Fast whole-slide cartography in colon cancer histology using superpixels and CNN classification

Whole-slide-image cartography is the process of automatically detecting and outlining different tissue types in digitized histological specimen. This semantic segmentation provides a basis for many follow-up analyses and can potentially guide subsequent medical decisions. Due to their large size, whole-slide-images typically have to be divided into smaller patches which are then analyzed individually using machine learning-based approaches. Thereby, local dependencies of image regions get lost and since a whole-slide-image comprises many thousands of such patches this process is inherently slow. We propose to subdivide the image into coherent regions prior to classification by grouping visually similar adjacent image pixels into larger segments, i.e. superpixels. Afterwards, only a random subset of patches per superpixel is classified and patch labels are combined into a single superpixel label. The algorithm has been developed and validated on a dataset of 159 hand-annotated whole-slide-images of colon resections and its performance has been compared to a standard patch-based approach. The algorithm shows an average speed-up of 41% on the test data and the overall accuracy is increased from 93.8% to 95.7%. We additionally propose a metric for identifying superpixels with an uncertain classification so they can be excluded from further analysis. Finally, we evaluate two potential medical applications, namely tumor area estimation including tumor invasive margin generation and tumor composition analysis.

Progressive Stochastic Binarization of Deep Networks

A plethora of recent research has focused on improving the memory footprint and inference speed of deep networks by reducing the complexity of (i) numerical representations (for example, by deterministic or stochastic quantization) and (ii) arithmetic operations (for example, by binarization of weights). We propose a stochastic binarization scheme for deep networks that allows for efficient inference on hardware by restricting itself to additions of small integers and fixed shifts. Unlike previous approaches, the underlying randomized approximation is progressive, thus permitting an adaptive control of the accuracy of each operation at run-time. In a low-precision setting, we match the accuracy of previous binarized approaches. Our representation is unbiased - it approaches continuous computation with increasing sample size. In a high-precision regime, the computational costs are competitive with previous quantization schemes. Progressive stochastic binarization also permits localized, dynamic accuracy control within a single network, thereby providing a new tool for adaptively focusing computational attention. We evaluate our method on networks of various architectures, already pretrained on ImageNet. With representational costs comparable to previous schemes, we obtain accuracies close to the original floating point implementation. This includes pruned networks, except the known special case of certain types of separated convolutions. By focusing computational attention using progressive sampling, we reduce inference costs on ImageNet further by a factor of up to 33% (before network pruning).