Selected Publications

An implicit goal in works on deep generative models is that such models should be able to generate novel examples that were not previously seen in the training data. In this paper, we investigate to what extent this property holds for widely employed variational autoencoder (VAE) architectures. VAEs maximize a lower bound on the log marginal likelihood, which implies that they will in principle overfit the training data when provided with a sufficiently expressive decoder. In the limit of an infinite capacity decoder, the optimal generative model is a uniform mixture over the training data. More generally, an optimal decoder should output a weighted average over the examples in the training data, where the magnitude of the weights is determined by the proximity in the latent space. This leads to the hypothesis that, for a sufficiently high capacity encoder and decoder, the VAE decoder will perform nearest-neighbor matching according to the coordinates in the latent space. To test this hypothesis, we investigate generalization on the MNIST dataset. We consider both generalization to new examples of previously seen classes, and generalization to the classes that were withheld from the training set. In both cases, we find that reconstructions are closely approximated by nearest neighbors for higher-dimensional parameterizations. When generalizing to unseen classes however, lower-dimensional parameterizations offer a clear advantage.
In CRACT, 2018

We describe a new multiresolution ‘nested encoder-decoder’ convolutional network architecture and use it to annotate morphological patterns in reflectance confocal microscopy (RCM) images of human skin for aiding cancer diagnosis. Skin cancers are the most common types of cancers, melanoma being the deadliest among them. RCM is an effective, non-invasive pre-screening tool for skin cancer diagnosis, with the required cellular resolution. However, images are complex, low-contrast, and highly variable, so that clinicians require months to years of expert-level training to be able to make accurate assessments. In this paper, we address classifying 4 key clinically important structural/textural patterns in RCM images. The occurrence and morphology of these patterns are used by clinicians for diagnosis of melanomas. The large size of RCM images, the large variance of pattern size, the large-scale range over which patterns appear, the class imbalance in collected images, and the lack of fully-labeled images all make this a challenging problem to address, even with automated machine learning tools. We designed a novel nested U-net architecture to cope with these challenges, and a selective loss function to handle partial labeling. Trained and tested on 56 melanoma-suspicious, partially labeled, 12k x 12k pixel images, our network automatically annotated diagnostic patterns with high sensitivity and specificity, providing consistent labels for unlabeled sections of the test images. Providing such annotation will aid clinicians in achieving diagnostic accuracy, and perhaps more important, dramatically facilitate clinical training, thus enabling much more rapid adoption of RCM into widespread clinical use process. In addition, our adaptation of U-net architecture provides an intrinsically multiresolution deep network that may be useful in other challenging biomedical image analysis applications. First two authors share first authorship.
MICCAI, 2018

Recent Publications

More Publications

. Can VAEs generate novel examples?. In CRACT, 2018.

PDF Poster Slides

. A Multiresolution Deep Learning Framework for Automated Annotation of Reflectance Confocal Microscopy Images. Microscopy Histopathology and Analytics, 2018.

Preprint PDF

. Delineation of Skin Strata in Reflectance Confocal Microscopy Images With Recurrent Convolutional Networks. In CVPRW, 2017.

PDF Slides

. Delineation of Skin Strata in Reflectance Confocal Microscopy Images using Recurrent Convolutional Networks with Toeplitz Attention. In ML4H, 2017.

Preprint Poster

. Deep learning based classification of morphological patterns in reflectance confocal microscopy to guide noninvasive diagnosis of melanocytic lesions. In SPIE Photonics West BioS 2017, 2017.

Slides

. Unsupervised delineation of stratum corneum using reflectance confocal microscopy and spectral clustering. In SRT, 2016.

PDF

. Expert diagnosis of plus disease in retinopathy of prematurity from computer-based image analysis. In JAMA Opthalmology, 2016.

PDF

. Computer-Based Image Analysis for Plus Disease Diagnosis in Retinopathy of Prematurity: Performance of the “i-ROP” System and Image Features Associated With Expert Diagnosis. In TVST, 2015.

PDF

Contact

  • alican@ece.neu.edu
  • Room 505, ISEC Building Interdisciplinary Science & Engineering Complex 805 Columbus Ave, Boston, MA 02120