Methods for medical image analysis using self-supervised learning

Abstract

The present invention relates to a method (1400) comprising obtaining a first teacher dataset comprising an unannotated multi-dimensional medical image (202), and performing a self-supervised mask image modeling (MIM) training process (200) to pre-train an image encoder (150) with the first teacher dataset. The method also comprises obtaining a second teacher dataset (203) comprising annotated multi-dimensional medical images (204). Here, each of the annotated multi-dimensional medical images comprises a plurality of image voxels (206) paired respectively with corresponding ground truth labels (208) indicating the class to which the corresponding image voxels belong. The method also comprises performing a supervised training process (160) to train an image analysis model (170) with the second teacher dataset to cause the image analysis model to learn a method for predicting ground truth labels corresponding to the plurality of image voxels of each of the annotated multi-dimensional medical images. The image analysis model incorporates the pre-trained image encoder.

Description

[Technical Field]

[0001] The present disclosure relates to medical image analysis using self-supervised learning. [Background technology]

[0002] Multidimensional medical images, such as three-dimensional (3D) medical images, provide an enhanced picture of the inside of a patient's body to help facilitate medical analysis, diagnosis, or treatment of the patient. Such medical images can be generated using a variety of modalities, including, for example, computed tomography (CT) or magnetic resonance imaging (MRI). Summary of the Invention

[0003] A first aspect of the present disclosure provides a computer-implemented method that, when executed on data processing hardware, causes the data processing hardware to perform operations including obtaining a first training dataset including a plurality of unannotated multidimensional medical images and performing a self-supervised masked image modeling (MIM) training process to pre-train an image encoder on the first training dataset. The operations also include obtaining a second training dataset including a plurality of annotated multidimensional medical images, each of the annotated multidimensional medical images including a plurality of image voxels, each paired with a corresponding ground-truth label indicating a class to which the corresponding image voxel belongs. The operations also include performing a supervised training process to train an image analysis model on the second training dataset, teaching the image analysis model to learn how to predict ground-truth labels corresponding to each of the plurality of image voxels in the annotated multidimensional medical images. The image analysis model incorporates the pre-trained image encoder.

[0004] Embodiments of the present disclosure may include one or more of the following optional features: In some embodiments, for each unannotated multidimensional medical image corresponding to the first training dataset, performing a self-supervised MIM training process to pre-train an image encoder includes: using an image tokenizer configured to receive the corresponding unannotated multidimensional medical image as input to generate a set of discrete visual tokens characterizing the corresponding unannotated multidimensional medical image; segmenting the corresponding unannotated multidimensional medical image into a plurality of image patches; and randomly masking some of the segmented image patches from the corresponding unannotated multidimensional medical image. For each masked image patch, the operations also include generating, using the image encoder, an encoded hidden representation for the masked image patch; and generating, using a decoder, a corresponding predicted token based on the encoded hidden representation. Here, the operations also include determining a training loss based on the predicted token generated for the masked image patch and the corresponding visual token from the set of discrete visual tokens matching the masked image patch; and updating parameters of the image encoder based on the training loss. In these embodiments, the image encoder may include multiple multi-head attention layers, and the decoder may include multiple multi-head attention layers. Additionally or alternatively, randomly masking the portion of the image patch may include randomly masking the portion of the image patch using one of a central region masking strategy, a block-wise masking strategy, or a uniformly random masking strategy using various masked patch sizes and masking ratios. The number of visual tokens in the series of discrete visual tokens may be equal to the number of image patches in the plurality of image patches.

[0005] In some examples, performing a self-supervised MIM training process for each unannotated multidimensional medical image corresponding to the first training dataset to pre-train an image encoder includes: dividing the corresponding unannotated multidimensional medical image into a plurality of image patches, each image patch represented by a corresponding set of raw voxel values; and randomly masking a portion of the divided image patch from the corresponding unannotated multidimensional medical image. For each masked image patch, the operation includes generating an encoded hidden representation for the masked image patch using an image encoder; and generating predicted voxel values ​​for the masked image patch based on the encoded hidden representation using a prediction head. Here, the operation also includes determining a training loss based on the predicted voxel values ​​generated for the masked image patch and the corresponding set of raw voxel values ​​representing the masked image patch; and updating parameters of the image encoder based on the training loss. In these examples, the image encoder may include multiple multi-head attention layers, and the prediction head may include a single linear layer prediction head and may be configured to generate predicted voxel values ​​from the encoded hidden representation without the use of a decoder. Additionally or alternatively, randomly masking portions of the image patches may include randomly masking portions of the image patches using one of a central region masking strategy, a block-wise masking strategy, or a uniform random masking strategy using various masked patch sizes and masking ratios. In an embodiment, the image analysis model includes a tumor segmentation model. By way of example, the image analysis model includes a multi-organ segmentation model.

[0006] Another aspect of the present disclosure provides a system including data processing hardware and memory hardware in communication with the data processing hardware. The memory hardware stores instructions that, when executed on the data processing hardware, cause the data processing hardware to perform operations including obtaining a first teacher dataset including a plurality of unannotated multidimensional medical images and performing a self-supervised masked image modeling (MIM) training process to pre-train an image encoder on the first teacher dataset. The operations also include obtaining a second teacher dataset including a plurality of annotated multidimensional medical images, where each annotated multidimensional medical image includes a plurality of image voxels, each paired with a corresponding ground truth label indicating a class to which the corresponding image voxel belongs. The operations also include performing a supervised training process to train an image analysis model on the second teacher dataset, teaching the image analysis model to learn how to predict a corresponding ground truth label for each of the plurality of image voxels in the annotated multidimensional medical images. The image analysis model incorporates the pre-trained image encoder.

[0007] This aspect may include one or more of the following optional features: In some embodiments, for each unannotated multidimensional medical image corresponding to the first training dataset, performing a self-supervised MIM training process to pre-train an image encoder includes: using an image tokenizer configured to receive the corresponding unannotated multidimensional medical image as input to generate a set of discrete visual tokens characterizing the corresponding unannotated multidimensional medical image; segmenting the corresponding unannotated multidimensional medical image into a plurality of image patches; and randomly masking some of the segmented image patches from the corresponding unannotated multidimensional medical image. For each masked image patch, the operations also include generating, using the image encoder, an encoded hidden representation for the masked image patch; and generating, using a decoder, a corresponding predicted token based on the encoded hidden representation. Here, the operations also include determining a training loss based on the predicted token generated for the masked image patch and the corresponding visual token from the set of discrete visual tokens that match the masked image patch; and updating parameters of the image encoder based on the training loss. In these embodiments, the image encoder may include multiple multi-head attention layers, and the decoder may include multiple multi-head attention layers. Additionally or alternatively, randomly masking the portion of the image patch may include randomly masking the portion of the image patch using one of a central region masking strategy, a block-wise masking strategy, or a uniform random masking strategy using various masked patch sizes and masking ratios. The number of visual tokens in the series of discrete visual tokens may be equal to the number of image patches in the plurality of image patches.

[0008] In some examples, performing a self-supervised MIM training process for each unannotated multidimensional medical image corresponding to the first training dataset to pre-train an image encoder includes: dividing the corresponding unannotated multidimensional medical image into a plurality of image patches, each image patch represented by a corresponding set of raw voxel values; and randomly masking a portion of the divided image patch from the corresponding unannotated multidimensional medical image. For each masked image patch, the operation includes generating an encoded hidden representation for the masked image patch using an image encoder; and generating predicted voxel values ​​for the masked image patch based on the encoded hidden representation using a prediction head. Here, the operation also includes determining a training loss based on the predicted voxel values ​​generated for the masked image patch and the corresponding set of raw voxel values ​​representing the masked image patch; and updating parameters of the image encoder based on the training loss. In these examples, the image encoder may include multiple multi-head attention layers, and the prediction head may include a single linear layer prediction head and may be configured to generate predicted voxel values ​​from the encoded hidden representation without the use of a decoder. Additionally or alternatively, randomly masking portions of the image patches may include randomly masking portions of the image patches using one of a central region masking strategy, a block-wise masking strategy, or a uniform random masking strategy using various masked patch sizes and masking ratios. In an embodiment, the image analysis model includes a tumor segmentation model. By way of example, the image analysis model includes a multi-organ segmentation model.

[0009] The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Other aspects, features, and advantages will be apparent from the description and drawings, and from the claims. [Brief explanation of the drawings]

[0010] [Figure 1] FIG. 1 is a schematic diagram of a system for pre-training an image encoder using self-supervised mask image modeling (MIM) and training an image analysis model that incorporates the pre-trained image encoder. [Figure 2A] FIG. 2B is a schematic diagram of an example of self-supervised MIM for pre-training the image encoder of FIG. 1. [Figure 2B] FIG. 2A is a schematic diagram of an example of self-supervised MIM for pre-training the image encoder of FIG. 1. [Figure 3] Figure 3 shows an example of an input, masked, and reconstructed 3D CT image using a pre-trained image encoder with a simple MIM architecture. [Figure 4] Figure 4 shows an example of an input, masked, and reconstructed 3D CT image using a pre-trained image encoder with a mask autoencoder (MAE) architecture. [Figure 5] FIG. 5 is a table showing Dice coefficients for multi-organ segmentation images using an image analysis model. [Figure 6] Figure 6 is a table listing the supplemental baseline settings for the supervised training process for training the image analysis model of Figure 1. [Figure 7] Figure 7 is a table listing the supplemental baseline settings for the supervised training process for training the image analysis model of Figure 1. [Figure 8] Figure 8 is a table listing the pre-training settings for the self-supervised MIM training process in Figure 1. [Figure 9] Figure 9 is a table revealing the results of using a machine learning model on brain tumor segmentation images after pre-training with the Bra TS teacher dataset. [Figure 10] Figure 10 shows a plot of self-supervised MIM training of an image encoder followed by downstream supervised fine-tuning. [Figure 11]FIG. 11 is a table showing the ablation studies applied for various masked patch sizes and masking ratios for a multi-organ segmentation task. [Figure 12] FIG. 12 is a table showing the ablation studies applied for different masked patch sizes and masking ratios for the brain tumor segmentation task. [Figure 13] FIG. 13 is a table showing the results of pre-training an image encoder with a fixed patch size and a fixed masking ratio. [Figure 14] FIG. 14 is a flowchart outlining example operations for training an image analysis model to perform vision tasks on multidimensional medical images. [Figure 15] FIG. 15 is a schematic diagram of an example computing device that may be used to implement the systems and methods described herein.

[0011] Like reference symbols in the various drawings indicate like elements. DETAILED DESCRIPTION OF THE INVENTION

[0012] Computer vision analysis is witnessing a paradigm shift from the use of convolutional neural networks to the use of multi-head attention-based architectures. While this disclosure references, as an example, a transformer-based architecture using self-attention as one form of multi-head attention-based architecture, this disclosure may use other forms of multi-head attention-based architectures that enhance multi-dimensional input images. In general, a transformer-based architecture (e.g., a vision transformer) divides a multi-dimensional input image into patches and produces patch embeddings as input to a transformer-based model for various vision tasks, including image classification, object detection, and image segmentation.

[0013] Three-dimensional (3D) medical imaging techniques, such as computed tomography (CT) or magnetic resonance imaging (MRI), are widely used to diagnose and treat a wide range of illnesses. In general, 3D medical stereoscopic images can help improve the speed and accuracy of diagnosing patient conditions. For example, accurately and quickly detecting and measuring tumor lesions from MRI or CT scans is crucial for disease prevention, early detection, and treatment plan optimization, and can foster the development of more effective clinical applications, ultimately improving patients' lives. A fundamental task performed in medical image analysis involves 3D image segmentation. Another fundamental task performed in medical image analysis involves image classification. The image classification task involves classifying input images into various categories. Generally, 3D image segmentation (also referred to as "3D semantic segmentation") aims to classify one or more specific objects by predicting the class corresponding to each voxel in a stereoscopic input image and separating each specific object from others by overlaying respective segmentation masks on the specific objects. 3D image segmentation has the potential to ease the burden of radiologists' daily workload by automating or assisting image interpretation workflow, ultimately improving clinical care and patient outcomes. 3D image segmentation tasks may include multi-organ segmentation, performed as a 13-class segmentation task with a single channel input, and brain tumor segmentation, performed as a 3-class segmentation task with a 4-channel input.

[0014] Training robust transformer-based image analysis models requires additionally annotated training data, exceeding the performance of traditional CNNs. However, the high expense of obtaining dedicated annotations of 3D medical volumetric images in specific domains often hinders attempts to leverage advanced techniques for clinical outcomes, such as using deep learning approaches to 3D medical image analysis. In short, annotation of large-scale 3D medical images by radiologists is limited by the high cost and time required to create them. Another limiting factor in 3D medical image processing is the sheer volume of data associated with the 3D medical images. The volume of data is determined by the increased dimensionality and resolution of the 3D images, resulting in significant processing complexity. As a result, the ability to effectively integrate radiomics endpoint information with other biomarker data for downstream tasks in clinical study design, such as tumor burden assessment and overall survival prediction, can be extremely challenging.

[0015] Transfer learning is the use of models learned from one context in another. Transfer learning from ordinary images can be used for medical image analysis, regardless of differences in image statistics, scale, and task-related characteristics. For example, transfer learning from ImageNet can accelerate convergence on medical images and can be useful when medical image training data is limited. Transfer learning using domain-specific data can also help resolve issues due to domain differences. For example, improved performance can be achieved following pre-training with labeled data from the same domain. However, this strategy can often be impractical due to the cost and time required to collect labeled data for various medical scenarios. Self-supervised learning offers a viable alternative, allowing the use of unlabeled / unannotated medical data.

[0016] Self-supervised learning is a training technique that emphasizes learning representations from unlabeled data, allowing low-capacity classifiers to achieve high accuracy using various embeddings. Contrastive learning is another example of a self-supervised learning strategy. Contrastive learning creates image similarities and dissimilarities (or simple similarities) between two or more domains, with data augmentation being important for contrast and related approaches. Self-supervised learning can be used in the medical field, such as for domain-specific, seemingly unrelated tasks, or for contrastive learning tailored to medical data. A range of self-supervised learning strategies can be applied to 3D medical images. For example, a model pre-trained on ImageNet can be applied to dermatology image classification. As another example, inpainting can be combined with contrastive learning in medical image segmentation.

[0017] Masked image modeling approaches typically mask out portions of the input image or encoded image tokens and have the model reconstruct the masked regions. Some existing MIM models use an encoder-decoder design followed by a projection head. The encoder assists in modeling the latent feature representation, while the decoder assists in resampling the latent vectors to the original image. The encoded or decoded embedding can then be matched to the original signal in the regions masked by the projection head. In particular, the decoder component can be designed to be lightweight to minimize training time. A lightweight decoder not only reduces computational complexity but also increases the encoder's ability to learn more generalizable representations that the decoder can easily grasp, transform, and propagate. The encoder can be used for fine-tuning. Encoding techniques such as SimMIM can eliminate the need for an entire decoder with a single projection layer.

[0018] Using a Vision Transformer (ViT), for example, an image can be divided into regular, non-overlapping patches (e.g., a 96x96x96 3D volume is divided into 216 patches of smaller 16x16x16 volumes), which are often considered as the basic processing unit of the Vision Transformer. There are several random masking techniques, including, but not limited to, a central region masking strategy, a complex block-by-block masking strategy, and / or a uniform random masking method at the patch level using various masked patch sizes and masking ratios.

[0019] In some examples, the image encoder includes a Vision Transformer (ViT) architecture, such as vanilla ViT (e.g., ViT3D, Swin Transformer 3D, and / or Attention Visual Network (e.g., VAN3D)), which inherits the attention mechanism to derive a hierarchical representation similar to, for example, Swin Transformer 3D, but using pure convolutions instead. Other forms of multi-head attention layers can be used by the image encoder, such as, but not limited to, a conformer layer, a performer layer, or a lightweight convolutional layer.

[0020] Embodiments of this document are directed to performing a self-supervised masked image modeling (MIM) training process to pre-train an image encoder on multiple unannotated (e.g., unlabeled) multidimensional medical images. As used herein, multidimensional images are referred to as 3D medical images, although the present disclosure is not limited thereto and may also include 4D medical images. The 3D medical images include volumetric slices from a CT or MRI of a region inside (or outside) a patient's body. The image encoder includes multiple multi-head attention layers. For example, the image encoder may include a transformer-based architecture that uses self-attention using a stack of transformer layers. As will become apparent, the image encoder is responsible for modeling latent feature representations of masked image patches, which can later be used to predict the original image signal in regions associated with the masked image patches. Through the self-supervised MIM training process, an image encoder pre-trained on unannotated 3D medical images can be adapted to a wide range of downstream vision tasks, such as 3D image segmentation and image classification.

[0021] The pre-trained image encoder may be integrated into an image analysis model and fine-tuned to use the annotated multidimensional medical images to perform a specific downstream vision task. The annotated multidimensional medical images used to fine-tune the pre-trained image encoder and ultimately train the medical image model to perform a specific vision task may each include a plurality of image voxels, each paired with a corresponding ground truth label indicating the class to which the corresponding image voxel belongs. In this manner, embodiments of the present disclosure are further directed to performing a supervised training process to train an image segmentation model on a plurality of annotated multidimensional medical images, thereby teaching the image segmentation model to learn how to predict ground truth labels corresponding to each of a plurality of image voxels in the annotated multidimensional medical images. The image segmentation model thereby includes a pre-trained image encoder that is initialized with unannotated multidimensional medical images via a self-supervised MIM training process and fine-tuned with annotated multidimensional medical images via a supervised training process. In some examples, the trained image analysis model includes an image segmentation model that performs 3D image segmentation tasks, such as multi-organ segmentation or tumor segmentation performed on 3D image slices from an MRI or CT scan of an internal body part. As described in more detail below, the trained image analysis model may receive as input multiple image patches from a multidimensional medical image (i.e., volumetric slices from an MRI or CT scan), generate an enhanced medical image based on features extracted from the multidimensional medical image, and perform image segmentation or image classification on the enhanced image. In an image segmentation scenario, the trained image analysis model may be trained to classify one or more specific objects (e.g., tumors or organs) in the enhanced image and separate each of the specific objects from one another by augmenting the enhanced image with respective segmentation masks that overlay the specific objects.As used herein, expanding an enhanced image that includes a segmentation mask includes expanding image voxels within the enhanced image that represent each object class and / or define the boundaries of each object class. Expanding the image voxels may include changing the color of the image voxels, adjusting the intensity of the image voxels, or expanding the image voxels in any suitable manner so that each classified object is distinct and identifiable within the enhanced image.

[0022] 1 illustrates an exemplary system 100 for pre-training an image encoder 150 via a self-supervised training process 200 to learn how to generate encoded feature representations 225 (FIGS. 2A and 2B) from unannotated 3D medical images 202, and fine-tuning the pre-trained image encoder 150 to perform downstream image tasks via a supervised training process 160. Specifically, the pre-trained image encoder 150 may be adapted for use with an image analysis model 170 to perform a specific vision task by training the image analysis model 170 on annotated 3D medical images 204. The system 100 includes a computing system 120 having data processing hardware 122 and memory hardware 124 in communication with the data processing hardware 122 and storing instructions that cause the data processing hardware 122 to perform operations. In some embodiments, the first computing system 120, 120a performs a self-supervised training process 200 to pre-train the image encoder 150, and then performs a supervised training process 160 to train an image analysis model 170 that incorporates the pre-trained image encoder 150 to perform downstream vision tasks on 3D medical images. In these embodiments, after the image analysis model 170 has been trained to perform downstream vision tasks, the first computing system 120a provides the trained image analysis model 170 to the second computing system 120, 120b, which may then execute the image analysis model 170 to generate enhanced 3D medical images 110, 110E from the raw 3D medical images 110, 110R and perform the downstream vision tasks on the enhanced 3D medical images 110E.

[0023] The first computing system 120a may include a distributed system (e.g., a cloud computing environment). The second computing system 120b may include a computing device (e.g., a desktop computer, workstation, laptop, tablet, etc.) that downloads the image analysis model 170 from the first computing system 120a. In some other embodiments, the first computing system 120a receives the 3D medical images 110R from the second computing system 120b and executes the image analysis model 170 to perform downstream vision tasks. In additional embodiments, the second computing system 120b receives the pre-trained image encoder 150 from the first computing system 120a via the self-supervised training process 200 and executes the supervised training process 160 to fine-tune the pre-trained image encoder on downstream vision tasks. In this scenario, the annotated MD images 204 may be processed locally on the second computing system 120b via the supervised training process 160, thereby protecting privacy and confidential data.

[0024] The self-supervised training process 200 trains the image encoder 150 with a first training dataset 201 including a plurality of unannotated multidimensional (MD) images 202. Specifically, and as described in more detail below with reference to FIGS. 2A and 2B , the self-supervised training process includes a self-supervised masked image modeling (MIM) training process. Each unannotated MD image 202 in the first training dataset 201 may include an image slice segmented from a patient's internal CT scan or MRI scan. As a result, the first training dataset 201 includes a corpus of unannotated MD medical images 202 relating to image slices from multiple patients' internal CT scans and / or MRI scans. As one example, the first training dataset 201 includes unannotated 3D CT scan images 202 obtained from The Cancer Imaging Archive-Covid19 (TCIA-Covid19) public dataset. Here, the unannotated 3D CT scan images include 771 unenhanced chest CT scans collected from 661 patients with Covid-19 infection.

[0025] In particular, self-supervised MIM training as disclosed herein is particularly advantageous for modeling 3D medical images by significantly accelerating training convergence and improving downstream performance. For example, when compared to simple control learning, when a trained image encoder 150 is adapted and fine-tuned to perform downstream vision tasks, training convergence can save up to 1.40x training costs to achieve the same or higher Dice coefficient. Similarly, downstream performance of the downstream vision task of image segmentation can achieve improvements of 5 percent (%) or more without any hyperparameter tuning. In addition, downstream applications incorporating an image encoder pre-trained via self-supervised MIM training are faster and more cost-effective than transfer learning to specific downstream tasks for prognosis, treatment sensitivity prediction, tissue segmentation, image classification, and digital patient representation. As will become apparent, training the image encoder 150 via the self-supervised MIM training process 200 enables prediction of raw voxel values ​​using a high masking ratio and a relatively small patch size. For simple reconstruction of the raw input 3D medical images 110R into enhanced 3D medical images 110E, a lightweight decoder may be implemented to receive the encoded feature representations 225 output by the image encoder 150 and perform reconstruction of the image signal with increased speed and reduced computational and storage costs. Self-supervised MIM training is versatile across raw input 3D medical images 110R with a variety of image resolutions and labeled data rates during the supervised training process 160.

[0026] Generally, MIM learning involves a learning task that involves masking a subset of the input signal (e.g., image patch 210) and predicting the masked signal. In other words, MIM learning / training is a self-supervised learning technique that learns representations through images corrupted by a mask. Masking can be provided as a noise type. Predicting the masked patch in self-supervised learning can predict missing voxels by inpainting large rectangular regions of the source region and grouping voxel values ​​into clusters to classify the unknown voxel values. Additionally, predicting the masked patch in self-supervised learning can be accomplished by predicting the average color of the image.

[0027] After the image encoder 150 is pre-trained via the self-supervised training process 200, a supervised training process 160 trains an image analysis model 170 on a second teacher dataset 203 that includes a plurality of annotated MD medical images 204. The supervised training process 160 fine-tunes the trained image encoder 150 integrated with the image analysis model 170, training the image analysis model 170 to perform downstream vision tasks, such as image segmentation or image classification. Each annotated MD medical image 204 includes a plurality of image voxels 206, each paired with a corresponding ground truth label 208 that indicates the class to which the corresponding image voxel 206 belongs. In particular, the unannotated 3D images 202 in the first teacher dataset 201 used to pre-train the image encoder 150 may be associated with a different medical domain than the annotated 3D images 204 in the annotated second teacher dataset 203. For example, the first data set 201 may include a chest CT scan, and the second data set 203 may include an abdominal CT scan or a multi-modal MRI scan of a brain tumor.

[0028] The image analysis model 170 may include a U-shaped encoder-decoder architecture including the image encoder 150 (used as a ViT-based encoder, a Swin transformer, or a VAN) to generate hierarchical encoded features 225 (FIGS. 2A and 2B) from the image patches 210 and the decoder 152. The decoder 152 may include UPerNet to perform image segmentation tasks based on the encoded features 225 output from the image encoder 150. That is, two layers of transposed convolutions can be used as projection heads 260 (FIG. 2A) during a self-supervised MIM training process to pre-train the image encoder 150, and the UPerNet decoder 152 can be implemented for use with the pre-trained image encoder 150 by the image analysis model 170 to perform downstream image segmentation. In some examples, the image encoder 150 includes a masked audio encoder (MAE) (see FIG. 2A) that uses a stack of multi-head attention layers. For example, the MAE may include an 8-layer stack of transformer blocks with 512 dimensions for use by the decoder 152. In another example, the image encoder includes a simple mask image model (SimMIM) (see FIG. 2), and a simple linear layer is used as the projection head instead of the decoder.

[0029] In one example, the second training dataset 203 includes annotated 3D CT scans obtained from the Beyond the Cranial Vault (BTCV) abdominal dataset, which includes abdominal CT scans from 30 participants / patients with 13 organ annotations, acquired by a human interpreter under the supervision of a clinical radiologist. Each 3D CT scan in the BTCV abdominal dataset is performed in the portal venous phase with contrast enhancement and includes 80 to 225 slices with 512 x 512 pixels and slice thicknesses ranging from 1 to 6 millimeters (mm). During preprocessing, each annotated 3D image 204 may be resampled with an isotropic voxel spacing of 1.5-2.0. In this example, the supervised training process 160 trains the image analysis model 170 as a multi-organ segmentation model performing 13-class segmentation with a single-channel output. As a result, the ground truth labels 208 of the image voxels 206 corresponding to each annotated 3D medical image 204 may include one of 13 different classes depending on the organ to which the corresponding image voxel 206 belongs.

[0030] In another example, the second training dataset 203 includes annotated 3D MRI scan images obtained from the Brain Tumor Segmentation (BraTS) public dataset, which includes multi-modality and multi-site MRI scans with ground-truth labels 208 for corresponding image voxels 206 representing regions of edema, non-enhancing core, and necrotic core. In this example, the supervised training process 160 trains the image analysis model 170 as a brain tumor segmentation model that performs three-class segmentation with four-channel input. The voxel spacing of the MRI images may be 1.0 x 1.0 x 1.0 mm. The voxel intensities may be preprocessed using normalization.

[0031] The self-supervised training process 200 may store the pre-trained image encoder 150 in data storage 180 overlaid on the memory hardware 124 of the computing system 120. Similarly, the supervised training process 160 may store the trained image analysis model 170 in data storage 180. The first computing system 120a and / or any number of second computing systems 120b may connect to / obtain the pre-trained image encoder 150 and / or the trained image analysis model 170 for execution thereof.

[0032] During inference, the image analysis model 170 incorporating the pre-trained and fine-tuned image encoder 150 executes on the second computing system 120b (or the first computing system 120a) to process and perform image analysis tasks on one or more raw input 3D medical images 110R. In particular, the image analysis tasks performed by the image analysis model 170 include downstream vision tasks (i.e., image segmentation or image classification), where the image analysis model 170 has been trained by a supervised training process 160. Each raw input 3D medical image 110R may correspond to a 3D image slice from a 3D CT scan or a 3D MRI scan of the patient's body. Optionally, the raw input 3D medical image 110R may correspond to a 3D image of a region within the patient's body. Each raw input 3D medical image 110R may undergo initial image pre-processing 184 to segment the raw input 3D medical image 110R into multiple image patches 210, 210a-n. While nine image patches are shown as an example, this example is not limiting, and pre-processing 184 may divide the image into any number of image patches 210. Image analysis model 170 may process image patches 210 to generate enhanced 3D medical images 110E and perform downstream vision tasks on the enhanced 3D medical images 110E. When image analysis model 170 performs the downstream vision task of 3D medical segmentation, model 170 predicts a class corresponding to each voxel in the volumetric enhanced 3D medical images 110E to classify one or more specific objects (e.g., tumor, tissue, organ), and separates each specific object from another by defining respective segmentation masks to overlay the voxels classifying each object. Example 3D image segmentation tasks may include multi-organ segmentation, performed as a 13-class segmentation task with a single channel, and brain tumor segmentation, performed as a 3-class segmentation task with a four-channel input.

[0033] The image augmenter 360 may receive the enhanced 3D medical image 110E, which has been segmented to identify voxels representing each particular object class, and may generate a corresponding segmentation mask to apply to at least some of the voxels representing the particular object class. Accordingly, the image augmenter 360 may enhance image voxels in the enhanced image that represent each object class and / or define the boundaries of each object class. Enhancement of the image voxels may include changing the color of the image voxels, adjusting the intensity of the image voxels, or enhancing the image voxels in any suitable manner so that each classified object is distinct and identifiable within the enhanced image 110E. The segmentation mask may include graphical features applied to the enhanced image to communicate the location of each object identified in the enhanced image 110E. The image augmenter 360 may output the enhanced and augmented image 110A, representing the segmentation mask that communicates the results of the segmentation performed by the analytical model 170. A graphic user interface 360 ​​executing on the computing system 120 may display the augmented image 110A on a screen in communication with the computing system 120. Additionally or alternatively, the enhanced image and / or the augmented image 110A may be provided as output to one or more additional downstream tasks.

[0034] 2A and 2B, in some embodiments, a self-supervised MIM training process 200 pre-trains an image encoder 150 with either a mask autoencoder (MAE) architecture (FIG. 2A) or a simple MIM (SimMIM) architecture (FIG. 2B). For each unannotated 3D medical image 202, the training process 200 first pre-processes the image 202 in a pre-processing stage 184 to divide the image 202 into multiple image patches 210, 210a-n. Because a full 3D image volume is generally difficult to load directly onto the data processing hardware 122 (e.g., a GPU) of the computing system 120, the self-supervised MIM training process 200 may implement a sliding window training strategy in which pre-processing divides the original 3D medical image 202 into several small 3D windows (e.g., 96 x 96 x 96). By default, the pre-processing stage 184 may implement a patch size of approximately 16. The pre-processing stage may downsample the image resolution of the unannotated 3D medical image 202. For example, a 96× volumetric resolution can be downsampled to a 9× volumetric resolution when the image encoder 150 includes a ViT-based image encoder, or to a 3× volumetric resolution when the image encoder 150 includes a Swin transformer or a VAN.

[0035] 2A shows an MIM training process 200 for training an image encoder 150 with an MAE architecture by randomly masking a portion of an image patch 210 segmented from a corresponding unannotated MD medical image 202. The training process 200 further randomly masks a portion of the image patch 210 using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using various masked patch sizes and masking ratios. The training process further generates a set of discrete visual tokens characterizing the corresponding unannotated MD medical image 202 using an image tokenizer 230 configured to receive the unannotated MD medical image 202 as input. The number of visual tokens in the set of discrete visual tokens 240 may be equal to the number of image patches 210 segmented from the unannotated MD medical image 202. The tokenizer 230 may map discrete image voxels from the medical image 202 to discrete visual tokens 240 according to a visual codebook that includes a token vocabulary that includes discrete token indices. Because the visual tokens 240 are discrete, the training process 200 is not differentiable. In some examples, the tokenizer 230 is trained via an autoencoding-style reconstruction process in which images are tokenized into discrete visual tokens according to a learned vocabulary.

[0036] As shown by way of example, the self-supervised MIM training process 200 adds a positional embedding 215 to an image patch 210. The image encoder 150 receives each masked image patch 210M, whereby each masked image patch may be replaced with a special masking embedding [M]. The special masking token [M] may be randomly initialized as a learnable vector optimized to reveal the corresponding masked image patch 210.

[0037] For each masked image patch [M], the image encoder 150 is configured to generate a corresponding encoded feature representation 225 (also referred to as an encoded hidden representation 225), and the decoder 250 decodes the corresponding encoded feature representation 225 to predict a corresponding predicted token 275 as output from the projection head 260. The goal of the MIM training process 200 is to train the image encoder 150 and the decoder 250 to learn how to predict a visual token 240 obtained from an original 3D image 202. Specifically, the training process 200 trains the encoder 150 to generate an encoded feature representation 225 of the masked image patch 210M that is used to generate a predicted token 275 that matches the visual token 240 obtained from the original 3D image 202. Here, the training process 200 may determine a training loss based on the predicted tokens 275 generated for the masked image patch 210M and the corresponding visual tokens from the set of discrete visual tokens 240 that match the masked image patch 210M (i.e., using the positional embeddings 215). The training process 200 then updates the parameters of the image encoder 150 (and optionally the decoder 250) based on the training loss.

[0038] The decoder may include multiple multi-head attention layers (e.g., transformer layers). In some examples, the masked image patches 210M are hidden from the encoder 150, so that only the decoder 250 has knowledge of the various tokens. This approach may save computation and memory without interfering with training.

[0039] 2B shows a self-supervised MIM training process 200 that trains an image encoder 150 with a SimMIM architecture to randomly mask portions of image patches 210 segmented from corresponding unannotated MD medical images 202. Each image patch 210 may be represented by a corresponding set of raw voxel values. The training process 200 further randomly masks portions of the image patches 210 using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using various masked patch sizes and masking ratios.

[0040] As shown by way of example, the self-supervised MIM training process 200 adds a positional embedding 215 to an image patch 210. The image encoder 150 receives each masked image patch 210M, whereby each masked image patch may be replaced with a special masking embedding [M]. The special masking token [M] may be randomly initialized as a learnable vector optimized to reveal the corresponding masked image patch 210.

[0041] For each masked image patch 210M, the image encoder 150 is configured to generate a corresponding encoded feature representation 225, and the prediction head 260 generates predicted voxel values ​​for the masked image patch 210M. In particular, the MIM training process 200 for pre-training an image encoder 150 with the SimMIM architecture omits the decoder and instead implements the prediction head 260 to predict raw voxel values ​​270 for each masked image patch 210M directly from the encoded feature representation 225 generated by the image encoder 225 for the corresponding masked image patch 210M. The training process 200 may determine a training loss based on the predicted voxel values ​​270 generated for the masked image patch and a corresponding set of raw voxel values ​​from the original, unannotated MD medical image 202 representing the masked image patch.

[0042] The training loss may be based on the distance in voxel spacing between the inpainted / estimated raw voxel values ​​270 and the original voxel values ​​from the set of corresponding raw voxel values ​​representing the masked image patch. The training loss may include either an l1 or l2 loss function. In particular, the training loss may only be calculated for the masked matches 210M to prevent the encoder 150 from self-reconstructing, potentially dominating the learning process and ultimately hindering knowledge acquisition. The training process 200 then updates the parameters of the image encoder 150 (and optionally the decoder 250) based on the training loss. The projection head can convert the predicted tokens 275 back to the original voxel spacing when preprocessing downsamples the resolution of the medical image 202. Optionally, two layers of transposed convolutions can upsample the compressed encoded feature representation 225 to the resolution of the original medical image 202.

[0043] Figure 3 shows example input, masked, and reconstructed 3D CT scan images from the validation set of TCIA-COVID19 applying a pre-trained image encoder 150 using SimMIM reconstruction. While all original images are 3D volumes, the reconstructed images are displayed in slice format for ease of illustration and understanding, with index numbers representing depth. For each triplet, the first or leftmost column shows the ground truth (e.g., the original image). The second or middle column shows the masked image. The third or rightmost column shows the machine learning model using SimMIM reconstruction. For the images shown in Figure 5, the ViT-Base backbone is applied to the encoder, with a masked patch size of approximately 16 (for all dimensions) and a masking ratio of approximately 75%.

[0044] Figure 4 shows example input, masked, and reconstructed 3D CT scan images from the TCIA-COVID19 validation set applying a machine learning model using MAE reconstruction. Similar to Figure 3, while all original images are 3D volumes, the reconstructed images are displayed in slice format for ease of explanation and understanding, with index numbers representing depth. For each triplet, the first or leftmost column shows the ground truth (e.g., the original image). The second or middle column shows the masked image. The third or rightmost column shows the machine learning model using MAE reconstruction. For the images shown in Figure 4, the ViT-Large backbone is applied to the encoder, the masked patch size is approximately 16 (for all dimensions), and the masking ratio is approximately 75%.

[0045] Figure 5 shows a table demonstrating that the MIM approach can generally outperform control learning techniques. The pre-trained image encoder 150 has both the MAE architecture and the SimMIM architecture achieving an average Dice coefficient of 0.752 to 0.758, while SimCLR has an average Dice coefficient of approximately 0.723, 4.5% lower. As used herein, the Dice coefficient is used to evaluate the accuracy of segmentation performed as a downstream vision task. For a given semantic task, G i and P i denote the ground truth and predicted values ​​for each corresponding voxel i, respectively. The following equation may be used to reveal the Dice coefficients:

number

[0046] Figure 6 shows a table listing supplemental baseline settings for the supervised training process 160 for training an image analysis model 170 on the BTCV dataset for multi-organ image segmentation. Figure 7 shows a table listing supplemental baseline settings for the supervised training process 160 for training an image analysis model 170 on the BraTS dataset for brain tumor segmentation. Figure 8 shows a table listing pre-training settings for a self-supervised training process using 3D CT image volumes as unannotated 3D medical images 202.

[0047] Figure 9 is a table revealing the results of using a machine learning model on brain tumor segmentation images after pre-training using the BraTS training dataset as annotated MD medical images 204. The BraTS segmentation results in Figure 8 follow a similar pattern to the segmentation results shown in Figure 5. While the average Dice coefficient for the mask image modeling approaches is slightly larger than 0.80, SimCLR obtains a Dice coefficient of 0.7739, which is 4.37% smaller than the best approach comparable to Figure 5. Another noteworthy point is that despite the similarity of the two MIM techniques, SimMIM is able to achieve slightly better performance than MAE, as revealed in both Figures 5 and 9. One explanation for this is that even if the encoder 150 does not obtain a generalizable representation, an efficient decoder (even a lightweight decoder) may be able to reconstruct the original image, thus periodically relaxing the encoder 150's motivation to learn a more efficient representation 225. One goal of self-supervised MIM learning is to learn efficient and generalizable representations of data rather than just self-converging. In comparison, SimMIM uses a lighter design by omitting the decoder entirely and running the encoder to perform more complex reconstruction and learning tasks.

[0048] The self-supervised MIM training process 200 increases training speed while reducing the cost of pre-training the image encoder 150 on a first training dataset 201. Figure 10 shows a plot representing how the self-supervised MIM training process 200 proceeds through the supervised training process 160. Here, the average Dice coefficients on the validation set are separated for the supervised baseline and various self-supervised MIM techniques using different masking ratios throughout the training phase. Pre-training masked image modeling saves training costs and produces better performance. The SimMIM-based architecture achieves a 1.76x Dice coefficient over 1.3k training phases. Furthermore, the MIM-based approach can reach a Dice coefficient of 0.7 with 1.4x less training time than the training time required by the supervised baseline.

[0049] In some implementations, various masked patch sizes and masking ratios are used to train models using self-supervised MIM. The results of applying machine learning models to 3D medical images using various MIM techniques and fine-tuning a pre-trained image encoder for downstream image segmentation are summarized in the tables of FIGS. 11 and 12. FIG. 11 includes a table showing an ablation study of various masked patch sizes and masking ratios for multi-organ segmentation. The machine learning model 160 applied to generate the results of FIG. 13 had the default backbone of ViT-B applied as the pre-trained encoder 150. Additionally, the machine learning model 160 was trained via a supervised training process 160 using the BTCV training dataset. FIG. 12 is a table showing an ablation study of various masked patch sizes and masking ratios for brain tumor segmentation. Similarly, the pre-training data includes the BraTS dataset itself, and ViT-B is applied as the encoder backbone of UNETR for segmentation fine-tuning.

[0050] Higher masking ratios are an important self-supervised learning task that continuously drives the model to build a general representation that can be efficiently translated to downstream tasks. For example, the best Dice coefficients in multi-organ segmentation and brain tumor segmentation are obtained when a masking ratio of approximately 0.75 is used across multiple patch sizes (e.g., 0.7183 for patch size 16 in Figure 11 and 0.8041 for patch sizes 24 and 32 in Figure 12). A high masking ratio combined with a small patch size results in relatively good performance when used in combination with SimMIM. As shown in Figures 11 and 12, when the patch size is equal to 16, the model can perform with Dice coefficients of approximately 0.7249 and 0.8077, respectively. However, as the patch size increases, the SimMIM method appears less sensitive to this masking ratio. For example, when the patch size is approximately 32, the model can achieve the largest Dice coefficient with a masking ratio of approximately 0.15, the smallest possible masking ratio. Medical images are generally raw, low-level signals with a large degree of spatial redundancy. Inpainting some unknown patches is done by directly copying nearby patches that have some comprehensive knowledge of the object and its surroundings. A single small masked patch may not be able to adequately mask complex and intersecting structures or locations, while a large patch size can hide more important signals by itself. As a result, a high masking ratio with a small patch size can be more fatal than a high masking ratio with a large patch size.

[0051] Generally, in supervised learning, more training data results in improved performance. FIG. 13 includes a table showing the Dice coefficients of an image encoder 150 pre-trained via a self-supervised MIM training process 200 and an image analysis model 170 incorporating a hand with an MAE architecture (FIG. 2A). The image encoder 150 may be pre-trained for various data sources with varying degrees of downsampling. The supervised training process 160 may train the image analysis model 170 on multi-organ segmentation datasets with various labeled data ratios. The results of the table show that models trained via the self-supervised MIM training process 200 with more unannotated 3D medical images 202 outperform models trained with fewer unannotated 3D medical images 202 (e.g., 0.7184 vs. 0.7543, a 4.9% improvement; 0.7018 vs. 0.7338, a 4.6% improvement). This advantage may be even more pronounced at lower image resolutions, as 0.6818 is 5.6% larger than 0.6552 when only half the labeled data is used for supervised training.

[0052] Figure 13 also illustrates how different resolutions of unannotated 3D medical images for pretraining affect downstream image task performance. For example, higher pretraining resolutions yield better segmentation results because the images contain more granular information. Here, different downsampling ratios can be used to represent the degree to which the original signal is compressed across all dimensions of each volume. As can be seen from Figure 13, pretrained encoder models with higher resolutions (e.g., 1.5×, 1.5×, 2.0) generally perform better than pretrained models with lower resolutions (e.g., 2.0×, 2.0×, 2.0). For example, the Dice coefficient of 0.7338 is 2.7% smaller than the Dice coefficient of models pretrained using higher resolutions with the same data source and labeled ratio.

[0053] 14 is a flowchart of an exemplary sequence of operations for a method 1400 of training an image analysis model to perform image analysis tasks on multidimensional medical images. The data processing hardware 122 of the computing system 120 may perform the operations by executing instructions stored on the memory hardware 124. At operation 1402, the method 1400 includes obtaining a first teacher data set 201 including a plurality of unannotated multidimensional medical images 202. At operation 1404, the method 1400 includes performing a self-supervised masked image modeling (MIM) training process 200 to pre-train the image encoder 150 on the first teacher data set 201.

[0054] At operation 1406, the method 1400 includes obtaining a second training data set 203 including a plurality of annotated multidimensional medical images 204, where each of the annotated multidimensional medical images 204 includes a plurality of image voxels 206, each paired with a corresponding ground truth label 208 indicating a class to which the corresponding image voxel belongs. At operation 1408, the method 1400 includes performing a supervised training process 160 to train an image analysis model 170 on the second training data set 203, where the image analysis model 170 learns how to predict the ground truth label 208 corresponding to each of the plurality of image voxels 206 of the annotated multidimensional medical images 204. Here, the image analysis model 170 incorporates a pre-trained image encoder 150. The supervised training process 160 fine-tunes the pre-trained image encoder 150, which was initialized via the self-supervised MIM training process 200.

[0055] A software application (i.e., a software resource) may refer to computer software that causes a computing device to perform a task. In some examples, a software application may be referred to as an "application," "app," or "program." Examples of applications include, but are not limited to, system diagnostic applications, system management applications, system maintenance applications, word processing applications, spreadsheet applications, messaging applications, media streaming applications, social networking applications, and gaming applications.

[0056] Non-transitory memory may be a physical device used to store programs (e.g., sequences of instructions) or data (e.g., program state information) on a temporary or permanent basis for use by a computing device. Non-transitory memory may be volatile and / or non-volatile addressable semiconductor memory. Examples of non-volatile memory include (but are not limited to) flash memory and read-only memory (ROM), programmable read-only memory (PROM), erasable programmable read-only memory (EPROM), and electronically erasable programmable read-only memory (EEPROM) (e.g., typically used for firmware such as boot programs). Examples of volatile memory include (but are not limited to) random access memory (RAM), dynamic random access memory (DRAM), static random access memory (SRAM), phase change memory (PCM), and disk or tape.

[0057] 15 is a schematic diagram of an example computing device 1500 that may be used to implement the systems and methods described herein. Computing device 1500 is intended to represent various forms of digital computers, such as laptops, desktops, workstations, personal digital assistants, servers, blade servers, mainframes, and other suitable computers. The connections and relationships and functional components shown here are meant to be merely exemplary and are not meant to limit the practice of the invention(s) described and / or claimed herein.

[0058] Computing device 1500 includes processor 1510, memory 1520, storage device 1530, high-speed interface / controller 1540 coupled to memory 1520 and high-speed expansion port 1550, and low-speed interface / controller 1560 coupled to low-speed bus 1570 and storage device 1530. Each of components 1510, 1520, 1530, 1540, 1550, and 1560 may be interconnected using various buses and may be mounted on a common motherboard or otherwise as needed. Processor 1510 can process instructions that execute within computing device 1500, including instructions stored in memory 1520 or storage device 1530 for displaying graphical information for a graphic user interface (GUI) on an external input / output device, such as display 1580 coupled to high-speed interface 1540. In other embodiments, multiple processors and / or multiple buses may be used, along with multiple memories and memory types, as needed. Additionally, multiple computing devices 1500 may be connected, with each device providing a portion of the required operations (eg, a bank of servers, a group of blade servers, or a multi-processor system).

[0059] Memory 1520 stores information non-temporarily within computing device 1500. Memory 1520 may be a computer-readable medium, a volatile memory unit, or a non-volatile memory unit. Non-transient memory 1520 may be a physical device used to store programs (e.g., sequences of instructions) or data (e.g., program state information) on a temporary or permanent basis for use by computing device 1500. Examples of non-volatile memory include, but are not limited to, flash memory and read-only memory (ROM), programmable read-only memory (PROM), erasable programmable read-only memory (EPROM), or electronically erasable programmable read-only memory (EEPROM) (e.g., typically used for firmware, such as boot programs). Examples of volatile memory include, but are not limited to, random access memory (RAM), dynamic random access memory (DRAM), static random access memory (SRAM), phase-change memory (PCM), and disk or tape.

[0060] Storage device 1530 can provide mass storage for computing device 1500. In some embodiments, storage device 1530 is a computer-readable medium. In various different embodiments, storage device 1530 can be an array of devices including a floppy disk device, a hard disk device, an optical disk device, or a tape device, a flash memory or other similar solid-state memory device, or a storage area network or other configuration of devices. In additional embodiments, a computer program product is tangibly embodied on an information medium. The computer program product includes instructions that, when executed, perform one or more methods, such as those described above. The information medium is a computer- or machine-readable medium, such as memory 1520, storage device 1530, or memory on processor 1510.

[0061] The high-speed controller 1540 manages bandwidth-intensive operations of the computing device 1500, while the low-speed controller 1560 manages low-bandwidth operations. Such role assignments are merely exemplary. In some embodiments, the high-speed controller 1540 is coupled to the memory 1520, the display 1580 (e.g., through a graphics processor or accelerator), and the high-speed expansion port 1550 (which may employ various expansion cards, not shown here). In some embodiments, the low-speed controller 1560 is coupled to the storage device 1530 and the low-speed expansion port 1590. The low-speed expansion port 1590 may include various communication ports (e.g., USB, Bluetooth, Ethernet, wireless Ethernet) and may be coupled to one or more input / output devices, such as a keyboard, a pointing device, a scanner, or a network device, such as a switch or router, through a network adapter.

[0062] The computing device 1500, as shown, may be implemented in several different forms, such as a standard server 1500a or a group of such servers 1500a, a laptop computer 1500b, or as part of a rack server system 1500c.

[0063] Various embodiments of the systems and techniques described herein may be realized in digital electrical and / or optical circuitry, integrated circuits (particularly ASICs (application-specific integrated circuits)), computer hardware, firmware, software, and / or combinations thereof. These various embodiments may include implementation in one or more computer programs, which may be executable and / or interpretable by a programmable system including at least one programmable processor, which may be special-purpose or general-purpose, and which may be coupled to receive data and instructions from, and transmit data and instructions to, a storage system, at least one input device, and at least one output device.

[0064] These computer programs (also known as programs, software, software applications, or code) include machine instructions for a programmable processor and may be implemented in a high-level procedural and / or object-oriented programming language and / or in assembly / machine language. As used herein, the terms "machine-readable medium" and "computer-readable medium" refer to any computer program product, non-transitory computer-readable medium, apparatus, and / or device (e.g., magnetic disks, optical disks, memory, programmable logic devices (PLDs)) used to provide machine instructions and / or data to a programmable processor, including machine-readable media that receive machine instructions as a machine-readable signal. The term "machine-readable signal" refers to any signal used to provide machine instructions and / or data to a programmable processor.

[0065] The processes and logic flows described herein may be performed by one or more programmable processors, also referred to as data processing hardware, which may execute one or more computer programs to perform functions by operating on input data and generating output. The processes and logic flows may also be performed by special-purpose logic circuitry (e.g., an FPGA (field-programmable gate array) or an ASIC (application-specific integrated circuit)). Processors suitable for executing computer programs include, by way of example, both general-purpose and special-purpose microprocessors, and one or more processors of any kind of digital computer. Typically, a processor receives instructions and data from a read-only memory or a random-access memory, or both. The essential elements of a computer are a processor for executing instructions and one or more memory devices for storing instructions and data. Typically, a computer also includes one or more mass storage devices (e.g., magnetic disks, magneto-optical disks, or optical disks) for storing data and is operably coupled to receive data from them, transmit data to them, or both. However, a computer need not include such devices. Computer-readable media suitable for storing computer program instructions and data include all forms of media and memory devices, including, by way of example, semiconductor memory devices (e.g., EPROM, EEPROM) and flash memory devices, magnetic disks (e.g., internal hard disk or removable disk), magneto-optical disks, CD-ROM and DVD-ROM disks. The processor and the memory can be supplemented by, or incorporated in, special purpose logic circuitry.

[0066] To provide for user interaction, one or more aspects of the present disclosure may be implemented on a computer that includes a display device (e.g., a CRT (cathode ray tube), LCD (liquid crystal display) monitor, or touch screen for displaying information to the user, and optionally, a keyboard and pointing device (e.g., a mouse or trackball) through which the user can provide input to the computer). Other types of devices may be used to provide for user interaction as well. For example, feedback provided to the user may be any form of sensory feedback, such as visual feedback, auditory feedback, or tactile feedback, and input from the user may be received in any form, including acoustic, speech, or tactile input. Additionally, the computer may interact with the user by sending documents to and receiving documents from devices used by the user, e.g., sending a web page to a web browser on a user client device in response to a request received from the web browser.

[0067] Although several embodiments have been described, it will be understood that various modifications may be made without departing from the spirit and scope of the present disclosure. Accordingly, other embodiments are within the scope of the following claims.

Claims

1. 1. A computer-implemented method executed on data processing hardware, the method comprising: obtaining a first training dataset comprising a plurality of unannotated multidimensional medical images; performing a self-supervised mask image modeling (MIM) training process to pre-train an image encoder on the first training dataset; obtaining a second training dataset including a plurality of annotated multidimensional medical images, each of the annotated multidimensional medical images including a plurality of image voxels each paired with a corresponding ground truth label indicating one of a plurality of candidate classes to which the corresponding image voxel belongs; performing a supervised training process to train an image analysis model on the second training dataset, thereby training the image analysis model to learn how to generate an enhanced multidimensional medical image for each corresponding annotated multidimensional medical image by learning how to predict ground truth labels corresponding to a plurality of image voxels in the corresponding annotated multidimensional medical image; Perform an action including the image analysis model incorporates the pre-trained image encoder; The enhanced multidimensional medical images generated by the image analysis model during execution of the supervised training process separate each class of the plurality of class candidates from each other class of a plurality of task candidates by defining a respective segmentation mask for overlaying each corresponding image voxel belonging to the respective class; the plurality of unannotated multidimensional medical images of the first training data set are associated with a different medical domain than the plurality of annotated multidimensional medical images of the second training data set; method.

2. The step of performing the self-supervised MIM training process to pre-train the image encoder includes, for each unannotated multidimensional medical image corresponding to the first training dataset: using an image tokenizer configured to receive as input a corresponding unannotated multidimensional medical image, and generating a set of discrete visual tokens that characterize the corresponding unannotated multidimensional medical image; Segmenting the corresponding unannotated multidimensional medical image into a plurality of image patches; randomly masking a portion of the image patches segmented from the corresponding unannotated multidimensional medical image; For each masked image patch, generating an encoded hidden representation for the masked image patch using the image encoder; generating, using a decoder, a corresponding predicted token based on the encoded hidden representation; and determining a training loss based on the predicted tokens generated for the masked image patch and corresponding visual tokens from the set of discrete visual tokens that match the masked image patch; updating parameters of the image encoder based on the training loss; Including, The method of claim 1.

3. the image encoder includes a plurality of multi-head attention layers; The decoder includes multiple multi-head attention layers. The method of claim 2.

4. randomly masking a portion of the image patch comprises randomly masking a portion of the image patch using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using different masked patch sizes and masking ratios; The method according to claim 2 or 3.

5. the number of visual tokens in the set of discrete visual tokens is equal to the number of image patches in the plurality of image patches; The method according to claim 2 or 3.

6. The step of performing the self-supervised MIM training process to pre-train the image encoder includes, for each unannotated multidimensional medical image corresponding to the first training dataset: dividing the corresponding unannotated multidimensional medical image into a plurality of image patches, each image patch being represented by a corresponding set of raw voxel values; randomly masking a portion of the image patches segmented from the corresponding unannotated multidimensional medical image; For each masked image patch, generating an encoded hidden representation for the masked image patch using the image encoder; generating predicted voxel values ​​(270) for the masked image patch based on the encoded hidden representation using a prediction head; and determining a training loss based on the predicted voxel values ​​generated for the masked image patch and the corresponding set of raw voxel values ​​representing the masked image patch; updating parameters of the image encoder based on the training loss; Including, The method according to any one of claims 1 to 3.

7. the image encoder includes a plurality of multi-head attention layers; the prediction head includes a single linear layer prediction head and is configured to generate the predicted voxel values ​​from the encoded hidden representation without the use of a decoder. The method of claim 6.

8. randomly masking a portion of the image patch comprises randomly masking a portion of the image patch using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using different masked patch sizes and masking ratios; The method of claim 6.

9. The image analysis model includes a tumor segmentation model. The method according to any one of claims 1 to 3.

10. The image analysis model includes a multi-organ segmentation model. The method according to any one of claims 1 to 3.

11. 1. A system comprising: data processing hardware; memory hardware in communication with said data processing hardware and storing instructions that, when executed by said data processing hardware, cause said data processing hardware to perform operations; Including, The operation is obtaining a first training dataset comprising a plurality of unannotated multidimensional medical images; performing a self-supervised mask image modeling (MIM) training process to pre-train an image encoder on the first training dataset; obtaining a second training dataset including a plurality of annotated multidimensional medical images, each of the annotated multidimensional medical images including a plurality of image voxels each paired with a corresponding ground truth label indicating one of a plurality of candidate classes to which the corresponding image voxel belongs; performing a supervised training process to train an image analysis model on the second training dataset, thereby training the image analysis model to learn how to generate an enhanced multidimensional medical image for each corresponding annotated multidimensional medical image by learning how to predict ground truth labels corresponding to a plurality of image voxels in the corresponding annotated multidimensional medical image; Including, the image analysis model incorporates the pre-trained image encoder; The enhanced multidimensional medical images generated by the image analysis model during execution of the supervised training process separate each class of the plurality of class candidates from each other class of a plurality of task candidates by defining a respective segmentation mask for overlaying each corresponding image voxel belonging to the respective class; the plurality of unannotated multidimensional medical images of the first training data set are associated with a different medical domain than the plurality of annotated multidimensional medical images of the second training data set; system.

12. The step of performing the self-supervised MIM training process to pre-train the image encoder includes, for each unannotated multidimensional medical image corresponding to the first training dataset: using an image tokenizer configured to receive as input a corresponding unannotated multidimensional medical image, and generating a set of discrete visual tokens that characterize the corresponding unannotated multidimensional medical image; Segmenting the corresponding unannotated multidimensional medical image into a plurality of image patches; randomly masking a portion of the image patches segmented from the corresponding unannotated multidimensional medical image; For each masked image patch, generating an encoded hidden representation for the masked image patch using the image encoder; generating, using a decoder, a corresponding predicted token based on the encoded hidden representation; and determining a training loss based on the predicted tokens generated for the masked image patch and corresponding visual tokens from the set of discrete visual tokens that match the masked image patch; updating parameters of the image encoder based on the training loss; Including, The system of claim 11.

13. the image encoder includes a plurality of multi-head attention layers; The decoder includes multiple multi-head attention layers. The system of claim 12.

14. randomly masking a portion of the image patch comprises randomly masking a portion of the image patch using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using different masked patch sizes and masking ratios; 14. A system according to claim 12 or 13.

15. the number of visual tokens in the set of discrete visual tokens is equal to the number of image patches in the plurality of image patches; 14. A system according to claim 12 or 13.

16. The step of performing the self-supervised MIM training process to pre-train the image encoder includes, for each unannotated multidimensional medical image corresponding to the first training dataset: dividing the corresponding unannotated multidimensional medical image into a plurality of image patches, each image patch being represented by a corresponding set of raw voxel values; randomly masking a portion of the image patches segmented from the corresponding unannotated multidimensional medical image; For each masked image patch, generating an encoded hidden representation for the masked image patch using the image encoder; generating predicted voxel values ​​for the masked image patch based on the encoded hidden representation using a prediction head; and determining a training loss based on the predicted voxel values ​​generated for the masked image patch and the corresponding set of raw voxel values ​​representing the masked image patch; updating parameters of an image encoder based on the training loss; Including, 14. A system according to any one of claims 11 to 13.

17. the image encoder includes a plurality of multi-head attention layers; the prediction head includes a single linear layer prediction head and is configured to generate the predicted voxel values ​​from the encoded hidden representation without the use of a decoder.

17. The system of claim 16.

18. randomly masking a portion of the image patch comprises randomly masking a portion of the image patch using one of a central region masking strategy, a block-by-block masking strategy, or a uniform random masking strategy using different masked patch sizes and masking ratios; 17. The system of claim 16.

19. The image analysis model includes a tumor segmentation model.

14. A system according to any one of claims 11 to 13.

20. The image analysis model includes a multi-organ segmentation model.

14. A system according to any one of claims 11 to 13.

Images