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DynaMMo: Dynamic Model Merging for Efficient Class Incremental Learning for Medical Images
Apr 22, 2024
Continual learning, the ability to acquire knowledge from new data while retaining previously learned information, is a fundamental challenge in machine learning. Various approaches, including memory replay, knowledge distillation, model regularization, and dynamic network expansion, have been proposed to address this issue. Thus far, dynamic network expansion methods have achieved state-of-the-art performance at the cost of incurring significant computational overhead. This is due to the need for additional model buffers, which makes it less feasible in resource-constrained settings, particularly in the medical domain. To overcome this challenge, we propose Dynamic Model Merging, DynaMMo, a method that merges multiple networks at different stages of model training to achieve better computational efficiency. Specifically, we employ lightweight learnable modules for each task and combine them into a unified model to minimize computational overhead. DynaMMo achieves this without compromising performance, offering a cost-effective solution for continual learning in medical applications. We evaluate DynaMMo on three publicly available datasets, demonstrating its effectiveness compared to existing approaches. DynaMMo offers around 10-fold reduction in GFLOPS with a small drop of 2.76 in average accuracy when compared to state-of-the-art dynamic-based approaches. The code implementation of this work will be available upon the acceptance of this work at https://github.com/BioMedIA-MBZUAI/DynaMMo.
TiBiX: Leveraging Temporal Information for Bidirectional X-ray and Report Generation
Mar 20, 2024
With the emergence of vision language models in the medical imaging domain, numerous studies have focused on two dominant research activities: (1) report generation from Chest X-rays (CXR), and (2) synthetic scan generation from text or reports. Despite some research incorporating multi-view CXRs into the generative process, prior patient scans and reports have been generally disregarded. This can inadvertently lead to the leaving out of important medical information, thus affecting generation quality. To address this, we propose TiBiX: Leveraging Temporal information for Bidirectional X-ray and Report Generation. Considering previous scans, our approach facilitates bidirectional generation, primarily addressing two challenging problems: (1) generating the current image from the previous image and current report and (2) generating the current report based on both the previous and current images. Moreover, we extract and release a curated temporal benchmark dataset derived from the MIMIC-CXR dataset, which focuses on temporal data. Our comprehensive experiments and ablation studies explore the merits of incorporating prior CXRs and achieve state-of-the-art (SOTA) results on the report generation task. Furthermore, we attain on-par performance with SOTA image generation efforts, thus serving as a new baseline in longitudinal bidirectional CXR-to-report generation. The code is available at https://github.com/BioMedIA-MBZUAI/TiBiX.
FissionFusion: Fast Geometric Generation and Hierarchical Souping for Medical Image Analysis
Mar 20, 2024
The scarcity of well-annotated medical datasets requires leveraging transfer learning from broader datasets like ImageNet or pre-trained models like CLIP. Model soups averages multiple fine-tuned models aiming to improve performance on In-Domain (ID) tasks and enhance robustness against Out-of-Distribution (OOD) datasets. However, applying these methods to the medical imaging domain faces challenges and results in suboptimal performance. This is primarily due to differences in error surface characteristics that stem from data complexities such as heterogeneity, domain shift, class imbalance, and distributional shifts between training and testing phases. To address this issue, we propose a hierarchical merging approach that involves local and global aggregation of models at various levels based on models' hyperparameter configurations. Furthermore, to alleviate the need for training a large number of models in the hyperparameter search, we introduce a computationally efficient method using a cyclical learning rate scheduler to produce multiple models for aggregation in the weight space. Our method demonstrates significant improvements over the model souping approach across multiple datasets (around 6% gain in HAM10000 and CheXpert datasets) while maintaining low computational costs for model generation and selection. Moreover, we achieve better results on OOD datasets than model soups. The code is available at https://github.com/BioMedIA-MBZUAI/FissionFusion.
MedMerge: Merging Models for Effective Transfer Learning to Medical Imaging Tasks
Mar 18, 2024
Transfer learning has become a powerful tool to initialize deep learning models to achieve faster convergence and higher performance. This is especially useful in the medical imaging analysis domain, where data scarcity limits possible performance gains for deep learning models. Some advancements have been made in boosting the transfer learning performance gain by merging models starting from the same initialization. However, in the medical imaging analysis domain, there is an opportunity in merging models starting from different initialisations, thus combining the features learnt from different tasks. In this work, we propose MedMerge, a method whereby the weights of different models can be merged, and their features can be effectively utilized to boost performance on a new task. With MedMerge, we learn kernel-level weights that can later be used to merge the models into a single model, even when starting from different initializations. Testing on various medical imaging analysis tasks, we show that our merged model can achieve significant performance gains, with up to 3% improvement on the F1 score. The code implementation of this work will be available at www.github.com/BioMedIA-MBZUAI/MedMerge.
XReal: Realistic Anatomy and Pathology-Aware X-ray Generation via Controllable Diffusion Model
Mar 14, 2024
Large-scale generative models have demonstrated impressive capacity in producing visually compelling images, with increasing applications in medical imaging. However, they continue to grapple with the challenge of image hallucination and the generation of anatomically inaccurate outputs. These limitations are mainly due to the sole reliance on textual inputs and lack of spatial control over the generated images, hindering the potential usefulness of such models in real-life settings. We present XReal, a novel controllable diffusion model for generating realistic chest X-ray images through precise anatomy and pathology location control. Our lightweight method can seamlessly integrate spatial control in a pre-trained text-to-image diffusion model without fine-tuning, retaining its existing knowledge while enhancing its generation capabilities. XReal outperforms state-of-the-art x-ray diffusion models in quantitative and qualitative metrics while showing 13% and 10% anatomy and pathology realism gain, respectively, based on the expert radiologist evaluation. Our model holds promise for advancing generative models in medical imaging, offering greater precision and adaptability while inviting further exploration in this evolving field. A large synthetically generated data with annotations and code is publicly available at https://github.com/BioMedIA-MBZUAI/XReal.
Multi-Task Learning Approach for Unified Biometric Estimation from Fetal Ultrasound Anomaly Scans
Nov 16, 2023Precise estimation of fetal biometry parameters from ultrasound images is vital for evaluating fetal growth, monitoring health, and identifying potential complications reliably. However, the automated computerized segmentation of the fetal head, abdomen, and femur from ultrasound images, along with the subsequent measurement of fetal biometrics, remains challenging. In this work, we propose a multi-task learning approach to classify the region into head, abdomen and femur as well as estimate the associated parameters. We were able to achieve a mean absolute error (MAE) of 1.08 mm on head circumference, 1.44 mm on abdomen circumference and 1.10 mm on femur length with a classification accuracy of 99.91\% on a dataset of fetal Ultrasound images. To achieve this, we leverage a weighted joint classification and segmentation loss function to train a U-Net architecture with an added classification head. The code can be accessed through \href{https://github.com/BioMedIA-MBZUAI/Multi-Task-Learning-Approach-for-Unified-Biometric-Estimation-from-Fetal-Ultrasound-Anomaly-Scans.git}{\texttt{Github}
PECon: Contrastive Pretraining to Enhance Feature Alignment between CT and EHR Data for Improved Pulmonary Embolism Diagnosis
Aug 27, 2023
Previous deep learning efforts have focused on improving the performance of Pulmonary Embolism(PE) diagnosis from Computed Tomography (CT) scans using Convolutional Neural Networks (CNN). However, the features from CT scans alone are not always sufficient for the diagnosis of PE. CT scans along with electronic heath records (EHR) can provide a better insight into the patients condition and can lead to more accurate PE diagnosis. In this paper, we propose Pulmonary Embolism Detection using Contrastive Learning (PECon), a supervised contrastive pretraining strategy that employs both the patients CT scans as well as the EHR data, aiming to enhance the alignment of feature representations between the two modalities and leverage information to improve the PE diagnosis. In order to achieve this, we make use of the class labels and pull the sample features of the same class together, while pushing away those of the other class. Results show that the proposed work outperforms the existing techniques and achieves state-of-the-art performance on the RadFusion dataset with an F1-score of 0.913, accuracy of 0.90 and an AUROC of 0.943. Furthermore, we also explore the explainability of our approach in comparison to other methods. Our code is publicly available at https://github.com/BioMedIA-MBZUAI/PECon.
FedSIS: Federated Split Learning with Intermediate Representation Sampling for Privacy-preserving Generalized Face Presentation Attack Detection
Aug 22, 2023
Lack of generalization to unseen domains/attacks is the Achilles heel of most face presentation attack detection (FacePAD) algorithms. Existing attempts to enhance the generalizability of FacePAD solutions assume that data from multiple source domains are available with a single entity to enable centralized training. In practice, data from different source domains may be collected by diverse entities, who are often unable to share their data due to legal and privacy constraints. While collaborative learning paradigms such as federated learning (FL) can overcome this problem, standard FL methods are ill-suited for domain generalization because they struggle to surmount the twin challenges of handling non-iid client data distributions during training and generalizing to unseen domains during inference. In this work, a novel framework called Federated Split learning with Intermediate representation Sampling (FedSIS) is introduced for privacy-preserving domain generalization. In FedSIS, a hybrid Vision Transformer (ViT) architecture is learned using a combination of FL and split learning to achieve robustness against statistical heterogeneity in the client data distributions without any sharing of raw data (thereby preserving privacy). To further improve generalization to unseen domains, a novel feature augmentation strategy called intermediate representation sampling is employed, and discriminative information from intermediate blocks of a ViT is distilled using a shared adapter network. The FedSIS approach has been evaluated on two well-known benchmarks for cross-domain FacePAD to demonstrate that it is possible to achieve state-of-the-art generalization performance without data sharing. Code: https://github.com/Naiftt/FedSIS
SEDA: Self-Ensembling ViT with Defensive Distillation and Adversarial Training for robust Chest X-rays Classification
Aug 15, 2023
Deep Learning methods have recently seen increased adoption in medical imaging applications. However, elevated vulnerabilities have been explored in recent Deep Learning solutions, which can hinder future adoption. Particularly, the vulnerability of Vision Transformer (ViT) to adversarial, privacy, and confidentiality attacks raise serious concerns about their reliability in medical settings. This work aims to enhance the robustness of self-ensembling ViTs for the tuberculosis chest x-ray classification task. We propose Self-Ensembling ViT with defensive Distillation and Adversarial training (SEDA). SEDA utilizes efficient CNN blocks to learn spatial features with various levels of abstraction from feature representations extracted from intermediate ViT blocks, that are largely unaffected by adversarial perturbations. Furthermore, SEDA leverages adversarial training in combination with defensive distillation for improved robustness against adversaries. Training using adversarial examples leads to better model generalizability and improves its ability to handle perturbations. Distillation using soft probabilities introduces uncertainty and variation into the output probabilities, making it more difficult for adversarial and privacy attacks. Extensive experiments performed with the proposed architecture and training paradigm on publicly available Tuberculosis x-ray dataset shows SOTA efficacy of SEDA compared to SEViT in terms of computational efficiency with 70x times lighter framework and enhanced robustness of +9%.
FeSViBS: Federated Split Learning of Vision Transformer with Block Sampling
Jun 26, 2023
Data scarcity is a significant obstacle hindering the learning of powerful machine learning models in critical healthcare applications. Data-sharing mechanisms among multiple entities (e.g., hospitals) can accelerate model training and yield more accurate predictions. Recently, approaches such as Federated Learning (FL) and Split Learning (SL) have facilitated collaboration without the need to exchange private data. In this work, we propose a framework for medical imaging classification tasks called Federated Split learning of Vision transformer with Block Sampling (FeSViBS). The FeSViBS framework builds upon the existing federated split vision transformer and introduces a block sampling module, which leverages intermediate features extracted by the Vision Transformer (ViT) at the server. This is achieved by sampling features (patch tokens) from an intermediate transformer block and distilling their information content into a pseudo class token before passing them back to the client. These pseudo class tokens serve as an effective feature augmentation strategy and enhances the generalizability of the learned model. We demonstrate the utility of our proposed method compared to other SL and FL approaches on three publicly available medical imaging datasets: HAM1000, BloodMNIST, and Fed-ISIC2019, under both IID and non-IID settings. Code: https://github.com/faresmalik/FeSViBS