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$\alpha$-Shape Sampler Paper Results

Code to reproduce analyses and results provided in the $\alpha$-shape sampler paper beyond what is given in the R package.

Directory Contents

The list of directories and their corresponding purpose in this repository include:

  • neutrophilML has all machine learning experiments for replication of analyses with the neutrophil data, including calculating shape characteristics and performing dimensionality reduction in python. In particular, we show how to implement the manifold regularized autoencoder (MRAE).
  • teeth_demo contains a subsampled dataset of primate mandibular molars and a notebook demonstrating how generate a new tooth.
  • mask_to_complex contains a notebook for converting a binary mask to a simplicial complex and vice versa in R.

Relevant Citations

D. Bhaskar, D. Lee, H. Knútsdóttir, C. Tan, M. Zhang, P. Dean, C. Roskelley, and L. Keshet. A methodology for morphological feature extraction and unsupervised cell classification. bioRxiv. 623793.

E.T. Winn-Nuñez, H. Witt, D. Bhaskar, R.Y. Huang, I.Y. Wong, J.S. Reichner, and L. Crawford. Generative modeling of biological shapes and images using a probabilistic $\alpha$-shape sampler. bioRxiv.