Artificial intelligence (AI) models trained using medical images for clinical tasks often exhibit bias in the form of disparities in performance between subgroups. Since not all sources of biases in real-world medical imaging data are easily identifiable, it is challenging to comprehensively assess how those biases are encoded in models, and how capable bias mitigation methods are at ameliorating performance disparities. In this article, we introduce a novel analysis framework for systematically and objectively investigating the impact of biases in medical images on AI models. We developed and tested this framework for conducting controlled in silico trials to assess bias in medical imaging AI using a tool for generating synthetic magnetic resonance images with known disease effects and sources of bias. The feasibility is showcased by using three counterfactual bias scenarios to measure the impact of simulated bias effects on a convolutional neural network (CNN) classifier and the efficacy of three bias mitigation strategies. The analysis revealed that the simulated biases resulted in expected subgroup performance disparities when the CNN was trained on the synthetic datasets. Moreover, reweighing was identified as the most successful bias mitigation strategy for this setup, and we demonstrated how explainable AI methods can aid in investigating the manifestation of bias in the model using this framework. Developing fair AI models is a considerable challenge given that many and often unknown sources of biases can be present in medical imaging datasets. In this work, we present a novel methodology to objectively study the impact of biases and mitigation strategies on deep learning pipelines, which can support the development of clinical AI that is robust and responsible.
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Microring resonators (MRRs) are promising devices for time-delay photonic reservoir computing, but the impact of the different physical effects taking place in the MRRs on the reservoir computing performance is yet to be fully understood. We numerically analyze the impact of linear losses as well as thermo-optic and free-carrier effects relaxation times on the prediction error of the time-series task NARMA-10. We demonstrate the existence of three regions, defined by the input power and the frequency detuning between the optical source and the microring resonance, that reveal the cavity transition from linear to nonlinear regimes. One of these regions offers very low error in time-series prediction under relatively low input power and number of nodes while the other regions either lack nonlinearity or become unstable. This study provides insight into the design of the MRR and the optimization of its physical properties for improving the prediction performance of time-delay reservoir computing.
Applying pre-trained medical segmentation models on out-of-domain images often yields predictions of insufficient quality. Several strategies have been proposed to maintain model performance, such as finetuning or unsupervised- and source-free domain adaptation. These strategies set restrictive requirements for data availability. In this study, we propose to combine domain generalization and test-time adaptation to create a highly effective approach for reusing pre-trained models in unseen target domains. Domain-generalized pre-training on source data is used to obtain the best initial performance in the target domain. We introduce the MIND descriptor previously used in image registration tasks as a further technique to achieve generalization and present superior performance for small-scale datasets compared to existing approaches. At test-time, high-quality segmentation for every single unseen scan is ensured by optimizing the model weights for consistency given different image augmentations. That way, our method enables separate use of source and target data and thus removes current data availability barriers. Moreover, the presented method is highly modular as it does not require specific model architectures or prior knowledge of involved domains and labels. We demonstrate this by integrating it into the nnUNet, which is currently the most popular and accurate framework for medical image segmentation. We employ multiple datasets covering abdominal, cardiac, and lumbar spine scans and compose several out-of-domain scenarios in this study. We demonstrate that our method, combined with pre-trained whole-body CT models, can effectively segment MR images with high accuracy in all of the aforementioned scenarios. Open-source code can be found here: //github.com/multimodallearning/DG-TTA
As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current methods often make assumptions about the relations between data that may not be valid in practice. In response, we introduce SAVAE (Survival Analysis Variational Autoencoder), a novel approach based on Variational Autoencoders. SAVAE contributes significantly to the field by introducing a tailored ELBO formulation for survival analysis, supporting various parametric distributions for covariates and survival time (as long as the log-likelihood is differentiable). It offers a general method that consistently performs well on various metrics, demonstrating robustness and stability through different experiments. Our proposal effectively estimates time-to-event, accounting for censoring, covariate interactions, and time-varying risk associations. We validate our model in diverse datasets, including genomic, clinical, and demographic data, with varying levels of censoring. This approach demonstrates competitive performance compared to state-of-the-art techniques, as assessed by the Concordance Index and the Integrated Brier Score. SAVAE also offers an interpretable model that parametrically models covariates and time. Moreover, its generative architecture facilitates further applications such as clustering, data imputation, and the generation of synthetic patient data through latent space inference from survival data.
Text normalization is a crucial technology for low-resource languages which lack rigid spelling conventions or that have undergone multiple spelling reforms. Low-resource text normalization has so far relied upon hand-crafted rules, which are perceived to be more data efficient than neural methods. In this paper we examine the case of text normalization for Ligurian, an endangered Romance language. We collect 4,394 Ligurian sentences paired with their normalized versions, as well as the first open source monolingual corpus for Ligurian. We show that, in spite of the small amounts of data available, a compact transformer-based model can be trained to achieve very low error rates by the use of backtranslation and appropriate tokenization.
Cubic-quartic regularization models for solving polynomial subproblems in third-order tensor methods
High-order tensor methods for solving both convex and nonconvex optimization problems have generated significant research interest, leading to algorithms with optimal global rates of convergence and local rates that are faster than Newton's method. On each iteration, these methods require the unconstrained local minimization of a (potentially nonconvex) multivariate polynomial of degree higher than two, constructed using third-order (or higher) derivative information, and regularized by an appropriate power of regularization. Developing efficient techniques for solving such subproblems is an ongoing topic of research, and this paper addresses the case of the third-order tensor subproblem. We propose the CQR algorithmic framework, for minimizing a nonconvex Cubic multivariate polynomial with Quartic Regularisation, by minimizing a sequence of local quadratic models that incorporate simple cubic and quartic terms. The role of the cubic term is to crudely approximate local tensor information, while the quartic one controls model regularization and progress. We provide necessary and sufficient optimality conditions that fully characterise the global minimizers of these cubic-quartic models. We then turn these conditions into secular equations that can be solved using nonlinear eigenvalue techniques. We show, using our optimality characterisations, that a CQR algorithmic variant has the optimal-order evaluation complexity of $\mathcal{O}(\epsilon^{-3/2})$ when applied to minimizing our quartically-regularised cubic subproblem, which can be further improved in special cases. We propose practical CQR variants that use local tensor information to construct the local cubic-quartic models. We test these variants numerically and observe them to be competitive with ARC and other subproblem solvers on typical instances and even superior on ill-conditioned subproblems with special structure.
The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, if not better than, the original dense networks. Sparsity can reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.
Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: //github.com/Luoxd1996/DTC
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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