RO-LLaMA: Generalist LLM for Radiation Oncology via Noise Augmentation and Consistency Regularization

Recent advancements in Artificial Intelligence (AI) have profoundly influenced medical fields, by providing tools to reduce clinical workloads. However, most AI models are constrained to execute uni-modal tasks, in stark contrast to the comprehensive approaches utilized by medical professionals. To address this, here we present RO-LLaMA, a versatile generalist large language model (LLM) tailored for the field of radiation oncology. This model seamlessly covers a wide range of the workflow of radiation oncologists, adept at various tasks such as clinical report summarization, radiation therapy plan suggestion, and plan-guided therapy target volume segmentation. In particular, to maximize the end-to-end performance, we further present a novel Consistency Embedding Fine-Tuning (CEFTune) technique, which boosts LLM's robustness to additional errors at the intermediates while preserving the capability of handling clean inputs, and creatively transform this concept into LLM-driven segmentation framework as Consistency Embedding Segmentation (CESEG). Experimental results on multi-centre cohort sets demonstrate our proposed RO-LLaMA's promising performance for diverse tasks with generalization capabilities.

LLM-driven Multimodal Target Volume Contouring in Radiation Oncology

Target volume contouring for radiation therapy is considered significantly more challenging than the normal organ segmentation tasks as it necessitates the utilization of both image and text-based clinical information. Inspired by the recent advancement of large language models (LLMs) that can facilitate the integration of the textural information and images, here we present a novel LLM-driven multi-modal AI that utilizes the clinical text information and is applicable to the challenging task of target volume contouring for radiation therapy, and validate it within the context of breast cancer radiation therapy target volume contouring. Using external validation and data-insufficient environments, which attributes highly conducive to real-world applications, we demonstrate that the proposed model exhibits markedly improved performance compared to conventional vision-only AI models, particularly exhibiting robust generalization performance and data-efficiency. To our best knowledge, this is the first LLM-driven multimodal AI model that integrates the clinical text information into target volume delineation for radiation oncology.

scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain

Single-cell RNA sequencing (scRNA-seq) has made significant strides in unraveling the intricate cellular diversity within complex tissues. This is particularly critical in the brain, presenting a greater diversity of cell types than other tissue types, to gain a deeper understanding of brain function within various cellular contexts. However, analyzing scRNA-seq data remains a challenge due to inherent measurement noise stemming from dropout events and the limited utilization of extensive gene expression information. In this work, we introduce scHyena, a foundation model designed to address these challenges and enhance the accuracy of scRNA-seq analysis in the brain. Specifically, inspired by the recent Hyena operator, we design a novel Transformer architecture called singe-cell Hyena (scHyena) that is equipped with a linear adaptor layer, the positional encoding via gene-embedding, and a {bidirectional} Hyena operator. This enables us to process full-length scRNA-seq data without losing any information from the raw data. In particular, our model learns generalizable features of cells and genes through pre-training scHyena using the full length of scRNA-seq data. We demonstrate the superior performance of scHyena compared to other benchmark methods in downstream tasks, including cell type classification and scRNA-seq imputation.

ED-NeRF: Efficient Text-Guided Editing of 3D Scene using Latent Space NeRF

Recently, there has been a significant advancement in text-to-image diffusion models, leading to groundbreaking performance in 2D image generation. These advancements have been extended to 3D models, enabling the generation of novel 3D objects from textual descriptions. This has evolved into NeRF editing methods, which allow the manipulation of existing 3D objects through textual conditioning. However, existing NeRF editing techniques have faced limitations in their performance due to slow training speeds and the use of loss functions that do not adequately consider editing. To address this, here we present a novel 3D NeRF editing approach dubbed ED-NeRF by successfully embedding real-world scenes into the latent space of the latent diffusion model (LDM) through a unique refinement layer. This approach enables us to obtain a NeRF backbone that is not only faster but also more amenable to editing compared to traditional image space NeRF editing. Furthermore, we propose an improved loss function tailored for editing by migrating the delta denoising score (DDS) distillation loss, originally used in 2D image editing to the three-dimensional domain. This novel loss function surpasses the well-known score distillation sampling (SDS) loss in terms of suitability for editing purposes. Our experimental results demonstrate that ED-NeRF achieves faster editing speed while producing improved output quality compared to state-of-the-art 3D editing models.

Ground-A-Video: Zero-shot Grounded Video Editing using Text-to-image Diffusion Models

Recent endeavors in video editing have showcased promising results in single-attribute editing or style transfer tasks, either by training text-to-video (T2V) models on text-video data or adopting training-free methods. However, when confronted with the complexities of multi-attribute editing scenarios, they exhibit shortcomings such as omitting or overlooking intended attribute changes, modifying the wrong elements of the input video, and failing to preserve regions of the input video that should remain intact. To address this, here we present a novel grounding-guided video-to-video translation framework called Ground-A-Video for multi-attribute video editing. Ground-A-Video attains temporally consistent multi-attribute editing of input videos in a training-free manner without aforementioned shortcomings. Central to our method is the introduction of Cross-Frame Gated Attention which incorporates groundings information into the latent representations in a temporally consistent fashion, along with Modulated Cross-Attention and optical flow guided inverted latents smoothing. Extensive experiments and applications demonstrate that Ground-A-Video's zero-shot capacity outperforms other baseline methods in terms of edit-accuracy and frame consistency. Further results and codes are provided at our project page (http://ground-a-video.github.io).

Prompt-tuning latent diffusion models for inverse problems

We propose a new method for solving imaging inverse problems using text-to-image latent diffusion models as general priors. Existing methods using latent diffusion models for inverse problems typically rely on simple null text prompts, which can lead to suboptimal performance. To address this limitation, we introduce a method for prompt tuning, which jointly optimizes the text embedding on-the-fly while running the reverse diffusion process. This allows us to generate images that are more faithful to the diffusion prior. In addition, we propose a method to keep the evolution of latent variables within the range space of the encoder, by projection. This helps to reduce image artifacts, a major problem when using latent diffusion models instead of pixel-based diffusion models. Our combined method, called P2L, outperforms both image- and latent-diffusion model-based inverse problem solvers on a variety of tasks, such as super-resolution, deblurring, and inpainting.

Steerable Conditional Diffusion for Out-of-Distribution Adaptation in Imaging Inverse Problems

Denoising diffusion models have emerged as the go-to framework for solving inverse problems in imaging. A critical concern regarding these models is their performance on out-of-distribution (OOD) tasks, which remains an under-explored challenge. Realistic reconstructions inconsistent with the measured data can be generated, hallucinating image features that are uniquely present in the training dataset. To simultaneously enforce data-consistency and leverage data-driven priors, we introduce a novel sampling framework called Steerable Conditional Diffusion. This framework adapts the denoising network specifically to the available measured data. Utilising our proposed method, we achieve substantial enhancements in OOD performance across diverse imaging modalities, advancing the robust deployment of denoising diffusion models in real-world applications.

C-DARL: Contrastive diffusion adversarial representation learning for label-free blood vessel segmentation

Blood vessel segmentation in medical imaging is one of the essential steps for vascular disease diagnosis and interventional planning in a broad spectrum of clinical scenarios in image-based medicine and interventional medicine. Unfortunately, manual annotation of the vessel masks is challenging and resource-intensive due to subtle branches and complex structures. To overcome this issue, this paper presents a self-supervised vessel segmentation method, dubbed the contrastive diffusion adversarial representation learning (C-DARL) model. Our model is composed of a diffusion module and a generation module that learns the distribution of multi-domain blood vessel data by generating synthetic vessel images from diffusion latent. Moreover, we employ contrastive learning through a mask-based contrastive loss so that the model can learn more realistic vessel representations. To validate the efficacy, C-DARL is trained using various vessel datasets, including coronary angiograms, abdominal digital subtraction angiograms, and retinal imaging. Experimental results confirm that our model achieves performance improvement over baseline methods with noise robustness, suggesting the effectiveness of C-DARL for vessel segmentation.

Generative AI for Medical Imaging: extending the MONAI Framework

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.

Energy-Based Cross Attention for Bayesian Context Update in Text-to-Image Diffusion Models

Despite the remarkable performance of text-to-image diffusion models in image generation tasks, recent studies have raised the issue that generated images sometimes cannot capture the intended semantic contents of the text prompts, which phenomenon is often called semantic misalignment. To address this, here we present a novel energy-based model (EBM) framework. Specifically, we first formulate EBMs of latent image representations and text embeddings in each cross-attention layer of the denoising autoencoder. Then, we obtain the gradient of the log posterior of context vectors, which can be updated and transferred to the subsequent cross-attention layer, thereby implicitly minimizing a nested hierarchy of energy functions. Our latent EBMs further allow zero-shot compositional generation as a linear combination of cross-attention outputs from different contexts. Using extensive experiments, we demonstrate that the proposed method is highly effective in handling various image generation tasks, including multi-concept generation, text-guided image inpainting, and real and synthetic image editing.