This paper explores methods for extracting information from radiology reports that generalize across exam modalities to reduce requirements for annotated data. We demonstrate that multi-pass T5-based text-to-text generative models exhibit better generalization across exam modalities compared to approaches that employ BERT-based task-specific classification layers. We then develop methods that reduce the inference cost of the model, making large-scale corpus processing more feasible for clinical applications. Specifically, we introduce a generative technique that decomposes complex tasks into smaller subtask blocks, which improves a single-pass model when combined with multitask training. In addition, we leverage target-domain contexts during inference to enhance domain adaptation, enabling use of smaller models. Analyses offer insights into the benefits of different cost reduction strategies.
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This study focuses on comparing deep learning methods for the segmentation and quantification of uncertainty in prostate segmentation from MRI images. The aim is to improve the workflow of prostate cancer detection and diagnosis. Seven different U-Net-based architectures, augmented with Monte-Carlo dropout, are evaluated for automatic segmentation of the central zone, peripheral zone, transition zone, and tumor, with uncertainty estimation. The top-performing model in this study is the Attention R2U-Net, achieving a mean Intersection over Union (IoU) of 76.3% and Dice Similarity Coefficient (DSC) of 85% for segmenting all zones. Additionally, Attention R2U-Net exhibits the lowest uncertainty values, particularly in the boundaries of the transition zone and tumor, when compared to the other models.
In this research, we investigate the possibility of applying a search strategy to genetic algorithms to explore the entire genetic tree structure. Several methods aid in performing tree searches; however, simpler algorithms such as breadth-first, depth-first, and iterative techniques are computation-heavy and often result in a long execution time. Adversarial techniques are often the preferred mechanism when performing a probabilistic search, yielding optimal results more quickly. The problem we are trying to tackle in this paper is the optimization of neural networks using genetic algorithms. Genetic algorithms (GA) form a tree of possible states and provide a mechanism for rewards via the fitness function. Monte Carlo Tree Search (MCTS) has proven to be an effective tree search strategy given states and rewards; therefore, we will combine these approaches to optimally search for the best result generated with genetic algorithms.
Particle methods based on evolving the spatial derivatives of the solution were originally introduced to simulate reaction-diffusion processes, inspired by vortex methods for the Navier--Stokes equations. Such methods, referred to as gradient random walk methods, were extensively studied in the '90s and have several interesting features, such as being grid free, automatically adapting to the solution by concentrating elements where the gradient is large and significantly reducing the variance of the standard random walk approach. In this work, we revive these ideas by showing how to generalize the approach to a larger class of partial differential equations, including hyperbolic systems of conservation laws. To achieve this goal, we first extend the classical Monte Carlo method to relaxation approximation of systems of conservation laws, and subsequently consider a novel particle dynamics based on the spatial derivatives of the solution. The methodology, combined with asymptotic-preserving splitting discretization, yields a way to construct a new class of gradient-based Monte Carlo methods for hyperbolic systems of conservation laws. Several results in one spatial dimension for scalar equations and systems of conservation laws show that the new methods are very promising and yield remarkable improvements compared to standard Monte Carlo approaches, either in terms of variance reduction as well as in describing the shock structure.
The purpose of this paper is to introduce a new numerical method to solve multi-marginal optimal transport problems with pairwise interaction costs. The complexity of multi-marginal optimal transport generally scales exponentially in the number of marginals $m$. We introduce a one parameter family of cost functions that interpolates between the original and a special cost function for which the problem's complexity scales linearly in $m$. We then show that the solution to the original problem can be recovered by solving an ordinary differential equation in the parameter $\epsilon$, whose initial condition corresponds to the solution for the special cost function mentioned above; we then present some simulations, using both explicit Euler and explicit higher order Runge-Kutta schemes to compute solutions to the ODE, and, as a result, the multi-marginal optimal transport problem.
Kinetic approaches are generally accurate in dealing with microscale plasma physics problems but are computationally expensive for large-scale or multiscale systems. One of the long-standing problems in plasma physics is the integration of kinetic physics into fluid models, which is often achieved through sophisticated analytical closure terms. In this paper, we successfully construct a multi-moment fluid model with an implicit fluid closure included in the neural network using machine learning. The multi-moment fluid model is trained with a small fraction of sparsely sampled data from kinetic simulations of Landau damping, using the physics-informed neural network (PINN) and the gradient-enhanced physics-informed neural network (gPINN). The multi-moment fluid model constructed using either PINN or gPINN reproduces the time evolution of the electric field energy, including its damping rate, and the plasma dynamics from the kinetic simulations. In addition, we introduce a variant of the gPINN architecture, namely, gPINN$p$ to capture the Landau damping process. Instead of including the gradients of all the equation residuals, gPINN$p$ only adds the gradient of the pressure equation residual as one additional constraint. Among the three approaches, the gPINN$p$-constructed multi-moment fluid model offers the most accurate results. This work sheds light on the accurate and efficient modeling of large-scale systems, which can be extended to complex multiscale laboratory, space, and astrophysical plasma physics problems.
To understand the ability and limitations of convolutional neural networks to generate time series that mimic complex temporal signals, we trained a generative adversarial network consisting of deep convolutional networks to generate chaotic time series and used nonlinear time series analysis to evaluate the generated time series. A numerical measure of determinism and the Lyapunov exponent, a measure of trajectory instability, showed that the generated time series well reproduce the chaotic properties of the original time series. However, error distribution analyses showed that large errors appeared at a low but non-negligible rate. Such errors would not be expected if the distribution were assumed to be exponential.
Hemodynamic velocity fields in coronary arteries could be the basis of valuable biomarkers for diagnosis, prognosis and treatment planning in cardiovascular disease. Velocity fields are typically obtained from patient-specific 3D artery models via computational fluid dynamics (CFD). However, CFD simulation requires meticulous setup by experts and is time-intensive, which hinders large-scale acceptance in clinical practice. To address this, we propose graph neural networks (GNN) as an efficient black-box surrogate method to estimate 3D velocity fields mapped to the vertices of tetrahedral meshes of the artery lumen. We train these GNNs on synthetic artery models and CFD-based ground truth velocity fields. Once the GNN is trained, velocity estimates in a new and unseen artery can be obtained with 36-fold speed-up compared to CFD. We demonstrate how to construct an SE(3)-equivariant GNN that is independent of the spatial orientation of the input mesh and show how this reduces the necessary amount of training data compared to a baseline neural network.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
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.
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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