Domain adaptation using optimal transport for invariant learning using histopathology datasets
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校贝克曼高级科学技术研究所）；Microsoft Research（微软研究院）
Kianoush Falahkheirkhah, Alex Lu, David Alvarez-Melis, Grace Huynh
Histopathology is critical for the diagnosis of many diseases, including cancer. These protocols typically require pathologists to manually evaluate slides under a microscope, which is time-consuming and subjective, leading to interest in machine learning to automate analysis. However, computational techniques are limited by batch effects, where technical factors like differences in preparation protocol or scanners can alter the appearance of slides, causing models trained on one institution to fail when generalizing to others. Here, we propose a domain adaptation method that improves the generalization of histopathological models to data from unseen institutions, without the need for labels or retraining in these new settings. Our approach introduces an optimal transport (OT) loss, that extends adversarial methods that penalize models if images from different institutions can be distinguished in their representation space. Unlike previous methods, which operate on single samples, our loss accounts for distributional differences between batches of images. We show that on the Camelyon17 dataset, while both methods can adapt to global differences in color distribution, only our OT loss can reliably classify a cancer phenotype unseen during training. Together, our results suggest that OT improves generalization on rare but critical phenotypes that may only make up a small fraction of the total tiles and variation in a slide.
Rutgers University（罗格斯大学）；Rutgers Cancer Institute of New Jersey（新泽西罗格斯癌症研究所）
Automatic and accurate Gleason grading of histopathology tissue slides is crucial for prostate cancer diagnosis, treatment, and prognosis. Usually, histopathology tissue slides from different institutions show heterogeneous appearances because of different tissue preparation and staining procedures, thus the predictable model learned from one domain may not be applicable to a new domain directly. Here we propose to adopt unsupervised domain adaptation to transfer the discriminative knowledge obtained from the source domain to the target domain without requiring labeling of images at the target…
The analysis of the tumor environment on digital histopathology slides is becoming key for the understanding of the immune response against cancer, supporting the development of novel immuno-therapies. We introduce here a novel deep learning solution to the related problem of tumor epithelium segmentation. While most existing deep learning segmentation approaches are trained on time-consuming and costly manual annotation on single stain domain (PD-L1), we leverage here semi-automatically labeled images from a second stain domain (Cytokeratin-CK). We introduce an end-to-end trainable network th…
Breast cancer is the most commonly diagnosed cancer worldwide, with over two million new cases each year. During diagnostic tumour grading, pathologists manually count the number of dividing cells (mitotic figures) in biopsy or tumour resection specimens. Since the process is subjective and time-consuming, data-driven artificial intelligence (AI) methods have been developed to automatically detect mitotic figures. However, these methods often generalise poorly, with performance reduced by variations in tissue types, staining protocols, or the scanners used to digitise whole-slide images. Domai…
While federated learning is a promising approach for training deep learning models over distributed sensitive datasets, it presents new challenges for machine learning, especially when applied in the medical domain where multi-centric data heterogeneity is common. Building on previous domain adaptation works, this paper proposes a novel federated learning approach for deep learning architectures via the introduction of local-statistic batch normalization (BN) layers, resulting in collaboratively-trained, yet center-specific models. This strategy improves robustness to data heterogeneity while …
The success of deep learning has set new benchmarks for many medical image analysis tasks. However, deep models often fail to generalize in the presence of distribution shifts between training (source) data and test (target) data. One method commonly employed to counter distribution shifts is domain adaptation: using samples from the target domain to learn to account for shifted distributions. In this work we propose an unsupervised domain adaptation approach that uses graph neural networks and, disentangled semantic and domain invariant structural features, allowing for better performance acr…
University of Maryland（马里兰大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Optimal Transport (OT) distances such as Wasserstein have been used in several areas such as GANs and domain adaptation. OT, however, is very sensitive to outliers (samples with large noise) in the data since in its objective function, every sample, including outliers, is weighed similarly due to the marginal constraints. To remedy this issue, robust formulations of OT with unbalanced marginal constraints have previously been proposed. However, employing these methods in deep learning problems such as GANs and domain adaptation is challenging due to the instability of their dual optimization s…
Shiraz University of Technology（设拉子理工大学）；National Brain Mapping Laboratory（国家脑图谱实验室）
We propose a two-step domain shift-invariant mitosis cell detection method based on Faster RCNN and a convolutional neural network (CNN). We generate various domain-shifted versions of existing histopathology images using a stain augmentation technique, enabling our method to effectively learn various stain domains and achieve better generalization. The performance of our method is evaluated on the preliminary test data set of the MIDOG-2021 challenge. The experimental results demonstrate that the proposed mitosis detection method can achieve promising performance for domain-shifted histopatho…
Despite their success in many computer vision tasks, convolutional networks tend to require large amounts of labeled data to achieve generalization. Furthermore, the performance is not guaranteed on a sample from an unseen domain at test time, if the network was not exposed to similar samples from that domain at training time. This hinders the adoption of these techniques in clinical setting where the imaging data is scarce, and where the intra- and inter-domain variance of the data can be substantial. We propose a domain adaptation technique that is especially suitable for deep networks to al…
North Carolina State University（北卡罗来纳州立大学）；Chalmers University（查尔姆斯大学）
In this paper, we address the problem of unsupervised Domain Adaptation. The need for such an adaptation arises when the distribution of the target data differs from that which is used to develop the model and the ground truth information of the target data is unknown. We propose an algorithm that uses optimal transport theory with a verifiably efficient and implementable solution to learn the best latent feature representation. This is achieved by minimizing the cost of transporting the samples from the target domain to the distribution of the source domain.
In this paper, we propose a novel approach for unsupervised domain adaptation, that relates notions of optimal transport, learning probability measures and unsupervised learning. The proposed approach, HOT-DA, is based on a hierarchical formulation of optimal transport, that leverages beyond the geometrical information captured by the ground metric, richer structural information in the source and target domains. The additional information in the labeled source domain is formed instinctively by grouping samples into structures according to their class labels. While exploring hidden structures i…
Prompt-Free Lightweight SAM Adaptation for Histopathology Nuclei Segmentation with Strong Cross-Dataset Generalization
School of Information and Communication Technology, Griffith University, QLD, Australia（信息与通信技术学院，格里菲斯大学，昆士兰，澳大利亚）；School of MDP -- Clinical Medicine, Griffith University, QLD, Australia（MDP临床医学学院，格里菲斯大学，昆士兰，澳大利亚）
ITMO University（ITMO大学）；Artificial Intelligence Research Institute（人工智能研究院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术学院）；Eberhard Karls Universität Tübingen（蒂宾根大学）
We present a novel algorithm for domain adaptation using optimal transport. In domain adaptation, the goal is to adapt a classifier trained on the source domain samples to the target domain. In our method, we use optimal transport to map target samples to the domain named source fiction. This domain differs from the source but is accurately classified by the source domain classifier. Our main idea is to generate a source fiction by c-cyclically monotone transformation over the target domain. If samples with the same labels in two domains are c-cyclically monotone, the optimal transport map bet…
Mind the Gap: Continuous Magnification Sampling for Pathology Foundation Models
Berlin Institute for the Foundations of Learning and Data (BIFOLD)（柏林学习与数据基础研究所）；Machine Learning Group, Technische Universität Berlin（柏林技术大学机器学习小组）；Aignostics（Aignostics公司）；Charité, Universitätsmedizin Berlin（柏林夏里特大学医学院）
University of Stavanger（斯塔万格大学）；Erasmus MC Cancer Institute, University Medical Center（伊拉斯姆斯医学中心癌症研究所，大学医学中心）
Accurate segmentation of tissue in histopathological images can be very beneficial for defining regions of interest (ROI) for streamline of diagnostic and prognostic tasks. Still, adapting to different domains is essential for histopathology image analysis, as the visual characteristics of tissues can vary significantly across datasets. Yet, acquiring sufficient annotated data in the medical domain is cumbersome and time-consuming. The labeling effort can be significantly reduced by leveraging active learning, which enables the selective annotation of the most informative samples. Our proposed…
Domain adaptation from one data space (or domain) to another is one of the most challenging tasks of modern data analytics. If the adaptation is done correctly, models built on a specific data space become more robust when confronted to data depicting the same semantic concepts (the classes), but observed by another observation system with its own specificities. Among the many strategies proposed to adapt a domain to another, finding a common representation has shown excellent properties: by finding a common representation for both domains, a single classifier can be effective in both and use …
Mila - Quebec AI Institute（米拉-魁北克人工智能研究所）；McGill University（麦吉尔大学）；Université de Montréal（蒙特利尔大学）
It is common in computer vision to be confronted with domain shift: images which have the same class but different acquisition conditions. In domain adaptation (DA), one wants to classify unlabeled target images using source labeled images. Unfortunately, deep neural networks trained on a source training set perform poorly on target images which do not belong to the training domain. One strategy to improve these performances is to align the source and target image distributions in an embedded space using optimal transport (OT). However OT can cause negative transfer, i.e. aligning samples with…
The Institute of Statistical Mathematics（统计数学研究所）；RIKEN AIP（理化学研究所先进智能项目中心）
Domain adaptation aims to transfer knowledge of labeled instances obtained from a source domain to a target domain to fill the gap between the domains. Most domain adaptation methods assume that the source and target domains have the same dimensionality. Methods that are applicable when the number of features is different in each domain have rarely been studied, especially when no label information is given for the test data obtained from the target domain. In this paper, it is assumed that common features exist in both domains and that extra (new additional) features are observed in the targe…
Unsupervised domain adaptation is one of the challenging problems in computer vision. This paper presents a novel approach to unsupervised domain adaptations based on the optimal transport-based distance. Our approach allows aligning target and source domains without the requirement of meaningful metrics across domains. In addition, the proposal can associate the correct mapping between source and target domains and guarantee a constraint of topology between source and target domains. The proposed method is evaluated on different datasets in various problems, i.e. (i) digit recognition on MNIS…
Univ Lyon（里昂大学）；INSA-Lyon（里昂国立应用科学学院）；Université Claude Bernard Lyon 1（里昂第一大学克洛德·贝尔纳大学）；UJM-Saint Etienne（圣艾蒂安大学（让·莫奈大学））；CNRS（法国国家科学研究中心）；Inserm（法国国家健康与医学研究院）
In this paper, we propose a new feature selection method for unsupervised domain adaptation based on the emerging optimal transportation theory. We build upon a recent theoretical analysis of optimal transport in domain adaptation and show that it can directly suggest a feature selection procedure leveraging the shift between the domains. Based on this, we propose a novel algorithm that aims to sort features by their similarity across the source and target domains, where the order is obtained by analyzing the coupling matrix representing the solution of the proposed optimal transportation prob…
Existing Unsupervised Domain Adaptation (UDA) literature adopts the covariate shift and conditional shift assumptions, which essentially encourage models to learn common features across domains. However, due to the lack of supervision in the target domain, they suffer from the semantic loss: the feature will inevitably lose non-discriminative semantics in source domain, which is however discriminative in target domain. We use a causal view -- transportability theory -- to identify that such loss is in fact a confounding effect, which can only be removed by causal intervention. However, the the…
Domain adaptation arises as an important problem in statistical learning theory when the data-generating processes differ between training and test samples, respectively called source and target domains. Recent theoretical advances show that the success of domain adaptation algorithms heavily relies on their ability to minimize the divergence between the probability distributions of the source and target domains. However, minimizing this divergence cannot be done independently of the minimization of other key ingredients such as the source risk or the combined error of the ideal joint hypothes…
We present a 2-step optimal transport approach that performs a mapping from a source distribution to a target distribution. Here, the target has the particularity to present new classes not present in the source domain. The first step of the approach aims at rejecting the samples issued from these new classes using an optimal transport plan. The second step solves the target (class ratio) shift still as an optimal transport problem. We develop a dual approach to solve the optimization problem involved at each step and we prove that our results outperform recent state-of-the-art performances. W…
NYU Grossman School of Medicine（纽约大学格罗斯曼医学院）；University of Toronto（多伦多大学）；Microsoft Research（微软研究院）
Scarcity of labeled histopathology data limits the applicability of deep learning methods to under-profiled cancer types and labels. Transfer learning allows researchers to overcome the limitations of small datasets by pre-training machine learning models on larger datasets similar to the small target dataset. However, similarity between datasets is often determined heuristically. In this paper, we propose a principled notion of distance between histopathology datasets based on a hierarchical generalization of optimal transport distances. Our method does not require any training, is agnostic t…
Technion, Israel Institute of Technology（以色列理工学院）；Technical University of Munich（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
In this paper, we address the problem of Domain Adaptation (DA) using Optimal Transport (OT) on Riemannian manifolds. We model the difference between two domains by a diffeomorphism and use the polar factorization theorem to claim that OT is indeed optimal for DA in a well-defined sense, up to a volume preserving map. We then focus on the manifold of Symmetric and Positive-Definite (SPD) matrices, whose structure provided a useful context in recent applications. We demonstrate the polar factorization theorem on this manifold. Due to the uniqueness of the weighted Riemannian mean, and by exploi…
In this paper, we propose a new strategy for learning inertial robotic navigation models. The proposed strategy enhances the generalisability of end-to-end inertial modelling, and is aimed at wheeled robotic deployments. Concretely, the paper describes the following. (1) Using precision robotics, we empirically characterise the effect of changing the sensor position during navigation on the distribution of raw inertial signals, as well as the corresponding impact on learnt latent spaces. (2) We propose neural architectures and algorithms to assimilate knowledge from an indexed set of sensor po…
This article investigates the quality of the estimator of the linear Monge mapping between distributions. We provide the first concentration result on the linear mapping operator and prove a sample complexity of $n^{-1/2}$ when using empirical estimates of first and second order moments. This result is then used to derive a generalization bound for domain adaptation with optimal transport. As a consequence, this method approaches the performance of theoretical Bayes predictor under mild conditions on the covariance structure of the problem. We also discuss the computational complexity of the l…
University of Genova（热那亚大学）；Istituto Italiano di Tecnologia（意大利理工学院）；École Polytechnique（巴黎综合理工学院）；Institut Polytechnique de Paris（巴黎理工学院）；Criteo AI Lab（科韬人工智能实验室）；University College London（伦敦大学学院）
The problem of domain adaptation on an unlabeled target dataset using knowledge from multiple labelled source datasets is becoming increasingly important. A key challenge is to design an approach that overcomes the covariate and target shift both among the sources, and between the source and target domains. In this paper, we address this problem from a new perspective: instead of looking for a latent representation invariant between source and target domains, we exploit the diversity of source distributions by tuning their weights to the target task at hand. Our method, named Weighted Joint Di…
National Institute of Information and Communications Technology（日本国立信息与通信技术研究所）；Research Center for Information Technology Innovation, Academic Sinica（中央研究院资讯科技创新研究中心）
Due to the mismatch of statistical distributions of acoustic speech between training and testing sets, the performance of spoken language identification (SLID) could be drastically degraded. In this paper, we propose an unsupervised neural adaptation model to deal with the distribution mismatch problem for SLID. In our model, we explicitly formulate the adaptation as to reduce the distribution discrepancy on both feature and classifier for training and testing data sets. Moreover, inspired by the strong power of the optimal transport (OT) to measure distribution discrepancy, a Wasserstein dist…
Optimal transport distances have found many applications in machine learning for their capacity to compare non-parametric probability distributions. Yet their algorithmic complexity generally prevents their direct use on large scale datasets. Among the possible strategies to alleviate this issue, practitioners can rely on computing estimates of these distances over subsets of data, {\em i.e.} minibatches. While computationally appealing, we highlight in this paper some limits of this strategy, arguing it can lead to undesirable smoothing effects. As an alternative, we suggest that the same min…
Winterlight Labs（温特莱特实验室）；Massachusetts Institute of Technology（麻省理工学院）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）；Microsoft Research（微软研究院）
Multi-language speech datasets are scarce and often have small sample sizes in the medical domain. Robust transfer of linguistic features across languages could improve rates of early diagnosis and therapy for speakers of low-resource languages when detecting health conditions from speech. We utilize out-of-domain, unpaired, single-speaker, healthy speech data for training multiple Optimal Transport (OT) domain adaptation systems. We learn mappings from other languages to English and detect aphasia from linguistic characteristics of speech, and show that OT domain adaptation improves aphasia d…
HOT: Harmonic-Constrained Optimal Transport for Remote Photoplethysmography Domain Adaptation
VNU University of Engineering and Technology, Hanoi, Vietnam（越南河内国立大学工程与技术大学）；VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, Vietnam（VinUni-Illinois智慧健康中心，VinUniversity，越南河内）；College of Engineering and Computer Science, VinUniversity, Hanoi, Vietnam（VinUniversity工程与计算机科学学院，越南河内）；Center for Innovations in Health Sciences, VinUniversity, Hanoi, Vietnam（VinUniversity健康科学创新中心，越南河内）
Histopathology image embedding is an active research area in computer vision. Most of the embedding models exclusively concentrate on a specific magnification level. However, a useful task in histopathology embedding is to train an embedding space regardless of the magnification level. Two main approaches for tackling this goal are domain adaptation and domain generalization, where the target magnification levels may or may not be introduced to the model in training, respectively. Although magnification adaptation is a well-studied topic in the literature, this paper, to the best of our knowle…
Univ.Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, UJM-Saint Etienne CNRS, Inserm, CREATIS UMR 5220, U1206（里昂大学，里昂国立应用科学学院，里昂第一大学，圣埃蒂安让·莫内大学，法国国家科学研究中心，法国国家健康与医学研究院，CREATIS实验室）；Univ. Lyon, UJM-Saint-Etienne CNRS, Lab. Hubert Curien UMR 5516（里昂大学，圣埃蒂安让·莫内大学，法国国家科学研究中心，于贝尔·居里安实验室）
Domain adaptation (DA) is an important and emerging field of machine learning that tackles the problem occurring when the distributions of training (source domain) and test (target domain) data are similar but different. Current theoretical results show that the efficiency of DA algorithms depends on their capacity of minimizing the divergence between source and target probability distributions. In this paper, we provide a theoretical study on the advantages that concepts borrowed from optimal transportation theory can bring to DA. In particular, we show that the Wasserstein metric can be used…
Université de Bretagne Sud（南布列塔尼大学）；IRISA（法国信息与随机系统研究所）；CNRS（法国国家科学研究中心）；Wageningen University（瓦赫宁根大学）；Université Côte d’Azur（蔚蓝海岸大学）；OCA（蔚蓝海岸天文台）；Laboratoire Lagrange（拉格朗日实验室）
In computer vision, one is often confronted with problems of domain shifts, which occur when one applies a classifier trained on a source dataset to target data sharing similar characteristics (e.g. same classes), but also different latent data structures (e.g. different acquisition conditions). In such a situation, the model will perform poorly on the new data, since the classifier is specialized to recognize visual cues specific to the source domain. In this work we explore a solution, named DeepJDOT, to tackle this problem: through a measure of discrepancy on joint deep representations/labe…
IBM Research Europe（IBM欧洲研究院）；ETH Zurich（苏黎世联邦理工学院）；Uppsala University（乌普萨拉大学）
Methods for unsupervised domain adaptation (UDA) help to improve the performance of deep neural networks on unseen domains without any labeled data. Especially in medical disciplines such as histopathology, this is crucial since large datasets with detailed annotations are scarce. While the majority of existing UDA methods focus on the adaptation from a labeled source to a single unlabeled target domain, many real-world applications with a long life cycle involve more than one target domain. Thus, the ability to sequentially adapt to multiple target domains becomes essential. In settings where…
In this work, we propose a mutual information (MI) based unsupervised domain adaptation (UDA) method for the cross-domain nuclei segmentation. Nuclei vary substantially in structure and appearances across different cancer types, leading to a drop in performance of deep learning models when trained on one cancer type and tested on another. This domain shift becomes even more critical as accurate segmentation and quantification of nuclei is an essential histopathology task for the diagnosis/ prognosis of patients and annotating nuclei at the pixel level for new cancer types demands extensive eff…
Optimal Transport has recently gained interest in machine learning for applications ranging from domain adaptation, sentence similarities to deep learning. Yet, its ability to capture frequently occurring structure beyond the "ground metric" is limited. In this work, we develop a nonlinear generalization of (discrete) optimal transport that is able to reflect much additional structure. We demonstrate how to leverage the geometry of this new model for fast algorithms, and explore connections and properties. Illustrative experiments highlight the benefit of the induced structured couplings for t…
ShanghaiTech University（上海科技大学）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉与成像工程技术研究中心）；University of Technology Sydney（悉尼科技大学）
Universal Domain Adaptation (UniDA) aims to transfer knowledge from a source domain to a target domain without any constraints on label sets. Since both domains may hold private classes, identifying target common samples for domain alignment is an essential issue in UniDA. Most existing methods require manually specified or hand-tuned threshold values to detect common samples thus they are hard to extend to more realistic UniDA because of the diverse ratios of common classes. Moreover, they cannot recognize different categories among target-private samples as these private samples are treated …
