Deep Metric Learning Meets Deep Clustering: An Novel Unsupervised Approach for Feature Embedding

Unsupervised Deep Distance Metric Learning (UDML) aims to learn sample similarities in the embedding space from an unlabeled dataset. Traditional UDML methods usually use the triplet loss or pairwise loss which requires the mining of positive and negative samples w.r.t. anchor data points. This is, however, challenging in an unsupervised setting as the label information is not available. In this paper, we propose a new UDML method that overcomes that challenge. In particular, we propose to use a deep clustering loss to learn centroids, i.e., pseudo labels, that represent semantic classes. During learning, these centroids are also used to reconstruct the input samples. It hence ensures the representativeness of centroids - each centroid represents visually similar samples. Therefore, the centroids give information about positive (visually similar) and negative (visually dissimilar) samples. Based on pseudo labels, we propose a novel unsupervised metric loss which enforces the positive concentration and negative separation of samples in the embedding space. Experimental results on benchmarking datasets show that the proposed approach outperforms other UDML methods.

Self-supervised Depth Estimation to Regularise Semantic Segmentation in Knee Arthroscopy

Intra-operative automatic semantic segmentation of knee joint structures can assist surgeons during knee arthroscopy in terms of situational awareness. However, due to poor imaging conditions (e.g., low texture, overexposure, etc.), automatic semantic segmentation is a challenging scenario, which justifies the scarce literature on this topic. In this paper, we propose a novel self-supervised monocular depth estimation to regularise the training of the semantic segmentation in knee arthroscopy. To further regularise the depth estimation, we propose the use of clean training images captured by the stereo arthroscope of routine objects (presenting none of the poor imaging conditions and with rich texture information) to pre-train the model. We fine-tune such model to produce both the semantic segmentation and self-supervised monocular depth using stereo arthroscopic images taken from inside the knee. Using a data set containing 3868 arthroscopic images captured during cadaveric knee arthroscopy with semantic segmentation annotations, 2000 stereo image pairs of cadaveric knee arthroscopy, and 2150 stereo image pairs of routine objects, we show that our semantic segmentation regularised by self-supervised depth estimation produces a more accurate segmentation than a state-of-the-art semantic segmentation approach modeled exclusively with semantic segmentation annotation.

Few-Shot Microscopy Image Cell Segmentation

Automatic cell segmentation in microscopy images works well with the support of deep neural networks trained with full supervision. Collecting and annotating images, though, is not a sustainable solution for every new microscopy database and cell type. Instead, we assume that we can access a plethora of annotated image data sets from different domains (sources) and a limited number of annotated image data sets from the domain of interest (target), where each domain denotes not only different image appearance but also a different type of cell segmentation problem. We pose this problem as meta-learning where the goal is to learn a generic and adaptable few-shot learning model from the available source domain data sets and cell segmentation tasks. The model can be afterwards fine-tuned on the few annotated images of the target domain that contains different image appearance and different cell type. In our meta-learning training, we propose the combination of three objective functions to segment the cells, move the segmentation results away from the classification boundary using cross-domain tasks, and learn an invariant representation between tasks of the source domains. Our experiments on five public databases show promising results from 1- to 10-shot meta-learning using standard segmentation neural network architectures.

Few-Shot Anomaly Detection for Polyp Frames from Colonoscopy

Anomaly detection methods generally target the learning of a normal image distribution (i.e., inliers showing healthy cases) and during testing, samples relatively far from the learned distribution are classified as anomalies (i.e., outliers showing disease cases). These approaches tend to be sensitive to outliers that lie relatively close to inliers (e.g., a colonoscopy image with a small polyp). In this paper, we address the inappropriate sensitivity to outliers by also learning from inliers. We propose a new few-shot anomaly detection method based on an encoder trained to maximise the mutual information between feature embeddings and normal images, followed by a few-shot score inference network, trained with a large set of inliers and a substantially smaller set of outliers. We evaluate our proposed method on the clinical problem of detecting frames containing polyps from colonoscopy video sequences, where the training set has 13350 normal images (i.e., without polyps) and less than 100 abnormal images (i.e., with polyps). The results of our proposed model on this data set reveal a state-of-the-art detection result, while the performance based on different number of anomaly samples is relatively stable after approximately 40 abnormal training images.

Region Proposals for Saliency Map Refinement for Weakly-supervised Disease Localisation and Classification

The deployment of automated systems to diagnose diseases from medical images is challenged by the requirement to localise the diagnosed diseases to justify or explain the classification decision. This requirement is hard to fulfil because most of the training sets available to develop these systems only contain global annotations, making the localisation of diseases a weakly supervised approach. The main methods designed for weakly supervised disease classification and localisation rely on saliency or attention maps that are not specifically trained for localisation, or on region proposals that can not be refined to produce accurate detections. In this paper, we introduce a new model that combines region proposal and saliency detection to overcome both limitations for weakly supervised disease classification and localisation. Using the ChestX-ray14 data set, we show that our proposed model establishes the new state-of-the-art for weakly-supervised disease diagnosis and localisation.

Self-supervised Monocular Trained Depth Estimation using Self-attention and Discrete Disparity Volume

Monocular depth estimation has become one of the most studied applications in computer vision, where the most accurate approaches are based on fully supervised learning models. However, the acquisition of accurate and large ground truth data sets to model these fully supervised methods is a major challenge for the further development of the area. Self-supervised methods trained with monocular videos constitute one the most promising approaches to mitigate the challenge mentioned above due to the wide-spread availability of training data. Consequently, they have been intensively studied, where the main ideas explored consist of different types of model architectures, loss functions, and occlusion masks to address non-rigid motion. In this paper, we propose two new ideas to improve self-supervised monocular trained depth estimation: 1) self-attention, and 2) discrete disparity prediction. Compared with the usual localised convolution operation, self-attention can explore a more general contextual information that allows the inference of similar disparity values at non-contiguous regions of the image. Discrete disparity prediction has been shown by fully supervised methods to provide a more robust and sharper depth estimation than the more common continuous disparity prediction, besides enabling the estimation of depth uncertainty. We show that the extension of the state-of-the-art self-supervised monocular trained depth estimator Monodepth2 with these two ideas allows us to design a model that produces the best results in the field in KITTI 2015 and Make3D, closing the gap with respect self-supervised stereo training and fully supervised approaches.

PAC-Bayesian Meta-learning with Implicit Prior

We introduce a new and rigorously-formulated PAC-Bayes few-shot meta-learning algorithm that implicitly learns a prior distribution of the model of interest. Our proposed method extends the PAC-Bayes framework from a single task setting to the few-shot learning setting to upper-bound generalisation errors on unseen tasks and samples. We also propose a generative-based approach to model the shared prior and the posterior of task-specific model parameters more expressively compared to the usual diagonal Gaussian assumption. We show that the models trained with our proposed meta-learning algorithm are well calibrated and accurate, with state-of-the-art calibration and classification results on few-shot classification (mini-ImageNet and tiered-ImageNet) and regression (multi-modal task-distribution regression) benchmarks.

Semi-supervised Multi-domain Multi-task Training for Metastatic Colon Lymph Node Diagnosis From Abdominal CT

The diagnosis of the presence of metastatic lymph nodes from abdominal computed tomography (CT) scans is an essential task performed by radiologists to guide radiation and chemotherapy treatment. State-of-the-art deep learning classifiers trained for this task usually rely on a training set containing CT volumes and their respective image-level (i.e., global) annotation. However, the lack of annotations for the localisation of the regions of interest (ROIs) containing lymph nodes can limit classification accuracy due to the small size of the relevant ROIs in this problem. The use of lymph node ROIs together with global annotations in a multi-task training process has the potential to improve classification accuracy, but the high cost involved in obtaining the ROI annotation for the same samples that have global annotations is a roadblock for this alternative. We address this limitation by introducing a new training strategy from two data sets: one containing the global annotations, and another (publicly available) containing only the lymph node ROI localisation. We term our new strategy semi-supervised multi-domain multi-task training, where the goal is to improve the diagnosis accuracy on the globally annotated data set by incorporating the ROI annotations from a different domain. Using a private data set containing global annotations and a public data set containing lymph node ROI localisation, we show that our proposed training mechanism improves the area under the ROC curve for the classification task compared to several training method baselines.

Photoshopping Colonoscopy Video Frames

The automatic detection of frames containing polyps from a colonoscopy video sequence is an important first step for a fully automated colonoscopy analysis tool. Typically, such detection system is built using a large annotated data set of frames with and without polyps, which is expensive to be obtained. In this paper, we introduce a new system that detects frames containing polyps as anomalies from a distribution of frames from exams that do not contain any polyps. The system is trained using a one-class training set consisting of colonoscopy frames without polyps -- such training set is considerably less expensive to obtain, compared to the 2-class data set mentioned above. During inference, the system is only able to reconstruct frames without polyps, and when it tries to reconstruct a frame with polyp, it automatically removes (i.e., photoshop) it from the frame -- the difference between the input and reconstructed frames is used to detect frames with polyps. We name our proposed model as anomaly detection generative adversarial network (ADGAN), comprising a dual GAN with two generators and two discriminators. We show that our proposed approach achieves the state-of-the-art result on this data set, compared with recently proposed anomaly detection systems.

Hidden Stratification Causes Clinically Meaningful Failures in Machine Learning for Medical Imaging

Machine learning models for medical image analysis often suffer from poor performance on important subsets of a population that are not identified during training or testing. For example, overall performance of a cancer detection model may be high, but the model still consistently misses a rare but aggressive cancer subtype. We refer to this problem as hidden stratification, and observe that it results from incompletely describing the meaningful variation in a dataset. While hidden stratification can substantially reduce the clinical efficacy of machine learning models, its effects remain difficult to measure. In this work, we assess the utility of several possible techniques for measuring and describing hidden stratification effects, and characterize these effects both on multiple medical imaging datasets and via synthetic experiments on the well-characterised CIFAR-100 benchmark dataset. We find evidence that hidden stratification can occur in unidentified imaging subsets with low prevalence, low label quality, subtle distinguishing features, or spurious correlates, and that it can result in relative performance differences of over 20% on clinically important subsets. Finally, we explore the clinical implications of our findings, and suggest that evaluation of hidden stratification should be a critical component of any machine learning deployment in medical imaging.