DCE-FORMER: A Transformer-based Model With Mutual Information And Frequency-based Loss Functions For Early And Late Response Prediction In Prostate DCE-MRI

Dynamic Contrast Enhanced Magnetic Resonance Imaging aids in the detection and assessment of tumor aggressiveness by using a Gadolinium-based contrast agent (GBCA). However, GBCA is known to have potential toxic effects. This risk can be avoided if we obtain DCE-MRI images without using GBCA. We propose, DCE-former, a transformer-based neural network to generate early and late response prostate DCE-MRI images from non-contrast multimodal inputs (T2 weighted, Apparent Diffusion Coefficient, and T1 pre-contrast MRI). Additionally, we introduce (i) a mutual information loss function to capture the complementary information about contrast uptake, and (ii) a frequency-based loss function in the pixel and Fourier space to learn local and global hyper-intensity patterns in DCE-MRI. Extensive experiments show that DCE-former outperforms other methods with improvement margins of +1.39 dB and +1.19 db in PSNR, +0.068 and +0.055 in SSIM, and -0.012 and -0.013 in Mean Absolute Error for early and late response DCE-MRI, respectively.

Geometric Learning-Based Transformer Network for Estimation of Segmentation Errors

Many segmentation networks have been proposed for 3D volumetric segmentation of tumors and organs at risk. Hospitals and clinical institutions seek to accelerate and minimize the efforts of specialists in image segmentation. Still, in case of errors generated by these networks, clinicians would have to manually edit the generated segmentation maps. Given a 3D volume and its putative segmentation map, we propose an approach to identify and measure erroneous regions in the segmentation map. Our method can estimate error at any point or node in a 3D mesh generated from a possibly erroneous volumetric segmentation map, serving as a Quality Assurance tool. We propose a graph neural network-based transformer based on the Nodeformer architecture to measure and classify the segmentation errors at any point. We have evaluated our network on a high-resolution micro-CT dataset of the human inner-ear bony labyrinth structure by simulating erroneous 3D segmentation maps. Our network incorporates a convolutional encoder to compute node-centric features from the input micro-CT data, the Nodeformer to learn the latent graph embeddings, and a Multi-Layer Perceptron (MLP) to compute and classify the node-wise errors. Our network achieves a mean absolute error of ~0.042 over other Graph Neural Networks (GNN) and an accuracy of 79.53% over other GNNs in estimating and classifying the node-wise errors, respectively. We also put forth vertex-normal prediction as a custom pretext task for pre-training the CNN encoder to improve the network's overall performance. Qualitative analysis shows the efficiency of our network in correctly classifying errors and reducing misclassifications.

HyperCoil-Recon: A Hypernetwork-based Adaptive Coil Configuration Task Switching Network for MRI Reconstruction

Parallel imaging, a fast MRI technique, involves dynamic adjustments based on the configuration i.e. number, positioning, and sensitivity of the coils with respect to the anatomy under study. Conventional deep learning-based image reconstruction models have to be trained or fine-tuned for each configuration, posing a barrier to clinical translation, given the lack of computational resources and machine learning expertise for clinicians to train models at deployment. Joint training on diverse datasets learns a single weight set that might underfit to deviated configurations. We propose, HyperCoil-Recon, a hypernetwork-based coil configuration task-switching network for multi-coil MRI reconstruction that encodes varying configurations of the numbers of coils in a multi-tasking perspective, posing each configuration as a task. The hypernetworks infer and embed task-specific weights into the reconstruction network, 1) effectively utilizing the contextual knowledge of common and varying image features among the various fields-of-view of the coils, and 2) enabling generality to unseen configurations at test time. Experiments reveal that our approach 1) adapts on the fly to various unseen configurations up to 32 coils when trained on lower numbers (i.e. 7 to 11) of randomly varying coils, and to 120 deviated unseen configurations when trained on 18 configurations in a single model, 2) matches the performance of coil configuration-specific models, and 3) outperforms configuration-invariant models with improvement margins of around 1 dB / 0.03 and 0.3 dB / 0.02 in PSNR / SSIM for knee and brain data. Our code is available at https://github.com/sriprabhar/HyperCoil-Recon

SDLFormer: A Sparse and Dense Locality-enhanced Transformer for Accelerated MR Image Reconstruction

Transformers have emerged as viable alternatives to convolutional neural networks owing to their ability to learn non-local region relationships in the spatial domain. The self-attention mechanism of the transformer enables transformers to capture long-range dependencies in the images, which might be desirable for accelerated MRI image reconstruction as the effect of undersampling is non-local in the image domain. Despite its computational efficiency, the window-based transformers suffer from restricted receptive fields as the dependencies are limited to within the scope of the image windows. We propose a window-based transformer network that integrates dilated attention mechanism and convolution for accelerated MRI image reconstruction. The proposed network consists of dilated and dense neighborhood attention transformers to enhance the distant neighborhood pixel relationship and introduce depth-wise convolutions within the transformer module to learn low-level translation invariant features for accelerated MRI image reconstruction. The proposed model is trained in a self-supervised manner. We perform extensive experiments for multi-coil MRI acceleration for coronal PD, coronal PDFS and axial T2 contrasts with 4x and 5x under-sampling in self-supervised learning based on k-space splitting. We compare our method against other reconstruction architectures and the parallel domain self-supervised learning baseline. Results show that the proposed model exhibits improvement margins of (i) around 1.40 dB in PSNR and around 0.028 in SSIM on average over other architectures (ii) around 1.44 dB in PSNR and around 0.029 in SSIM over parallel domain self-supervised learning. The code is available at https://github.com/rahul-gs-16/sdlformer.git

Automated Knowledge Modeling for Cancer Clinical Practice Guidelines

Clinical Practice Guidelines (CPGs) for cancer diseases evolve rapidly due to new evidence generated by active research. Currently, CPGs are primarily published in a document format that is ill-suited for managing this developing knowledge. A knowledge model of the guidelines document suitable for programmatic interaction is required. This work proposes an automated method for extraction of knowledge from National Comprehensive Cancer Network (NCCN) CPGs in Oncology and generating a structured model containing the retrieved knowledge. The proposed method was tested using two versions of NCCN Non-Small Cell Lung Cancer (NSCLC) CPG to demonstrate the effectiveness in faithful extraction and modeling of knowledge. Three enrichment strategies using Cancer staging information, Unified Medical Language System (UMLS) Metathesaurus & National Cancer Institute thesaurus (NCIt) concepts, and Node classification are also presented to enhance the model towards enabling programmatic traversal and querying of cancer care guidelines. The Node classification was performed using a Support Vector Machine (SVM) model, achieving a classification accuracy of 0.81 with 10-fold cross-validation.

Generalizing Supervised Deep Learning MRI Reconstruction to Multiple and Unseen Contrasts using Meta-Learning Hypernetworks

Meta-learning has recently been an emerging data-efficient learning technique for various medical imaging operations and has helped advance contemporary deep learning models. Furthermore, meta-learning enhances the knowledge generalization of the imaging tasks by learning both shared and discriminative weights for various configurations of imaging tasks. However, existing meta-learning models attempt to learn a single set of weight initializations of a neural network that might be restrictive for multimodal data. This work aims to develop a multimodal meta-learning model for image reconstruction, which augments meta-learning with evolutionary capabilities to encompass diverse acquisition settings of multimodal data. Our proposed model called KM-MAML (Kernel Modulation-based Multimodal Meta-Learning), has hypernetworks that evolve to generate mode-specific weights. These weights provide the mode-specific inductive bias for multiple modes by re-calibrating each kernel of the base network for image reconstruction via a low-rank kernel modulation operation. We incorporate gradient-based meta-learning (GBML) in the contextual space to update the weights of the hypernetworks for different modes. The hypernetworks and the reconstruction network in the GBML setting provide discriminative mode-specific features and low-level image features, respectively. Experiments on multi-contrast MRI reconstruction show that our model, (i) exhibits superior reconstruction performance over joint training, other meta-learning methods, and context-specific MRI reconstruction methods, and (ii) better adaptation capabilities with improvement margins of 0.5 dB in PSNR and 0.01 in SSIM. Besides, a representation analysis with U-Net shows that kernel modulation infuses 80% of mode-specific representation changes in the high-resolution layers. Our source code is available at https://github.com/sriprabhar/KM-MAML/.

Generalizable Deep Learning Method for Suppressing Unseen and Multiple MRI Artifacts Using Meta-learning

Magnetic Resonance (MR) images suffer from various types of artifacts due to motion, spatial resolution, and under-sampling. Conventional deep learning methods deal with removing a specific type of artifact, leading to separately trained models for each artifact type that lack the shared knowledge generalizable across artifacts. Moreover, training a model for each type and amount of artifact is a tedious process that consumes more training time and storage of models. On the other hand, the shared knowledge learned by jointly training the model on multiple artifacts might be inadequate to generalize under deviations in the types and amounts of artifacts. Model-agnostic meta-learning (MAML), a nested bi-level optimization framework is a promising technique to learn common knowledge across artifacts in the outer level of optimization, and artifact-specific restoration in the inner level. We propose curriculum-MAML (CMAML), a learning process that integrates MAML with curriculum learning to impart the knowledge of variable artifact complexity to adaptively learn restoration of multiple artifacts during training. Comparative studies against Stochastic Gradient Descent and MAML, using two cardiac datasets reveal that CMAML exhibits (i) better generalization with improved PSNR for 83% of unseen types and amounts of artifacts and improved SSIM in all cases, and (ii) better artifact suppression in 4 out of 5 cases of composite artifacts (scans with multiple artifacts).

SFT-KD-Recon: Learning a Student-friendly Teacher for Knowledge Distillation in Magnetic Resonance Image Reconstruction

Deep cascaded architectures for magnetic resonance imaging (MRI) acceleration have shown remarkable success in providing high-quality reconstruction. However, as the number of cascades increases, the improvements in reconstruction tend to become marginal, indicating possible excess model capacity. Knowledge distillation (KD) is an emerging technique to compress these models, in which a trained deep teacher network is used to distill knowledge to a smaller student network such that the student learns to mimic the behavior of the teacher. Most KD methods focus on effectively training the student with a pre-trained teacher unaware of the student model. We propose SFT-KD-Recon, a student-friendly teacher training approach along with the student as a prior step to KD to make the teacher aware of the structure and capacity of the student and enable aligning the representations of the teacher with the student. In SFT, the teacher is jointly trained with the unfolded branch configurations of the student blocks using three loss terms - teacher-reconstruction loss, student-reconstruction loss, and teacher-student imitation loss, followed by KD of the student. We perform extensive experiments for MRI acceleration in 4x and 5x under-sampling on the brain and cardiac datasets on five KD methods using the proposed approach as a prior step. We consider the DC-CNN architecture and setup teacher as D5C5 (141765 parameters), and student as D3C5 (49285 parameters), denoting a compression of 2.87:1. Results show that (i) our approach consistently improves the KD methods with improved reconstruction performance and image quality, and (ii) the student distilled using our approach is competitive with the teacher, with the performance gap reduced from 0.53 dB to 0.03 dB.

A Study of Representational Properties of Unsupervised Anomaly Detection in Brain MRI

Anomaly detection in MRI is of high clinical value in imaging and diagnosis. Unsupervised methods for anomaly detection provide interesting formulations based on reconstruction or latent embedding, offering a way to observe properties related to factorization. We study four existing modeling methods, and report our empirical observations using simple data science tools, to seek outcomes from the perspective of factorization as it would be most relevant to the task of unsupervised anomaly detection, considering the case of brain structural MRI. Our study indicates that anomaly detection algorithms that exhibit factorization related properties are well capacitated with delineatory capabilities to distinguish between normal and anomaly data. We have validated our observations in multiple anomaly and normal datasets.

Deep learning based non-contact physiological monitoring in Neonatal Intensive Care Unit

Preterm babies in the Neonatal Intensive Care Unit (NICU) have to undergo continuous monitoring of their cardiac health. Conventional monitoring approaches are contact-based, making the neonates prone to various nosocomial infections. Video-based monitoring approaches have opened up potential avenues for contactless measurement. This work presents a pipeline for remote estimation of cardiopulmonary signals from videos in NICU setup. We have proposed an end-to-end deep learning (DL) model that integrates a non-learning based approach to generate surrogate ground truth (SGT) labels for supervision, thus refraining from direct dependency on true ground truth labels. We have performed an extended qualitative and quantitative analysis to examine the efficacy of our proposed DL-based pipeline and achieved an overall average mean absolute error of 4.6 beats per minute (bpm) and root mean square error of 6.2 bpm in the estimated heart rate.