The work discusses the use of machine learning algorithms for anomaly detection in medical image analysis and how the performance of these algorithms depends on the number of annotators and the quality of labels. To address the issue of subjectivity in labeling with a single annotator, we introduce a simple and effective approach that aggregates annotations from multiple annotators with varying levels of expertise. We then aim to improve the efficiency of predictive models in abnormal detection tasks by estimating hidden labels from multiple annotations and using a re-weighted loss function to improve detection performance. Our method is evaluated on a real-world medical imaging dataset and outperforms relevant baselines that do not consider disagreements among annotators.
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Federated learning (FL) is an active area of research. One of the most suitable areas for adopting FL is the medical domain, where patient privacy must be respected. Previous research, however, does not provide a practical guide to applying FL in the medical domain. We propose empirical benchmarks and experimental settings for three representative medical datasets with different modalities: longitudinal electronic health records, skin cancer images, and electrocardiogram signals. The likely users of FL such as medical institutions and IT companies can take these benchmarks as guides for adopting FL and minimize their trial and error. For each dataset, each client data is from a different source to preserve real-world heterogeneity. We evaluate six FL algorithms designed for addressing data heterogeneity among clients, and a hybrid algorithm combining the strengths of two representative FL algorithms. Based on experiment results from three modalities, we discover that simple FL algorithms tend to outperform more sophisticated ones, while the hybrid algorithm consistently shows good, if not the best performance. We also find that a frequent global model update leads to better performance under a fixed training iteration budget. As the number of participating clients increases, higher cost is incurred due to increased IT administrators and GPUs, but the performance consistently increases. We expect future users will refer to these empirical benchmarks to design the FL experiments in the medical domain considering their clinical tasks and obtain stronger performance with lower costs.
Recent advances in deep learning-based medical image segmentation studies achieve nearly human-level performance in fully supervised manner. However, acquiring pixel-level expert annotations is extremely expensive and laborious in medical imaging fields. Unsupervised domain adaptation (UDA) can alleviate this problem, which makes it possible to use annotated data in one imaging modality to train a network that can successfully perform segmentation on target imaging modality with no labels. In this work, we propose SDC-UDA, a simple yet effective volumetric UDA framework for slice-direction continuous cross-modality medical image segmentation which combines intra- and inter-slice self-attentive image translation, uncertainty-constrained pseudo-label refinement, and volumetric self-training. Our method is distinguished from previous methods on UDA for medical image segmentation in that it can obtain continuous segmentation in the slice direction, thereby ensuring higher accuracy and potential in clinical practice. We validate SDC-UDA with multiple publicly available cross-modality medical image segmentation datasets and achieve state-of-the-art segmentation performance, not to mention the superior slice-direction continuity of prediction compared to previous studies.
Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model that is intended to segment user-defined objects of interest in an interactive manner. While the performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM's ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. We report the following findings: (1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM's performance generally improves only slightly while other methods' performance improves to the level that surpasses SAM's point-based performance. We also provide several illustrations for SAM's performance on all tested datasets, iterative segmentation, and SAM's behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it.
Link prediction problem has increasingly become prominent in many domains such as social network analyses, bioinformatics experiments, transportation networks, criminal investigations and so forth. A variety of techniques has been developed for link prediction problem, categorized into 1) similarity based approaches which study a set of features to extract similar nodes; 2) learning based approaches which extract patterns from the input data; 3) probabilistic statistical approaches which optimize a set of parameters to establish a model which can best compute formation probability. However, existing literatures lack approaches which utilize strength of each approach by integrating them to achieve a much more productive one. To tackle the link prediction problem, we propose an approach based on the combination of first and second group methods; the existing studied works use just one of these categories. Our two-phase developed method firstly determines new features related to the position and dynamic behavior of nodes, which enforce the approach more efficiency compared to approaches using mere measures. Then, a subspace clustering algorithm is applied to group social objects based on the computed similarity measures which differentiate the strength of clusters; basically, the usage of local and global indices and the clustering information plays an imperative role in our link prediction process. Some extensive experiments held on real datasets including Facebook, Brightkite and HepTh indicate good performances of our proposal method. Besides, we have experimentally verified our approach with some previous techniques in the area to prove the supremacy of ours.
Uncertainty quantification for inverse problems in imaging has drawn much attention lately. Existing approaches towards this task define uncertainty regions based on probable values per pixel, while ignoring spatial correlations within the image, resulting in an exaggerated volume of uncertainty. In this paper, we propose PUQ (Principal Uncertainty Quantification) -- a novel definition and corresponding analysis of uncertainty regions that takes into account spatial relationships within the image, thus providing reduced volume regions. Using recent advancements in stochastic generative models, we derive uncertainty intervals around principal components of the empirical posterior distribution, forming an ambiguity region that guarantees the inclusion of true unseen values with a user confidence probability. To improve computational efficiency and interpretability, we also guarantee the recovery of true unseen values using only a few principal directions, resulting in ultimately more informative uncertainty regions. Our approach is verified through experiments on image colorization, super-resolution, and inpainting; its effectiveness is shown through comparison to baseline methods, demonstrating significantly tighter uncertainty regions.
Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at //github.com/Arthur-Heng/NLGraph.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
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