SAM & SAM 2 in 3D Slicer: SegmentWithSAM Extension for Annotating Medical Images

Creating annotations for 3D medical data is time-consuming and often requires highly specialized expertise. Various tools have been implemented to aid this process. Segment Anything Model 2 (SAM 2) offers a general-purpose prompt-based segmentation algorithm designed to annotate videos. In this paper, we adapt this model to the annotation of 3D medical images and offer our implementation in the form of an extension to the popular annotation software: 3D Slicer. Our extension allows users to place point prompts on 2D slices to generate annotation masks and propagate these annotations across entire volumes in either single-directional or bi-directional manners. Our code is publicly available on https://github.com/mazurowski-lab/SlicerSegmentWithSAM and can be easily installed directly from the Extension Manager of 3D Slicer as well.

Rethinking Perceptual Metrics for Medical Image Translation

Modern medical image translation methods use generative models for tasks such as the conversion of CT images to MRI. Evaluating these methods typically relies on some chosen downstream task in the target domain, such as segmentation. On the other hand, task-agnostic metrics are attractive, such as the network feature-based perceptual metrics (e.g., FID) that are common to image translation in general computer vision. In this paper, we investigate evaluation metrics for medical image translation on two medical image translation tasks (GE breast MRI to Siemens breast MRI and lumbar spine MRI to CT), tested on various state-of-the-art translation methods. We show that perceptual metrics do not generally correlate with segmentation metrics due to them extending poorly to the anatomical constraints of this sub-field, with FID being especially inconsistent. However, we find that the lesser-used pixel-level SWD metric may be useful for subtle intra-modality translation. Our results demonstrate the need for further research into helpful metrics for medical image translation.

ContourDiff: Unpaired Image Translation with Contour-Guided Diffusion Models

Accurately translating medical images across different modalities (e.g., CT to MRI) has numerous downstream clinical and machine learning applications. While several methods have been proposed to achieve this, they often prioritize perceptual quality with respect to output domain features over preserving anatomical fidelity. However, maintaining anatomy during translation is essential for many tasks, e.g., when leveraging masks from the input domain to develop a segmentation model with images translated to the output domain. To address these challenges, we propose ContourDiff, a novel framework that leverages domain-invariant anatomical contour representations of images. These representations are simple to extract from images, yet form precise spatial constraints on their anatomical content. We introduce a diffusion model that converts contour representations of images from arbitrary input domains into images in the output domain of interest. By applying the contour as a constraint at every diffusion sampling step, we ensure the preservation of anatomical content. We evaluate our method by training a segmentation model on images translated from CT to MRI with their original CT masks and testing its performance on real MRIs. Our method outperforms other unpaired image translation methods by a significant margin, furthermore without the need to access any input domain information during training.

Anatomically-Controllable Medical Image Generation with Segmentation-Guided Diffusion Models

Diffusion models have enabled remarkably high-quality medical image generation, which can help mitigate the expenses of acquiring and annotating new images by supplementing small or imbalanced datasets, along with other applications. However, these are hampered by the challenge of enforcing global anatomical realism in generated images. To this end, we propose a diffusion model for anatomically-controlled medical image generation. Our model follows a multi-class anatomical segmentation mask at each sampling step and incorporates a \textit{random mask ablation} training algorithm, to enable conditioning on a selected combination of anatomical constraints while allowing flexibility in other anatomical areas. This also improves the network's learning of anatomical realism for the completely unconditional (unconstrained generation) case. Comparative evaluation on breast MRI and abdominal/neck-to-pelvis CT datasets demonstrates superior anatomical realism and input mask faithfulness over state-of-the-art models. We also offer an accessible codebase and release a dataset of generated paired breast MRIs. Our approach facilitates diverse applications, including pre-registered image generation, counterfactual scenarios, and others.

SegmentAnyBone: A Universal Model that Segments Any Bone at Any Location on MRI

Magnetic Resonance Imaging (MRI) is pivotal in radiology, offering non-invasive and high-quality insights into the human body. Precise segmentation of MRIs into different organs and tissues would be highly beneficial since it would allow for a higher level of understanding of the image content and enable important measurements, which are essential for accurate diagnosis and effective treatment planning. Specifically, segmenting bones in MRI would allow for more quantitative assessments of musculoskeletal conditions, while such assessments are largely absent in current radiological practice. The difficulty of bone MRI segmentation is illustrated by the fact that limited algorithms are publicly available for use, and those contained in the literature typically address a specific anatomic area. In our study, we propose a versatile, publicly available deep-learning model for bone segmentation in MRI across multiple standard MRI locations. The proposed model can operate in two modes: fully automated segmentation and prompt-based segmentation. Our contributions include (1) collecting and annotating a new MRI dataset across various MRI protocols, encompassing over 300 annotated volumes and 8485 annotated slices across diverse anatomic regions; (2) investigating several standard network architectures and strategies for automated segmentation; (3) introducing SegmentAnyBone, an innovative foundational model-based approach that extends Segment Anything Model (SAM); (4) comparative analysis of our algorithm and previous approaches; and (5) generalization analysis of our algorithm across different anatomical locations and MRI sequences, as well as an external dataset. We publicly release our model at https://github.com/mazurowski-lab/SegmentAnyBone.

High Efficiency Inference Accelerating Algorithm for NOMA-based Mobile Edge Computing

Splitting the inference model between device, edge server, and cloud can improve the performance of EI greatly. Additionally, the non-orthogonal multiple access (NOMA), which is the key supporting technologies of B5G/6G, can achieve massive connections and high spectrum efficiency. Motivated by the benefits of NOMA, integrating NOMA with model split in MEC to reduce the inference latency further becomes attractive. However, the NOMA based communication during split inference has not been properly considered in previous works. Therefore, in this paper, we integrate the NOMA into split inference in MEC, and propose the effective communication and computing resource allocation algorithm to accelerate the model inference at edge. Specifically, when the mobile user has a large model inference task needed to be calculated in the NOMA-based MEC, it will take the energy consumption of both device and edge server and the inference latency into account to find the optimal model split strategy, subchannel allocation strategy (uplink and downlink), and transmission power allocation strategy (uplink and downlink). Since the minimum inference delay and energy consumption cannot be satisfied simultaneously, and the variables of subchannel allocation and model split are discrete, the gradient descent (GD) algorithm is adopted to find the optimal tradeoff between them. Moreover, the loop iteration GD approach (Li-GD) is proposed to reduce the complexity of GD algorithm that caused by the parameter discrete. Additionally, the properties of the proposed algorithm are also investigated, which demonstrate the effectiveness of the proposed algorithms.

MoCo-Transfer: Investigating out-of-distribution contrastive learning for limited-data domains

Medical imaging data is often siloed within hospitals, limiting the amount of data available for specialized model development. With limited in-domain data, one might hope to leverage larger datasets from related domains. In this paper, we analyze the benefit of transferring self-supervised contrastive representations from moment contrast (MoCo) pretraining on out-of-distribution data to settings with limited data. We consider two X-ray datasets which image different parts of the body, and compare transferring from each other to transferring from ImageNet. We find that depending on quantity of labeled and unlabeled data, contrastive pretraining on larger out-of-distribution datasets can perform nearly as well or better than MoCo pretraining in-domain, and pretraining on related domains leads to higher performance than if one were to use the ImageNet pretrained weights. Finally, we provide a preliminary way of quantifying similarity between datasets.

Evaluating Model Performance in Medical Datasets Over Time

Machine learning (ML) models deployed in healthcare systems must face data drawn from continually evolving environments. However, researchers proposing such models typically evaluate them in a time-agnostic manner, splitting datasets according to patients sampled randomly throughout the entire study time period. This work proposes the Evaluation on Medical Datasets Over Time (EMDOT) framework, which evaluates the performance of a model class across time. Inspired by the concept of backtesting, EMDOT simulates possible training procedures that practitioners might have been able to execute at each point in time and evaluates the resulting models on all future time points. Evaluating both linear and more complex models on six distinct medical data sources (tabular and imaging), we show how depending on the dataset, using all historical data may be ideal in many cases, whereas using a window of the most recent data could be advantageous in others. In datasets where models suffer from sudden degradations in performance, we investigate plausible explanations for these shocks. We release the EMDOT package to help facilitate further works in deployment-oriented evaluation over time.

Model Evaluation in Medical Datasets Over Time

Machine learning models deployed in healthcare systems face data drawn from continually evolving environments. However, researchers proposing such models typically evaluate them in a time-agnostic manner, with train and test splits sampling patients throughout the entire study period. We introduce the Evaluation on Medical Datasets Over Time (EMDOT) framework and Python package, which evaluates the performance of a model class over time. Across five medical datasets and a variety of models, we compare two training strategies: (1) using all historical data, and (2) using a window of the most recent data. We note changes in performance over time, and identify possible explanations for these shocks.

WeLM: A Well-Read Pre-trained Language Model for Chinese

Large Language Models pre-trained with self-supervised learning have demonstrated impressive zero-shot generalization capabilities on a wide spectrum of tasks. In this work, we present WeLM: a well-read pre-trained language model for Chinese that is able to seamlessly perform different types of tasks with zero or few-shot demonstrations. WeLM is trained with 10B parameters by "reading" a curated high-quality corpus covering a wide range of topics. We show that WeLM is equipped with broad knowledge on various domains and languages. On 18 monolingual (Chinese) tasks, WeLM can significantly outperform existing pre-trained models with similar sizes and match the performance of models up to 25 times larger. WeLM also exhibits strong capabilities in multi-lingual and code-switching understanding, outperforming existing multilingual language models pre-trained on 30 languages. Furthermore, We collected human-written prompts for a large set of supervised datasets in Chinese and fine-tuned WeLM with multi-prompted training. The resulting model can attain strong generalization on unseen types of tasks and outperform the unsupervised WeLM in zero-shot learning. Finally, we demonstrate that WeLM has basic skills at explaining and calibrating the decisions from itself, which can be promising directions for future research. Our models can be applied from https://welm.weixin.qq.com/docs/api/.