Benchmarking and Boosting Radiology Report Generation for 3D High-Resolution Medical Images

Automatic radiology report generation can significantly benefit the labor-intensive process of report writing by radiologists, especially for 3D radiographs like CT scans, which are crucial for broad clinical diagnostics yet underexplored compared to 2D radiographs. Existing methods often handle 3D volumes either slice-wise or with aggressive downsampling due to current GPU memory limitations, which results in a loss of the inherent 3D nature and critical details. To overcome these issues, we introduce a novel framework that efficiently and effectively generates radiology reports for high-resolution (HR) 3D volumes, based on large language models (LLMs). Specifically, our framework utilizes low-resolution (LR) visual tokens as queries to mine information from HR tokens, preserving detailed HR information while reducing computational costs by only processing HR informed LR visual queries. Further benefiting the field, we curate and release BIMCV-RG, a new dataset with 5,328 HR 3D volumes and paired reports, establishing the first benchmarks for report generation from 3D HR medical images. Our method consistently surpasses existing methods on this benchmark across three different settings: normal-resolution, high-resolution inputs, and zero-shot domain transfer, all at an acceptable computational cost, trainable on a single A100-80G.

Noise2Noise Denoising of CRISM Hyperspectral Data

Hyperspectral data acquired by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) have allowed for unparalleled mapping of the surface mineralogy of Mars. Due to sensor degradation over time, a significant portion of the recently acquired data is considered unusable. Here a new data-driven model architecture, Noise2Noise4Mars (N2N4M), is introduced to remove noise from CRISM images. Our model is self-supervised and does not require zero-noise target data, making it well suited for use in Planetary Science applications where high quality labelled data is scarce. We demonstrate its strong performance on synthetic-noise data and CRISM images, and its impact on downstream classification performance, outperforming benchmark methods on most metrics. This allows for detailed analysis for critical sites of interest on the Martian surface, including proposed lander sites.

BIMCV-R: A Landmark Dataset for 3D CT Text-Image Retrieval

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Electrocardiogram Instruction Tuning for Report Generation

Electrocardiogram (ECG) serves as the primary non-invasive diagnostic tool for cardiac conditions monitoring, are crucial in assisting clinicians. Recent studies have concentrated on classifying cardiac conditions using ECG data but have overlooked ECG report generation, which is not only time-consuming but also requires clinical expertise. To automate ECG report generation and ensure its versatility, we propose the Multimodal ECG Instruction Tuning (MEIT) framework, the \textit{first} attempt to tackle ECG report generation with LLMs and multimodal instructions. To facilitate future research, we establish a benchmark to evaluate MEIT with various LLMs backbones across two large-scale ECG datasets. Our approach uniquely aligns the representations of the ECG signal and the report, and we conduct extensive experiments to benchmark MEIT with nine open source LLMs, using more than 800,000 ECG reports. MEIT's results underscore the superior performance of instruction-tuned LLMs, showcasing their proficiency in quality report generation, zero-shot capabilities, and resilience to signal perturbation. These findings emphasize the efficacy of our MEIT framework and its potential for real-world clinical application.

Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets.

Explainable Global Wildfire Prediction Models using Graph Neural Networks

Wildfire prediction has become increasingly crucial due to the escalating impacts of climate change. Traditional CNN-based wildfire prediction models struggle with handling missing oceanic data and addressing the long-range dependencies across distant regions in meteorological data. In this paper, we introduce an innovative Graph Neural Network (GNN)-based model for global wildfire prediction. We propose a hybrid model that combines the spatial prowess of Graph Convolutional Networks (GCNs) with the temporal depth of Long Short-Term Memory (LSTM) networks. Our approach uniquely transforms global climate and wildfire data into a graph representation, addressing challenges such as null oceanic data locations and long-range dependencies inherent in traditional models. Benchmarking against established architectures using an unseen ensemble of JULES-INFERNO simulations, our model demonstrates superior predictive accuracy. Furthermore, we emphasise the model's explainability, unveiling potential wildfire correlation clusters through community detection and elucidating feature importance via Integrated Gradient analysis. Our findings not only advance the methodological domain of wildfire prediction but also underscore the importance of model transparency, offering valuable insights for stakeholders in wildfire management.

Multi-fidelity physics constrained neural networks for dynamical systems

Physics-constrained neural networks are commonly employed to enhance prediction robustness compared to purely data-driven models, achieved through the inclusion of physical constraint losses during the model training process. However, one of the major challenges of physics-constrained neural networks consists of the training complexity especially for high-dimensional systems. In fact, conventional physics-constrained models rely on singular-fidelity data necessitating the assessment of physical constraints within high-dimensional fields, which introduces computational difficulties. Furthermore, due to the fixed input size of the neural networks, employing multi-fidelity training data can also be cumbersome. In this paper, we propose the Multi-Scale Physics-Constrained Neural Network (MSPCNN), which offers a novel methodology for incorporating data with different levels of fidelity into a unified latent space through a customised multi-fidelity autoencoder. Additionally, multiple decoders are concurrently trained to map latent representations of inputs into various fidelity physical spaces. As a result, during the training of predictive models, physical constraints can be evaluated within low-fidelity spaces, yielding a trade-off between training efficiency and accuracy. In addition, unlike conventional methods, MSPCNN also manages to employ multi-fidelity data to train the predictive model. We assess the performance of MSPCNN in two fluid dynamics problems, namely a two-dimensional Burgers' system and a shallow water system. Numerical results clearly demonstrate the enhancement of prediction accuracy and noise robustness when introducing physical constraints in low-fidelity fields. On the other hand, as expected, the training complexity can be significantly reduced by computing physical constraint loss in the low-fidelity field rather than the high-fidelity one.

Data Assimilation using ERA5, ASOS, and the U-STN model for Weather Forecasting over the UK

In recent years, the convergence of data-driven machine learning models with Data Assimilation (DA) offers a promising avenue for enhancing weather forecasting. This study delves into this emerging trend, presenting our methodologies and outcomes. We harnessed the UK's local ERA5 850 hPa temperature data and refined the U-STN12 global weather forecasting model, tailoring its predictions to the UK's climate nuances. From the ASOS network, we sourced T2m data, representing ground observations across the UK. We employed the advanced kriging method with a polynomial drift term for consistent spatial resolution. Furthermore, Gaussian noise was superimposed on the ERA5 T850 data, setting the stage for ensuing multi-time step synthetic observations. Probing into the assimilation impacts, the ASOS T2m data was integrated with the ERA5 T850 dataset. Our insights reveal that while global forecast models can adapt to specific regions, incorporating atmospheric data in DA significantly bolsters model accuracy. Conversely, the direct assimilation of surface temperature data tends to mitigate this enhancement, tempering the model's predictive prowess.

Freeze the backbones: A Parameter-Efficient Contrastive Approach to Robust Medical Vision-Language Pre-training

Modern healthcare often utilises radiographic images alongside textual reports for diagnostics, encouraging the use of Vision-Language Self-Supervised Learning (VL-SSL) with large pre-trained models to learn versatile medical vision representations. However, most existing VL-SSL frameworks are trained end-to-end, which is computation-heavy and can lose vital prior information embedded in pre-trained encoders. To address both issues, we introduce the backbone-agnostic Adaptor framework, which preserves medical knowledge in pre-trained image and text encoders by keeping them frozen, and employs a lightweight Adaptor module for cross-modal learning. Experiments on medical image classification and segmentation tasks across three datasets reveal that our framework delivers competitive performance while cutting trainable parameters by over 90% compared to current pre-training approaches. Notably, when fine-tuned with just 1% of data, Adaptor outperforms several Transformer-based methods trained on full datasets in medical image segmentation.

T3D: Towards 3D Medical Image Understanding through Vision-Language Pre-training

Expert annotation of 3D medical image for downstream analysis is resource-intensive, posing challenges in clinical applications. Visual self-supervised learning (vSSL), though effective for learning visual invariance, neglects the incorporation of domain knowledge from medicine. To incorporate medical knowledge into visual representation learning, vision-language pre-training (VLP) has shown promising results in 2D image. However, existing VLP approaches become generally impractical when applied to high-resolution 3D medical images due to GPU hardware constraints and the potential loss of critical details caused by downsampling, which is the intuitive solution to hardware constraints. To address the above limitations, we introduce T3D, the first VLP framework designed for high-resolution 3D medical images. T3D incorporates two text-informed pretext tasks: (\lowerromannumeral{1}) text-informed contrastive learning; (\lowerromannumeral{2}) text-informed image restoration. These tasks focus on learning 3D visual representations from high-resolution 3D medical images and integrating clinical knowledge from radiology reports, without distorting information through forced alignment of downsampled volumes with detailed anatomical text. Trained on a newly curated large-scale dataset of 3D medical images and radiology reports, T3D significantly outperforms current vSSL methods in tasks like organ and tumor segmentation, as well as disease classification. This underlines T3D's potential in representation learning for 3D medical image analysis. All data and code will be available upon acceptance.