Treatment-wise Glioblastoma Survival Inference with Multi-parametric Preoperative MRI

In this work, we aim to predict the survival time (ST) of glioblastoma (GBM) patients undergoing different treatments based on preoperative magnetic resonance (MR) scans. The personalized and precise treatment planning can be achieved by comparing the ST of different treatments. It is well established that both the current status of the patient (as represented by the MR scans) and the choice of treatment are the cause of ST. While previous related MR-based glioblastoma ST studies have focused only on the direct mapping of MR scans to ST, they have not included the underlying causal relationship between treatments and ST. To address this limitation, we propose a treatment-conditioned regression model for glioblastoma ST that incorporates treatment information in addition to MR scans. Our approach allows us to effectively utilize the data from all of the treatments in a unified manner, rather than having to train separate models for each of the treatments. Furthermore, treatment can be effectively injected into each convolutional layer through the adaptive instance normalization we employ. We evaluate our framework on the BraTS20 ST prediction task. Three treatment options are considered: Gross Total Resection (GTR), Subtotal Resection (STR), and no resection. The evaluation results demonstrate the effectiveness of injecting the treatment for estimating GBM survival.

Disentangled Multimodal Brain MR Image Translation via Transformer-based Modality Infuser

Multimodal Magnetic Resonance (MR) Imaging plays a crucial role in disease diagnosis due to its ability to provide complementary information by analyzing a relationship between multimodal images on the same subject. Acquiring all MR modalities, however, can be expensive, and, during a scanning session, certain MR images may be missed depending on the study protocol. The typical solution would be to synthesize the missing modalities from the acquired images such as using generative adversarial networks (GANs). Yet, GANs constructed with convolutional neural networks (CNNs) are likely to suffer from a lack of global relationships and mechanisms to condition the desired modality. To address this, in this work, we propose a transformer-based modality infuser designed to synthesize multimodal brain MR images. In our method, we extract modality-agnostic features from the encoder and then transform them into modality-specific features using the modality infuser. Furthermore, the modality infuser captures long-range relationships among all brain structures, leading to the generation of more realistic images. We carried out experiments on the BraTS 2018 dataset, translating between four MR modalities, and our experimental results demonstrate the superiority of our proposed method in terms of synthesis quality. In addition, we conducted experiments on a brain tumor segmentation task and different conditioning methods.

Is Registering Raw Tagged-MR Enough for Strain Estimation in the Era of Deep Learning?

Magnetic Resonance Imaging with tagging (tMRI) has long been utilized for quantifying tissue motion and strain during deformation. However, a phenomenon known as tag fading, a gradual decrease in tag visibility over time, often complicates post-processing. The first contribution of this study is to model tag fading by considering the interplay between $T_1$ relaxation and the repeated application of radio frequency (RF) pulses during serial imaging sequences. This is a factor that has been overlooked in prior research on tMRI post-processing. Further, we have observed an emerging trend of utilizing raw tagged MRI within a deep learning-based (DL) registration framework for motion estimation. In this work, we evaluate and analyze the impact of commonly used image similarity objectives in training DL registrations on raw tMRI. This is then compared with the Harmonic Phase-based approach, a traditional approach which is claimed to be robust to tag fading. Our findings, derived from both simulated images and an actual phantom scan, reveal the limitations of various similarity losses in raw tMRI and emphasize caution in registration tasks where image intensity changes over time.

Posterior Estimation for Dynamic PET imaging using Conditional Variational Inference

This work aims efficiently estimating the posterior distribution of kinetic parameters for dynamic positron emission tomography (PET) imaging given a measurement of time of activity curve. Considering the inherent information loss from parametric imaging to measurement space with the forward kinetic model, the inverse mapping is ambiguous. The conventional (but expensive) solution can be the Markov Chain Monte Carlo (MCMC) sampling, which is known to produce unbiased asymptotical estimation. We propose a deep-learning-based framework for efficient posterior estimation. Specifically, we counteract the information loss in the forward process by introducing latent variables. Then, we use a conditional variational autoencoder (CVAE) and optimize its evidence lower bound. The well-trained decoder is able to infer the posterior with a given measurement and the sampled latent variables following a simple multivariate Gaussian distribution. We validate our CVAE-based method using unbiased MCMC as the reference for low-dimensional data (a single brain region) with the simplified reference tissue model.

Speech Audio Synthesis from Tagged MRI and Non-Negative Matrix Factorization via Plastic Transformer

The tongue's intricate 3D structure, comprising localized functional units, plays a crucial role in the production of speech. When measured using tagged MRI, these functional units exhibit cohesive displacements and derived quantities that facilitate the complex process of speech production. Non-negative matrix factorization-based approaches have been shown to estimate the functional units through motion features, yielding a set of building blocks and a corresponding weighting map. Investigating the link between weighting maps and speech acoustics can offer significant insights into the intricate process of speech production. To this end, in this work, we utilize two-dimensional spectrograms as a proxy representation, and develop an end-to-end deep learning framework for translating weighting maps to their corresponding audio waveforms. Our proposed plastic light transformer (PLT) framework is based on directional product relative position bias and single-level spatial pyramid pooling, thus enabling flexible processing of weighting maps with variable size to fixed-size spectrograms, without input information loss or dimension expansion. Additionally, our PLT framework efficiently models the global correlation of wide matrix input. To improve the realism of our generated spectrograms with relatively limited training samples, we apply pair-wise utterance consistency with Maximum Mean Discrepancy constraint and adversarial training. Experimental results on a dataset of 29 subjects speaking two utterances demonstrated that our framework is able to synthesize speech audio waveforms from weighting maps, outperforming conventional convolution and transformer models.

Bias and Fairness in Chatbots: An Overview

Chatbots have been studied for more than half a century. With the rapid development of natural language processing (NLP) technologies in recent years, chatbots using large language models (LLMs) have received much attention nowadays. Compared with traditional ones, modern chatbots are more powerful and have been used in real-world applications. There are however, bias and fairness concerns in modern chatbot design. Due to the huge amounts of training data, extremely large model sizes, and lack of interpretability, bias mitigation and fairness preservation of modern chatbots are challenging. Thus, a comprehensive overview on bias and fairness in chatbot systems is given in this paper. The history of chatbots and their categories are first reviewed. Then, bias sources and potential harms in applications are analyzed. Considerations in designing fair and unbiased chatbot systems are examined. Finally, future research directions are discussed.

MomentaMorph: Unsupervised Spatial-Temporal Registration with Momenta, Shooting, and Correction

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

Incremental Learning for Heterogeneous Structure Segmentation in Brain Tumor MRI

Deep learning (DL) models for segmenting various anatomical structures have achieved great success via a static DL model that is trained in a single source domain. Yet, the static DL model is likely to perform poorly in a continually evolving environment, requiring appropriate model updates. In an incremental learning setting, we would expect that well-trained static models are updated, following continually evolving target domain data -- e.g., additional lesions or structures of interest -- collected from different sites, without catastrophic forgetting. This, however, poses challenges, due to distribution shifts, additional structures not seen during the initial model training, and the absence of training data in a source domain. To address these challenges, in this work, we seek to progressively evolve an ``off-the-shelf" trained segmentation model to diverse datasets with additional anatomical categories in a unified manner. Specifically, we first propose a divergence-aware dual-flow module with balanced rigidity and plasticity branches to decouple old and new tasks, which is guided by continuous batch renormalization. Then, a complementary pseudo-label training scheme with self-entropy regularized momentum MixUp decay is developed for adaptive network optimization. We evaluated our framework on a brain tumor segmentation task with continually changing target domains -- i.e., new MRI scanners/modalities with incremental structures. Our framework was able to well retain the discriminability of previously learned structures, hence enabling the realistic life-long segmentation model extension along with the widespread accumulation of big medical data.

Attentive Continuous Generative Self-training for Unsupervised Domain Adaptive Medical Image Translation

Self-training is an important class of unsupervised domain adaptation (UDA) approaches that are used to mitigate the problem of domain shift, when applying knowledge learned from a labeled source domain to unlabeled and heterogeneous target domains. While self-training-based UDA has shown considerable promise on discriminative tasks, including classification and segmentation, through reliable pseudo-label filtering based on the maximum softmax probability, there is a paucity of prior work on self-training-based UDA for generative tasks, including image modality translation. To fill this gap, in this work, we seek to develop a generative self-training (GST) framework for domain adaptive image translation with continuous value prediction and regression objectives. Specifically, we quantify both aleatoric and epistemic uncertainties within our GST using variational Bayes learning to measure the reliability of synthesized data. We also introduce a self-attention scheme that de-emphasizes the background region to prevent it from dominating the training process. The adaptation is then carried out by an alternating optimization scheme with target domain supervision that focuses attention on the regions with reliable pseudo-labels. We evaluated our framework on two cross-scanner/center, inter-subject translation tasks, including tagged-to-cine magnetic resonance (MR) image translation and T1-weighted MR-to-fractional anisotropy translation. Extensive validations with unpaired target domain data showed that our GST yielded superior synthesis performance in comparison to adversarial training UDA methods.

Posterior Estimation Using Deep Learning: A Simulation Study of Compartmental Modeling in Dynamic PET

Background: In medical imaging, images are usually treated as deterministic, while their uncertainties are largely underexplored. Purpose: This work aims at using deep learning to efficiently estimate posterior distributions of imaging parameters, which in turn can be used to derive the most probable parameters as well as their uncertainties. Methods: Our deep learning-based approaches are based on a variational Bayesian inference framework, which is implemented using two different deep neural networks based on conditional variational auto-encoder (CVAE), CVAE-dual-encoder and CVAE-dual-decoder. The conventional CVAE framework, i.e., CVAE-vanilla, can be regarded as a simplified case of these two neural networks. We applied these approaches to a simulation study of dynamic brain PET imaging using a reference region-based kinetic model. Results: In the simulation study, we estimated posterior distributions of PET kinetic parameters given a measurement of time-activity curve. Our proposed CVAE-dual-encoder and CVAE-dual-decoder yield results that are in good agreement with the asymptotically unbiased posterior distributions sampled by Markov Chain Monte Carlo (MCMC). The CVAE-vanilla can also be used for estimating posterior distributions, although it has an inferior performance to both CVAE-dual-encoder and CVAE-dual-decoder. Conclusions: We have evaluated the performance of our deep learning approaches for estimating posterior distributions in dynamic brain PET. Our deep learning approaches yield posterior distributions, which are in good agreement with unbiased distributions estimated by MCMC. All these neural networks have different characteristics and can be chosen by the user for specific applications. The proposed methods are general and can be adapted to other problems.