Step in the Democratization of NLP in the Biomedical Area

OBJECTIVES

To analyse the content of publications within the medical Natural Language Processing (NLP) domain in 2022.

METHODS

Automatic and manual preselection of publications to be reviewed, and selection of the best NLP papers of the year. Analysis of the important issues.

RESULTS

Three best papers have been selected. We also propose an analysis of the content of the NLP publications in 2022, stressing on some of the topics.

CONCLUSION

The main trend in 2022 is certainly related to the availability of large language models, especially those based on Transformers, and to their use by non-NLP researchers. This leads to the democratization of the NLP methods. We also observe the renewal of interest to languages other than English, the continuation of research on information extraction and prediction, the massive use of data from social media, and the consideration of needs and interests of patients.