An adaptive learning framework for digital pathology

Abstract

The present disclosure relates to techniques for efficient development of an initial model using an adaptive learning framework, as well as for efficient model updating and / or adaptation to different image domains. For efficient development of the initial model, a two-stage development strategy may be implemented as follows. That is, stage 1; pre-adjustment of the model, in which an artificial intelligence system utilizes existing annotated datasets and improves learning skills through training on these datasets, and stage 2: target model training, in which the artificial intelligence system utilizes the learning skills learned in stage 1 to expand to a different image domain (target domain) that requires a smaller number of annotations in the target domain than conventional learning methods. To efficiently perform model updating and adaptation to new datasets after the initial model development, a digital pathology scenario is identified, an adaptive learning method is selected based on the scenario, and the model is updated and adapted to the new dataset using the adaptive learning method.

Description

[Technical Field]

[0001] The present disclosure relates to digital pathology, and in particular to techniques for efficient development of initial models, as well as efficient model updating and / or adaptation to different image domains using an adaptive learning framework. [Background technology]

[0002] Digital pathology involves scanning slides (e.g., histopathology or cytopathology glass slides) into interpretable digital images on a computer screen. The tissues and / or cells in the digital images can then be examined by digital pathology image analysis and / or interpreted by a pathologist for a variety of reasons, including diagnosing disease, assessing response to treatment, and developing drugs to combat disease. To examine the tissues and / or cells (which are substantially transparent) in the digital images, pathology slides can be prepared using various staining assays (e.g., immunohistochemistry) that selectively bind to tissue and / or cellular components. Immunofluorescence (IF) is a technique for analyzing assays that bind fluorescent dyes to antigens. Multiple assays responding to different wavelengths can be utilized on the same slide. These multiplexed IF slides enable understanding of the complexity and heterogeneity of the immune landscape of the tumor microenvironment and its potential impact on tumor response to immunotherapy. In some assays, the target antigen for the stain in the tissue is sometimes referred to as a biomarker. Digital pathology image analysis can then be performed on the digital images of the stained tissues and / or cells to identify and quantify staining for antigens (e.g., biomarkers indicative of various cells, such as tumor cells) in the biological tissue.

[0003] Artificial intelligence and machine learning-based methods and / or techniques have shown great promise in digital pathology image analysis, such as cell detection, counting, localization, classification, and patient prognosis. Many computing systems equipped with machine learning techniques, including convolutional neural networks (CNNs), have been proposed for image classification and digital pathology image analysis, such as cell detection and classification. For example, a CNN can have a series of convolutional layers as hidden layers, and this network structure enables the extraction of representational features for object / image classification and digital pathology image analysis. In addition to object / image classification, machine learning techniques have also been implemented for image segmentation. Image segmentation is the process of dividing a digital image into multiple segments (sets of pixels, also known as image objects). The purpose of segmentation is to simplify and / or change the representation of the image to one that is more meaningful and easier to analyze. For example, image segmentation is typically used to find objects such as cells and boundaries (lines, curves, etc.) within an image. To perform image segmentation for large data sets (e.g., whole-slide pathology images), the image is first divided into many small patches. A computing system equipped with machine learning techniques is trained to classify each pixel of these patches, all pixels of the same class are combined into one segmented area for each patch, and then all segmented patches are combined into one segmented image (e.g., a segmented whole-slide pathology image). Machine learning techniques can then be further implemented to predict or further classify the segmented areas (e.g., positive cells for a given biomarker, negative cells for a given biomarker, or cells with no staining expression) based on the expression features associated with the segmented areas. Summary of the Invention

[0004] Artificial intelligence and machine learning-based techniques have achieved excellent performance in digital pathology. However, developing such models is very time-consuming and resource-intensive. Not only do hundreds of thousands of annotations need to be built from scratch in the initial development phase to build a reliable model from scratch, but once developed, the model has limited generalizability to unseen data, leading to unavoidable continuous investment in developing new models even for related tasks. Disclosed herein is a framework for reducing resource requirements throughout the entire development process of AI-based digital pathology algorithms, including initial model development and subsequent model updating, improvement, and adaptation to different datasets. Specifically, disclosed herein is a model preconditioning phase using an existing annotated dataset that is related to, but not necessarily similar to, the target dataset for building the model, such that initial model development requires only a small number of annotations to generate a model with reasonable accuracy. In the subsequent model updating and adaptation phase, an adaptive learning workflow is used for multiple digital pathology scenarios and strategies to select the best learning method for efficient model updating without the need to train on all data from scratch.

[0005] In various embodiments, a computer-implemented method is provided that includes, in a data processing system, obtaining a first annotated training set of images for training a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in the images, the first annotated training set of images being in a first image domain; dividing, by the data processing system, the first annotated training set of images into mini-sets of images, each mini-set representing a separate modeling subtask and including a limited number of examples; and running, by the data processing system, the first-stage machine learning algorithm using the mini-sets of images to generate a conditioned machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in the new images. labeling, by a data processing system, a limited number of images from the target dataset to generate a second annotated training set of images for training the machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in the images, wherein the second annotated training set of images is in a second image domain; and training, by the data processing system, a second-stage preconditioned machine learning model using the second annotated training set of images to generate a target machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in the new images, wherein the number of classes targeted in the first stage is a subset of or matches the number of classes targeted in the second stage.

[0006] In some embodiments, the first annotated training set of images are digital pathology images that include one or more types of cells.

[0007] In some embodiments, the splitting includes either: if only one mini-set of images is available, then for each distinct modeling subtask, selecting a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples based on the selected subset of classes; and if multiple mini-sets of images are available, then for each distinct modeling subtask, (i) mixing examples from the multiple mini-sets of images, selecting a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples from the mixed examples based on the selected subset of classes; or (ii) selecting one mini-set of images from the multiple mini-sets of images, selecting a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples from the selected mini-set of images based on the selected subset of classes.

[0008] In some embodiments, the second stage further includes applying the conditioned machine learning model to generate a feature vector representation for each example in the second annotated training set of images; combining feature vector representations from examples of the same class to generate one representation per target class and use the one representation per target class as a prototype in the target class; generating feature vector representations for images or image regions of the remainder of the images that are unlabeled from the target dataset; and comparing each feature vector representation from the unlabeled images to a prototype in the target class based on a distance between the feature vector representation from the unlabeled images and the prototype for the target class.

[0009] In some embodiments, the first stage further includes an inner learning loop in which the machine learning algorithm updates model weights or parameters on one subtask for a predetermined or flexible number of epochs to initialize the preconditioned machine learning model for adaptation to the target dataset, generating a loss on the validation set of images after model updating, denoted as L-subtask-i for the i-th subtask; and an outer learning loop in which the goal is to search for a set of model initializations that, when each is used to update all subtasks with only a limited number of examples, generate a preconditioned machine learning model by finding a model initialization that minimizes the sum of all losses, denoted as the sum of L-subtask-i, where i ranges from 1 to the number of subtasks calculated from the validation set of images for the subtask for model initialization.

[0010] In some embodiments, the first stage of training involves performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the mini-set of images that maximizes or minimizes a cost function, where each iteration involves finding a set of parameters for the machine learning algorithm such that the value of the cost function using the set of parameters is greater or less than the value of the cost function using another set of parameters in the previous iteration, and the cost function is constructed to measure the difference between predictions made for some or all of the regions or objects using the machine learning algorithm and the ground truth labels assigned to the mini-set of images.

[0011] In some embodiments, training the second stage includes performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the second annotated training set of images that maximizes or minimizes a cost function, where each iteration involves finding a set of parameters for the preconditioned machine learning model such that the value of the cost function using the set of parameters is greater or less than the value of the cost function using another set of parameters in a previous iteration, and the cost function is constructed to measure the difference between predictions made for some or all of the regions or objects using the preconditioned machine learning model and ground truth labels assigned to the second annotated training set of images.

[0012] In some embodiments, the computer-implemented method further includes identifying a digital pathology scenario, selecting an adaptive continuous learning method for updating the target machine learning model in light of the digital pathology scenario, and updating the target machine learning model based on the adaptive continuous learning method to generate an updated machine learning model.

[0013] In some embodiments, the digital pathology scenario is a data incremental scenario, a domain incremental scenario, a class incremental scenario, or a task incremental scenario.

[0014] In some embodiments, the adaptive continuous learning method is selected from the group including Elastic Weight Reinforcement (EWC), Lean Without Forgetting (LWF), Incremental Learner and Representation Learning (iCaRL), Continuous Prototype Evaluation (CoPE), A-GEM, and Parameter Separation methods.

[0015] In some embodiments, the computer-implemented method further includes providing a target machine learning model and / or an updated machine learning model.

[0016] In some embodiments, providing includes deploying the targeted machine learning model and / or the updated machine learning model to a digital pathology system.

[0017] In some embodiments, the computer-implemented method further includes receiving, by the data processing system, a new image; inputting the new image into a target machine learning model or an updated machine learning model; detecting, characterizing, classifying, or a combination thereof, some or all regions or objects in the new image with the target machine learning model or the updated machine learning model; and outputting, by the target machine learning model or the updated machine learning model, an inference based on the detection, characterization, classification, or a combination thereof.

[0018] In some embodiments, the computer-implemented method further includes determining, by a user, a diagnosis of a subject associated with the new image, the diagnosis being determined based on the inferences output by the target machine learning model or the updated machine learning model.

[0019] In some embodiments, the computer-implemented method further includes administering, by the user, a treatment to the subject based on (i) the inferences output by the target machine learning model or the updated machine learning model, and / or (ii) the subject's diagnosis.

[0020] In some embodiments, training the machine learning algorithm includes implementing meta-learning principles to enable a first stage to generate a conditioned machine learning model using a limited number of examples.

[0021] In some embodiments, training the conditioned machine learning model includes implementing meta-learning principles to enable the second stage to generate a targeted machine learning model using a limited number of images.

[0022] In some embodiments, a system is provided that includes one or more data processors and a non-transitory computer-readable storage medium containing instructions that, when executed on the one or more data processors, cause the one or more data processors to perform some or all of one or more of the methods disclosed herein.

[0023] In some embodiments, a computer program product is provided that is tangibly embodied in a non-transitory machine-readable storage medium and includes instructions configured to cause one or more data processors to perform some or all of one or more of the methods disclosed herein.

[0024] The terms and expressions which have been employed are used as terms of description rather than of limitation, and there is no intention in the use of such terms and expressions to exclude all equivalents of the features shown and described or portions thereof, recognizing that various modifications are possible within the scope of the claimed invention. Thus, although the claimed invention has been specifically disclosed by embodiments and optional features, it is to be understood that modifications and variations of the concepts disclosed herein may be reclassified by those skilled in the art, and that such modifications and variations are deemed to be within the scope of the invention as defined by the appended claims. [Brief explanation of the drawings]

[0025] Aspects and features of various embodiments will become more apparent from the following detailed description of the preferred embodiments taken in conjunction with the accompanying drawings.

[0026] [Figure 1] We present the challenges for artificial intelligence-based digital pathology algorithms to efficiently adapt to ever-increasing data complexity.

[0027] [Figure 2] 1 illustrates efficient model development using an adaptive learning framework according to various embodiments.

[0028] [Figure 3] We present a comparison of resource demands for training from scratch, transfer learning, and adaptive learning.

[0029] [Figure 4] 1 illustrates an exemplary network for generating digital pathology images according to some embodiments.

[0030] [Figure 5] 1 illustrates an overview of an adaptive learning framework according to various embodiments.

[0031] [Figure 6] 1 shows examples of IHC images and ground truth for cell detection according to various embodiments.

[0032] [Figure 7] 10 illustrates an example of adaptively learning an increasing number of data with similarity for hematoxylin and eosin (H&E) tissue type classification (data incremental) according to various embodiments.

[0033] [Figure 8] 1 illustrates an example of adaptively learning an increasing number of data sources for H&E tissue type classification (domain incremental) according to various embodiments.

[0034] [Figure 9] 1 illustrates an example of adaptive learning of an increasing number of tissue types for H&E tissue type classification (class incremental) according to various embodiments.

[0035] [Figure 10] 1 illustrates an exemplary computing environment for processing digital pathology images using machine learning / deep learning models according to various embodiments.

[0036] [Figure 11]1 shows a flowchart illustrating a process for training and using a machine learning model according to various embodiments of the present disclosure.

[0037] [Figure 12] 1 illustrates an example of an image from a CRC training dataset according to various embodiments.

[0038] [Figure 13] 1 illustrates an example of an image from a PatchCam dataset according to various embodiments.

[0039] [Figure 14] 10 shows the accuracy of the test stream at the end of each primary experience under the class incremental setting with the extended CRC dataset using COPE with two baselines according to various embodiments.

[0040] [Figure 15] 1 illustrates example images from an augmented training dataset according to various embodiments.

[0041] [Figure 16] 10 shows the accuracy (left) and forgetting (right) of the test stream at the end of each main experience under the domain incremental setting with the extended CRC dataset using LwF according to various embodiments.

[0042] [Figure 17] 10 shows the accuracy of the test stream at the end of each primary experience under a data incremental setting with an extended CRC dataset using iCaRL according to various embodiments.

[0043] [Figure 18] 1 shows the overall accuracy at the end of the training data, domain and class incremental scenario from different continuous learning methods according to various embodiments, along with two baselines.

[0044] [Figure 19] 1 illustrates the performance of a continuous learning method in a data incremental scenario according to various embodiments.

[0045] [Figure 20] 1 illustrates the performance of a continuous learning method in a domain incremental scenario according to various embodiments.

[0046] [Figure 21] 1 illustrates the performance of a continuous learning method in a class-incremental scenario according to various embodiments.

[0047] [Figure 22] 10 shows results from an A-GEM with extended CRC data set as a task incremental scenario according to various embodiments.

[0048] [Figure 23] 10 shows the accuracy of the last test stream of each main experience under the domain incremental setting with the extended CRC dataset using CoPE according to various embodiments.

[0049] [Figure 24] 10 illustrates the impact of class grouping and experience settings on class incremental performance using iCaRL according to various embodiments.

[0050] [Figure 25] 1 illustrates sequential learning from different tumor types in a domain incremental setting using LwF according to various embodiments. DETAILED DESCRIPTION OF THE INVENTION

[0051] While specific embodiments are described, these embodiments are presented by way of example only and are not intended to limit the scope of protection. The apparatus, methods, and systems described herein may be embodied in various other forms. Furthermore, various omissions, substitutions, and changes in form of the exemplary methods and systems described herein may be made without departing from the scope of protection.

[0052] I. Overview Artificial intelligence and machine learning-based methods have achieved unprecedented performance in solving complex problems in digital pathology analysis, automatically suggesting potential lesions, thus improving diagnostic confidence and reducing pathologist workload by reducing subjectivity. A common strategy to ensure reliable and trustworthy digital pathology algorithm performance is to collect and train models with numerous annotations for each target image domain in digital pathology from scratch, both during (a) the initial model training phase and (b) the model update phase for performance improvement or adaptation to different image domains. However, fundamental tasks for histopathology image analysis, such as image classification, semantic segmentation, and object detection, require manual creation and curation of annotations by pathologists. Such time-consuming and resource-intensive model development has led to two major challenges in digital pathology.

[0053] First, there is the challenge of efficiently and effectively establishing artificial intelligence models for targeted digital pathology datasets. Due to their data-intensive nature and limited generalizability to unseen data distributions, most deep learning models take months to develop, requiring a large set of annotations specific to the target dataset to be generated and validated by certified experts. However, such a time-consuming and resource-intensive development process presents challenges in meeting the ever-increasing demand for such models. Given emerging multiplexing technologies on the market, a diverse set of new assays will be developed alongside deep learning-based digital pathology analysis. Furthermore, constantly evolving patient populations and unpredictable disease outbreaks require efficient model development strategies to address changing diagnostic needs.

[0054] Second, there is the challenge of efficiently adapting existing model systems to related but different datasets. Image digitization requirements are constantly evolving, especially with technological advances. The use of different staining chromogens, variations in staining, digital scanners, and vendor platforms result in variations in the appearance of digitized images. The widespread availability and widespread availability of digital pathology also results in a nearly continuous stream of data with biological variance due to the heterogeneous disease samples to be analyzed. The ever-increasing volume and complexity of data necessitates the development of artificial intelligence algorithms that can adapt and maintain performance under various conditions. Traditional approaches, which use manual task-specific annotations and retrain on newer data batches, rapidly increase demands on data storage, training time, and computing power, subsequently increasing costs and delaying product releases, ultimately reaching a point where they are prohibitively expensive for organizations, as shown in Figure 1.

[0055] Active learning-based techniques have been designed since the pre-deep learning era to reduce the number of annotations required for model development. These techniques utilize heuristic scoring strategies to query a small subset of the most informative unlabeled examples within a dataset. By iteratively adding only a small set of such selected examples for model retraining, active learning aims to incrementally improve model performance, thus avoiding the need to annotate many potentially uninformative examples. However, models developed using active learning are only applied to test images with the same or identical distribution as the training images. For example, a model trained using active learning on one immunohistochemistry (IHC) assay (Domain 1) cannot generalize to another domain, such as another IHC assay (Domain 2). As another example, a model trained on one tissue type cannot be easily transferred to other tissue types. Therefore, such techniques, unlike the adaptive learning framework disclosed herein, cannot fully address the challenges of model inflexibility and lack of model adaptability. In addition, active learning cannot help reduce the demands on computational power and storage space, as it requires iterative model retraining with all existing examples and newly annotated examples at each development iteration.

[0056] Alternatively, transfer learning and domain adaptation have been used to improve model generalization to some extent. In transfer learning, all or part of the model weights are targeted with a large annotated dataset to be applied to a new image domain, while domain adaptation aims to use only a few or no annotations from the target domain for model development. However, both frameworks can suffer from catastrophic forgetting: when a model targeted in one image domain (the source domain) is utilized to train in another image domain (the target domain), its performance in the source domain is significantly degraded, thus "forgetting" the knowledge learned from the previous training process on the source domain data. Although domain adaptation algorithms aim to generate models with good performance for both the source and target domains even without annotations from the target domain (unsupervised domain adaptation), current practice still relies on a validation set from the target domain for model selection, which inevitably tends to overfit the validation set.

[0057] To address these and other challenges, various embodiments disclosed herein relate to methods, systems, and computer-readable storage media for (1) reducing the resource demands required to develop artificial intelligence models for unseen distributions of digital pathology data in the initial model development stage, and (2) reducing the resource demands for subsequent iterations of model development aimed at improving or adapting the initial artificial intelligence model built in accordance with (1) to related but not entirely identical datasets.

[0058] To reduce resource demands during the initial model development phase, techniques are implemented to precondition artificial intelligence systems to learn useful features from existing digital pathology data. Such designs leverage existing annotated digital pathology datasets that are related to, but not necessarily similar to, the target data, allowing the artificial intelligence system to distill its learning skills through a pre-training phase using these related datasets. As used herein, "learning skills" include one or more of the following: the best set of model initializations, the best set of model weights that can generalize to unseen data, the best set of model architectures, etc. These learning skills allow the preconditioned model to achieve reasonable performance, requiring only a small set of annotations. For example, achieving 75% accuracy with <50 annotated images to classify tissue type from tumor types on which the model is not trained, and >2,000 images to train a model specific to this tumor type using a conventional artificial intelligence model.

[0059] To reduce resource requirements for subsequent model development or model adaptation to different datasets, continuous learning techniques and algorithms are implemented to enable model updating using sequentially acquired data without having to train the model from scratch on all existing and new datasets. Continuous learning algorithms offer a solution for learning from a series of data streams, but ensuring that old knowledge is not forgotten (catastrophic forgetting) remains a challenge. To select the most effective continuous learning algorithm for diverse digital pathology data, a set of strategies is designed to target various model update requirements commonly encountered in digital pathology applications, and corresponding algorithms are implemented to continuously learn without training from scratch and without model performance degradation on previously encountered data (e.g., catastrophic forgetting by machine learning models).

[0060] These various techniques and algorithms are implemented in an adaptive learning framework that includes the following features and advantages:

[0061] (1) Effectively reduce resource requirements throughout the development process of AI-based digital pathology algorithms. The adaptive learning framework, as shown in Figure 2, addresses the resource-intensive process of both initial model development and subsequent model update / adaptation. Compared to traditional AI strategies (training from scratch), the adaptive learning framework enables efficient initial model development with fewer annotations (e.g., less than 50) and faster model improvement (adaptive learning) to reach convergence on good model performance. The arrows indicate the model update process, and various methods can be applied, including self-supervised learning, continuous adaptive learning, preconditioned continuous adaptive learning (with a small set of annotations), and traditional training (with sufficient annotations).

[0062] (2) The adaptive learning framework can be applied to develop models targeting images from different image domains in digital pathology. Herein, an image domain refers to a set of images with a specific sample distribution. Examples of different image domains include different image modalities (IHC images vs. H&E images), IHC assays (IHC targeting Ki67 vs. CK7 vs. PDL1-CK7), tumor types and subtypes (breast cancer vs. lung cancer), scanners from different vendors, etc.

[0063] (3) The adaptive learning framework leverages existing digital pathology datasets (from one or more image domains) during the preconditioning phase for initial model development, and the corresponding preconditioning model can be applied to the same or related but different image domains as the image domain in the preconditioning phase.

[0064] (4) The designed algorithm for model update strategy selection enables effective extension of existing models to adapt to different image domains after initial model development.

[0065] (5) Users, such as developers, can flexibly apply only the initial model development strategy, only the model update strategy, or both, depending on the availability of the initial model and the need to update the model to new image datasets or new domains. Alternatively, self-supervised pre-training can be combined with the preconditioning and model update strategies in one or all of the multiple model development iterations.

[0066] (6) The adaptive learning framework is domain-independent and can be applied to other imaging modalities as well as other computational studies such as multimodal analysis, gene sequencing signal analysis, and survival modeling.

[0067] Figure 3 shows a comparison of resource requirements for training from scratch, transfer learning, and the adaptive learning framework described herein. Resources (y-axis) refer to the total number of images that need to be computed for model training of various subsequent model versions (x-axis); if one image is processed N times, it counts as N images. Training from scratch consumes the most resources, and demands increase rapidly. Transfer learning only requires resources to compute a new batch of data. Adaptive learning requires similar computational resources as transfer learning, with a negligible increase.

[0068] In one exemplary embodiment, a computer-implemented process is provided that includes, in a data processing system, obtaining a first annotated training set of images for training a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in images, the first annotated training set of images being in a first image domain; dividing, by the data processing system, the first annotated training set of images into mini-sets of images, each mini-set representing a separate modeling subtask and including a limited number of examples; and generating, by the data processing system, a conditioned machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in new images, using the mini-sets of images in a first stage. training a machine learning algorithm; labeling, by a data processing system, a limited number of images from the target dataset to generate a second annotated training set of images for training the machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in the images, wherein the second annotated training set of images is in a second image domain; and training, by the data processing system, a second-stage preconditioned machine learning model using the second annotated training set of images to generate a target machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in new images, wherein the number of classes targeted in the first stage is a subset of or matches the number of classes targeted in the second stage.

[0069] In some embodiments, the computer-implemented process further includes identifying a digital pathology scenario, selecting an adaptive continuous learning method for updating the target machine learning model in light of the digital pathology scenario, and updating the target machine learning model based on the adaptive continuous learning method to generate an updated machine learning model.

[0070] Advantageously, the various techniques described herein can improve the robustness of machine learning models (e.g., improve the accuracy of cell classification).

[0071] II. Definition As used herein, when an action is "based on" something, this means that the action is based at least in part on at least a part of the something.

[0072] As used herein, the terms "substantially," "approximately," and "about" are defined as being largely, but not necessarily entirely, specified (and including) what is entirely specified, as would be understood by one of ordinary skill in the art. In any disclosed embodiment, the terms "substantially," "approximately," or "about" may be replaced with "within [percentage]" of what is specified, where percentages include 0.1, 1, 5, and 10%.

[0073] As used herein, the terms "sample," "biological sample," "tissue," or "tissue sample" refer to any sample containing biomolecules (e.g., proteins, peptides, nucleic acids, lipids, carbohydrates, or combinations thereof) obtained from any organism, including viruses. Other examples of organisms include mammals (e.g., veterinary animals such as humans, cats, dogs, horses, cows, and pigs, and laboratory animals such as mice, rats, and primates), insects, annelids, arachnids, marsupials, reptiles, amphibians, bacteria, and fungi. Biological samples include tissue samples (such as tissue sections and needle biopsies of tissue), cell samples (such as cytological smears, such as Pap smears or blood smears, or samples of cells obtained by microdissection), or cell fractions, fragments, or organelles (such as those obtained by lysing cells and separating their components, such as by centrifugation). Other examples of biological samples include blood, serum, urine, semen, feces, cerebrospinal fluid, interstitial fluid, mucus, tears, sweat, pus, biopsy tissue (e.g., obtained by surgical or needle biopsy), nipple aspirate, earwax, milk, vaginal fluid, saliva, swabs (such as oral swabs), or any material containing biomolecules derived from an initial biological sample. In certain embodiments, the term "biological sample," as used herein, refers to a sample prepared from a tumor or portion thereof obtained from a subject (such as a homogenized or liquefied sample).

[0074] As used herein, the terms "biological material," "biological structure," or "cellular structure" refer to naturally occurring materials or structures that comprise all or part of a biological structure (e.g., a cell nucleus, cell membrane, cytoplasm, chromosomes, DNA, cell, cell mass, etc.).

[0075] As used herein, "digital pathology image" refers to a digital image of a stained sample.

[0076] As used herein, the term "cell detection" refers to the detection of the location and characteristics of a cell or cell structure (e.g., cell nucleus, cell membrane, cytoplasm, chromosome, DNA, cell, cell mass, etc.) pixel.

[0077] As used herein, the term "target region" refers to a region of an image containing image data intended to be evaluated in an image analysis process. Target regions include any region, such as a tissue region of an image, intended to be analyzed in an image analysis process (e.g., tumor cells or stain expression).

[0078] As used herein, the term "tile" or "tile image" refers to a single image corresponding to a portion of an entire image or an entire slide. In some embodiments, a "tile" or "tile image" refers to a region of an entire slide scan or an area of ​​interest having (x,y) pixel dimensions (e.g., 1000 pixels by 1000 pixels). For example, consider an entire image divided into M columns of tiles and N rows of tiles. Each tile in the MxN mosaic contains a portion of the entire image; i.e., the tile at location M1, N1 contains a first portion of the image, the tile at location M1, N2 contains a second portion of the image, and the first and second portions are different. In some embodiments, the tiles may each have the same dimensions (pixel size by pixel size). In some instances, the tiles may overlap, representing overlapping regions of the entire slide scan or area of ​​interest.

[0079] As used herein, the terms "patch," "image patch," or "mask patch" refer to a container of pixels corresponding to a portion of an entire image, entire slide, or entire mask. In some embodiments, a "patch," "image patch," or "mask patch" refers to a region of an image or mask, or an area of ​​interest having (x,y) pixel dimensions (e.g., 256 pixels by 256 pixels). For example, a 1000 pixel by 1000 pixel image divided into 100 pixel by 100 pixel patches will contain 10 patches (each patch containing 1000 pixels). In other embodiments, the patches have (x,y) pixel dimensions and overlap with each "patch," "image patch," or "mask patch" sharing one or more pixels with another "patch," "image patch," or "mask patch."

[0080] III. Generation of digital pathology images Digital pathology involves the interpretation of digitized images to accurately diagnose a subject and guide therapeutic decision-making. In a digital pathology solution, an image analysis workflow can be established to automatically detect or classify biological objects of interest, such as positive and negative tumor cells. An exemplary digital pathology solution workflow includes acquiring a tissue slide, scanning a preselected area or the entire tissue slide with a digital image scanner (e.g., a whole slide imaging (WSI) scanner) to acquire a digital image, performing image analysis on the digital image using one or more image analysis algorithms, and potentially detecting and quantifying each object of interest (e.g., counting or identifying object-specific regions or cumulative areas of each object of interest) based on the image analysis (e.g., quantitative or semi-quantitative scoring such as positive, negative, moderate, weak, etc.).

[0081] 4 shows an exemplary network 400 for generating digital pathology images. A fixation / embedding system 405 fixes and / or embeds tissue samples (e.g., samples containing at least a portion of at least one tumor) using a fixative (e.g., a liquid fixative such as a formaldehyde solution) and / or an embedding substance (e.g., a histology wax such as paraffin wax, and / or one or more resins such as styrene or polyethylene). Each sample may be fixed by exposing the sample to a fixative for a predetermined period of time (e.g., at least 3 hours) and then dehydrating the sample (e.g., via exposure to an ethanol solution and / or a clearing intermediate agent). The embedding substance may become infiltrated when the sample is in a liquid state (e.g., upon heating).

[0082] Fixation and / or embedding of samples is used to preserve samples and slow their degradation. In histology, fixation generally refers to an irreversible process using chemicals to preserve chemical composition, preserve natural sample structure, and protect cellular structures from degradation. Fixation may also harden cells or tissues for sectioning. Fixatives may enhance sample and cell preservation using cross-linking proteins. Fixatives may bind to and cross-link some proteins and denature others through dehydration, which can harden tissue and inactivate enzymes that might otherwise degrade the sample. Fixatives may also kill bacteria.

[0083] Fixatives can be administered, for example, by perfusion and immersion of the prepared sample. Various fixatives can be used, including methanol, buprenorphine fixatives, and / or formaldehyde fixatives, such as neutral buffered formalin (NBF) or paraffin-formalin (paraformaldehyde-PFA). If the sample is a liquid sample (e.g., a blood sample), the sample may be smeared onto a slide and allowed to dry before fixation. While the fixation process can help preserve the structure of the sample and cells for histological examination, fixation can mask tissue antigens, thereby reducing antigen detection. Therefore, fixation is generally considered a limiting factor in immunohistochemistry, as formalin can crosslink antigens and mask epitopes. In some instances, additional processes are performed to reverse the effects of crosslinking, including treating the fixed sample with citraconic anhydride (a reversible protein crosslinker) and heating.

[0084] Embedding can involve infiltrating a sample (e.g., a fixed tissue sample) with an appropriate histological wax, such as paraffin wax. Histological waxes can be insoluble in water or alcohol, but soluble in paraffin solvents such as xylene. Therefore, it may be necessary to replace the water in the tissue with xylene. To do so, the sample may first be dehydrated by gradually replacing the water in the sample with alcohol. This can be achieved by passing the tissue through increasing concentrations of ethyl alcohol (e.g., from 0 to approximately 100%). After replacing the water with alcohol, the alcohol can be replaced with xylene, which is miscible with alcohol. Because histological waxes can be soluble in xylene, the molten wax can be filled with xylene, filling the spaces previously filled with water. The wax-filled sample can be cooled to form a hardened block, which can be clamped to a microtome, vibratome, or compressome to cut sections. In some cases, deviations from the above exemplary procedure may result in infiltration of the paraffin wax, inhibiting penetration of antibodies, chemicals, or other fixatives.

[0085] The tissue slicer 410 can then be used to section the fixed and / or embedded tissue sample (e.g., a tumor sample). Sectioning is the process of cutting thin slices (e.g., 4-5 μm thick) of a sample from a tissue block for mounting on a microscope slide for examination. Sectioning may be performed using a microtome, vibratome, or compressome. In some cases, tissue can be rapidly frozen in dry ice or isopentane and then cut with a cold knife in a refrigerated cabinet (e.g., a cryostat). Other types of coolants, such as liquid nitrogen, can be used to freeze tissue. Sections for use in brightfield and fluorescence microscopy are generally on the order of 4-10 μm thick. In some cases, sections can be embedded in epoxy or acrylic resin, which may allow for cutting thinner sections (e.g., <2 μm). These sections may then be mounted on one or more glass slides. A coverslip may be placed on top to protect the sample section.

[0086] Because tissue sections and the cells therein are substantially transparent, slide preparation typically further includes staining the tissue sections (e.g., automated staining) to make relevant structures more visible. In some cases, the staining is performed manually. In some cases, the staining is performed semi-automatically or automatically using a staining system 415. The staining process involves exposing sections of the tissue sample or fixed liquid sample to one or more different stains (e.g., sequentially or simultaneously) to reveal different properties of the tissue.

[0087] For example, stains can be used to mark specific types of cells and / or flag specific types of nucleic acids and / or proteins to aid in microscopy. The staining process generally involves adding a dye or stain to a sample to confirm or quantify the presence of a particular compound, structure, molecule, or feature (e.g., a subcellular feature). For example, stains can help identify or highlight specific biomarkers in tissue sections. In other examples, stains can be used to identify or highlight biological tissues (e.g., muscle fibers or connective tissue), cell populations (e.g., different blood cells), or organelles within individual cells.

[0088] One exemplary type of tissue stain is a histochemical stain, which uses one or more chemical dyes (e.g., acid dyes, basic dyes, chromogens) to stain tissue structures. Histochemical stains may be used to reveal general aspects of tissue morphology and / or cellular microanatomy (e.g., distinguishing cell nuclei from cytoplasm, revealing lipid droplets, etc.). One example of a histochemical stain is H&E. Other examples of histochemical stains include trichrome stains (e.g., Masson's trichrome), periodic acid-Schiff (PAS), silver stains, and iron stains. The molecular weight of histochemical stains (e.g., dyes) is generally about 500 kilodaltons (kD) or less, although some histochemical stains (e.g., Alcian blue, phosphomolybdic acid (PMA)) may have molecular weights up to 2000 or 3000 kD. One example of a high molecular weight histochemical stain is α-amylase (about 55 kD), which may be used to reveal glycogen.

[0089] Another type of tissue staining is IHC, also known as "immunostaining," which uses a primary antibody that specifically binds to a target antigen of interest (also called a biomarker). IHC can be direct or indirect. In direct IHC, the primary antibody is directly conjugated to a label (e.g., a chromophore or fluorophore). In indirect IHC, a primary antibody is first bound to the target antigen, and then a secondary antibody conjugated to a label (e.g., a chromophore or fluorophore) is bound to the primary antibody. Because antibodies have a molecular weight of approximately 150 kD or greater, the molecular weight of IHC reagents is much larger than that of histochemical staining reagents.

[0090] Various types of staining protocols may be used to perform staining. For example, an exemplary IHC staining protocol includes using a hydrophobic barrier around the sample (e.g., tissue section) to prevent leakage of reagents from the slide during incubation, treating the tissue section with reagents to block endogenous sources of nonspecific staining (e.g., enzymes, free aldehyde groups, immunoglobulins, and other unrelated molecules that may mimic specific staining), incubating the sample with a permeabilization buffer to promote penetration of antibodies and other staining reagents into the tissue, incubating the tissue section with a primary antibody at a specific temperature (e.g., room temperature, 6-8 °C) for a certain period of time (e.g., 1-24 hours), rinsing the sample with a wash buffer, and then incubating the sample (tissue section) with a secondary antibody at another specific temperature (e.g., room temperature) for another period of time, rinsing the sample again with a water buffer, incubating the rinsed sample with a chromogen (e.g., DAB: 3,3'-diaminobenzidine), and washing off the chromogen to stop the reaction. In some instances, a counterstain is then used to identify the overall "landscape" of the sample and serve as the primary color reference used to detect tissue targets. Counterstains can include, for example, hematoxylin (a blue-to-purple stain), methylene blue (a blue stain), toluidine blue (a stain that renders nuclei deep blue and polysaccharides pink to red), nuclear fast red (also known as Kern Echtrot dye, a red stain), methyl green (a green stain), non-nucleogenic stains such as eosin (a pink stain), and the like. As will be appreciated by those skilled in the art, other immunohistochemical staining techniques can be implemented to achieve staining.

[0091] In another example, an H&E staining protocol can be performed to stain tissue sections. The H&E staining protocol involves applying hematoxylin stain mixed with a metal salt or mordant to the sample. The sample can then be rinsed in a weak acid solution to remove excess stain (differentiation), followed by bluing in weak alkaline water. After application of hematoxylin, the sample can be counterstained with eosin. It will be understood that other H&E staining techniques can be performed.

[0092] In some embodiments, staining can be performed using various types of stains depending on which features of interest are targeted. For example, DAB can be used on various tissue sections for IHC staining, producing a brown color that represents the feature of interest in the stained image. In another example, alkaline phosphatase (AP) can be used on skin tissue sections for IHC staining because the DAB color can be masked by melanin pigments. Regarding primary staining techniques, applicable stains can include, for example, basophilic and eosinophilic stains, hematein and hematoxylin, silver nitrate, trichrome stains, etc. Acidic dyes can react with cationic or basic components in tissues or cells, such as proteins and other components in the cytoplasm. Basic dyes can react with anionic or acidic components in tissues or cells, such as nucleic acids. As mentioned above, one example of a staining system is H&E. Eosin can be a negatively charged pink acidic dye, and hematoxylin can be a purple or blue basic dye containing hematein and aluminum ions. Other examples of stains may include Periodic Acid-Schiff (PAS) stain, Masson's trichrome, Alcian blue, Van Gieson, reticulin stain, etc. In some embodiments, different types of stains may be used in combination.

[0093] The sections may then be mounted on corresponding slides, which the imaging system 420 can then scan or image to generate raw digital pathology images 425a-n. A microscope (e.g., an electron microscope or an optical microscope) can be used to magnify the stained sample. For example, an optical microscope may have a resolution of less than 1 μm, such as on the order of several hundred nanometers. To observe finer details in the nanometer or sub-nanometer range, an electron microscope may be used. An imaging device (combined with or separate from the microscope) images the magnified biological sample to obtain image data, such as a multichannel image (e.g., multichannel fluorescence) having several (e.g., 10-16) channels. The imaging device may include, but is not limited to, a camera (e.g., an analog camera, a digital camera, etc.), optical elements (e.g., one or more lenses, a sensor-focusing lens group, a microscope objective, etc.), an imaging sensor (e.g., a charge-coupled device (CCD), a complementary metal-oxide semiconductor (CMOS) image sensor, etc.), photographic film, etc. In digital embodiments, the imaging device may include multiple lenses that cooperate to provide on-the-fly focusing. An image sensor, such as a CCD sensor, may capture digital images of the biological sample. In some embodiments, the imaging device is a bright-field imaging system, a multispectral imaging (MSI) system, or a fluorescence microscope system. The imaging device may utilize invisible electromagnetic radiation (e.g., UV light) or other imaging techniques to capture images. For example, the imaging device may include a microscope and a camera configured to capture images magnified by the microscope. The image data received by the analysis system may be identical to and / or derived from the raw image data captured by the imaging device.

[0094] Images of the stained sections may then be stored on a storage device 425, such as a server. The images may be stored locally, remotely, and / or on a cloud server. Each image may be stored in association with a subject identifier and a date (e.g., the date the sample was collected and / or the date the image was captured). The images may then be transmitted to another system (e.g., a system associated with a pathologist, an automated or semi-automated image analysis system, or a machine learning training and deployment system, as described in more detail herein).

[0095] It is understood that modifications to the process described with respect to network 400 are contemplated. For example, if the sample is a liquid sample, embedding and / or sectioning may be omitted from the process.

[0096] IV. Adaptive Learning Framework 5 shows that the adaptive learning framework includes two components: (505) initial model development, and (510) model updating and / or adaptation to different image domains. The two components 505; 510 can be applied separately or all together, such as initial model development and subsequent model updating and / or adaptation to different image domains.

[0097] Development of the initial model For efficient development of an initial model, a two-stage development strategy (illustrated in Figure 5) is as follows: Stage 1 Model Preconditioning, in which an artificial intelligence system (e.g., the artificial intelligence system described in detail with respect to Figure 10) leverages existing annotated datasets and improves its learning skills through training with these datasets. Stage 2 Targeted Model Training, in which an artificial intelligence system utilizes the learning skills learned from Stage 1 to extend itself to a different image domain (the target domain) that requires fewer annotations in the target domain than traditional learning methods.

[0098] The aforementioned "learning skill" includes one or more of the following: best set of model initialization, best set of model weights that can generalize to unseen data, best set of model architecture, etc. The best set is determined using one or more metrics for measuring model performance, such as accuracy or area under the curve (AUC). The learning skill is then applied to a target image domain, such that fewer annotations are required for the target domain than traditional machine learning.

[0099] To achieve model preconditioning, a meta-learning strategy may be employed in which an existing dataset (e.g., a training dataset) is divided into mini-sets, each mini-set representing a distinct modeling subtask and containing only a small number of examples, thus forming multiple subtasks. The division can be performed at training time, with different data divisions being performed in each model training iteration. Training an AI system using these subtasks allows the AI ​​system to search for superior solutions in the model optimization landscape, which can generalize to any related smaller subtasks without overfitting to a specific subtask, thus preconditioning the AI ​​system for the unseen target domain in Stage 2. Generally, the number of classes in Stage 1 training is set to match a portion of or the number of classes in Stage 2 training. In a class-incremental scenario for Stage 2, the number of classes in Stage 1 can be increased, while in a domain and data-incremental scenario for Stage 2, the number of classes from Stage 1 must match. In a specific example, the number of classes in Stage 2 can be greater than that in Stage 1 (as described in detail in connection with FIG. 9 ). In classification tasks (e.g., binary and multi-class classification), class labels are at the image level, e.g., a class (or multiple classes) is assigned to the entire image. In prediction tasks (e.g., dense prediction), such as image segmentation and object detection, class labels are at a finer level, e.g., in the case of object detection, each distinct object in an image has its class and location label. The training datasets used for model preconditioning are related to each other but can have varying degrees of similarity to that of the target domain.

[0100] The following criteria may be implemented to sample existing annotated datasets: (1) If only one annotated dataset is available, for each subtask, a subset of classes may be randomly selected to be a fraction of or match the number of classes in stage 2, and some examples may be randomly selected from the selected classes. In this scenario, there are many subtasks with different or partially different classes. (2) If multiple annotated datasets are available, for each subtask, examples may be mixed from multiple datasets, and the mixed dataset may then be implemented in the same way as in (1), or a specific dataset may be first randomly selected, and then a subset of classes within that dataset may be randomly selected to be a fraction of or match the number of classes in stage 2. In both scenarios, (a) sampling strategies other than complete randomness may also be employed, e.g., some classes or some datasets may be sampled more frequently than others, and / or (b) examples within each subtask may be divided into a training subset and a validation subset.

[0101] More specifically, for image-level prediction, e.g., image classification tasks, an "example" refers to an image in the dataset with that class label; that is, each subtask consists of a set of images all belonging to a selected class. Within each subtask, image class labels are redefined for the Phase 1 training process. For example, 15 images, e.g., five images per class, for a total of three classes, may be selected. Regardless of each image's original class label, a random ordering of the classes is generated for Phase 1 training, whereby one of the three classes can be set as Class No. 0, another class can be set as Class No. 1, and the last class can be set as Class No. 2. For the next subtask, another 15 images can be selected from a different set of classes, and then their class labels are reset in a random order to 0, 1, and 2 again. In this way, the model becomes class-independent in the sense that it is not focused on learning information from each specific class, but rather learns how to improve its learning skills for all possible subtasks it encounters.

[0102] For prediction tasks (e.g., dense prediction), an example includes all annotated entities (regions or objects) of the same class in an image along with their labels. When sampling some examples from a selected subset of classes, some images containing at least one labeled entity from the selected class are first selected, and then labeled entities not from the selected class are set to the background class. For example, in an image segmentation task, class labels may include a foreground class and a background class (i.e., regions of no interest for modeling purposes). If the selected classes are tumor nests and blood vessels, all regions in the image that do not belong to these two classes are relabeled as the background class, all regions belonging to tumor nests are randomly relabeled as class No. 0 or No. 1, and blood vessel regions are relabeled as whichever class index remains after relabeling tumor regions.

[0103] The subtask learning methods can be thought of as follows: Metric-based methods that learn representations for existing datasets and distill from these datasets the skill of comparing the similarity between examples of any class from an unseen target domain. In these methods, the representations learned in Stage 1 can be applied in Stage 2 in the following way: (a) select a small number of images in the target domain; (b) annotate these images and apply a preconditioned model for each example to generate a feature vector representation (e.g., the output of the last layer in a convolutional network before the classification layer); (c) combine representations from examples of the same class to generate one representation per target class; (d) use these processed representations as prototypes of the target class; (e) generate feature vector representations for the remaining unlabeled images or image regions (or other entities in the case of dense prediction tasks) in the target domain; and (f) compare each feature vector representation from the unlabeled target domain with the prototype by calculating the distance between these vectors, e.g., the cosine distance, and then assign the class label in the unlabeled image or image region as the prototype class with the smallest distance (e.g., most similar). Other techniques for learning subtasks may be used in combination with metric-based methods, such as generative adversarial models, which synthesize images based on a distribution of existing images and use the generated images to increase the number of examples per class in the target image domain.

[0104] Alternatively, optimization-based methods for learning the best model weights for initializing a model can efficiently adapt to unseen target datasets with only a few examples. In these methods, training in Stage 1 involves two model optimization loops: (a) an inner learning loop in which the artificial intelligence model updates its model weights on one subtask for a predetermined or flexible number of epochs, producing a loss on its validation set after the model update for the i-th subtask, denoted as L-subtask-i; and (b) an outer learning loop in which the objective is to search for a set of model initializations that produces the best model when used to update all subtasks, each of which involves only a few annotated examples, by finding a model initialization that minimizes the sum of all losses calculated from the validation sets of the subtasks on their validation set for those model initializations (summing L-subtask-i, where i ranges from 1 to the number of subtasks). Other techniques for learning subtasks may be used in combination with optimization-based methods. For example, not only searching for the best model initialization, but also searching for the best model architecture (e.g., performing a neural architecture search).

[0105] The workflow described here for the design of initial model development was applied to cell detection in brightfield IHC assays and tissue type classification in H&E assays as follows: However, a similar workflow can also be applied to other staining methods, such as special stains in brightfield assays (e.g., Trichrome Masson assays, which simultaneously stain muscle, collagen fibers, red blood cells, and cell nuclei) and fluorescent IHC assays.

[0106] (i) Model preconditioning for cell detection in IHC assays: The goal is to identify the staining phenotype, cell type, and cell location in each image. For example, in the case of a DAB-Ki67 IHC assay, a cell detection model can be designed to identify tumor cells that are positively stained with Ki67 (Ki67+ tumor), tumor cells that are negatively stained with Ki67 (Ki67- tumor), and all other cell types / staining types, along with the location of each cell nucleus center in a single pixel, or along with the bounding box of each cell nucleus (e.g., the pixel location of the rectangle circumscribing each cell nucleus), or along with the pixel of each cell nucleus (e.g., a nuclear segmentation mask).

[0107] Generally, images from brightfield IHC assays are related and share a certain level of similarity in appearance; i.e., hematoxylin staining is used in most of these assays to stain cell nuclei and serve as a pointer to where cells are located within the whole slide image. However, one or more biomarkers are targeted by the IHC staining protocol, and correspondingly, cells expressing these biomarkers exhibit color through the application of a chromogen. "Staining pattern" refers to the appearance of image areas positive for the target biomarker in terms of (a) the intracellular and / or subcellular localization of the biomarker, (b) the stained cell type, (c) staining intensity, (d) frequency of occurrence, and (e) the spatial distribution of the positive areas. For example, Ki67 has a nuclear staining pattern; positive staining signals in IHC images from Ki67 assays are observed to be primarily located in cell nuclei, either in scattered tumor cells or clustered tumor nests, with positive staining signals ranging from low to very high intensity.

[0108] A workflow for preconditioning may be designed using images from various IHC assays with various chromogens and biomarker staining patterns (see Table 1 for assays, for example). An example workflow may include the following: (1) If one or more chromogens used in an existing annotated dataset are the same as those in one or more target IHC assays: (1.1) If annotations from only one assay are available, in each model training iteration, divide this dataset into subtasks and sample one subtask for training, which has a small number of images with cell annotations from one or more classes. Ensure that cells from all classes selected for this development stage are present in at least one of the images. For example, apply the preconditioning to the DAB-Ki67 assay and the DAB-PDL1 assay. Figure 6 shows an example of a DAB-Ki67 IHC image (A). In this case, the brown signal is the image area where the chromogen DAB generated color, indicating those cells where Ki67 expressed in the cell nuclei was detected by this IHC assay, and the grayish-blue signal is the hematoxylin-stained cell nuclei. An example ground truth (B) is also shown for cell detection in the image in (A), with different colored dots overlaid on the cell nuclei centers indicating the class label of each cell. (1.2) If annotations from multiple assays are available, in each model training iteration, an assay may first be selected from all assays, and then several examples may be sampled from this assay to train a preconditioned artificial intelligence system that is as assay-independent as possible. For example, the artificial intelligence system may be preconditioned on the DAB-Ki67 and DAB-CK7 assays and applied to the DAB-PDL1 assay.

[0109] (2) If the chromogens used in the existing annotated dataset are different from those of the target IHC assay, a workflow similar to (1.1) or (1.2) can be performed. Furthermore, to match the chromogens in both Steps 1 and 2, stain unmixing can be performed to decompose the IHC image into its individual stain components and remix these components with the color vectors extracted from the target IHC assay. For example, an artificial intelligence system can be used as a preconditioner for a Tamra-PDL1 / Dabsyl-CK7 duplex assay or applied to a DAB-Ki67 assay. The training system or user can choose to decompose the Tamra-PDL1 / Dabsyl-CK7 duplex image into PDL1, CK7, and hematoxylin gray-scale intensity images and remix them with the DAB color vector to obtain two image sets for the preconditioning step: a composite DAB-PDL1 single-strand image and a composite DAB-CK7 single-strand image. Figure 6 shows an exemplary Tamra-PDL1-Dabsyl-CK7 IHC image (C). An exemplary ground truth (D) is also shown for a DAB-PR IHC image in which different colored dots overlaid on the cell nucleus center indicate the class label of each cell.

[0110] The assays used in the preconditioning stage do not necessarily have to have a high degree of similarity to the target domain assay, but some level of similarity can be beneficial for the accumulation of both learning skills and learned knowledge in Stage 1. [Table 1]

[0111] (ii) Model preconditioning for tissue type classification in H&E assays: In this case, the goal is to generate a model for identifying the tissue type of each image tile from the whole slide image. For example, build a model that can classify each image tile into tumor, stroma, normal tissue, and other types. Model preconditioning can be performed using a similar workflow described herein with existing datasets from other disease types outside the target domain (e.g., different tumor types), different disease stages, etc. Each subtask can sample from the same dataset or from a mixture of different datasets, if available.

[0112] Model Update and Adaptation To efficiently perform model updating and adaptation to new datasets after initial model development, we identified scenarios commonly encountered in digital pathology settings and developed techniques for selecting the optimal adaptive learning method for the scenario. Tissue type classification of H&E images is used as an example to illustrate these techniques. However, it should be understood that the described techniques for model updating and adaptation can be applied to a variety of other scenarios commonly encountered in digital pathology.

[0113] When the model is trained continuously, the stream of data can vary in different ways. Commonly encountered situations in digital pathology have been categorized into the following scenarios: 1. Data Incremental Scenario: Creating a pathologist-curated, annotated dataset is a time-consuming process, and it is preferable to train the model in batches as and when data arrives. Incoming data, considered as a new stream for training the model, has minimal differences from previous data, and is typically from the same underlying distribution, with all classes as seen before. 2. Domain Incremental: When successive streams of data are from different domains or distributions, it is considered a domain incremental scenario. This scenario is similar to the data incremental scenario in that all data streams have all classes represented in them. 3. Class Incremental: The class incremental scenario is when the model is expanded with respect to the number of classes. The clinical need for this scenario arises when a batch of annotated images contains a different subset of classes or when the model definition changes to classify the data into more tissue subtypes. It should be understood that each data stream may contain images from new unseen classes as well as images of seen classes introduced in previous data streams. 4. Task Incremental: Any of the above scenarios can be considered task incremental if each data stream is defined as a new task. This scenario uses a different architectural design, where the network has shared layers between tasks and task-specific layers.

[0114] Each incremental data stream is called an experience. Each experience is then divided into training, validation, and test streams. The model is targeted in the training stream, validated in the validation stream at the end of every epoch, and evaluated in the test stream at the end of each experience. Model performance is evaluated on the test stream from all experiences at the end of training for all experiences to study forward and backward movement.

[0115] (i) Data-incremental digital pathology model update: (1.1) Digital Pathology Scenario: After the initial development of an AI-based digital pathology algorithm, more annotated data from the same domain (e.g., slight differences and near-similarities; from the same underlying data distribution) may need to be incorporated into the model. In a digital pathology setting, it is common to expect annotated data to arrive in batches because expertly annotated and / or expertly validated annotations are time-consuming and may not be available during initial model development. In addition, due to the large number of parameters in AI models, especially deep neural networks, it is common to prevent model overfitting by learning from additional data. For example, an initial model may be trained to classify tumor tissue versus normal tissue from colon cancer images (as shown in Figure 7—the plot in the lower left corner shows the class labels and number of examples in each model version). In subsequent model development / updates, similar examples of the same class may be integrated into the model, arriving in batches over time.

[0116] (1.2) Workflow for selecting the best adaptive learning method: (1.2a) To efficiently and effectively update a model without training from scratch using existing data and newly arrived data, a benchmark dataset is established from a given digital pathology domain, data assets are randomly divided into batches, and sequentially arriving data is simulated. (1.2b) To evaluate how effective a candidate learning method is in the presence of small random variations in individual examples within each batch, an augmented dataset may be created to simulate such small variations, and the image order may be randomly shuffled so that each data batch contains images augmented in a different way. The various types and degrees of variations to the original data may be carefully balanced so as not to distort the distribution of the entire dataset. Data augmentation can be performed dynamically during training or proactively for each training iteration. Exemplary dilation techniques include (i) changing the stain space, where stain decomposition is first performed (e.g., unmixing), and then each stain is remixed with a predetermined color vector to change the hue, saturation, and intensity of each stain; (ii) increasing the image resolution by resizing the image and then restoring it to the original size; (iii) the same; or (iv) any combination thereof.

[0117] (1.3) Artificial Intelligence Based Methods for Adaptive Learning: The batch of benchmark data generated from (1.2b) can be run against candidate learning methods as follows:

[0118] (1.3a) Regularization-Based Methods: These methods primarily focus on prioritizing privacy and reducing memory. Privacy is maintained by avoiding storing raw inputs. Among different regularization-based methods, two common methods are elastic weight reinforcement (EWC) and forgetting-free learning (LWF). EWC is a priori focused method in which model parameters are used as priors when learning from new data, and the method estimates distributions over the model parameters. On the other hand, LWF is a data-focused method. The main design of data-focused methods is based on knowledge distillation from a previous model to a current model targeted with new data. This concept is also introduced in LWF, which handles forgetting with a knowledge transfer mechanism. These methods prevent the model from forgetting learned knowledge by applying constraints to the current model weights, so that when updating the current model, the model weights do not deviate significantly from their current version.

[0119] (1.3b) Replay-based methods: These methods retain the most informative examples or their feature representations (e.g., feature vectors extracted from the hidden layer of a neural network) from existing data batches and revisit them during training on newly arrived data. To overcome forgetting, previous examples of the task are replayed during the process of learning a new task. Among the various methods in this category are incremental learner and representation learning (iCaRL), continuous prototype evaluation (CoPE), and A-GEM. iCaRL methods memorize a subset of the best examples per class selected according to the approximate class means in the learned feature space. The upper bound of this method is determined by joint training of past and current tasks. CoPE is an online data-incremental learner with prototypes that persistently represent the most salient features of the class population. Rapidly evolving prototypes enable learning and prediction at any point in time. CoPE is robust to class imbalance using a replay and balanced memory population scheme. GEM is designed based on the task-incremental setting. This method focuses only on new tasks by limiting their updates, thus not interfering with previous tasks. This is achieved by projecting the computed gradient direction onto the feasible region outlined by the previous task gradients via a first-order Taylor series approximation. The A-GEM method is an improved version of the GEM method. A-GEM helps alleviate the problem of projecting onto a single direction estimated by a randomly selected sample from the previous task data buffer. A-GEM provides performance accuracy similar to GEM with computational and memory efficiency similar to regularization methods.

[0120] (1,3c) A method combining regularization and reproduction

[0121] (1.3d) A method that exploits meta-learning principles to allow model updating on several examples in each batch (see the “CoPE” method implemented in the experimental section).

[0122] (1.3e) Parameter isolation methods: These methods assign different model parameters to each task to deal with forgetting. There is no fixed architecture in these methods, as no constraints are applied to the size of the architecture. Therefore, new branches can grow for new tasks. This can be achieved by freezing previous task parameters or by dedicating a model copy to each task. These types of architectures are called dynamic architectures.

[0123] (1.3f) Other techniques applied in conjunction with the above methods. For example, running self-supervised learning on new, unlabeled data before applying the above methods. Another example is running a generative adversarial model to generate examples similar to these from previous batches of data.

[0124] (ii) Domain-incremental digital pathology model updating: (2.1) Digital Pathology Scenario: After the initial development of an artificial intelligence-based digital pathology algorithm, it may be necessary to incorporate annotated data from different domains (e.g., similar but from different underlying data distributions) into the model. In the digital pathology setting, there is a practical need to be able to generate models that are (a) robust to changes in experimental settings, such as changes or differences in (i) staining reagents, (ii) staining protocols or equipment, (iii) scanner suppliers, and (iv) sample sources (e.g., different clinical sites or tissue banks), and (b) robust to changes in other aspects, such as tissue type, organ type, patient population, disease stage, and disease subtype (e.g., tumor type and subtype).

[0125] (2.2) Workflow for Selecting the Best Adaptive Learning Method: (2.2a) To efficiently and effectively update the model without training from scratch using both existing and newly arrived data, a benchmark dataset is established from the DP domain, and synthetic images simulating realistic changes are generated as data from different sources / domains. (2.2b) To evaluate which candidate adaptive learning method is most effective for this scenario, an augmented dataset may be created to simulate multiple types of domain shifts, and how well the candidate method performs under such changes may be evaluated. Data augmentation can be performed dynamically during training or proactively for each training iteration. Exemplary augmentation techniques include (i) changing the stain space, where stain decomposition is first performed (e.g., unmixing), and then each stain is remixed with a predetermined color vector to change the hue, saturation, and intensity of each stain; (ii) increasing the image resolution by resizing the image and then restoring it to its original size; (iii) etc., or (iv) any combination thereof. One or more types of changes can be applied to each subset to simulate a series of successive domain shifts. For example, for H&E images with the same tissue type for a classification task, the dataset may be randomly split to generate expanded subsets for the following reasons: (i) one of the stains becomes more intense due to a change in protocol; (ii) both stains fade (i.e., decrease in staining intensity) due to aging of the prepared slides; (iii) one stain becomes more saturated in the HSV color space than the other due to a change in staining agent; and (iv) both stains change hue in the HSV color space due to a change in scanner. Figure 8 illustrates the changes described in (i) and (ii) above (the plot in the lower left corner shows the class labels and number of examples for each model version).

[0126] (2.3) Artificial intelligence-based methods for adaptive learning: The batches of benchmark data generated from (2.2b) may be run against candidate learning methods, such as: (2.3a) Regularization-based methods: These methods prevent the model from forgetting learned knowledge by applying constraints to the current model weights, so that when updating the current model, the model weights do not deviate significantly from their current version; (2.3b) Regeneration-based methods: These methods retain the most informative examples or their feature representations (e.g., feature vectors extracted from the hidden layer of a neural network) from existing data batches and revisit them during training on newly arrived data; (2.3c) Methods that combine regularization and regeneration; (2.3d) Methods that leverage meta-learning principles to enable model updating with several examples from each batch (see the "CoPE" method implemented in the Experimental Section); (2.3e) Parameter isolation methods; (2.3f) Other techniques applied in conjunction with the aforementioned methods. For example, self-supervised learning can be performed on new, unlabeled data before applying the aforementioned methods. Another example is running a generative adversarial model to generate similar examples from previous data batches.

[0127] (iii) Class Incremental Digital Pathology Model Update: (3.1) Digital Pathology Scenario: After the initial development of an artificial intelligence-based digital pathology algorithm, it may be necessary to expand the model in terms of the number of classes. In the digital pathology setting, this scenario is commonly encountered due to: (i) changing end-user needs; (ii) annotated data comes in batches, each batch having a set of classes that are partially or completely different from those of the existing data; and / or (iii) model design choices, e.g., a model initially designed to classify tumor vs. normal finds it necessary to identify necrosis and lymphocyte clusters to ensure good model performance.

[0128] (3.2) Workflow for Selecting the Best Adaptive Learning Method: (3.2a) To efficiently and effectively update the model without training both existing and new data from scratch, a benchmark dataset from the digital pathology domain may be established, in which classes may be divided into several different subsets, and corresponding examples are then divided according to their class labels. For example, Figure 9 shows such class divisions for each model version (the plot in the lower left shows the class labels and number of examples in each model version). (3.2b) Next, candidate adaptive learning methods may be evaluated to determine which adaptive learning method is most effective at incrementally learning classes, and their performance in learning different sets of class orders for each data batch may be compared. (3.3) Artificial intelligence-based methods for adaptive learning: The batches of benchmark data generated from (3.2b) may be run against candidate learning methods, such as: (3.3a) Regularization-based methods: These methods prevent the model from forgetting learned knowledge by applying constraints to the current model weights, so that when updating the current model, the model weights do not deviate significantly from their current version; (3.3b) Regeneration-based methods: These methods retain the most informative examples or their feature representations (e.g., feature vectors extracted from the hidden layer of a neural network) from existing data batches and revisit them during training on newly arrived data; (3.3c) Methods that combine regularization and regeneration; (3.3d) Methods that leverage meta-learning principles to enable model updating with several examples from each batch (see the "CoPE" method implemented in the Experimental Section); (3.3e) Parameter isolation methods; (3.3e) Other techniques applied in conjunction with the aforementioned methods. For example, self-supervised learning can be performed on new, unlabeled data before applying the aforementioned methods. Another example is running a generative adversarial model to generate similar examples from previous data batches.

[0129] (iv) Task Incremental Digital Pathology Model Update: (4.1) In each of the above scenarios, a decision may be made as to whether to formulate each different batch of data as a new task, and thus whether to apply a task incremental method. Such a method may specify a separate model component (e.g., a separate set of neurons or a separate layer in a neural network model) for each task, and in each model iteration, only the model-specific component is trained, while the rest of the previously trained component remains unchanged. Thus, the model can adapt to changes in the data with separate components and avoid forgetting knowledge learned from previous tasks.

[0130] Applying the Adaptive Learning Framework to Other Modalities The adaptive learning framework may be applied to other imaging modalities and other research fields. The adaptive learning framework is domain-independent in the following aspects: (1) The preconditioning strategy for initial model training can be applied to other types of data where a large number of annotations are required to generate the initial model. (2) The three adaptive learning scenarios for model updating / adaptation have commonality with scenarios encountered in other computational biomedical research, and therefore the adaptive learning method selection strategy can be leveraged by these studies.

[0131] The adaptive learning framework may be applied to federated learning, which aims to update a global model without sharing data from individual data sources and without explicitly sharing local models. The adaptive learning framework can be leveraged by federated learning in the following ways: (1) preconditioning the local and / or global models to enable more effective and efficient model updates with a smaller number of annotations in the target image domain, and (2) updating the local and / or global models via one or more adaptive learning methods to continuously update the models without retraining on previous data and selecting the best learning method by applying the model selection workflow described herein.

[0132] The adaptive learning framework may be applied to multi-model learning. Multimodal learning aims to integrate knowledge learned from different modalities of data. The adaptive learning framework can be leveraged by multi-model learning in the following ways: (1) preconditioning a model from one or more data modalities to enable more effective and efficient model updating with fewer annotations in the target image domain; (2) updating from one or more data modalities via one or more adaptive learning methods to continuously update the model without retraining on previous data and selecting the best learning method by applying the model selection workflow described herein; and (3) generating a model for adaptively integrating representations from data of multiple modalities by applying the adaptive learning framework for the initial iteration of learning and / or continuous updating / adaptation.

[0133] V. An Exemplary System for Adaptive Learning 10 shows a block diagram illustrating a computing environment 1000 for processing digital pathology images using an artificial intelligence system (e.g., one or more machine learning models). As described further herein, processing the digital pathology images may include training a machine learning algorithm using the digital pathology images and / or converting some or all of the digital pathology images into one or more results using a trained (or partially trained) version of the machine learning algorithm (i.e., a machine learning model).

[0134] As shown in FIG. 10, the computing environment 1000 includes several stages: an image storage stage 1005, a preprocessing stage 1010, a labeling stage 1015, a data augmentation stage 1017, a training stage 1020, and a result generation stage 1025.

[0135] The image storage stage 1005 includes one or more image data stores 1030 (e.g., storage device 430 described in connection with FIG. 4 ) that are accessed (e.g., by the pre-processing stage 1010) to provide a set of digital images 1035 of pre-selected areas from a biological specimen slide (e.g., a histology slide) or the entire biological specimen slide. Each digital image 1035 stored in each image data store 1030 and accessed by the image storage stage 1010 may include a digital pathology image generated according to some or all of the processes described with respect to the network 400 displayed in FIG. 4 . In some embodiments, each digital image 1035 includes image data from one or more scanned slides. Each of the digital images 1035 may correspond to image data from a single specimen and / or from a single day on which the underlying image data corresponding to the image was collected.

[0136] The image data may include the image, as well as any information about the color or wavelength channels, and details about the imaging platform on which the image was generated. For example, a tissue section may need to be stained by applying a staining assay containing one or more different biomarkers associated with a chromogenic stain for brightfield imaging or a fluorophore for fluorescence imaging. The staining assay may use a chromogenic stain for brightfield imaging, an organic fluorophore for fluorescence imaging, quantum dots, or a combination of organic fluorophores and quantum dots, or any other combination of stains, biomarkers, and observation or imaging devices. Examples of biomarkers include estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), human Ki-67 protein, progesterone receptor (PR), programmed cell death protein 1 (PD1), etc., where the tissue section is detectably labeled with a binding agent (e.g., an antibody) for ER, HER2, Ki-67, PR, PD1, etc., respectively. In some embodiments, digital image and data analysis operations such as classification, scoring, Cox modeling, and risk stratification depend on the type of biomarkers used and field of view (FOV) selection and annotation. Furthermore, typical tissue sections are processed in an automated staining / assay platform that applies a staining assay to the tissue section, thereby obtaining a stained sample. Various commercial products suitable for use as staining / assay platforms exist on the market, one example being the VENTANA® SYMPHONY® product from the assignee, Ventana Medical Systems, Inc. The stained tissue sections may be fed into an imaging system, such as a microscope or whole-slide scanner with a microscope and / or imaging component, one example being the VENTANA® iScan Coreo® / VENTANA® DP200 product from the assignee, Ventana Medical Systems, Inc. Multiple tissue slides may be scanned with an equivalent multiple-slide scanner system.Additional information provided by the imaging system may include any information regarding the staining platform, including the concentration of chemicals used for staining, the reaction time of the chemicals applied to the tissue in the staining, and / or the pre-analysis conditions of the tissue, such as the age of the tissue, fixation method, duration, embedding method for sections, and cutting method.

[0137] In the preprocessing stage 1010, one, more, or all of the set of digital images 1035 are each preprocessed using one or more techniques to generate corresponding preprocessed images 1040. Preprocessing may include cropping the image. In some examples, preprocessing may further include standardizing or rescaling (e.g., normalizing) all features to the same scale (e.g., the same size scale or the same color or saturation scale). In particular cases, the image is resized to a minimum size (width or height) of a predetermined number of pixels (e.g., 2500 pixels) or a maximum size (width or height) of a predetermined number of pixels (e.g., 3000 pixels), optionally maintaining the original aspect ratio. Preprocessing may further include removing noise. For example, the image may be smoothed, such as by applying a Gaussian function or Gaussian blur, to remove unwanted noise.

[0138] The preprocessed images 1040 may include one or more training images, validation input images, and unlabeled images. It should be understood that the preprocessed images 1040 corresponding to the training group, validation group, and unlabeled group need not be accessed simultaneously. For example, an initial set of training and validation preprocessed images 1040 may be initially accessed and used to train the machine learning algorithm 1055, and subsequently, unlabeled input images may be accessed or received (e.g., one or more times thereafter) and used by the trained machine learning model 1060 to provide a desired output (e.g., cell classification).

[0139] In some examples, the machine learning algorithm 1055 is trained using supervised training, and some or all of the preprocessed images 1040 are manually, semi-automatically, or automatically partially or fully labeled in a labeling stage 1015 with labels 1045 that identify the "correct" interpretation (i.e., "ground truth") of various biological materials and structures within the preprocessed images 1040. For example, the labels 1045 may identify features of interest (for example), a cellular classification, a binary indication as to whether a given cell is a particular type of cell, a binary indication as to whether the preprocessed images 1040 (or particular regions of the preprocessed images 1040) contain a particular type of indication (e.g., necrosis or artifact), slide-level or region-specific categorical features of indication (e.g., identifying a particular type of cell), a count (e.g., identifying the amount of a particular type of cell within a region, the amount of represented artifact, or the amount of necrotic area), the presence or absence of one or more biomarkers, etc. In some cases, the labels 1045 include a location. For example, the label 1045 may identify the point location of the nucleus of a particular type of cell, or the point location of a particular type of cell (e.g., a raw dot label). As another example, the label 1045 may include the border or boundary of a depicted tumor, blood vessel, necrotic region, etc. As another example, the label 1045 may include one or more biomarkers identified based on biomarker patterns observed using one or more stains. For example, a tissue slide stained for a biomarker, such as programmed cell death protein 1 (“PD1”), may be observed and / or processed to label cells as either positive or negative cells, taking into account the expression level and pattern of PD1 in the tissue. Depending on the feature of interest, a given labeled preprocessed image 1040 may be associated with a single label 1045 or multiple labels 1045. In the latter case, each label 1045 may be associated with (for example) an indication as to which location or portion within the preprocessed image 1045 the label corresponds to.

[0140] The labels 1045 assigned in the labeling step 1015 may be identified based on input from a human user (e.g., a pathologist or image scientist) and / or an algorithm (e.g., an annotation tool) configured to define the labels 1045. In some examples, the labeling step 1015 may include transmitting and / or presenting some or all of the one or more preprocessed images 1040 to a computing device operated by a user. In some examples, the labeling step 1015 includes utilizing an interface presented by the labeling controller 1050 (e.g., using an API) at the computing device operated by the user, the interface including an input component for accepting input identifying the labels 1045 for features of interest. For example, a user interface may be presented by the labeling controller 1050 that enables selection of an image or region of an image (e.g., FOV) for labeling. A user operating a terminal may select the image or FOV using the user interface. Several image or FOV selection mechanisms may be provided, such as specifying a known or irregular shape or defining an anatomical region of interest (e.g., tumor region). In one example, the image or FOV is an entire tumor region selected on an IHC slide stained with a combination of H&E stains. The selection of the image or FOV can be performed by a user or by an automated image analysis algorithm, such as tumor region segmentation on an H&E tissue slide. For example, a user may select that the image or FOV be the entire slide or the entire tumor, or the entire slide or the entire tumor region, which can be automatically designated as the image or FOV using a segmentation algorithm. The user operating the terminal may then select one or more labels 1045 to be applied to the selected image or FOV, such as point locations on cells, positive markers for biomarkers expressed by cells, negative biomarkers for biomarkers not expressed by cells, or a boundary around the cells.

[0141] In some examples, the interface may identify which particular labels 1045 are requested and / or how many are requested, which may be communicated to the user via (for example) text instructions and / or visualization. For example, a particular color, size, and / or symbol may indicate that a label 1045 is requested for a particular indication within an image (e.g., a particular cell or region or staining pattern) relative to other indications. If labels 1045 corresponding to multiple indications are requested, the interface may identify each of the indications simultaneously, or may identify each indication sequentially (such that providing a label for one identified indication triggers the identification of the next indication for labeling). In some examples, each image is presented until the user identifies a particular number of labels 1045 (e.g., of a particular type). For example, a given full slide image or a given patch of a full slide image may be presented until the user identifies the presence or absence of three different biomarkers, at which point the interface may present images of a different full slide image or different patches (e.g., until a threshold number of images or patches have been labeled). Thus, in some examples, the interface is configured to request and / or accept labels 1045 of an incomplete subset of features of interest, and the user may decide which of the potentially many representations will be labeled.

[0142] In some examples, the labeling stage 1015 includes a labeling controller 1050 that implements an annotation algorithm to semi-automatically or automatically label various features of an image or a region of interest within the image. The labeling controller 1050 annotates the image or FOV on a first slide according to user input or an annotation algorithm and maps the annotations across the remainder of the slides. Depending on the defined FOV, several methods for annotation and alignment are possible. For example, the entire tumor region annotated on an H&E slide from multiple consecutive slides can be selected automatically or by the user on an interface such as VIRTUOSO / VERSO™. Because the other tissue slides correspond to serial sections from the same tissue block, the labeling controller 1050 performs a marker-to-marker alignment operation to map and transfer the entire tumor annotation from the H&E slide to each of the remaining IHC slides in the series. Exemplary methods for marker-to-marker registration are described in further detail in commonly assigned International Publication No. WO 2014140070, "Whole slide image registration and cross-image annotation devices, systems and methods," filed March 12, 2014, which is incorporated by reference herein in its entirety for all purposes. In some embodiments, any other method for image registration and generation of whole-tumor annotations may be used. For example, a qualified radiologist, such as a pathologist, may annotate whole-tumor regions on any other IHC slides and execute the labeling controller 1050 to map the whole-tumor annotations on other digitized slides. For example, a pathologist (or an automated detection algorithm) may annotate whole-tumor regions on an H&E slide and trigger analysis of all adjacent serially sectioned IHC slides to determine a whole-slide tumor score for the annotated regions on all slides.

[0143] In the augmentation step 1017, a training set of labeled or unlabeled images (original images) from the preprocessed images 1040 is augmented with synthetic images 1052 generated using an augmentation control 1054 that executes one or more augmentation algorithms. Augmentation techniques are used to artificially increase the amount and / or type of training data by adding slightly modified synthetic copies of existing training data or newly created synthetic data from existing training data. As described herein, variations between scanners and laboratories can cause intensity and color variability in digital images. Furthermore, poor scanning can result in gradient variations and blurring effects, assay staining can result in staining artifacts such as background washout, and different tissue / patient samples can result in cell size variations. These variations and perturbations can adversely affect the quality and reliability of deep learning and artificial intelligence systems. The augmentation techniques implemented in the augmentation step 1017 act as regularizers of these variations and perturbations and can help reduce overfitting when training machine learning models. Examples of enhancement techniques include (i) varying in dye space, where dye decomposition (e.g., unmixing) is first performed and then each dye is remixed with a predetermined color vector to change the hue, saturation, and intensity of each dye; (ii) increasing the image resolution by resizing the image and then restoring it to the original size; (iii) the same; or (iv) any combination thereof.

[0144] During the training stage 1020, the labels 1045 and corresponding preprocessed images 1040 can be used by the training controller 1065 to train a machine learning algorithm 1055 according to various workflows described herein. For example, to train the algorithm 1055, the preprocessed images 1040 may be partitioned into a subset of images 1040a (e.g., 90%) for training and a subset of images 1040b (e.g., 10%) for validation. The partitioning may be performed randomly (e.g., 90 / 10% or 70 / 30%), or according to more complex validation techniques such as K-fold cross-validation, leave-one-out cross-validation, leave-one-out cross-validation, nested cross-validation, etc. to minimize sampling bias and overfitting. The partitioning may also be performed based on the inclusion of augmented or synthetic images 1052 in the preprocessed images 1040. For example, it may be beneficial to limit the number or proportion of synthetic images 1052 included in the subset of training images 1040a. In some examples, the ratio of the original image 1035 to the composite image 1052 is maintained at 1:1, 1:2, 2:1, 1:3, 3:1, 1:4, or 4:1.

[0145] In some examples, the machine learning algorithm 1055 includes a CNN, a modified CNN with the encoding layer replaced by a residual neural network ("Resnet"), or a modified CNN with the encoding and decoding layers replaced by Resnet. In other examples, the machine learning algorithm 1055 may be any suitable machine learning algorithm configured to localize, classify, and / or analyze the preprocessed image 1040, such as a two-dimensional CNN ("2DCNN"), Mask R-CNN, U-Net, feature pyramid network (FPN), dynamic time warping ("DTW") technique, hidden Markov model ("HMM"), pure attention-based model, or a combination of one or more of such techniques, such as a visual transformer, CNN-HMM, or MCNN (multiscale convolutional neural network). The computing environment 1000 may employ the same type of machine learning algorithm or different types of machine learning algorithms trained to detect and classify different cells. For example, the computing environment 1000 may include a first machine learning algorithm (e.g., U-Net) for detecting and classifying PD1. The computing environment 500 may also include a second machine learning algorithm (e.g., 2DCNN) for detecting and classifying cluster of differentiation 68 ("CD68"). The computing environment 1000 may also include a third machine learning algorithm (e.g., U-Net) for detecting and classifying PD1 and CD68 in combination. The computing environment 1000 may also include a fourth machine learning algorithm (e.g., HMM) for diagnosing disease for treatment or prognosis of a subject, such as a patient. In other examples according to the present disclosure, still other types of machine learning algorithms may be implemented.

[0146] The training process of the machine learning algorithm 1055 includes selecting hyperparameters for the machine learning algorithm 1055 from the parameter data store 1063, inputting a subset of images 1040a (e.g., labels 1045 and corresponding preprocessed images 1040) into the machine learning algorithm 1055, and performing iterative operations to learn a set of parameters (e.g., one or more coefficients and / or weights) for the machine learning algorithm 1055. Hyperparameters are settings that can be adjusted or optimized to control the behavior of the machine learning algorithm 1055. Most algorithms explicitly define hyperparameters that control different aspects of the algorithm, such as memory or execution cost. However, additional hyperparameters may be defined to adapt the algorithm to specific scenarios. For example, hyperparameters may include the number of hidden units of the algorithm, the learning rate of the algorithm (e.g., 1e-4), the convolution kernel width, or the number of kernels of the algorithm. In some examples, the number of model parameters is reduced for each convolutional and deconvolutional layer, and / or the number of kernels is reduced by half for each convolutional and deconvolutional layer compared to a typical CNN.

[0147] The subset of images 1040a may be input to the machine learning algorithm 1055 in batches of a predetermined size. The batch size limits the number of images shown to the machine learning algorithm 1055 before parameter updates can be performed. Alternatively, the subset of images 1040a may be input to the machine learning algorithm 1055 as a time series or sequentially. In either case, if augmented or composite images 1052 are included in the preprocessed images 1040a, the number of original images 1035 versus the number of composite images 1052 included in each batch, or the manner in which the original images 1035 and phenotypic images 1052 are fed to the algorithm (e.g., every other batch or image is an original batch of images or an original image), can be defined as a hyperparameter.

[0148] Each parameter is a tunable variable such that values ​​for the parameter are adjusted during training. For example, a cost function or objective function may be configured to optimize accurate classification of displayed expressions, optimize characterization of a given type of feature (e.g., characterization of shape, size, uniformity, etc.), optimize detection of a given type of feature, and / or optimize accurate localization of a given type of feature. Each iteration may include learning a set of parameters for the machine learning algorithm 1055 that minimizes or maximizes a cost function of the machine learning algorithm 1055, such that the value of the cost function using a set of parameters may be smaller or larger than the value of the cost function using a different set of parameters in a previous iteration. The cost function may be configured to measure the difference between the predicted output using the machine learning algorithm 1055 and the labels 1045 included in the training data. For example, in the case of a supervised learning-based model, the goal of training is to learn a function “h()” (sometimes called a hypothesis function) that maps a training input space X to a target value space Y, h:X→Y, such that h(x) is a good predictor of the corresponding value of y. A variety of different techniques may be used to learn this hypothesis function. In some techniques, as part of deriving the hypothesis function, a cost or loss function may be defined that measures the difference between a ground truth value for an input and a predicted value for that input. As part of training, techniques such as backpropagation, random feedback, direct feedback alignment (DFA), indirect feedback alignment (IFA), Hebbian learning, and the like are used to minimize this cost or loss function.

[0149] The training iterations continue until a stopping condition is met. The training completion condition may be configured to be met (for example) when a predetermined number of training iterations are completed, when a statistical value generated based on testing or validation exceeds a predetermined threshold (e.g., a classification accuracy threshold), when a statistical value generated based on a confidence metric (e.g., the mean or median of the confidence metric or the percentage of the confidence metric above a particular value) exceeds a predetermined confidence threshold, and / or when a user device involved in the training review closes the training application executed by the training controller 1065. Once a set of model parameters is identified through training, the machine learning algorithm 1055 is trained, and the training controller 1065 performs an additional process of testing or validation using a subset of images 1040b (a testing or validation dataset). The validation process may include iterative operations of inputting images from the subset of images 1040b into the machine learning algorithm 1055 using validation techniques such as k-fold cross-validation, leave-one-out cross-validation, leave-one-out cross-validation, nested cross-validation, etc., to adjust the hyperparameters and ultimately find an optimal set of hyperparameters. Once the optimal set of hyper-parameters is obtained, a reserved test set of images from the subset of images 1040b is input into the machine learning algorithm 1055 to obtain an output, which is evaluated against the ground truth by using correlation techniques such as the Bland-Altman method and Spearman's rank correlation coefficient, and calculating performance metrics such as error, precision, precision, recall, receiver operating characteristic curves (ROC), etc. In some cases, a new training iteration may be initiated in response to receiving a corresponding request or trigger condition from the user device (e.g., initial model development, model update / adaptation, continuous learning, drift determined within the trained machine learning model 1060, etc.).

[0150] As will be appreciated, other training / validation mechanisms are contemplated and may be implemented within the computing environment 1000. For example, a machine learning algorithm 1055 may be trained and hyperparameters may be tuned on images from the subset of images 1040a, while images from the subset of images 1040b may be used solely to test and evaluate the performance of the machine learning algorithm 1055. Furthermore, the training mechanisms described herein focus on training new machine learning algorithms 1055. These training mechanisms may also be utilized for initial model development, model updating / adaptation, and continuous learning of existing machine learning models 1060 trained from other datasets, as described in detail herein. For example, in some cases, the machine learning model 1060 may have been preconditioned using images of other objects or biological structures, or from sections from other subjects or studies (e.g., human or mouse studies). In those cases, the machine learning model 1060 may be used for initial model development, model updating / adaptation, and continuous learning using the preprocessed images 1040.

[0151] The trained machine learning model 1060 can then be used (in a result generation stage 1025) to process the new preprocessed image 1040 to generate predictions or inferences, such as predicting cell center and / or location probabilities, classifying cell types, generating cell masks (e.g., segmentation masks for each pixel of the image), predicting a disease diagnosis or prognosis for a subject, such as a patient, or any combination thereof. In some examples, the masks identify the locations of displayed cells associated with one or more biomarkers. For example, given tissue stained for a single biomarker, the trained machine learning model 1060 can be configured to (i) infer cell centers and / or locations, (ii) classify cells based on staining pattern features associated with the biomarker, and (iii) output a cell detection mask for positive cells and a cell detection mask for negative cells. As another example, given tissue stained for two biomarkers, the trained machine learning model 1060 may be configured to (i) infer cell centers and / or locations, (ii) classify the cells based on staining pattern features associated with the two biomarkers, and (iii) output a cell detection mask for cells positive for a first biomarker, a cell detection mask for cells negative for the first biomarker, a cell detection mask for cells positive for a second biomarker, and a cell detection mask for cells negative for the second biomarker. As another example, given tissue stained for a single biomarker, the trained machine learning model 1060 may be configured to (i) infer cell centers and / or locations, (ii) classify the cells based on cell features and staining pattern associated with the biomarker, and (iii) output a cell detection mask for positive cells and a cell detection mask for negative cell codes, as well as mask cells classified as tissue cells.

[0152] In some examples, the analysis controller 1080 generates analysis results 1085 that are utilized by the entity that requested processing of the underlying image. The analysis results 1085 may include a mask output from the trained machine learning model 1060 overlaid on the new preprocessed image 1040. Additionally or alternatively, the analysis results 1085 may include information calculated or determined from the output of the trained machine learning model, such as a whole-slide tumor score. In exemplary embodiments, the automated analysis of the tissue slide uses Assignee VENTANA's FDA-cleared 510(k) approved algorithm. Alternatively or additionally, any other automated algorithm may be used to analyze selected regions of the image (e.g., masked images) and generate a score. In some embodiments, the analysis controller 1080 may further respond to instructions received from a computing device from a pathologist, physician, investigator (e.g., associated with a clinical trial), subject, medical professional, etc. In some examples, the communication from the computing device includes an identifier for each of a particular set of subjects and corresponds to a request to perform an iteration of the analysis for each subject represented in the set. The computing device may further perform analysis based on the machine learning model and / or the output of analysis controller 1080 and / or may provide a recommended diagnosis / treatment to the subject.

[0153] It will be understood that computing environment 1000 is exemplary and that computing environments 1000 having different stages and / or using different components are contemplated. For example, in some instances, the network may omit preprocessing stage 1010, such that the images used to train the algorithm and / or images processed by the model are raw images (e.g., from an image data store). As another example, it will be understood that each of preprocessing stage 1010 and training stage 1020 can include a controller for performing one or more operations described herein. Similarly, although labeling stage 1015 is shown in association with labeling controller 1050 and result generation stage 1025 is shown in association with analysis controller 1080, the controllers associated with each stage may additionally or alternatively facilitate other operations described herein other than generating labels and / or generating analysis results. 10 lacks displayed representations of devices associated with the programmer (e.g., who selected the architecture of the machine learning algorithm 1055, which defined how various interfaces would function, etc.), devices associated with the user providing the initial label or label review (e.g., in the labeling stage 1015), and devices associated with the user requesting model processing of a given image (which may be the same user as the user who provided the initial label or label review or a different user). Despite the lack of representations of these devices, the computing environment 1000 may include use of one, more, or all of the devices, and may in fact include use of multiple devices associated with a corresponding number of users providing the initial label or label review and / or a corresponding number of users requesting model processing of various images.

[0154] VI. Techniques for Training Machine Learning Algorithms Using an Adaptive Learning Framework FIG. 11 is a flowchart illustrating a process 1100 for using a training set of images to train a machine learning algorithm according to various embodiments. The process 1100 illustrated in FIG. 11 may be implemented in software (e.g., code, instructions, programs) executed by one or more processing units (e.g., processors, cores) of a respective system, hardware, or combination thereof. The software may be stored in a non-transitory storage medium (e.g., a memory device). The process 1100 presented in FIG. 11 and described below is intended to be exemplary and non-limiting. While FIG. 11 illustrates various processing steps occurring in a particular sequence or order, this is not intended to be limiting. In certain alternative embodiments, steps may be performed in several different orders, or some steps may be performed in parallel. In certain embodiments, such as those illustrated in FIGS. 4 and 10, the process illustrated in FIG. 11 may be performed as part of a training phase (e.g., algorithm training 1020) that uses a training set of images to train a machine learning algorithm to generate a machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects within an image.

[0155] Process 1100 begins at block 1105, where a first annotated training set of images is obtained to train a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects within an image. The first annotated training set of images is in a first image domain (e.g., preprocessed images 1040 of the computing environment 1000 described with reference to FIG. 10 ). In some cases, the first annotated training set of images is a digital pathology image including one or more types of cells. The first annotated training set of images may depict cells having staining patterns associated with biomarkers. In some cases, the first annotated training set of images shows cells having multiple staining patterns associated with multiple biomarkers. The first annotated training set of images may be annotated with training labels (e.g., supervised, semi-supervised, or weakly supervised).

[0156] At block 1110, the first annotated training set of images is divided into mini-sets of images, each mini-set representing a distinct modeling subtask and containing a limited number of examples. Optionally, the division includes, if only one mini-set of images is available, selecting, for each distinct modeling subtask, a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples based on the selected subset of classes; and, if multiple mini-sets of images are available, for each distinct modeling subtask, either (i) mixing examples from multiple mini-sets of images, selecting a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples from the mixed examples based on the selected subset of classes, or (ii) selecting one mini-set of images from multiple mini-sets of images, selecting a subset of classes that is a fraction of or matches the number of classes targeted in the second stage, and selecting a limited number of examples from the selected mini-set of images based on the selected subset of classes.

[0157] In block 1115, the machine learning algorithm is trained in a first stage using the mini-set of images to generate a preconditioned machine learning model configured to detect, characterize, or classify, or a combination thereof, some or all regions or objects in new images. Optionally, the first stage further includes an inner learning loop in which the machine learning algorithm updates model weights or parameters on one subtask for a predetermined or flexible number of epochs to initialize the preconditioned machine learning model for adaptation to the target dataset, generating a loss on a validation set of images after model updating, denoted as L-subtask-i, for the i-th subtask, and an outer learning loop whose goal is to search for a set of model initializations that, when used to update all subtasks with only a limited number of examples, generate a preconditioned machine learning model by finding a model initialization that minimizes the sum of all losses, denoted as L-subtask-i summed up, where i ranges from 1 to the number of subtasks calculated from the validation set of images for the subtask for model initialization.

[0158] In some cases, the first stage of training includes performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the mini-set of images that maximizes or minimizes a cost function, where each iteration involves finding a set of parameters for the machine learning algorithm such that the value of the cost function using the set of parameters is greater or less than the value of the cost function using another set of parameters in the previous iteration, and the cost function is constructed to measure the difference between predictions made for some or all of the regions or objects using the machine learning algorithm and ground truth labels assigned to the mini-set of images.

[0159] At block 1120, a limited number of images from the target dataset are labeled to generate a second annotated training set of images for training a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in the images. The second annotated training set of images is in a second image domain (different from the first image domain). In particular examples, the limited number of images is less than 50 images, 30 images, or 20 images.

[0160] At block 1125, the preconditioned machine learning model is trained in a second stage using a second annotated training set of images to generate a target machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in new images. The number of classes targeted in the first stage is a subset of or equal to the number of classes targeted in the second stage. Optionally, the second stage further includes applying the preconditioned machine learning model to generate a feature vector representation for each example in the second annotated training set of images, combining feature vector representations from examples of the same class to generate one representation for each target class and use the one representation for each target class as a prototype in the target class, generating feature vector representations for images or image regions of the remaining unlabeled images from the target dataset, and comparing each feature vector representation from the unlabeled images to a prototype in the target class based on a distance between the feature vector representation from the unlabeled images and the prototype for the target class.

[0161] In some embodiments, training the second stage includes performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the second annotated training set of images that maximizes or minimizes a cost function, where each iteration involves finding a set of parameters for the preconditioned machine learning model such that the value of the cost function using the set of parameters is greater or less than the value of the cost function using another set of parameters in a previous iteration, and the cost function is constructed to measure the difference between predictions made for some or all of the regions or objects using the preconditioned machine learning model and ground truth labels assigned to the second annotated training set of images.

[0162] At optional block 1130, a target machine learning model is provided. For example, the target machine learning model may be deployed to run in an image analysis environment, as described with respect to FIG.

[0163] A digital pathology scenario is identified at block 1135. The digital pathology scenario may be a data incremental scenario, a domain incremental scenario, a class incremental scenario, or a task incremental scenario.

[0164] At block 1140, an adaptive continuous learning method is selected to update the target machine learning model in light of the digital pathology scenario. In some examples, the adaptive continuous learning method is selected from a group including Elastic Weight Reinforcement (EWC), No Forgetting (LWF), Incremental Learner and Representation Learning (iCaRL), Continuous Prototype Evaluation (CoPE), A-GEM, and parameter separation methods. In other examples, the adaptive continuous learning method includes EWC, LWF, iCaRL, CoPE, A-GEM, parameter separation methods, similar continuous learning methods, or any combination thereof.

[0165] In block 1145, the target machine learning model is updated based on an adaptive continuous learning method to generate an updated machine learning model.

[0166] At optional block 1150, an updated machine learning model is provided. For example, the updated machine learning model may be deployed for execution in an image analysis environment, as described with respect to FIG.

[0167] At block 1155, a new image is received. The new image may be divided into image patches of a predetermined size. For example, full slide images typically have random sizes, and machine learning algorithms such as modified CNNs learn more efficiently with normalized image sizes (e.g., parallel computing on batches of images of the same size, memory constraints), so the image may be divided into image patches having a specific size to optimize analysis. In some embodiments, the image is divided into image patches having a predetermined size of 64 pixels by 64 pixels, 128 pixels by 128 pixels, 256 pixels by 256 pixels, or 512 pixels by 512 pixels.

[0168] The new image or image patch is input to the target or updated machine learning model at block 1160. At block 1165, the target or updated machine learning model detects, characterizes, classifies, or a combination thereof, some or all regions or objects in the new image or image patch, and outputs inferences based on the detection, characterization, classification, or a combination thereof.

[0169] At optional block 1170, a diagnosis of the subject associated with the image or image patch is determined based on the inferences output by the revised machine learning model.

[0170] In optional block 1175, an action is applied to the object associated with the image or image patch. In some examples, the action is applied based on (i) the inference output by the machine learning model or revised machine learning model, and / or (ii) the diagnosis of the object determined in block 1170.

[0171] VII. Examples The systems and methods implemented in various embodiments may be better understood with reference to the following examples.

[0172] data CRC: In the following experiments, we used 100,000 non-overlapping patches from H&E-stained histological images of human colorectal cancer (CRC) consisting of nine tissue classes, including adipose tissue (ADI), background (BACK), debris (DEB), lymphocytes (LYM), mucus (MUC), smooth muscle (MUS), normal colon mucosa (NORM), cancer-associated stroma (STR), and colorectal adenocarcinoma epithelium (TUM), for training. Some example images are shown in Figure 12. The test set contained 7,180 image patches that did not overlap with the training data. All images were color normalized using Macenko's method.

[0173] The CRC dataset was extended by varying stain intensity, color, and saturation individually and in combination to simulate data collected from different stainers, scanners, and chromogens. Images were unmixed using nonnegative matrix factorization. Four settings of color, saturation, and intensity were applied to individual stains from non-overlapping subsets of the original dataset. Each synthetic setting was used with the original dataset to create different adaptive learning scenarios. 1. Each augmentation setting was recognized as a shift in domain from the original dataset. Thus, the dataset can be split into five data streams, each representing a different augmentation or domain setting resulting in five experience domain incremental scenarios (although five was used in the experiments disclosed herein, it should be understood that the dataset can be split into any number of "n" data streams, each representing a different augmentation or domain setting resulting in "n" experience domain incremental scenarios). The model learns to classify images in the new domain setting in every experience the model was targeted to. 2. The different augmentations were also mixed uniformly across classes. This mixed dataset was used to create five data streams or experiences of equal size with representations from all classes (although five was used in the experiments disclosed herein, it should be understood that the dataset can be divided into any number "n" of data streams or experiences of equal size with representations from all classes). This constitutes a data incremental scenario, where each subsequent experience is added to the model's training data. 3. The uniformly mixed dataset was also divided into subsets, or experiences, each containing a different class, forming a class-incremental scenario. Depending on how the data was divided, the model was exposed to a different class in each experience, and all classes were targeted during the training process.

[0174] Sequential Training Scenarios: Each synthetic setting can be used with the original dataset to create different sequential training scenarios. Each augmented setting is a domain shift from the original dataset. They were used separately as separate data streams or experiences in domain incremental settings. Images from different augmented settings were uniformly mixed across classes and split into experiences with equal class representation to form data incremental scenarios. The uniformly mixed dataset was also split into experiences, each containing a different class, to form class incremental scenarios.

[0175] PatchCam: The PatchCam benchmark dataset consists of 327,680 patches extracted from 400 H&E-stained whole-slide images of lymph node sections from breast tissue, 96 x 96 pixels in size at 10x magnification. A 75 / 12.5 / 12.5% ​​train / valid / test split was selected using a hard-negative mining regime. The dataset has two classes (normal and tumor) to indicate the presence of metastatic tissue. For consistency and easy comparison with the CRC dataset, this dataset was also normalized using Macenko's method. Normalized examples from both classes are shown in Figure 13. The top row contains samples from the normal class, and the bottom row contains examples from the tumor class.

[0176] Sequential learning scenario: A dramatic domain shift in the data stream was evaluated by training a model with the original CRC images (stain-normalized) in the first experience and the normalized PatchCam dataset in the second experience.

[0177] method We experimented with the following continuous learning methods, processing three scenarios: EWC and online EWC, LwF, iCaRL, CoPE, and A-GEM. All methods were compared to two baselines: 1) training from scratch (upper bound), in which the same network architecture, an 18-layer ResNet, was trained on all available data from all experiences seen so far; and 2) transfer learning or fine-tuning (lower bound), in which the model was trained with the same design as continuous learning, only exposing it to data available during a specific experience, but instead of using a strategy to mitigate forgetting, the model was simply fine-tuned to adapt to new classes. For all experiments, we set the training epochs to 15 and the batch size to 16. We used the same ResNet architecture in a multi-head setup, where each head was used for a different task when testing with A-GEM according to their findings. A stochastic gradient descent optimizer was used, starting with a learning rate of 0.1, momentum of 0.9, and weight decay of 0.00001 applied after epochs 10 and 13.

[0178] Example 1.- Data Incremental Setting The first experiment involved a data incremental scenario in which more data was sequentially fed into the model, and then the model was updated based only on the most recent data without accessing any of the older datasets on which it was previously trained. The newer data streams have the same classes as the older streams, but there may be a shift in distribution. The mixed datasets used in this experiment should have a uniform distribution across experiences.

[0179] To train the model in this setting, we used a method called continuous prototype evaluation (CoPE). CoPE is an online data incremental algorithm that uses prototypes to represent the most important features from the data. The prototypes continuously evolve as the model learns to keep up with changes in the data, enabling it to make accurate predictions. CoPE also incorporates balanced replays to ensure all classes are well represented in the replay ensemble. The data was supplied online as mini-batches or mini-experiences; that is, the model only sees each data sample once and is therefore trained in a single epoch. To reduce forgetting, we used a mini-experience size of 128 samples (i.e., each mini-experience had only 128 samples) for training with a batch size of 10 and momentum of 0.99. Therefore, for the data incremental scenarios created for the augmented dataset, each of the five experiences had 99 mini-experiences.

[0180] At the end of training, the test stream with samples from different experiences had an average accuracy of 76%. Figure 14 shows the accuracy of the test stream at the end of each main experience under the data incremental setting using the extended CRC dataset with CoPE. The experiences were divided into user-defined sizes of 128 images, resulting in 99 mini-experiences within each experience, which were fed to the model in an online fashion. The numbers shown on the plot were the end of the 99th mini-experience or the end of all main experiences. Classification accuracy gradually increased, indicating that the model benefited from more data. The accuracy of individual test streams also increased as the model learned from more recent training streams, indicating that the model had not forgotten what it had previously learned. Equal presentation of all synthetic domains in each experience resulted in transfer learning and test streams benefiting from all data. It is also noteworthy that the model performed similarly on test streams from subsequent experiences. For example, at the end of main experience 1, the model performed similarly on test stream 1 as well as test streams 2, 3, and 4, indicating some transfer learning. The mixed-augmented dataset used here has equal representation from all synthetic domains, resulting in similar distributions across experiences. Accuracy also improved by less than 1% between experiences 3 and 4, indicating that the model performed similarly on 80% of the data.

[0181] Example 2.- Domain incremental configuration The second experiment involved five domain incremental scenarios in which the hue, saturation, and intensity values ​​of two stains, eosin and hematoxylin, were varied to different degrees to mimic images acquired using different stains, scanners, and reagents. Examples from the five experiences are shown in Figure 15. Each row corresponds to one of nine tissue types, and three example images are plotted from each enhancement setting (i.e., domain). Domain 0 (columns 1–3): Stain-normalized CRC dataset. Domain 1 (columns 4–6): Simulating scenarios of increased eosin staining intensity, increased eosin solution concentration, or extended staining time. Domain 2 (columns 7–9): Simulating scenarios of decreased eosin intensity, aging slides with faded stains. Domain 3 (columns 10–12): Differences in hue changes between hematoxylin and eosin. Domain 4 (columns 13–15): Changes in hue and increased saturation levels for both eosin and hematoxylin. Each of the three column sections can be considered a separate domain in the domain incremental scenario. The domains can be mixed and divided into experiences each with representations from all classes for the data incremental scenario, or mixed domain experiences each with a non-overlapping subset of classes for the class incremental scenario.

[0182] For this scenario, a method called learning without forgetting (LwF) was adopted. LwF is a combination of fine-tuning and distillation. LwF uses only the most recent data corresponding to the current task to learn task-specific parameters for the new / current task without compromising performance on the old task. Unlike traditional regularization, which penalizes parameter changes based on their importance, LwF penalizes changes in the input-to-output mapping. The loss function consists of two terms: a cross-entropy loss for the current task and a distillation loss to prevent previously acquired knowledge from being forgotten.

[0183] LwF performed well in three of the five predefined domains, with accuracies exceeding 86%. Evaluation accuracies for Domains 1 and 2 during the training were 88% and 93%, respectively. Although the model was targeted at the corresponding domains, knowledge retention was poor. However, when specific domain data was no longer available, nearly 28% of the acquired domain-specific knowledge was forgotten, particularly in Domains 1 and 2. The results are shown in Figure 16, which shows the accuracy (left) and forgetting (right) of the test stream at the end of each primary training session under the domain-incremental setting with the extended CRC dataset using LwF. At the end of training, the model performed with accuracies ranging from 86 to 94% in three of the five predefined domains. While the model performed well in Domain 1 (88%) and Domain 2 (93%), the acquired domain-specific knowledge was forgotten during the training session after the specific domain data was no longer available. The test stream forgetting metric was approximately 28% at the end of training, indicating accuracy loss from Domains 1 and 2 over the course of training. This experiment demonstrated that a model presented with data from different domains in a continuous data stream can be trained to adapt reasonably well to the new domain while still maintaining performance in the previous domain that it no longer has access to.

[0184] Example 3.- Class incremental configuration In the third experiment, we trained the model in the class-incremental setting described herein with three experiences and six classes, such that the model had access to data from only two classes during each experience, and newer classes were gradually added with each experience. Incremental class and representation learning (iCaRL) was the adaptive learning strategy used here. iCaRL dynamically selects examples from the data stream, with each class having its own set of examples. iCaRL updates both parameters and examples when it sees new data. iCaRL performs classification by nearest-neighbor average of examples. iCaRL includes representation learning by distillation and prototype rehearsal, where the augmented dataset includes data from the current task, and the stored examples and model parameters were updated based on the cross-entropy loss of the newer classes and the distillation loss of the previously trained classes.

[0185] The iCaRL algorithm is compared to two baselines: 1) training from scratch (upper bound), in which the same neural network is trained on all available data up to a particular experience. That is, the iCaRL algorithm is trained from scratch on two classes during the first experience, four classes during the second experience, and all six classes during the third experience. The other baseline is 2) transfer learning or fine-tuning (lower bound), in which the model is trained with the same design as adaptive learning, exposing it to only two classes during each of the three experiences, but instead of using a strategy to mitigate forgetting, the model is simply fine-tuned to adapt to the newer classes. The results are shown in Figure 17. As shown, iCaRL was observed to perform comparably to the upper bound of training from scratch, which utilizes only a portion of the data, and therefore also provides a significant computational advantage. Transfer learning performed well in experience 0, but forgot previously acquired knowledge upon exposure and learning of the newer classes. While computationally comparable to iCaRL, transfer learning performance was poor at catastrophic forgetting.

[0186] Example 4.- Comparing methods Sequential training was performed using the extended CRC dataset. For fair comparison, the domain and data incremental experiment had five experiences, while the class incremental experiment had four experiences, with the first three experiences each having two classes and the final experience having the remaining three classes. A-GEM was found to provide the best results with the task descriptor, so it was treated as a task incremental method, with each experience introducing a new set of classes to the model with task IDs. The hyperparameters for each method were determined by grid search. CoPE and A-GEM were treated as online, few-shot methods, training in just one epoch. iCaRL was experimented with three settings. The first setting had four experiences, with the first three having two classes each, and the final experience having the remaining three classes. The second setting also had four experiences, but the first experience had three classes and the remaining experiences had two classes each. The final setting had three experiences with three classes each. The class order was the same across settings, ascending. LwF is experimented to successively train the original CRC dataset and the normalized PatchCam dataset in a domain incremental setting, where one tumor type is considered as one domain.

[0187] The evaluation accuracy at the end of training for the three designed scenarios (data, domain, and class incremental) for the sequential learning methods is shown in Figure 18. In the data and domain incremental scenarios, LwF and iCaRL were comparable to the upper-bound baseline. The class incremental scenario was an overall more difficult task to learn. iCaRL had the highest accuracy at 83%. A-GEM was the only method tested and evaluated in the task incremental scenario.

[0188] Data-incremental scenario: LwF had an overall accuracy of 93% at the end of training, forgetting <1% of previously acquired knowledge. This was 4% better than the lower bound and within 0.5% of the upper bound. The accuracy numbers per experience are shown in Figure 19. Specifically, Figure 19 shows data-incremental experiences tested with different CL methods, as listed in the legend, including two baselines. Each experience consists of its own test stream containing examples from a smaller batch of data belonging exclusively to that experience. Each subplot shows how the model performed on the test stream evaluated at the end of training for all experiences. The grayed-out areas indicate experiences that the model has not yet been targeted; the model is expected to perform less well on these experiences. However, once targeted by a particular experience, ideally it should not forget what it learned and should retain knowledge throughout the remainder of the training process; i.e., accuracy should remain high in the non-grayed-out areas for all test streams. LwF had the highest overall accuracy at the end of training.

[0189] The classification accuracy gradually increased, indicating that the model benefited from more data. The accuracy of each test stream also increased as the model learned from more recent training streams, indicating that the model did not forget what it had learned previously. Another observation is the performance of the iCaRL method. Although iCaRL was designed as a class-incremental method, the concept of storing examples representing classes within each domain should theoretically have performed better than EWC and LwF. The maximum memory size tested is not sufficient to store only "n" classes as in class-incremental, but is capable of storing "n" classes x "d" domains.

[0190] Domain-incremental scenario: As shown in Figure 20, iCaRL performed better than EWC and LwF with the best hyperparameters selected from the grid search. As shown in Figure 20, we tested five domain-incremental experiences with different CL methods, as listed in the legend, including two baselines. Each experience consisted of its own test stream containing examples from the domain exclusively belonging to that experience. Each subplot shows how the model performed on the test stream evaluated at the end of training for all experiences. The grayed-out areas indicate experiences that the model has not yet been targeted; the model is expected to perform less well on these experiences. However, once targeted with a particular experience, it ideally should not forget what it learned and should retain knowledge throughout the remainder of the training process; that is, accuracy should remain high in the non-grayed-out areas for all test streams. We can see that iCaRL performed comparable to the upper-bound baseline, while EWC and LwF performed closer to the lower-bound baseline. In the first experience, the upper limit is low (accuracy 0.57) because there are few training examples (20% of all examples).

[0191] Interestingly, 1) the model retained knowledge from some domains better than others. Specifically, it was more difficult to retain learned knowledge for datasets in which eosin intensity increased (Domain 1; columns 4–6 in Figure 15) or decreased (Domain 2; columns 7–9 in Figure 15), but there was some transfer learning between domains for changes in stain hue and / or saturation (Domains 3 and 4) (not shown in Figure 15). Even after training only on Domain 0, the model performed well on the test stream corresponding to Domain 4. Performance in these two domains remained high even at the end of the training process. Because the fourth domain was generated using hue variations for the stain, these results suggest that the model can handle a range of hue variations when continuously learning and retaining knowledge from continuous data streams.

[0192] Class-incremental scenario: iCaRL performed significantly better than the other methods. None of the tested methods, including the lower-bound baseline, were able to retain knowledge about classes learned in previous experiences. iCaRL's overall accuracy was 88%, which is approximately 6% lower than the joint training upper bound. This is still beneficial given its lower data storage and resource demands. Figure 21 shows the four-class incremental experiences tested with different CL methods, as listed in the legend, including the two baselines. Each experience consists of its own test stream containing examples from classes belonging exclusively to that experience. Each subplot shows how the model performed on the test stream evaluated at the end of training for all experiences. Grayed-out areas indicate experiences for which the model has not yet been trained; the model is expected to perform poorly on these experiences. However, once the model is targeted with a particular experience, ideally, it should not forget what it learned and retain the knowledge throughout the remainder of the training process. That is, accuracy should remain high in the non-grayed-out areas for all test streams. We find that iCaRL is the only CL method that performs well on the current experience and does not completely forget previous knowledge. Experience 0, which the model is initially targeted at, is the most forgotten experience at the end of the training process with 64% accuracy.

[0193] Few-shot online continuous learning: The greatest gains from both CoPE and A-GEM come with the amount of training data with each experience. A-GEM was tested using a class-incremental setting with task IDs, and model updates were based only on 128 randomly selected examples stored in memory for one epoch, rather than an online method, producing results comparable to iCaRL trained over 15 epochs. Overall accuracy at the end of training was 79%, more than 50% better than the lower-bound baseline. Detailed results are shown in Figure 22—the dataset was initially designed as a class-incremental scenario, with each experience assigned a separate task ID and targeted online with a multi-head architecture. Overall accuracy was approximately 79%, compared to the baseline lower-bound of 27%. A-GEM also performed significantly worse when used without task IDs. A-GEM was unable to retain any of the prior knowledge gained.

[0194] CoPE was tested in a domain-incremental scenario, simulating online training by dividing the dataset into mini-experiences, each with the same number of examples as the mini-batch size. This had an overall accuracy 67%-11% better than the lower-bound baseline. It is interesting to compare the results from CoPE with those from LwF and EWC, both of which were performed in domain-incremental scenarios. In both of the latter methods, the model performed poorly on test streams from Domains 1 and 2. While CoPE did not help retain knowledge from Domain 1 (less than 25% accuracy), the model had 60% accuracy from Domain 2. It is possible that the online setting helped retain more information. CoPE was also found to be sensitive to the softmax temperature. As opposed to using a temperature >1, as in other distillation methods, we tested temperatures lower than the stiffer softmax distribution, as recommended in the literature. Finer sweeps of the hyperparameters can yield better results. Another point to note is how each experience is divided into mini-batches or mini-experiences in CoPE. Each experience in the tested configuration had 128 samples or examples. Not all classes are equally represented in each mini-experience, which can also affect overall accuracy.

[0195] A comparison of CoPE with the baseline is shown in Figure 23. The experience was divided into user-defined portions of 128 images, resulting in 99 mini-experiences within each experience, which were fed to the model in an online fashion. The numbers shown in the left plot are the end of the 99th mini-experience or the end of all main experiences. On the right are results from the fine-tuning / naive baseline. Equal representation from all synthetic domains in each experience resulted in transfer learning and test streams that benefited from all data for both CoPE and the baseline, but overall accuracy was better for CoPE.

[0196] The effects of class grouping on sequential learning The results of the third experiment using different class grouping settings are shown in Figure 24. Three settings were tested: A. four experiences with two of the first three classes and the last three; B. four experiences with three classes in the first experience and two classes in the remaining experiences; and C. three experiences with three classes each. Comparing the first two subplots, both of which have four experiences, the overall accuracy drops by approximately 6.5%. The difference between the two settings is the number of classes the model targeted in the first experience. The hypothesis here is based on curriculum learning, where knowledge is better captured when more difficult tasks follow easier tasks. Here, starting with three classes may make it more difficult for the model to learn and retain knowledge, which is reflected in the drop in accuracy despite the remaining experiences targeting only two classes each in both settings. The same is true for the third setting. Despite having fewer experiences, the model must learn three more classes in each experience compared to two classes in setting 1, resulting in an almost 8% drop in accuracy.

[0197] Sequential learning from multiple tumor types Both EWC and LwF were evaluated in this experiment, with LwF producing slightly better results, as shown in Figure 25. CRC was designed to be the first domain and PatchCam the second. The model started well with over 90% accuracy on the CRC test stream, but by the end of training, it forgot some of the knowledge gained in its initial experience. At the end of the training process, the model produced an accuracy of approximately 70% on the CRC test stream and approximately 76% on the PatchCam test stream.

[0198] conclusion This systematic study characterized the performance of various sequential learning methods for different scenarios using augmented digital pathology images and evaluated the models when presented with different tumor types. The datasets were evaluated with regularization and regeneration methods. EWC and LwF performed relatively well in data- and domain-incremental scenarios, while the rehearsal methods iCaRL and A-GEM were necessary to prevent catastrophic forgetting in the more challenging class-incremental scenarios. The few online methods tested require additional fine-tuning of hyperparameters and experimental setups to fully understand their effectiveness. Furthermore, it would be interesting to investigate how changes in images from a clinical perspective due to shifts in patient populations, disease progression, and / or disease (sub)types affect the performance of these CL methods, which would provide insight into the feasibility of applying these methods in clinical settings. These experiments found that while knowledge about staining intensity is difficult to retain, the models appear to be insensitive to hue changes within the range tested. Although some results demonstrate the difficulty of learning tumor classification from DP images, this work demonstrates the potential for continuous learning in adapting to changes in clinicopathological image acquisition factors.

[0199] VIII. Further Considerations Some embodiments of the present disclosure include a system including one or more data processors. In some embodiments, the system includes a non-transitory computer-readable storage medium containing instructions that, when executed on the one or more data processors, cause the one or more data processors to perform some or all of one or more methods and / or some or all of one or more processes disclosed herein. Some embodiments of the present disclosure include a computer program product tangibly embodied in a non-transitory machine-readable storage medium, the computer program product including instructions configured to cause one or more data processors to perform some or all of one or more methods and / or some or all of one or more processes disclosed herein.

[0200] The terms and expressions which have been employed are used as terms of description rather than of limitation, and there is no intention in the use of such terms and expressions to exclude all equivalents of the features shown and described or portions thereof, recognizing that various modifications are possible within the scope of the claimed invention. Thus, although the claimed invention has been specifically disclosed by embodiments and optional features, it is to be understood that modifications and variations of the concepts disclosed herein may be reclassified by those skilled in the art, and that such modifications and variations are deemed to be within the scope of the invention as defined by the appended claims.

[0201] The following description provides only preferred exemplary embodiments and is not intended to limit the scope, applicability, or configuration of the present disclosure. Rather, the following description of preferred exemplary embodiments will provide those skilled in the art with an enabling description for implementing various embodiments. It will be understood that various changes may be made in the function and arrangement of elements without departing from the spirit and scope as set forth in the appended claims.

[0202] In the following description, specific details are given to provide a comprehensive understanding of the embodiments. However, it will be understood that the embodiments may be practiced without these specific details. For example, circuits, systems, networks, processes, and other components may be shown as components in block diagram form in order to avoid obscuring the embodiments in unnecessary detail. In other instances, well-known circuits, processes, algorithms, structures, and techniques may be shown without unnecessary detail in order to avoid obscuring the embodiments.

Claims

1. In a data processing system, obtaining a first annotated training set of images for training a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects in the images, wherein the first annotated training set of images is in a first image domain; dividing, by the data processing system, the first annotated training set of images into mini-sets of images, each mini-set representing a separate modeling subtask and including a limited number of examples; training, by the data processing system, the machine learning algorithm in a first stage using the mini-set of images to generate a pre-trained machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in new images; labeling, with the data processing system, a limited number of images from the target dataset to generate a second annotated training set of images for training a machine learning algorithm to detect, characterize, classify, or a combination thereof, some or all regions or objects within the images, wherein the second annotated training set of images is in a second image domain; training, by the data processing system, the pre-trained machine learning model in a second stage using the second annotated training set of images to generate a target machine learning model configured to detect, characterize, classify, or a combination thereof, some or all regions or objects in the new image, wherein some classes targeted in the first stage are part of or coincide with some classes targeted in the second stage; 10. A computer-implemented method comprising:

2. The computer-implemented method of claim 1 , wherein the first annotated training set of images are digital pathology images containing one or more types of cells.

3. The dividing step comprises: selecting, for each distinct modeling subtask if only one mini-set of images is available, a subset of classes that are part of or coincide with the classes targeted in the second stage, and selecting the limited number of examples based on the selected subset of classes; and If multiple mini-sets of images are available, for each distinct modeling subtask, either: (i) blending examples from the multiple mini-sets of images, selecting a subset of classes that are part of or match the several classes targeted in the second stage, and selecting the limited number of examples from the blended examples based on the selected subset of classes; or (ii) selecting one mini-set of images from the multiple mini-sets of images, selecting a subset of classes that are part of or match the several classes targeted in the second stage, and selecting the limited number of examples from the selected mini-set of images based on the selected subset of classes. The computer-implemented method of claim 1 , comprising:

4. The second stage comprises: applying the pre-trained machine learning model to generate a feature vector representation for each example in the second annotated training set of images; combining the feature vector representations from examples of the same class to generate one representation per target class and use the one representation per target class as a prototype for the target class; generating a feature vector representation for the remaining images or image regions of the unlabeled image from the target dataset; comparing each feature vector representation from the unlabeled image to the prototype for a target class based on a distance between the feature vector representation from the unlabeled image and the prototype for the target class; The computer-implemented method of claim 1 further comprising:

5. The first stage comprises: an inner training loop, in which the machine learning algorithm updates model weights or parameters on one subtask for a predetermined or flexible number of epochs to initialize the pre-trained machine learning model for adaptation to the target dataset, producing a loss on a validation set of images after model updating, denoted as L-subtask-i for the i-th subtask; an outer training loop whose goal is to search for a set of model initializations that, when used to update all subtasks with only a limited number of examples, produces the pre-tuned machine learning model by finding a model initialization that minimizes the sum of all losses, denoted as the sum of L-subtasks-i, where i ranges from 1 to the number of subtasks computed from a validation set of images for said subtasks for model initialization; The computer-implemented method of claim 1 further comprising:

6. 2. The computer-implemented method of claim 1, wherein the training of the first stage includes performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the mini-set of images that maximizes or minimizes a cost function, each iteration involving finding a set of parameters for the machine learning algorithm such that a value of the cost function using the set of parameters is greater or less than a value of the cost function using another set of parameters in a previous iteration, the cost function being constructed to measure the difference between predictions made for some or all of the regions or objects using the machine learning algorithm and ground truth labels assigned to the mini-set of images.

7. 2. The computer-implemented method of claim 1, wherein the training of the second stage includes performing iterative operations to learn a set of parameters to detect, characterize, classify, or a combination thereof, some or all of the regions or objects in the second annotated training set of images that maximizes or minimizes a cost function, each iteration involving finding a set of parameters for the pre-trained machine learning model such that a value of the cost function using the set of parameters is greater or less than a value of the cost function using another set of parameters in a previous iteration, the cost function being constructed to measure the difference between predictions made for some or all of the regions or objects using the pre-trained machine learning model and ground truth labels assigned to the second annotated training set of images.

8. Identifying digital pathology scenarios; selecting an adaptive continuous learning method for updating a target machine learning model in light of the digital pathology scenario; and updating the target machine learning model based on the adaptive continuous learning method to generate an updated machine learning model; The computer-implemented method of claim 1 further comprising:

9. The computer-implemented method of claim 8 , wherein the digital pathology scenario is a data incremental scenario, a domain incremental scenario, a class incremental scenario, or a task incremental scenario.

10. The adaptive continuous learning method is selected from the group including Elastic Weight Consolidation (EWC), No Forgetting Learning (LWF), Incremental Learner and Representation Learning (iCaRL), Continuous Prototype Evaluation (CoPE), A-GEM, and Parameter Separation Methods.

9. The computer-implemented method of claim 8.

11. The computer-implemented method of claim 8 , further comprising providing a target machine learning model and / or an updated machine learning model.

12. 12. The computer-implemented method of claim 11, wherein the providing comprises deploying the target machine learning model and / or the updated machine learning model to a digital pathology system.

13. receiving, by said data processing system, a new image; inputting the new image into a target machine learning model or an updated machine learning model; detecting, characterizing, classifying, or a combination thereof, some or all regions or objects in the new image with the target machine learning model or the updated machine learning model; outputting an inference based on the detection, characterization, classification, or a combination thereof, by the target machine learning model or the updated machine learning model; The computer-implemented method of claim 1 further comprising:

14. 14. The computer-implemented method of claim 13, further comprising determining, by a user, a diagnosis of a subject associated with the new image, the diagnosis being determined based on the inferences output by the target machine learning model or the updated machine learning model.

15. 15. The computer-implemented method of claim 14, further comprising administering, by the user, a treatment to the subject based on (i) an inference output by the target machine learning model or the updated machine learning model, and / or (ii) the diagnosis of the subject.

16. 2. The computer-implemented method of claim 1, wherein training the machine learning algorithm includes implementing meta-learning principles to enable the first stage to generate the pre-tuned machine learning model using the limited number of examples.

17. 2. The computer-implemented method of claim 1, wherein training the pre-trained machine learning model includes implementing meta-learning principles to enable the second stage to generate a targeted machine learning model using the limited number of images.

18. one or more data processors; a non-transitory computer-readable storage medium containing instructions that, when executed on the one or more data processors, cause the one or more data processors to perform any of the steps of the method of any one of claims 1 to 17; and A system comprising:

19. A computer program comprising instructions configured to cause one or more data processors to perform any of the steps of the method of any one of claims 1 to 17.

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