Browsing by Author "Biostatistics & Health Data Science, School of Medicine"

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    AI in Medical Imaging Informatics: Current Challenges and Future Directions
    (IEEE, 2020-07) Panayides, Andreas S.; Amini, Amir; Filipovic, Nenad D.; Sharma, Ashish; Tsaftaris, Sotirios A.; Young, Alistair; Foran, David; Do, Nhan; Golemati, Spyretta; Kurc, Tahsin; Huang, Kun; Nikita, Konstantina S.; Veasey, Ben P.; Zervakis, Michalis; Saltz, Joel H.; Pattichis, Constantinos S.; Biostatistics & Health Data Science, School of Medicine
    This paper reviews state-of-the-art research solutions across the spectrum of medical imaging informatics, discusses clinical translation, and provides future directions for advancing clinical practice. More specifically, it summarizes advances in medical imaging acquisition technologies for different modalities, highlighting the necessity for efficient medical data management strategies in the context of AI in big healthcare data analytics. It then provides a synopsis of contemporary and emerging algorithmic methods for disease classification and organ/ tissue segmentation, focusing on AI and deep learning architectures that have already become the de facto approach. The clinical benefits of in-silico modelling advances linked with evolving 3D reconstruction and visualization applications are further documented. Concluding, integrative analytics approaches driven by associate research branches highlighted in this study promise to revolutionize imaging informatics as known today across the healthcare continuum for both radiology and digital pathology applications. The latter, is projected to enable informed, more accurate diagnosis, timely prognosis, and effective treatment planning, underpinning precision medicine.
  • Thumbnail Image
    Item
    An Automated Line-of-Therapy Algorithm for Adults With Metastatic Non-Small Cell Lung Cancer: Validation Study Using Blinded Manual Chart Review
    (JMIR Publications, 2021-10-12) Meng, Weilin; Mosesso, Kelly M.; Lane, Kathleen A.; Roberts, Anna R.; Griffith, Ashley; Ou, Wanmei; Dexter, Paul R.; Biostatistics & Health Data Science, School of Medicine
    Background: Extraction of line-of-therapy (LOT) information from electronic health record and claims data is essential for determining longitudinal changes in systemic anticancer therapy in real-world clinical settings. Objective: The aim of this retrospective cohort analysis is to validate and refine our previously described open-source LOT algorithm by comparing the output of the algorithm with results obtained through blinded manual chart review. Methods: We used structured electronic health record data and clinical documents to identify 500 adult patients treated for metastatic non-small cell lung cancer with systemic anticancer therapy from 2011 to mid-2018; we assigned patients to training (n=350) and test (n=150) cohorts, randomly divided proportional to the overall ratio of simple:complex cases (n=254:246). Simple cases were patients who received one LOT and no maintenance therapy; complex cases were patients who received more than one LOT and/or maintenance therapy. Algorithmic changes were performed using the training cohort data, after which the refined algorithm was evaluated against the test cohort. Results: For simple cases, 16 instances of discordance between the LOT algorithm and chart review prerefinement were reduced to 8 instances postrefinement; in the test cohort, there was no discordance between algorithm and chart review. For complex cases, algorithm refinement reduced the discordance from 68 to 62 instances, with 37 instances in the test cohort. The percentage agreement between LOT algorithm output and chart review for patients who received one LOT was 89% prerefinement, 93% postrefinement, and 93% for the test cohort, whereas the likelihood of precise matching between algorithm output and chart review decreased with an increasing number of unique regimens. Several areas of discordance that arose from differing definitions of LOTs and maintenance therapy could not be objectively resolved because of a lack of precise definitions in the medical literature. Conclusions: Our findings identify common sources of discordance between the LOT algorithm and clinician documentation, providing the possibility of targeted algorithm refinement.
  • Thumbnail Image
    Item
    How an effective response to post‐acute sequelae of SARS‐CoV‐2 infection (PASC) relies on nursing research
    (Wiley, 2021-10) Pinto, Melissa D.; Downs, Charles A.; Lambert, Natalie; Burton, Candace W.; Biostatistics & Health Data Science, School of Medicine
  • Thumbnail Image
    Item
    Identifying Gene–Environment Interactions With Robust Marginal Bayesian Variable Selection
    (Frontiers Media, 2021-12-08) Lu, Xi; Fan, Kun; Ren, Jie; Wu, Cen; Biostatistics & Health Data Science, School of Medicine
    In high-throughput genetics studies, an important aim is to identify gene-environment interactions associated with the clinical outcomes. Recently, multiple marginal penalization methods have been developed and shown to be effective in G×E studies. However, within the Bayesian framework, marginal variable selection has not received much attention. In this study, we propose a novel marginal Bayesian variable selection method for G×E studies. In particular, our marginal Bayesian method is robust to data contamination and outliers in the outcome variables. With the incorporation of spike-and-slab priors, we have implemented the Gibbs sampler based on Markov Chain Monte Carlo (MCMC). The proposed method outperforms a number of alternatives in extensive simulation studies. The utility of the marginal robust Bayesian variable selection method has been further demonstrated in the case studies using data from the Nurse Health Study (NHS). Some of the identified main and interaction effects from the real data analysis have important biological implications.
  • Thumbnail Image
    Item
    TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery
    (BMC, 2021-10-25) Liu, Yusong; Ye, Xiufen; Yu, Christina Y.; Shao, Wei; Hou, Jie; Feng, Weixing; Zhang, Jie; Huang, Kun; Biostatistics & Health Data Science, School of Medicine
    Background: Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. However, these algorithms have limitations such as insufficient granularity and unbalanced module size, which prevent full acquisition of knowledge from data mining. In addition, it is difficult to incorporate prior knowledge in current co-expression module detection algorithms. Results: In this paper, we propose a novel module detection algorithm based on topology potential and spectral clustering algorithm to detect co-expressed modules in gene co-expression networks. By testing on TCGA data, our novel method can provide more complete coverage of genes, more balanced module size and finer granularity than current methods in detecting modules with significant overall survival difference. In addition, the proposed algorithm can identify modules by incorporating prior knowledge. Conclusion: In summary, we developed a method to obtain as much as possible information from networks with increased input coverage and the ability to detect more size-balanced and granular modules. In addition, our method can integrate data from different sources. Our proposed method performs better than current methods with complete coverage of input genes and finer granularity. Moreover, this method is designed not only for gene co-expression networks but can also be applied to any general fully connected weighted network.