Assessing equivalent and inverse change in genes between diverse experiments

Background: It is important to identify when two exposures impact a molecular marker (e.g., a gene's expression) in similar ways, for example, to learn that a new drug has a similar effect to an existing drug. Currently, statistically robust approaches for making comparisons of equivalence of effect sizes obtained from two independently run treatment vs. control comparisons have not been developed. Results: Here, we propose two approaches for evaluating the question of equivalence between effect sizes of two independent studies: a bootstrap test of the Equivalent Change Index (ECI), which we previously developed, and performing Two One-Sided t-Tests (TOST) on the difference in log-fold changes directly. The ECI of a gene is computed by taking the ratio of the effect size estimates obtained from the two different studies, weighted by the maximum of the two p-values and giving it a sign indicating if the effects are in the same or opposite directions, whereas TOST is a test of whether the difference in log-fold changes lies outside a region of equivalence. We used a series of simulation studies to compare the two tests on the basis of sensitivity, specificity, balanced accuracy, and F1-score. We found that TOST is not efficient for identifying equivalently changed gene expression values (F1-score = 0) because it is too conservative, while the ECI bootstrap test shows good performance (F1-score = 0.95). Furthermore, applying the ECI bootstrap test and TOST to publicly available microarray expression data from pancreatic cancer showed that, while TOST was not able to identify any equivalently or inversely changed genes, the ECI bootstrap test identified genes associated with pancreatic cancer. Additionally, when investigating publicly available RNAseq data of smoking vs. vaping, no equivalently changed genes were identified by TOST, but ECI bootstrap test identified genes associated with smoking. Conclusion: A bootstrap test of the ECI is a promising new statistical approach for determining if two diverse studies show similarity in the differential expression of genes and can help to identify genes which are similarly influenced by a specific treatment or exposure. The R package for the ECI bootstrap test is available at https://github.com/Hecate08/ECIbootstrap.

Expanding Horizons: The Realities of CAD, the Promise of Artificial Intelligence, and Machine Learning's Role in Breast Imaging beyond Screening Mammography

Artificial intelligence (AI) applications in mammography have gained significant popular attention; however, AI has the potential to revolutionize other aspects of breast imaging beyond simple lesion detection. AI has the potential to enhance risk assessment by combining conventional factors with imaging and improve lesion detection through a comparison with prior studies and considerations of symmetry. It also holds promise in ultrasound analysis and automated whole breast ultrasound, areas marked by unique challenges. AI's potential utility also extends to administrative tasks such as MQSA compliance, scheduling, and protocoling, which can reduce the radiologists' workload. However, adoption in breast imaging faces limitations in terms of data quality and standardization, generalizability, benchmarking performance, and integration into clinical workflows. Developing methods for radiologists to interpret AI decisions, and understanding patient perspectives to build trust in AI results, will be key future endeavors, with the ultimate aim of fostering more efficient radiology practices and better patient care.