Rajath Elias Soans

Justin Namuk Kim, Yiqiao Liu, Rajath Soans et al.

Accurate segmentation of longitudinal CT scans is important for monitoring tumor progression and evaluating treatment responses. However, existing 3D segmentation models solely focus on spatial information. To address this gap, we propose OmniMamba4D, a novel segmentation model designed for 4D medical images (3D images over time). OmniMamba4D utilizes a spatio-temporal tetra-orientated Mamba block to effectively capture both spatial and temporal features. Unlike traditional 3D models, which analyze single-time points, OmniMamba4D processes 4D CT data, providing comprehensive spatio-temporal information on lesion progression. Evaluated on an internal dataset comprising of 3,252 CT scans, OmniMamba4D achieves a competitive Dice score of 0.682, comparable to state-of-the-arts (SOTA) models, while maintaining computational efficiency and better detecting disappeared lesions. This work demonstrates a new framework to leverage spatio-temporal information for longitudinal CT lesion segmentation.

Ruiwen Ding, Lin Li, Rajath Soans et al.

Inflammatory bowel disease (IBD) involves chronic inflammation of the digestive tract, with treatment options often burdened by adverse effects. Identifying biomarkers for personalized treatment is crucial. While immune cells play a key role in IBD, accurately identifying ulcer regions in whole slide images (WSIs) is essential for characterizing these cells and exploring potential therapeutics. Multiple instance learning (MIL) approaches have advanced WSI analysis but they lack spatial context awareness. In this work, we propose a weakly-supervised model called DomainGCN that employs a graph convolution neural network (GCN) and incorporates domain-specific knowledge of ulcer features, specifically, the presence of epithelium, lymphocytes, and debris for WSI-level ulcer prediction in IBD. We demonstrate that DomainGCN outperforms various state-of-the-art (SOTA) MIL methods and show the added value of domain knowledge.

Rajath Soans, Alexa Gleason, Tosha Shah et al.

In this paper, we propose a deep learning-based method to segment the skeletal structures in the micro-CT images of Dutch-Belted rabbit fetuses which can assist in the assessment of drug-induced skeletal abnormalities as a required study in developmental and reproductive toxicology (DART). Our strategy leverages sub-optimal segmentation labels of 22 skull bones from 26 micro-CT volumes and maps them to 250 unlabeled volumes on which a deep CNN-based segmentation model is trained. In the experiments, our model was able to achieve an average Dice Similarity Coefficient (DSC) of 0.89 across all bones on the testing set, and 14 out of the 26 skull bones reached average DSC >0.93. Our next steps are segmenting the whole body followed by developing a model to classify abnormalities.

Sivaramakrishnan Sankarapandian, Saul Kohn, Vaughn Spurrier et al.

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.

Julianna D. Ianni, Rajath E. Soans, Sivaramakrishnan Sankarapandian et al.

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.