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Zero-Shot Medical Phrase Grounding with Off-the-shelf Diffusion Models
Apr 19, 2024
Localizing the exact pathological regions in a given medical scan is an important imaging problem that requires a large amount of bounding box ground truth annotations to be accurately solved. However, there exist alternative, potentially weaker, forms of supervision, such as accompanying free-text reports, which are readily available. The task of performing localization with textual guidance is commonly referred to as phrase grounding. In this work, we use a publicly available Foundation Model, namely the Latent Diffusion Model, to solve this challenging task. This choice is supported by the fact that the Latent Diffusion Model, despite being generative in nature, contains mechanisms (cross-attention) that implicitly align visual and textual features, thus leading to intermediate representations that are suitable for the task at hand. In addition, we aim to perform this task in a zero-shot manner, i.e., without any further training on target data, meaning that the model's weights remain frozen. To this end, we devise strategies to select features and also refine them via post-processing without extra learnable parameters. We compare our proposed method with state-of-the-art approaches which explicitly enforce image-text alignment in a joint embedding space via contrastive learning. Results on a popular chest X-ray benchmark indicate that our method is competitive wih SOTA on different types of pathology, and even outperforms them on average in terms of two metrics (mean IoU and AUC-ROC). Source code will be released upon acceptance.
Benchmarking Counterfactual Image Generation
Mar 29, 2024
Counterfactual image generation is pivotal for understanding the causal relations of variables, with applications in interpretability and generation of unbiased synthetic data. However, evaluating image generation is a long-standing challenge in itself. The need to evaluate counterfactual generation compounds on this challenge, precisely because counterfactuals, by definition, are hypothetical scenarios without observable ground truths. In this paper, we present a novel comprehensive framework aimed at benchmarking counterfactual image generation methods. We incorporate metrics that focus on evaluating diverse aspects of counterfactuals, such as composition, effectiveness, minimality of interventions, and image realism. We assess the performance of three distinct conditional image generation model types, based on the Structural Causal Model paradigm. Our work is accompanied by a user-friendly Python package which allows to further evaluate and benchmark existing and future counterfactual image generation methods. Our framework is extendable to additional SCM and other causal methods, generative models, and datasets.
Boosting Few-Shot Learning with Disentangled Self-Supervised Learning and Meta-Learning for Medical Image Classification
Mar 26, 2024
Background and objective: Employing deep learning models in critical domains such as medical imaging poses challenges associated with the limited availability of training data. We present a strategy for improving the performance and generalization capabilities of models trained in low-data regimes. Methods: The proposed method starts with a pre-training phase, where features learned in a self-supervised learning setting are disentangled to improve the robustness of the representations for downstream tasks. We then introduce a meta-fine-tuning step, leveraging related classes between meta-training and meta-testing phases but varying the granularity level. This approach aims to enhance the model's generalization capabilities by exposing it to more challenging classification tasks during meta-training and evaluating it on easier tasks but holding greater clinical relevance during meta-testing. We demonstrate the effectiveness of the proposed approach through a series of experiments exploring several backbones, as well as diverse pre-training and fine-tuning schemes, on two distinct medical tasks, i.e., classification of prostate cancer aggressiveness from MRI data and classification of breast cancer malignity from microscopic images. Results: Our results indicate that the proposed approach consistently yields superior performance w.r.t. ablation experiments, maintaining competitiveness even when a distribution shift between training and evaluation data occurs. Conclusion: Extensive experiments demonstrate the effectiveness and wide applicability of the proposed approach. We hope that this work will add another solution to the arsenal of addressing learning issues in data-scarce imaging domains.
Inference Stage Denoising for Undersampled MRI Reconstruction
Feb 12, 2024Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.
Group Distributionally Robust Knowledge Distillation
Nov 01, 2023Knowledge distillation enables fast and effective transfer of features learned from a bigger model to a smaller one. However, distillation objectives are susceptible to sub-population shifts, a common scenario in medical imaging analysis which refers to groups/domains of data that are underrepresented in the training set. For instance, training models on health data acquired from multiple scanners or hospitals can yield subpar performance for minority groups. In this paper, inspired by distributionally robust optimization (DRO) techniques, we address this shortcoming by proposing a group-aware distillation loss. During optimization, a set of weights is updated based on the per-group losses at a given iteration. This way, our method can dynamically focus on groups that have low performance during training. We empirically validate our method, GroupDistil on two benchmark datasets (natural images and cardiac MRIs) and show consistent improvement in terms of worst-group accuracy.
Compositional Representation Learning for Brain Tumour Segmentation
Oct 10, 2023For brain tumour segmentation, deep learning models can achieve human expert-level performance given a large amount of data and pixel-level annotations. However, the expensive exercise of obtaining pixel-level annotations for large amounts of data is not always feasible, and performance is often heavily reduced in a low-annotated data regime. To tackle this challenge, we adapt a mixed supervision framework, vMFNet, to learn robust compositional representations using unsupervised learning and weak supervision alongside non-exhaustive pixel-level pathology labels. In particular, we use the BraTS dataset to simulate a collection of 2-point expert pathology annotations indicating the top and bottom slice of the tumour (or tumour sub-regions: peritumoural edema, GD-enhancing tumour, and the necrotic / non-enhancing tumour) in each MRI volume, from which weak image-level labels that indicate the presence or absence of the tumour (or the tumour sub-regions) in the image are constructed. Then, vMFNet models the encoded image features with von-Mises-Fisher (vMF) distributions, via learnable and compositional vMF kernels which capture information about structures in the images. We show that good tumour segmentation performance can be achieved with a large amount of weakly labelled data but only a small amount of fully-annotated data. Interestingly, emergent learning of anatomical structures occurs in the compositional representation even given only supervision relating to pathology (tumour).
FairTune: Optimizing Parameter Efficient Fine Tuning for Fairness in Medical Image Analysis
Oct 08, 2023Training models with robust group fairness properties is crucial in ethically sensitive application areas such as medical diagnosis. Despite the growing body of work aiming to minimise demographic bias in AI, this problem remains challenging. A key reason for this challenge is the fairness generalisation gap: High-capacity deep learning models can fit all training data nearly perfectly, and thus also exhibit perfect fairness during training. In this case, bias emerges only during testing when generalisation performance differs across subgroups. This motivates us to take a bi-level optimisation perspective on fair learning: Optimising the learning strategy based on validation fairness. Specifically, we consider the highly effective workflow of adapting pre-trained models to downstream medical imaging tasks using parameter-efficient fine-tuning (PEFT) techniques. There is a trade-off between updating more parameters, enabling a better fit to the task of interest vs. fewer parameters, potentially reducing the generalisation gap. To manage this tradeoff, we propose FairTune, a framework to optimise the choice of PEFT parameters with respect to fairness. We demonstrate empirically that FairTune leads to improved fairness on a range of medical imaging datasets.
Unveiling Fairness Biases in Deep Learning-Based Brain MRI Reconstruction
Sep 25, 2023Deep learning (DL) reconstruction particularly of MRI has led to improvements in image fidelity and reduction of acquisition time. In neuroimaging, DL methods can reconstruct high-quality images from undersampled data. However, it is essential to consider fairness in DL algorithms, particularly in terms of demographic characteristics. This study presents the first fairness analysis in a DL-based brain MRI reconstruction model. The model utilises the U-Net architecture for image reconstruction and explores the presence and sources of unfairness by implementing baseline Empirical Risk Minimisation (ERM) and rebalancing strategies. Model performance is evaluated using image reconstruction metrics. Our findings reveal statistically significant performance biases between the gender and age subgroups. Surprisingly, data imbalance and training discrimination are not the main sources of bias. This analysis provides insights of fairness in DL-based image reconstruction and aims to improve equity in medical AI applications.
Cine cardiac MRI reconstruction using a convolutional recurrent network with refinement
Sep 23, 2023
Cine Magnetic Resonance Imaging (MRI) allows for understanding of the heart's function and condition in a non-invasive manner. Undersampling of the $k$-space is employed to reduce the scan duration, thus increasing patient comfort and reducing the risk of motion artefacts, at the cost of reduced image quality. In this challenge paper, we investigate the use of a convolutional recurrent neural network (CRNN) architecture to exploit temporal correlations in supervised cine cardiac MRI reconstruction. This is combined with a single-image super-resolution refinement module to improve single coil reconstruction by 4.4\% in structural similarity and 3.9\% in normalised mean square error compared to a plain CRNN implementation. We deploy a high-pass filter to our $\ell_1$ loss to allow greater emphasis on high-frequency details which are missing in the original data. The proposed model demonstrates considerable enhancements compared to the baseline case and holds promising potential for further improving cardiac MRI reconstruction.
Generative AI for Medical Imaging: extending the MONAI Framework
Jul 27, 2023
Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.