Chul Moon

Esteban Fernández Morales, Cong Zhang, Guanghua Xiao et al.

With the advanced imaging technology, digital pathology imaging of tumor tissue slides is becoming a routine clinical procedure for cancer diagnosis. This process produces massive imaging data that capture histological details in high resolution. Recent developments in deep-learning methods have enabled us to automatically detect and characterize the tumor regions in pathology images at large scale. From each identified tumor region, we extracted 30 well-defined descriptors that quantify its shape, geometry, and topology. We demonstrated how those descriptor features were associated with patient survival outcome in lung adenocarcinoma patients from the National Lung Screening Trial (n=143). Besides, a descriptor-based prognostic model was developed and validated in an independent patient cohort from The Cancer Genome Atlas Program program (n=318). This study proposes new insights into the relationship between tumor shape, geometrical, and topological features and patient prognosis. We provide software in the form of R code on GitHub: https://github.com/estfernandez/Slide_Image_Segmentation_and_Extraction.

Chul Moon, Qiwei Li, Guanghua Xiao

Tumor shape is a key factor that affects tumor growth and metastasis. This paper proposes a topological feature computed by persistent homology to characterize tumor progression from digital pathology and radiology images and examines its effect on the time-to-event data. The proposed topological features are invariant to scale-preserving transformation and can summarize various tumor shape patterns. The topological features are represented in functional space and used as functional predictors in a functional Cox proportional hazards model. The proposed model enables interpretable inference about the association between topological shape features and survival risks. Two case studies are conducted using consecutive 133 lung cancer and 77 brain tumor patients. The results of both studies show that the topological features predict survival prognosis after adjusting clinical variables, and the predicted high-risk groups have worse survival outcomes than the low-risk groups. Also, the topological shape features found to be positively associated with survival hazards are irregular and heterogeneous shape patterns, which are known to be related to tumor progression.

Noah Giansiracusa, Robert Giansiracusa, Chul Moon

The fingerprint classification problem is to sort fingerprints into pre-determined groups, such as arch, loop, and whorl. It was asserted in the literature that minutiae points, which are commonly used for fingerprint matching, are not useful for classification. We show that, to the contrary, near state-of-the-art classification accuracy rates can be achieved when applying topological data analysis (TDA) to 3-dimensional point clouds of oriented minutiae points. We also apply TDA to fingerprint ink-roll images, which yields a lower accuracy rate but still shows promise, particularly since the only preprocessing is cropping; moreover, combining the two approaches outperforms each one individually. These methods use supervised learning applied to persistent homology and allow us to explore feature selection on barcodes, an important topic at the interface between TDA and machine learning. We test our classification algorithms on the NIST fingerprint database SD-27.