Label-Efficient Deep Learning in Medical Image Analysis: Challenges and Future Directions (2303.12484v4)
Abstract: Deep learning has seen rapid growth in recent years and achieved state-of-the-art performance in a wide range of applications. However, training models typically requires expensive and time-consuming collection of large quantities of labeled data. This is particularly true within the scope of medical imaging analysis (MIA), where data are limited and labels are expensive to be acquired. Thus, label-efficient deep learning methods are developed to make comprehensive use of the labeled data as well as the abundance of unlabeled and weak-labeled data. In this survey, we extensively investigated over 300 papers to provide a comprehensive overview of recent progress on label-efficient learning strategies in MIA. We first present the background of label-efficient learning and categorize the approaches into different schemes. Next, we examine the current state-of-the-art methods in detail through each scheme. Specifically, we provide an in-depth investigation, covering not only canonical semi-supervised, self-supervised, and multi-instance learning schemes, but also recently emerged active and annotation-efficient learning strategies. Moreover, as a comprehensive contribution to the field, this survey not only elucidates the commonalities and unique features of the surveyed methods but also presents a detailed analysis of the current challenges in the field and suggests potential avenues for future research.
- Divide-and-rule: self-supervised learning for survival analysis in colorectal cancer, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 480–489.
- Slic superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Pattern Anal. Mach. Intell. 34, 2274–2282.
- Anatomically-aware uncertainty for semi-supervised image segmentation. Medical Image Analysis , 103011.
- Ifss-net: Interactive few-shot siamese network for faster muscle segmentation and propagation in volumetric ultrasound. IEEE Trans. Med. Imaging 40, 2615–2628.
- Bigbrain: an ultrahigh-resolution 3d human brain model. Science 340, 1472–1475.
- Efficient and generalizable statistical models of shape and appearance for analysis of cardiac mri. Med. Image Anal. 12, 335–357.
- Bach: Grand challenge on breast cancer histology images. Med. Image Anal. 56, 122–139.
- The lung image database consortium (lidc) and image database resource initiative (idri): a completed reference database of lung nodules on ct scans. Med. Phys. 38, 915–931.
- Automated gleason grading of prostate cancer tissue microarrays via deep learning. Scientific reports 8, 1–11.
- Mitosis domain generalization challenge, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, pp. 1–15.
- Foundational models in medical imaging: A comprehensive survey and future vision. arXiv preprint arXiv:2310.18689 .
- Big self-supervised models advance medical image classification, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 3478–3488.
- Self-supervised learning for cardiac mr image segmentation by anatomical position prediction, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 541–549.
- Semi-supervised learning for network-based cardiac mr image segmentation, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 253–260.
- Bidirectional copy-paste for semi-supervised medical image segmentation, in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 11514–11524.
- Label-efficient semantic segmentation with diffusion models. arXiv:2112.03126.
- Pseudo-label guided contrastive learning for semi-supervised medical image segmentation, in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 19786--19797.
- Consistency regularisation in varying contexts and feature perturbations for semi-supervised semantic segmentation of histology images. Medical Image Analysis 91, 102997.
- Deep active learning for joint classification & segmentation with weak annotator, in: Proc. IEEE Winter Conf. App. Comput. Vis., pp. 3338--3347.
- Deep learning techniques for automatic mri cardiac multi-structures segmentation and diagnosis: is the problem solved? IEEE Trans. Med. Imaging 37, 2514--2525.
- Mixmatch: A holistic approach to semi-supervised learning. Proc. Adv. Neural Inf. Process. Syst. 32.
- Retouch: the retinal oct fluid detection and segmentation benchmark and challenge. IEEE Trans. Med. Imaging 38, 1858--1874.
- Semi-supervised medical image segmentation via learning consistency under transformations, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 810--818.
- A survey on active learning and human-in-the-loop deep learning for medical image analysis. Med. Image Anal. 71, 102062.
- The panda challenge: Prostate cancer grade assessment using the gleason grading system. MICCAI challenge .
- Dual-distribution discrepancy with self-supervised refinement for anomaly detection in medical images. arXiv preprint arXiv:2210.04227 .
- Clinical-grade computational pathology using weakly supervised deep learning on whole slide images. Nat. Med. 25, 1301--1309.
- Query learning with large margin classifiers, in: ICML, p. 0.
- Learning to segment medical images with scribble-supervision alone, in: Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support. Springer, pp. 236--244.
- Auto-gan: self-supervised collaborative learning for medical image synthesis, in: AAAI Conf. Artif. Intell., pp. 10486--10493.
- Uncertainty aware temporal-ensembling model for semi-supervised abus mass segmentation. IEEE Trans. Med. Imaging 40, 431--443.
- Orf-net: Deep omni-supervised rib fracture detection from chest ct scans, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 238--248.
- Local contrastive loss with pseudo-label based self-training for semi-supervised medical image segmentation. Medical Image Analysis 87, 102792.
- Semi-supervised task-driven data augmentation for medical image segmentation. Med. Image Anal. 68, 101934.
- Generalizing few-shot classification of whole-genome doubling across cancer types, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 3382--3392.
- Semi-supervised learning (chapelle, o. et al., eds.; 2006)[book reviews]. IEEE Transactions on Neural Networks 20, 542--542.
- Image quality-aware diagnosis via meta-knowledge co-embedding, in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 19819--19829.
- Towards generalizable diabetic retinopathy grading in unseen domains, in: International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer. pp. 430--440.
- Tri-net for semi-supervised deep learning, in: Proceedings of twenty-seventh international joint conference on artificial intelligence, pp. 2014--2020.
- Dcan: deep contour-aware networks for accurate gland segmentation, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 2487--2496.
- Semi-supervised unpaired medical image segmentation through task-affinity consistency. IEEE Transactions on Medical Imaging 42, 594--605.
- Self-supervised learning for medical image analysis using image context restoration. Med. Image Anal. 58, 101539.
- Scaling vision transformers to gigapixel images via hierarchical self-supervised learning, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 16144--16155.
- A general-purpose self-supervised model for computational pathology. arXiv preprint arXiv:2308.15474 .
- A simple framework for contrastive learning of visual representations, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 1597--1607.
- C-cam: Causal cam for weakly supervised semantic segmentation on medical image, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 11676--11685.
- Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis. Med. Image Anal. 54, 280--296.
- Multiple instance learning with center embeddings for histopathology classification, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 519--528.
- The cancer imaging archive (tcia): maintaining and operating a public information repository. Journal of digital imaging 26, 1045--1057.
- Skin lesion analysis toward melanoma detection: A challenge at the 2017 international symposium on biomedical imaging (isbi), hosted by the international skin imaging collaboration (isic), in: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), IEEE. pp. 168--172.
- Group equivariant convolutional networks, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 2990--2999.
- Multiple instance learning for heterogeneous images: Training a cnn for histopathology, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 254--262.
- A unified framework for generalized low-shot medical image segmentation with scarce data. IEEE Trans. Med. Imaging 40, 2656--2671.
- Multiple instance learning of deep convolutional neural networks for breast histopathology whole slide classification, in: Proc. IEEE Int. Symp. Biomed. Imaging, IEEE. pp. 578--581.
- Federated learning for predicting clinical outcomes in patients with covid-19. Nat. Med. 27, 1735--1743.
- Feedback on a publicly distributed image database: the messidor database. Image Anal. Stereol. 33, 231--234.
- Multi-prototype few-shot learning in histopathology, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 620--628.
- Retinal image synthesis and semi-supervised learning for glaucoma assessment. IEEE Trans. Med. Imaging 38, 2211--2218.
- Federated contrastive learning for decentralized unlabeled medical images, in: MICCAI, Springer. pp. 378--387.
- Scribble-based domain adaptation via co-segmentation, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 479--489.
- Inter extreme points geodesics for end-to-end weakly supervised image segmentation, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 615--624.
- Weakly supervised instance learning for thyroid malignancy prediction from whole slide cytopathology images. Med. Image Anal. 67, 101814.
- Weakly supervised object detection with 2d and 3d regression neural networks. Med. Image Anal. 65, 101767.
- Diabetic retinopathy detection challenge. https://www.kaggle.com/c/diabetic-retinopathy-detection.
- A survey on semi-supervised learning. Machine Learning 109, 373--440.
- Inf-net: Automatic covid-19 lung infection segmentation from ct images. IEEE Trans. Med. Imaging 39, 2626--2637.
- Cancer survival prediction from whole slide images with self-supervised learning and slide consistency. IEEE Transactions on Medical Imaging .
- Adam challenge: Detecting age-related macular degeneration from fundus images. IEEE Transactions on Medical Imaging .
- Dmnet: difference minimization network for semi-supervised segmentation in medical images, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 532--541.
- Quantitative classification of eyes with and without intermediate age-related macular degeneration using optical coherence tomography. Ophthalmology 121, 162--172.
- Interactive few-shot learning: Limited supervision, better medical image segmentation. IEEE Trans. Med. Imaging 40, 2575--2588.
- Model-agnostic meta-learning for fast adaptation of deep networks, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 1126--1135.
- Apictorial jigsaw puzzles: The computer solution of a problem in pattern recognition. IEEE Transactions on Electronic Computers , 118--127.
- Weakly supervised segmentation of tumor lesions in pet-ct hybrid imaging. J. Med. Imaging 8, 054003.
- Palm: Pathologic myopia challenge. IEEE Dataport .
- Dropout as a bayesian approximation: Representing model uncertainty in deep learning, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 1050--1059.
- Deep bayesian active learning with image data, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 1183--1192.
- A semi-supervised multi-task learning framework for cancer classification with weak annotation in whole-slide images. Medical Image Analysis 83, 102652.
- Self-supervised learning from 100 million medical images. arXiv preprint arXiv:2201.01283 .
- Multi-organ abdominal ct reference standard segmentations. This data set was developed as part of independent research supported by Cancer Research UK (Multidisciplinary C28070/A19985) and the National Institute for Health Research UCL/UCL Hospitals Biomedical Research Centre .
- Automatic multi-organ segmentation on abdominal ct with dense v-networks. IEEE Trans. Med. Imaging 37, 1822--1834.
- & whyntie, t., 2018. niftynet: a deep-learning platform for medical imaging. Comput. Methods Programs Biomed. 158, 113--122.
- Weakly-supervised localization of diabetic retinopathy lesions in retinal fundus images, in: Proc. IEEE Int. Conf. Image Process., IEEE. pp. 2069--2073.
- Generative adversarial nets. Proc. Adv. Neural Inf. Process. Syst. 27.
- Dense steerable filter cnns for exploiting rotational symmetry in histology images. IEEE Trans. Med. Imaging 39, 4124--4136.
- Semi-supervised learning by entropy minimization. Proc. Adv. Neural Inf. Process. Syst. 17.
- Bootstrap your own latent-a new approach to self-supervised learning. Proc. Adv. Neural Inf. Process. Syst. 33, 21271--21284.
- Improved training of wasserstein gans. Proc. Adv. Neural Inf. Process. Syst. 30.
- Sac-net: Learning with weak and noisy labels in histopathology image segmentation. Medical Image Analysis 86, 102790.
- Curriculumnet: Weakly supervised learning from large-scale web images, in: Proc. Eur. Conf. Comput. Vis., pp. 135--150.
- Multi-level semantic adaptation for few-shot segmentation on cardiac image sequences. Med. Image Anal. 73, 102170.
- Benchmarking of deep architectures for segmentation of medical images. IEEE Trans. Med. Imaging 41, 3231--3241.
- Skin lesion analysis toward melanoma detection: A challenge at the international symposium on biomedical imaging (isbi) 2016, hosted by the international skin imaging collaboration (isic). arXiv preprint arXiv:1605.01397 .
- Semi-supervised medical image classification with global latent mixing, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 604--613.
- Semi-supervised learning by disentangling and self-ensembling over stochastic latent space, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 766--774.
- Learning semantics-enriched representation via self-discovery, self-classification, and self-restoration, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 137--147.
- Dira: Discriminative, restorative, and adversarial learning for self-supervised medical image analysis, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 20824--20834.
- Diabetic retinopathy grading by digital curvelet transform. Comput. Math. Methods Med. 2012.
- The rsna pediatric bone age machine learning challenge. Radiology 290, 498.
- Accurate screening of covid-19 using attention-based deep 3d multiple instance learning. IEEE Trans. Med. Imaging 39, 2584--2594.
- Multi-scale domain-adversarial multiple-instance cnn for cancer subtype classification with unannotated histopathological images, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 3852--3861.
- Deep residual learning for image recognition, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 770--778.
- Few-shot learning for deformable medical image registration with perception-correspondence decoupling and reverse teaching. IEEE J. Biomed. Health. Inf. .
- Geometric visual similarity learning in 3d medical image self-supervised pre-training, in: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 9538--9547.
- Retinal image understanding emerges from self-supervised multimodal reconstruction, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 321--328.
- Denoising diffusion probabilistic models. Adv. Neural Inf. Process Syst. 33, 6840--6851.
- Entropy-based active learning for object recognition, in: 2008 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, IEEE. pp. 1--8.
- Semi-supervised semantic segmentation of vessel images using leaking perturbations, in: Proc. IEEE Winter Conf. App. Comput. Vis., pp. 2625--2634.
- Bayesian active learning for classification and preference learning. arXiv preprint arXiv:1112.5745 .
- Weakly supervised instance segmentation using the bounding box tightness prior. Proc. Adv. Neural Inf. Process. Syst. 32.
- O2u-net: A simple noisy label detection approach for deep neural networks, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 3326--3334.
- Self-transfer learning for weakly supervised lesion localization, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 239--246.
- Attention-based deep multiple instance learning, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 2127--2136.
- Constrained deep weak supervision for histopathology image segmentation. IEEE Trans. Med. Imaging 36, 2376--2388.
- Anatomical invariance modeling and semantic alignment for self-supervised learning in 3d medical image analysis, in: Proceedings of the IEEE/CVF International Conference on Computer Vision, pp. 15859--15869.
- Self-supervised visual feature learning with deep neural networks: A survey. IEEE Trans. Pattern Anal. Mach. Intell. 43, 4037--4058.
- Mimic-cxr, a de-identified publicly available database of chest radiographs with free-text reports. Sci. Data 6, 1--8.
- Vtgan: Semi-supervised retinal image synthesis and disease prediction using vision transformers, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 3235--3245.
- Empowering multiple instance histopathology cancer diagnosis by cell graphs, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 228--235.
- Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study. PLoS Med. 16, e1002730.
- Multi-class texture analysis in colorectal cancer histology. Scientific reports 6, 1--11.
- Chaos challenge-combined (ct-mr) healthy abdominal organ segmentation. Med. Image Anal. 69, 101950.
- Diffusion models for medical image analysis: A comprehensive survey. arXiv preprint arXiv:2211.07804 .
- Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis. Communications biology 3, 1--12.
- Candishare: a resource for pediatric neuroimaging data. Neuroinformatics 10, 319--322.
- Identifying medical diagnoses and treatable diseases by image-based deep learning. Cell 172, 1122--1131.
- Extreme points derived confidence map as a cue for class-agnostic interactive segmentation using deep neural network, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 66--73.
- Domain generalizer: A few-shot meta learning framework for domain generalization in medical imaging, in: Domain Adaptation and Representation Transfer, and Distributed and Collaborative Learning. Springer, pp. 73--84.
- Auto-encoding variational bayes. arXiv preprint arXiv:1312.6114 .
- Segmentation of page images using the area voronoi diagram. Comput. Vis. Image Underst. 70, 370--382.
- Siamese neural networks for one-shot image recognition, in: ICML deep learning workshop, Lille. p. 0.
- Geometry in active learning for binary and multi-class image segmentation. Comput. Vis. Image Underst. 182, 1--16.
- Self-path: Self-supervision for classification of pathology images with limited annotations. IEEE Trans. Med. Imaging 40, 2845--2856.
- A framework for automated spine and vertebrae interpolation-based detection and model-based segmentation. IEEE Trans. Med. Imaging 34, 1649--1662.
- Macro-operators: A weak method for learning. Artif. Intell. 26, 35--77.
- Efficient inference in fully connected crfs with gaussian edge potentials. Proc. Adv. Neural Inf. Process. Syst. 24.
- A dataset and a technique for generalized nuclear segmentation for computational pathology. IEEE Trans. Med. Imaging 36, 1550--1560.
- Data efficient deep learning for medical image analysis: A survey. arXiv preprint arXiv:2310.06557 .
- Temporal ensembling for semi-supervised learning. arXiv preprint arXiv:1610.02242 .
- Miccai multi-atlas labeling beyond the cranial vault--workshop and challenge, in: Proc. MICCAI Multi-Atlas Labeling Beyond Cranial Vault—Workshop Challenge, p. 12.
- Pseudo-label: The simple and efficient semi-supervised learning method for deep neural networks, in: Workshop on challenges in representation learning, ICML, p. 896.
- Scribble2label: Scribble-supervised cell segmentation via self-generating pseudo-labels with consistency, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 14--23.
- A curated mammography data set for use in computer-aided detection and diagnosis research. Sci. Data 4, 1--9.
- Semi-supervised medical image segmentation using adversarial consistency learning and dynamic convolution network. IEEE Transactions on Medical Imaging .
- Single image super-resolution for whole slide image using convolutional neural networks and self-supervised color normalization. Med. Image Anal. 68, 101938.
- Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 14318--14328.
- Llava-med: Training a large language-and-vision assistant for biomedicine in one day. arXiv preprint arXiv:2306.00890 .
- Semantic segmentation with generative models: Semi-supervised learning and strong out-of-domain generalization, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 8300--8311.
- Learning to generalize: Meta-learning for domain generalization, in: AAAI Conf. Artif. Intell.
- A generic fundus image enhancement network boosted by frequency self-supervised representation learning. Medical Image Analysis 90, 102945.
- Domain generalization with adversarial feature learning, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 5400--5409.
- Domain generalization for medical imaging classification with linear-dependency regularization. NIPS 33, 3118--3129.
- Sacnn: Self-attention convolutional neural network for low-dose ct denoising with self-supervised perceptual loss network. IEEE Trans. Med. Imaging 39, 2289--2301.
- Shape-aware semi-supervised 3d semantic segmentation for medical images, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 552--561.
- Pathal: An active learning framework for histopathology image analysis. IEEE Trans. Med. Imaging .
- Multi-site fmri analysis using privacy-preserving federated learning and domain adaptation: Abide results. Med. Image Anal. 65, 101765.
- Rotation-oriented collaborative self-supervised learning for retinal disease diagnosis. IEEE Trans. Med. Imaging 40, 2284--2294.
- Self-supervised feature learning via exploiting multi-modal data for retinal disease diagnosis. IEEE Trans. Med. Imaging 39, 4023--4033.
- Semi-supervised skin lesion segmentation via transformation consistent self-ensembling model. arXiv preprint arXiv:1808.03887 .
- Transformation-consistent self-ensembling model for semisupervised medical image segmentation. IEEE Trans. Neural Networks Learn. Syst. 32, 523--534.
- Deep weakly-supervised breast tumor segmentation in ultrasound images with explicit anatomical constraints. Med. Image Anal. 76, 102315.
- Feature-critic networks for heterogeneous domain generalization, in: Proc. Int. Conf. Mach. Learn., PMLR. pp. 3915--3924.
- A novel multiple instance learning framework for covid-19 severity assessment via data augmentation and self-supervised learning. Med. Image Anal. 69, 101978.
- Iteratively-refined interactive 3d medical image segmentation with multi-agent reinforcement learning, in: Proc. IEEE Conf. Comput. Vis. Pattern Recogn., pp. 9394--9402.
- Seg4reg+: Consistency learning between spine segmentation and cobb angle regression, in: Proc. Int. Conf. Med. Image Comput. Comput.-Assisted Intervention, Springer. pp. 490--499.
- Nuclei segmentation with point annotations from pathology images via self-supervised learning and co-training. Medical Image Analysis 89, 102933.
- Cheng Jin (76 papers)
- Zhengrui Guo (11 papers)
- Yi Lin (103 papers)
- Luyang Luo (39 papers)
- Hao Chen (1006 papers)