Federated learning has emerged as a compelling paradigm for medical image segmentation, particularly in light of increasing privacy concerns. However, most of the existing research relies on relatively stringent assumptions regarding the uniformity and completeness of annotations across clients. Contrary to this, this paper highlights a prevalent challenge in medical practice: incomplete annotations. Such annotations can introduce incorrectly labeled pixels, potentially undermining the performance of neural networks in supervised learning. To tackle this issue, we introduce a novel solution, named FedIA. Our insight is to conceptualize incomplete annotations as noisy data (i.e., low-quality data), with a focus on mitigating their adverse effects. We begin by evaluating the completeness of annotations at the client level using a designed indicator. Subsequently, we enhance the influence of clients with more comprehensive annotations and implement corrections for incomplete ones, thereby ensuring that models are trained on accurate data. Our method's effectiveness is validated through its superior performance on two extensively used medical image segmentation datasets, outperforming existing solutions. The code is available at https://github.com/HUSTxyy/FedIA.

Distantly-Supervised Named Entity Recognition effectively alleviates the burden of time-consuming and expensive annotation in the supervised setting. But the context-free matching process and the limited coverage of knowledge bases introduce inaccurate and incomplete annotation noise respectively. Previous studies either considered only incomplete annotation noise or indiscriminately handle two types of noise with the same strategy. In this paper, we argue that the different causes of two types of noise bring up the requirement of different strategies in model architecture. Therefore, we propose the SANTA to handle these two types of noise separately with (1) Memory-smoothed Focal Loss and Entity-aware KNN to relieve the entity ambiguity problem caused by inaccurate annotation, and (2) Boundary Mixup to alleviate decision boundary shifting problem caused by incomplete annotation and a noise-tolerant loss to improve the robustness. Benefiting from our separate tailored strategies, we confirm in the experiment that the two types of noise are well mitigated. SANTA also achieves a new state-of-the-art on five public datasets.

Segmentation is one of the most primary tasks in deep learning for medical imaging, owing to its multiple downstream clinical applications. However, generating manual annotations for medical images is time-consuming, requires high skill, and is an expensive effort, especially for 3D images. One potential solution is to aggregate knowledge from partially annotated datasets from multiple groups to collaboratively train global models using Federated Learning. To this end, we propose SegViz, a federated learning-based framework to train a segmentation model from distributed non-i.i.d datasets with partial annotations. The performance of SegViz was compared against training individual models separately on each dataset as well as centrally aggregating all the datasets in one place and training a single model. The SegViz framework using FedBN as the aggregation strategy demonstrated excellent performance on the external BTCV set with dice scores of 0.93, 0.83, 0.55, and 0.75 for segmentation of liver, spleen, pancreas, and kidneys, respectively, significantly (p < 0.05) better (except spleen) than the dice scores of 0.87, 0.83, 0.42, and 0.48 for the baseline models. In contrast, the central aggregation model significantly (p < 0.05) performed poorly on the test dataset with dice scores of 0.65, 0, 0.55, and 0.68. Our results demonstrate the potential of the SegViz framework to train multi-task models from distributed datasets with partial labels. All our implementations are open-source and available at https://anonymous.4open.science/r/SegViz-B746

Methods to detect malignant lesions from screening mammograms are usually trained with fully annotated datasets, where images are labelled with the localisation and classification of cancerous lesions. However, real-world screening mammogram datasets commonly have a subset that is fully annotated and another subset that is weakly annotated with just the global classification (i.e., without lesion localisation). Given the large size of such datasets, researchers usually face a dilemma with the weakly annotated subset: to not use it or to fully annotate it. The first option will reduce detection accuracy because it does not use the whole dataset, and the second option is too expensive given that the annotation needs to be done by expert radiologists. In this paper, we propose a middle-ground solution for the dilemma, which is to formulate the training as a weakly- and semi-supervised learning problem that we refer to as malignant breast lesion detection with incomplete annotations. To address this problem, our new method comprises two stages, namely: 1) pre-training a multi-view mammogram classifier with weak supervision from the whole dataset, and 2) extending the trained classifier to become a multi-view detector that is trained with semi-supervised student-teacher learning, where the training set contains fully and weakly-annotated mammograms. We provide extensive detection results on two real-world screening mammogram datasets containing incomplete annotations, and show that our proposed approach achieves state-of-the-art results in the detection of malignant breast lesions with incomplete annotations.

State-of-the-art Named Entity Recognition(NER) models rely heavily on large amountsof fully annotated training data. However, ac-cessible data are often incompletely annotatedsince the annotators usually lack comprehen-sive knowledge in the target domain. Normallythe unannotated tokens are regarded as non-entities by default, while we underline thatthese tokens could either be non-entities orpart of any entity. Here, we study NER mod-eling with incomplete annotated data whereonly a fraction of the named entities are la-beled, and the unlabeled tokens are equiva-lently multi-labeled by every possible label.Taking multi-labeled tokens into account, thenumerous possible paths can distract the train-ing model from the gold path (ground truthlabel sequence), and thus hinders the learn-ing ability. In this paper, we propose AdaK-NER, named the adaptive top-Kapproach, tohelp the model focus on a smaller feasible re-gion where the gold path is more likely to belocated. We demonstrate the superiority ofour approach through extensive experimentson both English and Chinese datasets, aver-agely improving 2% in F-score on the CoNLL-2003 and over 10% on two Chinese datasetscompared with the prior state-of-the-art works.