Re-mixing Embeddings for Patient Augmentation in Data Scarce Multiple Instance Learning
Computational Health Center & Helmholtz AI, Helmholtz Munich（计算健康中心与亥姆霍兹AI，亥姆霍兹慕尼黑）；Computer Aided Medical Procedures, Technical University of Munich（计算机辅助医疗程序，慕尼黑工业大学）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心）；Department of Medicine III, Ludwig Maximilian University Hospital（路德维希·马克西米利安大学医院第三内科）；Department of Physics, Ludwig-Maximilians-Universität München（慕尼黑路德维希-马克西米利安大学物理系）；DKTK, German Cancer Consortium, partner site Munich（德国癌症联盟DKTK，慕尼黑合作站点）
Muhammed Furkan Dasdelen, Fatih Ozlugedik, Anastasia Litinetskaya, Nassir Navab, Carsten Marr, Ario Sadafi
备注：
Accepted for publication at the 29th International Conference on Medical Image Computing and Computer Assisted Intervention - MICCAI 2026
Data scarcity is a major bottleneck in medical Multiple Instance Learning (MIL), especially for rare diseases or expensive modalities. We introduce a statistically grounded patient augmentation approach that generates realistic patients directly in embedding space. Using Gaussian Mixture Models as a probabilistic clustering approach on pooled instance embeddings from all patients, our method learns disease-specific "recipes"-statistical distributions of instances across unsupervised clusters. New patients are then generated by sampling embeddings from clusters based on learned recipes. Unlike existing methods that require examples from all categories, our method can generate patients offline by re-mixing pooled embeddings. Generated patients are further selected based on uncertainty quantification to improve MIL performance. We evaluate our method across three clinically relevant scarcity scenarios: (i) cross-dataset transfer, where an entirely missing "healthy" class is generated using statistics from an external cohort; (ii) low-data regimes, where class sizes are extremely limited; and (iii) small-cohort non-image tasks, including single-cell RNA-seq and flow cytometry. Across all experiments, our method improves performance over baseline, often outperforming other bag-mixing strategies. Notably, in the missing-class scenario, a performance comparable to full-dataset training is achieved, demonstrating its potential for rare disease diagnostic and privacy-preserving patient augmentation. The code is available at https://github.com/marrlab/RECIPE
Unlocking Out-of-Distribution Generalization in Dynamics through Physics-Guided Augmentation
University of Science and Technology of China（科学技术大学）；Tsinghua University（清华大学）；Nanyang Technological University（南洋理工大学）；Beijing Jiaotong University（北京交通大学）；Tencent（腾讯）
Impact of Data Augmentation on Confidence Calibration in Melanoma Classification
Technological University Dublin（都柏林理工大学）；Research Ireland Centre for Research Training in Machine Learning（爱尔兰研究机器学习研究培训中心）；University College Dublin（都柏林大学学院）；Dublin City University（都柏林城市大学）
Region-of-Interest Augmentation for Mammography Classification under Patient-Level Cross-Validation
Department of Computer Science University of Texas at Arlington（计算机科学系德克萨斯大学阿灵顿分校）；Department of Civil Engineering University of Texas at Arlington（土木工程系德克萨斯大学阿灵顿分校）；Department of Computer Science Colorado State University（计算机科学系科罗拉多州立大学）
Harvard Medical School（哈佛医学院）；Massachusetts Institute of Technology（麻省理工学院）
Medical datasets often face the problem of data scarcity, as ground truth labels must be generated by medical professionals. One mitigation strategy is to pretrain deep learning models on large, unlabelled datasets with self-supervised learning (SSL). Data augmentations are essential for improving the generalizability of SSL-trained models, but they are typically handcrafted and tuned manually. We use an adversarial model to generate masks as augmentations for 12-lead electrocardiogram (ECG) data, where masks learn to occlude diagnostically-relevant regions of the ECGs. Compared to random augm…
Data augmentation has proven its usefulness to improve model generalization and performance. While it is commonly applied in computer vision application when it comes to multi-view systems, it is rarely used. Indeed geometric data augmentation can break the alignment among views. This is problematic since multi-view data tend to be scarce and it is expensive to annotate. In this work we propose to solve this issue by introducing a new multi-view data augmentation pipeline that preserves alignment among views. Additionally to traditional augmentation of the input image we also propose a second …
Shape-informed cardiac mechanics surrogates in data-scarce regimes via geometric encoding and generative augmentation
MOX Laboratory, Department of Mathematics, Politecnico di Milano（米兰Politecnico大学数学系MOX实验室）；Division 2.2 Process Simulation, Bundesanstalt für Materialforschung und -prüfung (BAM)（材料研究所（BAM）第2.2过程模拟部）；Department of Mathematics, University of Trento（特伦托大学数学系）
Stanford University（斯坦福大学）；Chalmers University of Technology（查尔姆斯理工大学）
Data augmentation has led to substantial improvements in the performance and generalization of deep models, and remain a highly adaptable method to evolving model architectures and varying amounts of data---in particular, extremely scarce amounts of available training data. In this paper, we present a novel method of applying Mobius transformations to augment input images during training. Mobius transformations are bijective conformal maps that generalize image translation to operate over complex inversion in pixel space. As a result, Mobius transformations can operate on the sample level and …
University of Southern California（南加利福尼亚大学）；Clarifai Inc（克拉里菲人工智能公司）；Northeastern University（东北大学）
Recent advances in the field of artificial intelligence have been made possible by deep neural networks. In applications where data are scarce, transfer learning and data augmentation techniques are commonly used to improve the generalization of deep learning models. However, fine-tuning a transfer model with data augmentation in the raw input space has a high computational cost to run the full network for every augmented input. This is particularly critical when large models are implemented on embedded devices with limited computational and energy resources. In this work, we propose a method …
University of Waterloo（滑铁卢大学）；McGill University（麦吉尔大学）；St. Mary’s Hospital（圣玛丽医院）；Waterloo AI Institute（滑铁卢人工智能研究院）；DarwinAI Corp.（达尔文人工智能公司）
As the global population continues to face significant negative impact by the on-going COVID-19 pandemic, there has been an increasing usage of point-of-care ultrasound (POCUS) imaging as a low-cost and effective imaging modality of choice in the COVID-19 clinical workflow. A major barrier with widespread adoption of POCUS in the COVID-19 clinical workflow is the scarcity of expert clinicians that can interpret POCUS examinations, leading to considerable interest in deep learning-driven clinical decision support systems to tackle this challenge. A major challenge to building deep neural networ…
Domain adaptation aims to exploit a label-rich source domain for learning classifiers in a different label-scarce target domain. It is particularly challenging when there are significant divergences between the two domains. In the paper, we propose a novel unsupervised domain adaptation method based on progressive domain augmentation. The proposed method generates virtual intermediate domains via domain interpolation, progressively augments the source domain and bridges the source-target domain divergence by conducting multiple subspace alignment on the Grassmann manifold. We conduct experimen…
Hong Kong Polytechnic University（香港理工大学）；Sony AI（索尼人工智能）；Nara Institute of Science and Technology（奈良先端科学技術大学院大学）；University of Alberta（阿尔伯塔大学）；Osaka University（大阪大学）
Clinicians prescribe antibiotics by looking at the patient's health record with an experienced eye. However, the therapy might be rendered futile if the patient has drug resistance. Determining drug resistance requires time-consuming laboratory-level testing while applying clinicians' heuristics in an automated way is difficult due to the categorical or binary medical events that constitute health records. In this paper, we propose a novel framework for rapid clinical intervention by viewing health records as graphs whose nodes are mapped from medical events and edges as correspondence between…
FAAGC: Feature Augmentation on Adaptive Geodesic Curve Based on the shape space theory
School of Computer Engineering and Science, Shanghai University（上海大学计算机工程与科学学院）；Key Laboratory of Silicate Cultural Relics Conservation (Shanghai University), Ministry of Education（上海大学硅酸盐文物保护重点实验室（教育部））
ETH Zürich（苏黎世联邦理工学院）；Amazon（亚马逊）；MPI-IS（马克斯·普朗克智能系统研究所）
Intensive care units (ICU) are increasingly looking towards machine learning for methods to provide online monitoring of critically ill patients. In machine learning, online monitoring is often formulated as a supervised learning problem. Recently, contrastive learning approaches have demonstrated promising improvements over competitive supervised benchmarks. These methods rely on well-understood data augmentation techniques developed for image data which do not apply to online monitoring. In this work, we overcome this limitation by supplementing time-series data augmentation techniques with …
In the current COVID-19 pandemic situation, there is an urgent need to screen infected patients quickly and accurately. Using deep learning models trained on chest X-ray images can become an efficient method for screening COVID-19 patients in these situations. Deep learning approaches are already widely used in the medical community. However, they require a large amount of data to be accurate. The open-source community collectively has made efforts to collect and annotate the data, but it is not enough to train an accurate deep learning model. Few-shot learning is a sub-field of machine learni…
IQVIA（艾昆纬）；The Pennsylvania State University（宾夕法尼亚州立大学）；Georgia Institute of Technology（佐治亚理工学院）
Rare diseases affect hundreds of millions of people worldwide but are hard to detect since they have extremely low prevalence rates (varying from 1/1,000 to 1/200,000 patients) and are massively underdiagnosed. How do we reliably detect rare diseases with such low prevalence rates? How to further leverage patients with possibly uncertain diagnosis to improve detection? In this paper, we propose a Complementary pattern Augmentation (CONAN) framework for rare disease detection. CONAN combines ideas from both adversarial training and max-margin classification. It first learns self-attentive and h…
University of Electronic Science and Technology of China（电子科技大学）；University of Toronto（多伦多大学）；The Hospital for Sick Children (SickKids)（SickKids 儿童医院（病童医院））；Sinai Health System（西奈卫生系统）；University Health Network（大学健康网络）；Lunenfeld-Tanenbaum Research Institute（卢嫩菲尔德-塔南鲍姆研究所）；Sunnybrook Research Institute（桑尼布鲁克研究所）
Data augmentation refers to a group of techniques whose goal is to battle limited amount of available data to improve model generalization and push sample distribution toward the true distribution. While different augmentation strategies and their combinations have been investigated for various computer vision tasks in the context of deep learning, a specific work in the domain of medical imaging is rare and to the best of our knowledge, there has been no dedicated work on exploring the effects of various augmentation methods on the performance of deep learning models in prostate cancer detect…
AnemiaVision: Non-Invasive Anemia Detection via Smartphone Imagery Using EfficientNet-B3 with TrivialAugmentWide, Mixup Augmentation, and Persistent Patient History Management
Department of Electronics and Communication Engineering（电子与通信工程系）；Indian Institute of Information Technology, Surat（萨拉特信息科技大学）；India（印度）
Sapienza University of Rome（罗马大学）；Dpt. of Computer, Control, and Management Engineering（计算机、控制与管理工程系）
In this work, we perform a wide variety of experiments with different deep learning architectures on datasets of limited size. According to our study, we show that model complexity is a critical factor when only a few samples per class are available. Differently from the literature, we show that in some configurations, the state of the art can be improved using low complexity models. For instance, in problems with scarce training samples and without data augmentation, low-complexity convolutional neural networks perform comparably well or better than state-of-the-art architectures. Moreover, w…
Mask-guided Data Augmentation for Multiparametric MRI Generation with a Rare Hepatocellular Carcinoma
Universidad Industrial de Santander（桑坦德工业大学）；University of Toulouse（图卢兹大学）；Université Paul Sabatier Toulouse 3（图卢兹第三大学（保罗·萨巴蒂埃大学））；Bicêtre University Hospital（比塞特尔大学医院）；Assistance publique des hôpitaux de Paris（巴黎公共援助医院）；Université Claude Bernard Lyon 1（里昂第一大学（克洛德·贝尔纳里昂第一大学））
École de Technologie Superiéure, Université du Québec（魁北克大学高等技术学院）；State University of Ponta Grossa (UEPG)（蓬塔格罗萨州立大学）；Pontifical Catholic University of Paraná（巴拉那天主教大学）；Federal University of Paraná（巴拉那联邦大学）
Data imbalance is a major problem that affects several machine learning (ML) algorithms. Such a problem is troublesome because most of the ML algorithms attempt to optimize a loss function that does not take into account the data imbalance. Accordingly, the ML algorithm simply generates a trivial model that is biased toward predicting the most frequent class in the training data. In the case of histopathologic images (HIs), both low-level and high-level data augmentation (DA) techniques still present performance issues when applied in the presence of inter-patient variability; whence the model…
Massachusetts Institute of Technology（麻省理工学院）；Massachusetts General Hospital（麻省总医院）
Neural network models have demonstrated impressive performance in predicting pathologies and outcomes from the 12-lead electrocardiogram (ECG). However, these models often need to be trained with large, labelled datasets, which are not available for many predictive tasks of interest. In this work, we perform an empirical study examining whether training time data augmentation methods can be used to improve performance on such data-scarce ECG prediction problems. We investigate how data augmentation strategies impact model performance when detecting cardiac abnormalities from the ECG. Motivated…
Tel Aviv University（特拉维夫大学）；Sheba Medical Center（示巴医疗中心）；Bar-Ilan University（巴伊兰大学）
In this work we propose a method for anatomical data augmentation that is based on using slices of computed tomography (CT) examinations that are adjacent to labeled slices as another resource of labeled data for training the network. The extended labeled data is used to train a U-net network for a pixel-wise classification into different hepatic lesions and normal liver tissues. Our dataset contains CT examinations from 140 patients with 333 CT images annotated by an expert radiologist. We tested our approach and compared it to the conventional training process. Results indicate superiority o…
University of Reading（雷丁大学）；Imperial College London（帝国理工学院）；Leiden University（莱顿大学）；European Centre for Medium-Range Weather Forecasts（欧洲中期天气预报中心）
Can we improve machine-learning (ML) emulators with synthetic data? If data are scarce or expensive to source and a physical model is available, statistically generated data may be useful for augmenting training sets cheaply. Here we explore the use of copula-based models for generating synthetically augmented datasets in weather and climate by testing the method on a toy physical model of downwelling longwave radiation and corresponding neural network emulator. Results show that for copula-augmented datasets, predictions are improved by up to 62 % for the mean absolute error (from 1.17 to 0.4…
Maharaja Agrasen Institute of Technology（马哈拉贾·阿格拉森技术学院）；Near East University（近东大学）；State University of Ceará（塞阿拉州立大学）；University of Fortaleza（福塔莱萨大学）
Coronavirus (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spread of COVID-19 seems to have a detrimental effect on the global economy and health. A positive chest X-ray of infected patients is a crucial step in the battle against COVID-19. Early results suggest that abnormalities exist in chest X-rays of patients suggestive of COVID-19. This has led to the introduction of a variety of deep learning systems and studies have shown that the accuracy of COVID-19 patient detection through the use of chest X-rays is strongly optimistic. Dee…
Data is one of the essential ingredients to power deep learning research. Small datasets, especially specific to medical institutes, bring challenges to deep learning training stage. This work aims to develop a practical deep multimodal that can classify patients into abnormal and normal categories accurately as well as assist radiologists to detect visual and textual anomalies by locating areas of interest. The detection of the anomalies is achieved through a novel technique which extends the integrated gradients methodology with an unsupervised clustering algorithm. This technique also intro…
The application of Deep Learning (DL) for medical diagnosis is often hampered by two problems. First, the amount of training data may be scarce, as it is limited by the number of patients who have acquired the condition to be diagnosed. Second, the training data may be corrupted by various types of noise. Here, we study the problem of brain tumor detection from magnetic resonance spectroscopy (MRS) data, where both types of problems are prominent. To overcome these challenges, we propose a new method for training a deep neural network that distills particularly representative training examples…
Peking University（北京大学）；Shanghai University of Finance and Economics（上海财经大学）
There are significant regional inequities in health resources around the world. It has become one of the most focused topics to improve health services for data-scarce hospitals and promote health equity through knowledge sharing among medical institutions. Because electronic medical records (EMRs) contain sensitive personal information, privacy protection is unavoidable and essential for multi-hospital collaboration. In this paper, for a common disease in ICU patients, sepsis, we propose a novel cross-center collaborative learning framework guided by medical knowledge, SofaNet, to achieve ear…
Aalto University（阿尔托大学）；Sony Group Corporation（索尼集团公司）
Data augmentation methods have shown great importance in diverse supervised learning problems where labeled data is scarce or costly to obtain. For sound event localization and detection (SELD) tasks several augmentation methods have been proposed, with most borrowing ideas from other domains such as images, speech, or monophonic audio. However, only a few exploit the spatial properties of a full 3D audio scene. We propose Spatial Mixup, as an application of parametric spatial audio effects for data augmentation, which modifies the directional properties of a multi-channel spatial audio signal…
Computer Network Information Center, CAS and University of Chinese Academy of Sciences（中国科学院计算机网络信息中心和中国科学院大学）；Department of Computer Science, Portland State University（波特兰州立大学计算机科学系）；Department of Computer and Information Science, The State Key Laboratory of Internet of Things for Smart City, University of Macau（澳门大学计算机与信息科学系、智能城市物联网国家重点实验室）；Arizona State University（亚利桑那州立大学）；Virginia Tech（弗吉尼亚理工大学）；IBM T. J. Watson Research Center（IBM T.J. Watson研究部）；Duke University（杜克大学）
Imperial College London（帝国理工学院）；Accenture Labs（埃森哲实验室）
Class imbalance can often degrade predictive performance of supervised learning algorithms. Balanced classes can be obtained by oversampling exact copies, with noise, or interpolation between nearest neighbours (as in traditional SMOTE methods). Oversampling tabular data using augmentation, as is typical in computer vision tasks, can be achieved with deep generative models. Deep generative models are effective data synthesisers due to their ability to capture complex underlying distributions. Synthetic data in healthcare can enhance interoperability between healthcare providers by ensuring pat…
MedDiffusion: Boosting Health Risk Prediction via Diffusion-based Data Augmentation
The Pennsylvania State University（宾夕法尼亚州立大学）；Purdue University（普渡大学）；Georgia State University（佐治亚州立大学）；Iowa State University（爱荷华州立大学）；Stony Brook University（石溪大学）
Artificial Intelligence Algorithms for the Detection of Pathologies Related to Lung Cancer through Image Analysis using Convolutional Neural Networks and Data Augmentation: a systematic mapping of the literature
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）
Children's automatic speech recognition (ASR) is always difficult due to, in part, the data scarcity problem, especially for kindergarten-aged kids. When data are scarce, the model might overfit to the training data, and hence good starting points for training are essential. Recently, meta-learning was proposed to learn model initialization (MI) for ASR tasks of different languages. This method leads to good performance when the model is adapted to an unseen language. However, MI is vulnerable to overfitting on training tasks (learner overfitting). It is also unknown whether MI generalizes to …
University of Cambridge（剑桥大学）；Carnegie Mellon University（卡内基梅隆大学）；Alan Turing Institute（阿兰·图灵研究所）；Imperial College London（伦敦帝国学院）
Reinforcement learning (RL) algorithms usually require a substantial amount of interaction data and perform well only for specific tasks in a fixed environment. In some scenarios such as healthcare, however, usually only few records are available for each patient, and patients may show different responses to the same treatment, impeding the application of current RL algorithms to learn optimal policies. To address the issues of mechanism heterogeneity and related data scarcity, we propose a data-efficient RL algorithm that exploits structural causal models (SCMs) to model the state dynamics, w…
Advances in computational cognitive neuroimaging research are related to the availability of large amounts of labeled brain imaging data, but such data are scarce and expensive to generate. While powerful data generation mechanisms, such as Generative Adversarial Networks (GANs), have been designed in the last decade for computer vision, such improvements have not yet carried over to brain imaging. A likely reason is that GANs training is ill-suited to the noisy, high-dimensional and small-sample data available in functional neuroimaging. In this paper, we introduce Conditional Independent Com…
Patients who suffer an acute coronary syndrome are at elevated risk for adverse cardiovascular events such as myocardial infarction and cardiovascular death. Accurate assessment of this risk is crucial to their course of care. We focus on estimating a patient's risk of cardiovascular death after an acute coronary syndrome based on a patient's raw electrocardiogram (ECG) signal. Learning from this signal is challenging for two reasons: 1) positive examples signifying a downstream cardiovascular event are scarce, causing drastic class imbalance, and 2) each patient's ECG signal consists of thous…
University of Georgia（佐治亚大学）；South China University of Technology（华南理工大学）；Lehigh University（利哈伊大学）；Carnegie Mellon University（卡内基梅隆大学）；Mayo Clinic（梅奥诊所）；University of Virginia（弗吉尼亚大学）；The University of Texas at Arlington（德克萨斯大学阿灵顿分校）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Text data augmentation is an effective strategy for overcoming the challenge of limited sample sizes in many natural language processing (NLP) tasks. This challenge is especially prominent in the few-shot learning scenario, where the data in the target domain is generally much scarcer and of lowered quality. A natural and widely-used strategy to mitigate such challenges is to perform data augmentation to better capture the data invariance and increase the sample size. However, current text data augmentation methods either can't ensure the correct labeling of the generated data (lacking faithfu…
