A Pathology Deep Learning System Capable of Triage of Melanoma Specimens Utilizing Dermatopathologist Consensus as Ground Truth

Although melanoma occurs more rarely than several other skin cancers, patients' long term survival rate is extremely low if the diagnosis is missed. Diagnosis is complicated by a high discordance rate among pathologists when distinguishing between melanoma and benign melanocytic lesions. A tool that allows pathology labs to sort and prioritize melanoma cases in their workflow could improve turnaround time by prioritizing challenging cases and routing them directly to the appropriate subspecialist. We present a pathology deep learning system (PDLS) that performs hierarchical classification of digitized whole slide image (WSI) specimens into six classes defined by their morphological characteristics, including classification of "Melanocytic Suspect" specimens likely representing melanoma or severe dysplastic nevi. We trained the system on 7,685 images from a single lab (the reference lab), including the the largest set of triple-concordant melanocytic specimens compiled to date, and tested the system on 5,099 images from two distinct validation labs. We achieved Area Underneath the ROC Curve (AUC) values of 0.93 classifying Melanocytic Suspect specimens on the reference lab, 0.95 on the first validation lab, and 0.82 on the second validation lab. We demonstrate that the PDLS is capable of automatically sorting and triaging skin specimens with high sensitivity to Melanocytic Suspect cases and that a pathologist would only need between 30% and 60% of the caseload to address all melanoma specimens.

$β$-Annealed Variational Autoencoder for glitches

Gravitational wave detectors such as LIGO and Virgo are susceptible to various types of instrumental and environmental disturbances known as glitches which can mask and mimic gravitational waves. While there are 22 classes of non-Gaussian noise gradients currently identified, the number of classes is likely to increase as these detectors go through commissioning between observation runs. Since identification and labelling new noise gradients can be arduous and time-consuming, we propose $\beta$-Annelead VAEs to learn representations from spectograms in an unsupervised way. Using the same formulation as \cite{alemi2017fixing}, we view Bottleneck-VAEs~cite{burgess2018understanding} through the lens of information theory and connect them to $\beta$-VAEs~cite{higgins2017beta}. Motivated by this connection, we propose an annealing schedule for the hyperparameter $\beta$ in $\beta$-VAEs which has advantages of: 1) One fewer hyperparameter to tune, 2) Better reconstruction quality, while producing similar levels of disentanglement.

Augmenting the Pathology Lab: An Intelligent Whole Slide Image Classification System for the Real World

Standard of care diagnostic procedure for suspected skin cancer is microscopic examination of hematoxylin \& eosin stained tissue by a pathologist. Areas of high inter-pathologist discordance and rising biopsy rates necessitate higher efficiency and diagnostic reproducibility. We present and validate a deep learning system which classifies digitized dermatopathology slides into 4 categories. The system is developed using 5,070 images from a single lab, and tested on an uncurated set of 13,537 images from 3 test labs, using whole slide scanners manufactured by 3 different vendors. The system's use of deep-learning-based confidence scoring as a criterion to consider the result as accurate yields an accuracy of up to 98\%, and makes it adoptable in a real-world setting. Without confidence scoring, the system achieved an accuracy of 78\%. We anticipate that our deep learning system will serve as a foundation enabling faster diagnosis of skin cancer, identification of cases for specialist review, and targeted diagnostic classifications.