Ruizhe Li

Ruizhe Li, Xin Chen

Cardiac Magnetic Resonance Imaging (MRI) plays an important role in the analysis of cardiac function. However, the acquisition is often accompanied by motion artefacts because of the difficulty of breath-hold, especially for acute symptoms patients. Therefore, it is essential to assess the quality of cardiac MRI for further analysis. Time-consuming manual-based classification is not conducive to the construction of an end-to-end computer aided diagnostic system. To overcome this problem, an automatic cardiac MRI quality estimation framework using ensemble and transfer learning is proposed in this work. Multiple pre-trained models were initialised and fine-tuned on 2-dimensional image patches sampled from the training data. In the model inference process, decisions from these models are aggregated to make a final prediction. The framework has been evaluated on CMRxMotion grand challenge (MICCAI 2022) dataset which is small, multi-class, and imbalanced. It achieved a classification accuracy of 78.8% and 70.0% on the training set (5-fold cross-validation) and a validation set, respectively. The final trained model was also evaluated on an independent test set by the CMRxMotion organisers, which achieved the classification accuracy of 72.5% and Cohen's Kappa of 0.6309 (ranked top 1 in this grand challenge). Our code is available on Github: https://github.com/ruizhe-l/CMRxMotion.

James Mitchell-White, Reza Omdivar, Benjamin Partridge et al.

This paper introduces Llettuce, an open-source tool designed to address the complexities of converting medical terms into OMOP standard concepts. Unlike existing solutions such as the Athena database search and Usagi, which struggle with semantic nuances and require substantial manual input, Llettuce leverages advanced natural language processing, including large language models and fuzzy matching, to automate and enhance the mapping process. Developed with a focus on GDPR compliance, Llettuce can be deployed locally, ensuring data protection while maintaining high performance in converting informal medical terms to standardised concepts.

Ruizhe Li, Grazziela Figueredo, Dorothee Auer et al.

Deformable image registration (alignment) is highly sought after in numerous clinical applications, such as computer aided diagnosis and disease progression analysis. Deep Convolutional Neural Network (DCNN)-based image registration methods have demonstrated advantages in terms of registration accuracy and computational speed. However, while most methods excel at global alignment, they often perform worse in aligning local regions. To address this challenge, this paper proposes a mask-guided encoder-decoder DCNN-based image registration method, named as MrRegNet. This approach employs a multi-resolution encoder for feature extraction and subsequently estimates multi-resolution displacement fields in the decoder to handle the substantial deformation of images. Furthermore, segmentation masks are employed to direct the model's attention toward aligning local regions. The results show that the proposed method outperforms traditional methods like Demons and a well-known deep learning method, VoxelMorph, on a public 3D brain MRI dataset (OASIS) and a local 2D brain MRI dataset with large deformations. Importantly, the image alignment accuracies are significantly improved at local regions guided by segmentation masks. Github link:https://github.com/ruizhe-l/MrRegNet.

Eduardo Aguilar-Bejarano, Daniel Lea, Karthikeyan Sivakumar et al.

Helix is an open-source, extensible, Python-based software framework to facilitate reproducible and interpretable machine learning workflows for tabular data. It addresses the growing need for transparent experimental data analytics provenance, ensuring that the entire analytical process -- including decisions around data transformation and methodological choices -- is documented, accessible, reproducible, and comprehensible to relevant stakeholders. The platform comprises modules for standardised data preprocessing, visualisation, machine learning model training, evaluation, interpretation, results inspection, and model prediction for unseen data. To further empower researchers without formal training in data science to derive meaningful and actionable insights, Helix features a user-friendly interface that enables the design of computational experiments, inspection of outcomes, including a novel interpretation approach to machine learning decisions using linguistic terms all within an integrated environment. Released under the MIT licence, Helix is accessible via GitHub and PyPI, supporting community-driven development and promoting adherence to the FAIR principles.

Ruizhe Li, Grazziela Figueredo, Dorothee Auer et al.

Semi-supervised learning, which leverages both annotated and unannotated data, is an efficient approach for medical image segmentation, where obtaining annotations for the whole dataset is time-consuming and costly. Traditional semi-supervised methods primarily focus on extracting features and learning data distributions from unannotated data to enhance model training. In this paper, we introduce a novel approach incorporating an image registration model to generate pseudo-labels for the unannotated data, producing more geometrically correct pseudo-labels to improve the model training. Our method was evaluated on a 2D brain data set, showing excellent performance even using only 1\% of the annotated data. The results show that our approach outperforms conventional semi-supervised segmentation methods (e.g. teacher-student model), particularly in a low percentage of annotation scenario. GitHub: https://github.com/ruizhe-l/UniSegReg.

Ruizhe Li, Yanjun Gao

Large Language Models (LLMs), such as the GPT-4 and LLaMA families, have demonstrated considerable success across diverse tasks, including multiple-choice questions (MCQs). However, these models exhibit a positional bias, particularly an even worse anchored bias in the GPT-2 family, where they consistently favour the first choice 'A' in MCQs during inference. This anchored bias challenges the integrity of GPT-2's decision-making process, as it skews performance based on the position rather than the content of the choices in MCQs. In this study, we utilise the mechanistic interpretability approach to identify the internal modules within GPT-2 models responsible for this bias. We focus on the Multi-Layer Perceptron (MLP) layers and attention heads, using the "logit lens" method to trace and modify the specific value vectors that contribute to the bias. By updating these vectors within MLP and recalibrating attention patterns to neutralise the preference for the first choice 'A', we effectively mitigate the anchored bias. Our interventions not only mitigate the bias but also improve the overall MCQ prediction accuracy for the GPT-2 family across various datasets. This work represents the first comprehensive mechanistic analysis of anchored bias from the failing cases in MCQs within the GPT-2 models, introducing targeted, minimal-intervention strategies that significantly enhance GPT2 model robustness and accuracy in MCQs. Our code is available at https://github.com/ruizheliUOA/Anchored_Bias_GPT2.

Ruizhe Li, Matteo Bastiani, Dorothee Auer et al.

Brain age estimation based on magnetic resonance imaging (MRI) is an active research area in early diagnosis of some neurodegenerative diseases (e.g. Alzheimer, Parkinson, Huntington, etc.) for elderly people or brain underdevelopment for the young group. Deep learning methods have achieved the state-of-the-art performance in many medical image analysis tasks, including brain age estimation. However, the performance and generalisability of the deep learning model are highly dependent on the quantity and quality of the training data set. Both collecting and annotating brain MRI data are extremely time-consuming. In this paper, to overcome the data scarcity problem, we propose a generative adversarial network (GAN) based image synthesis method. Different from the existing GAN-based methods, we integrate a task-guided branch (a regression model for age estimation) to the end of the generator in GAN. By adding a task-guided loss to the conventional GAN loss, the learned low-dimensional latent space and the synthesised images are more task-specific. It helps to boost the performance of the down-stream task by combining the synthesised images and real images for model training. The proposed method was evaluated on a public brain MRI data set for age estimation. Our proposed method outperformed (statistically significant) a deep convolutional neural network based regression model and the GAN-based image synthesis method without the task-guided branch. More importantly, it enables the identification of age-related brain regions in the image space. The code is available on GitHub (https://github.com/ruizhe-l/tgb-gan).

Kang Wang, Chen Qin, Zhang Shi et al.

Deep learning models have achieved state-of-the-art performance in automated Cardiac Magnetic Resonance (CMR) analysis. However, the efficacy of these models is highly dependent on the availability of high-quality, artifact-free images. In clinical practice, CMR acquisitions are frequently degraded by respiratory motion, yet the robustness of deep learning models against such artifacts remains an underexplored problem. To promote research in this domain, we organized the MICCAI CMRxMotion challenge. We curated and publicly released a dataset of 320 CMR cine series from 40 healthy volunteers who performed specific breathing protocols to induce a controlled spectrum of motion artifacts. The challenge comprised two tasks: 1) automated image quality assessment to classify images based on motion severity, and 2) robust myocardial segmentation in the presence of motion artifacts. A total of 22 algorithms were submitted and evaluated on the two designated tasks. This paper presents a comprehensive overview of the challenge design and dataset, reports the evaluation results for the top-performing methods, and further investigates the impact of motion artifacts on five clinically relevant biomarkers. All resources and code are publicly available at: https://github.com/CMRxMotion

Ruizhe Li, Dorothee Auer, Christian Wagner et al.

Deep learning based image segmentation has achieved the state-of-the-art performance in many medical applications such as lesion quantification, organ detection, etc. However, most of the methods rely on supervised learning, which require a large set of high-quality labeled data. Data annotation is generally an extremely time-consuming process. To address this problem, we propose a generic semi-supervised learning framework for image segmentation based on a deep convolutional neural network (DCNN). An encoder-decoder based DCNN is initially trained using a few annotated training samples. This initially trained model is then copied into sub-models and improved iteratively using random subsets of unlabeled data with pseudo labels generated from models trained in the previous iteration. The number of sub-models is gradually decreased to one in the final iteration. We evaluate the proposed method on a public grand-challenge dataset for skin lesion segmentation. Our method is able to significantly improve beyond fully supervised model learning by incorporating unlabeled data.