Chloe Min Seo Choi

Jue Jiang, Chloe Min Seo Choi, Maria Thor et al.

Background: Voxel-based analysis (VBA) for population level radiotherapy (RT) outcomes modeling requires topology preserving inter-patient deformable image registration (DIR) that preserves tumors on moving images while avoiding unrealistic deformations due to tumors occurring on fixed images. Purpose: We developed a tumor-aware recurrent registration (TRACER) deep learning (DL) method and evaluated its suitability for VBA. Methods: TRACER consists of encoder layers implemented with stacked 3D convolutional long short term memory network (3D-CLSTM) followed by decoder and spatial transform layers to compute dense deformation vector field (DVF). Multiple CLSTM steps are used to compute a progressive sequence of deformations. Input conditioning was applied by including tumor segmentations with 3D image pairs as input channels. Bidirectional tumor rigidity, image similarity, and deformation smoothness losses were used to optimize the network in an unsupervised manner. TRACER and multiple DL methods were trained with 204 3D CT image pairs from patients with lung cancers (LC) and evaluated using (a) Dataset I (N = 308 pairs) with DL segmented LCs, (b) Dataset II (N = 765 pairs) with manually delineated LCs, and (c) Dataset III with 42 LC patients treated with RT. Results: TRACER accurately aligned normal tissues. It best preserved tumors, blackindicated by the smallest tumor volume difference of 0.24\%, 0.40\%, and 0.13 \% and mean square error in CT intensities of 0.005, 0.005, 0.004, computed between original and resampled moving image tumors, for Datasets I, II, and III, respectively. It resulted in the smallest planned RT tumor dose difference computed between original and resampled moving images of 0.01 Gy and 0.013 Gy when using a female and a male reference.

Jue Jiang, Aneesh Rangnekar, Chloe Min Seo Choi et al.

Pretraining vision transformers (ViT) with attention guided masked image modeling (MIM) has shown to increase downstream accuracy for natural image analysis. Hierarchical shifted window (Swin) transformer, often used in medical image analysis cannot use attention guided masking as it lacks an explicit [CLS] token, needed for computing attention maps for selective masking. We thus enhanced Swin with semantic class attention. We developed a co-distilled Swin transformer that combines a noisy momentum updated teacher to guide selective masking for MIM. Our approach called \textsc{s}e\textsc{m}antic \textsc{a}ttention guided co-distillation with noisy teacher \textsc{r}egularized Swin \textsc{T}rans\textsc{F}ormer (SMARTFormer) was applied for analyzing 3D computed tomography datasets with lung nodules and malignant lung cancers (LC). We also analyzed the impact of semantic attention and noisy teacher on pretraining and downstream accuracy. SMARTFormer classified lesions (malignant from benign) with a high accuracy of 0.895 of 1000 nodules, predicted LC treatment response with accuracy of 0.74, and achieved high accuracies even in limited data regimes. Pretraining with semantic attention and noisy teacher improved ability to distinguish semantically meaningful structures such as organs in a unsupervised clustering task and localize abnormal structures like tumors. Code, models will be made available through GitHub upon paper acceptance.