AI Accelerated Human-in-the-loop Structuring of Radiology Reports.

Rule-based Natural Language Processing (NLP) pipelines depend on robust domain knowledge. Given the long tail of important terminology in radiology reports, it is not uncommon for standard approaches to miss items critical for understanding the image. AI techniques can accelerate the concept expansion and phrasal grouping tasks to efficiently create a domain specific lexicon ontology for structuring reports. Using Chest X-ray (CXR) reports as an example, we demonstrate that with robust vocabulary, even a simple NLP pipeline can extract 83 directly mentioned abnormalities (Ave. recall=93.83%, precision=94.87%) and 47 abnormality/normality descriptions of key anatomies. The richer vocabulary enables identification of additional label mentions in 10 out of 13 labels (compared to baseline methods). Furthermore, it captures expert insight into critical differences between observed and inferred descriptions, and image quality issues in reports. Finally, we show how the CXR ontology can be used to anatomically structure labeled output.

Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2.

Scientific progress depends on formulating testable hypotheses informed by the literature. In many domains, however, this model is strained because the number of research papers exceeds human readability. Here, we developed computational assistance to analyze the biomedical literature by reading PubMed abstracts to suggest new hypotheses. The approach was tested experimentally on the tumor suppressor p53 by ranking its most likely kinases, based on all available abstracts. Many of the best-ranked kinases were found to bind and phosphorylate p53 (P value = 0.005), suggesting six likely p53 kinases so far. One of these, NEK2, was studied in detail. A known mitosis promoter, NEK2 was shown to phosphorylate p53 at Ser315 in vitro and in vivo and to functionally inhibit p53. These bona fide validations of text-based predictions of p53 phosphorylation, and the discovery of an inhibitory p53 kinase of pharmaceutical interest, suggest that automated reasoning using a large body of literature can generate valuable molecular hypotheses and has the potential to accelerate scientific discovery.