Eleftheria Panagiotaki

Snigdha Sen, Saurabh Singh, Hayley Pye et al.

Purpose: Demonstrating and assessing self-supervised machine learning fitting of the VERDICT (Vascular, Extracellular and Restricted DIffusion for Cytometry in Tumours) model for prostate. Methods: We derive a self-supervised neural network for fitting VERDICT (ssVERDICT) that estimates parameter maps without training data. We compare the performance of ssVERDICT to two established baseline methods for fitting diffusion MRI models: conventional nonlinear least squares (NLLS) and supervised deep learning. We do this quantitatively on simulated data, by comparing the Pearson's correlation coefficient, mean-squared error (MSE), bias, and variance with respect to the simulated ground truth. We also calculate in vivo parameter maps on a cohort of 20 prostate cancer patients and compare the methods' performance in discriminating benign from cancerous tissue via Wilcoxon's signed-rank test. Results: In simulations, ssVERDICT outperforms the baseline methods (NLLS and supervised DL) in estimating all the parameters from the VERDICT prostate model in terms of Pearson's correlation coefficient, bias, and MSE. In vivo, ssVERDICT shows stronger lesion conspicuity across all parameter maps, and improves discrimination between benign and cancerous tissue over the baseline methods. Conclusion: ssVERDICT significantly outperforms state-of-the-art methods for VERDICT model fitting, and shows for the first time, fitting of a complex three-compartment biophysical model with machine learning without the requirement of explicit training labels.

Tanishq Patil, Snigdha Sen, Malwina Molendowska et al.

Diffusion MRI (dMRI) enables non-invasive assessment of prostate microstructure but conventional metrics such as the Apparent Diffusion Coefficient in multiparametric MRI lack specificity to underlying histology. Integrating dMRI with the compartment-based biophysical VERDICT (Vascular, Extracellular, and Restricted Diffusion for Cytometry in Tumours) framework offers richer microstructural insights, though clinical gradient systems (40-80 mT/m) suffer from poor signal-to-noise ratio (SNR) at stronger diffusion weightings due to prolonged echo times. Ultra-strong gradients (up to 300 mT/m) can mitigate these limitations by improving SNR and contrast-to-noise ratios (CNR) but their adoption has until recently been limited to research environments due to challenges with peripheral nerve stimulation thresholds and gradient non-uniformity. This study investigates whether physics-informed self-supervised VERDICT (ssVERDICT) fitting applied to ultra-strong gradients enhances prostate cancer characterization relative to current clinical acquisitions. We developed enhanced ssVERDICT fitting approaches using dense multilayer perceptron (Dense MLP) and convolutional U-Net architectures, benchmarking them against non-linear least-squares (NLLS) fitting and Diffusion Kurtosis Imaging across clinical- to ultra-strong gradient systems. Dense ssVERDICT at ultra-strong gradient notably outperformed NLLS VERDICT, boosting median CNR by 47%, cutting inter-patient Coefficient of Variation by 52%, and reducing pooled f_ic variation by 50%. Overall, it delivered the highest CNR, the most stable parameter estimates, and the clearest tumour-normal contrast compared with conventional methods and clinical gradient systems. These findings highlight the potential of advanced gradient systems and deep learning-based modelling to improve non-invasive prostate cancer characterization and reduce unnecessary biopsies.

Eleni Chiou, Eleftheria Panagiotaki, Iasonas Kokkinos

In this work we challenge the common approach of using a one-to-one mapping ('translation') between the source and target domains in unsupervised domain adaptation (UDA). Instead, we rely on stochastic translation to capture inherent translation ambiguities. This allows us to (i) train more accurate target networks by generating multiple outputs conditioned on the same source image, leveraging both accurate translation and data augmentation for appearance variability, (ii) impute robust pseudo-labels for the target data by averaging the predictions of a source network on multiple translated versions of a single target image and (iii) train and ensemble diverse networks in the target domain by modulating the degree of stochasticity in the translations. We report improvements over strong recent baselines, leading to state-of-the-art UDA results on two challenging semantic segmentation benchmarks. Our code is available at https://github.com/elchiou/Beyond-deterministic-translation-for-UDA.

Chen Jin, Ryutaro Tanno, Thomy Mertzanidou et al.

Many computer vision systems require low-cost segmentation algorithms based on deep learning, either because of the enormous size of input images or limited computational budget. Common solutions uniformly downsample the input images to meet memory constraints, assuming all pixels are equally informative. In this work, we demonstrate that this assumption can harm the segmentation performance because the segmentation difficulty varies spatially. We combat this problem by introducing a learnable downsampling module, which can be optimised together with the given segmentation model in an end-to-end fashion. We formulate the problem of training such downsampling module as optimisation of sampling density distributions over the input images given their low-resolution views. To defend against degenerate solutions (e.g. over-sampling trivial regions like the backgrounds), we propose a regularisation term that encourages the sampling locations to concentrate around the object boundaries. We find the downsampling module learns to sample more densely at difficult locations, thereby improving the segmentation performance. Our experiments on benchmarks of high-resolution street view, aerial and medical images demonstrate substantial improvements in terms of efficiency-and-accuracy trade-off compared to both uniform downsampling and two recent advanced downsampling techniques.

Eleni Chiou, Francesco Giganti, Shonit Punwani et al.

Any novel medical imaging modality that differs from previous protocols e.g. in the number of imaging channels, introduces a new domain that is heterogeneous from previous ones. This common medical imaging scenario is rarely considered in the domain adaptation literature, which handles shifts across domains of the same dimensionality. In our work we rely on stochastic generative modeling to translate across two heterogeneous domains at pixel space and introduce two new loss functions that promote semantic consistency. Firstly, we introduce a semantic cycle-consistency loss in the source domain to ensure that the translation preserves the semantics. Secondly, we introduce a pseudo-labelling loss, where we translate target data to source, label them by a source-domain network, and use the generated pseudo-labels to supervise the target-domain network. Our results show that this allows us to extract systematically better representations for the target domain. In particular, we address the challenge of enhancing performance on VERDICT-MRI, an advanced diffusion-weighted imaging technique, by exploiting labeled mp-MRI data. When compared to several unsupervised domain adaptation approaches, our approach yields substantial improvements, that consistently carry over to the semi-supervised and supervised learning settings.

Eleni Chiou, Francesco Giganti, Shonit Punwani et al.

The need for training data can impede the adoption of novel imaging modalities for learning-based medical image analysis. Domain adaptation methods partially mitigate this problem by translating training data from a related source domain to a novel target domain, but typically assume that a one-to-one translation is possible. Our work addresses the challenge of adapting to a more informative target domain where multiple target samples can emerge from a single source sample. In particular we consider translating from mp-MRI to VERDICT, a richer MRI modality involving an optimized acquisition protocol for cancer characterization. We explicitly account for the inherent uncertainty of this mapping and exploit it to generate multiple outputs conditioned on a single input. Our results show that this allows us to extract systematically better image representations for the target domain, when used in tandem with both simple, CycleGAN-based baselines, as well as more powerful approaches that integrate discriminative segmentation losses and/or residual adapters. When compared to its deterministic counterparts, our approach yields substantial improvements across a broad range of dataset sizes, increasingly strong baselines, and evaluation measures.