Purpose: To develop an open-source, fully-automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT) data. Methods: We used a dataset of 715 OCT B-scans (82 subjects, 115 eyes) from 3 clinical studies related to systemic disease. Ground truth segmentations were generated using a clinically validated, semi-automatic choroid segmentation method, Gaussian Process Edge Tracing (GPET). We finetuned a UNet with MobileNetV3 backbone pre-trained on ImageNet. Standard segmentation agreement metrics, as well as derived measures of choroidal thickness and area, were used to evaluate DeepGPET, alongside qualitative evaluation from a clinical ophthalmologist. Results: DeepGPET achieves excellent agreement with GPET on data from 3 clinical studies (AUC=0.9994, Dice=0.9664; Pearson correlation of 0.8908 for choroidal thickness and 0.9082 for choroidal area), while reducing the mean processing time per image on a standard laptop CPU from 34.49s ($\pm$15.09) using GPET to 1.25s ($\pm$0.10) using DeepGPET. Both methods performed similarly according to a clinical ophthalmologist, who qualitatively judged a subset of segmentations by GPET and DeepGPET, based on smoothness and accuracy of segmentations. Conclusions: DeepGPET, a fully-automatic, open-source algorithm for choroidal segmentation, will enable researchers to efficiently extract choroidal measurements, even for large datasets. As no manual interventions are required, DeepGPET is less subjective than semi-automatic methods and could be deployed in clinical practice without necessitating a trained operator.
With the increasing demand of intelligent systems capable of operating in different contexts (e.g. users on the move) the correct interpretation of the user-need by such systems has become crucial to give consistent answers to the user questions. The most effective applications addressing such task are in the fields of natural language processing and semantic expansion of terms. These techniques are aimed at estimating the goal of an input query reformulating it as an intent, commonly relying on textual resources built exploiting different semantic relations like \emph{synonymy}, \emph{antonymy} and many others. The aim of this paper is to generate such resources using the labels of a given taxonomy as source of information. The obtained resources are integrated into a plain classifier for reformulating a set of input queries as intents and tracking the effect of each relation, in order to quantify the impact of each semantic relation on the classification. As an extension to this, the best tradeoff between improvement and noise introduction when combining such relations is evaluated. The assessment is made generating the resources and their combinations and using them for tuning the classifier which is used to reformulate the user questions as labels. The evaluation employs a wide and varied taxonomy as a use-case, exploiting its labels as basis for the semantic expansion and producing several corpora with the purpose of enhancing the pseudo-queries estimation.
Dynamical systems across the sciences, from electrical circuits to ecological networks, undergo qualitative and often catastrophic changes in behavior, called bifurcations, when their underlying parameters cross a threshold. Existing methods predict oncoming catastrophes in individual systems but are primarily time-series-based and struggle both to categorize qualitative dynamical regimes across diverse systems and to generalize to real data. To address this challenge, we propose a data-driven, physically-informed deep-learning framework for classifying dynamical regimes and characterizing bifurcation boundaries based on the extraction of topologically invariant features. We focus on the paradigmatic case of the supercritical Hopf bifurcation, which is used to model periodic dynamics across a wide range of applications. Our convolutional attention method is trained with data augmentations that encourage the learning of topological invariants which can be used to detect bifurcation boundaries in unseen systems and to design models of biological systems like oscillatory gene regulatory networks. We further demonstrate our method's use in analyzing real data by recovering distinct proliferation and differentiation dynamics along pancreatic endocrinogenesis trajectory in gene expression space based on single-cell data. Our method provides valuable insights into the qualitative, long-term behavior of a wide range of dynamical systems, and can detect bifurcations or catastrophic transitions in large-scale physical and biological systems.
Compressed Sensing (CS) encompasses a broad array of theoretical and applied techniques for recovering signals, given partial knowledge of their coefficients. Its applications span various fields, including mathematics, physics, engineering, and several medical sciences. Motivated by our interest in the mathematics behind Magnetic Resonance Imaging (MRI) and CS, we employ convex analysis techniques to analytically determine equivalents of Lagrange multipliers for optimization problems with inequality constraints, specifically a weighted LASSO with voxel-wise weighting. We investigate this problem under assumptions on the fidelity term $\Vert{Ax-b}\Vert_2^2$, either concerning the sign of its gradient or orthogonality-like conditions of its matrix. To be more precise, we either require the sign of each coordinate of $2(Ax-b)^TA$ to be fixed within a rectangular neighborhood of the origin, with the side lengths of the rectangle dependent on the constraints, or we assume $A^TA$ to be diagonal. The objective of this work is to explore the relationship between Lagrange multipliers and the constraints of a weighted variant of LASSO, specifically in the mentioned cases where this relationship can be computed explicitly. As they scale the regularization terms of the weighted LASSO, Lagrange multipliers serve as tuning parameters for the weighted LASSO, prompting the question of their potential effective use as tuning parameters in applications like MR image reconstruction and denoising. This work represents an initial step in this direction.
A class of (block) rational Krylov subspace based projection method for solving large-scale continuous-time algebraic Riccati equation (CARE) $0 = \mathcal{R}(X) := A^HX + XA + C^HC - XBB^HX$ with a large, sparse $A$ and $B$ and $C$ of full low rank is proposed. The CARE is projected onto a block rational Krylov subspace $\mathcal{K}_j$ spanned by blocks of the form $(A^H+ s_kI)C^H$ for some shifts $s_k, k = 1, \ldots, j.$ The considered projections do not need to be orthogonal and are built from the matrices appearing in the block rational Arnoldi decomposition associated to $\mathcal{K}_j.$ The resulting projected Riccati equation is solved for the small square Hermitian $Y_j.$ Then the Hermitian low-rank approximation $X_j = Z_jY_jZ_j^H$ to $X$ is set up where the columns of $Z_j$ span $\mathcal{K}_j.$ The residual norm $\|R(X_j )\|_F$ can be computed efficiently via the norm of a readily available $2p \times 2p$ matrix. We suggest to reduce the rank of the approximate solution $X_j$ even further by truncating small eigenvalues from $X_j.$ This truncated approximate solution can be interpreted as the solution of the Riccati residual projected to a subspace of $\mathcal{K}_j.$ This gives us a way to efficiently evaluate the norm of the resulting residual. Numerical examples are presented.
Due to their intrinsic capabilities on parallel signal processing, optical neural networks (ONNs) have attracted extensive interests recently as a potential alternative to electronic artificial neural networks (ANNs) with reduced power consumption and low latency. Preliminary confirmation of the parallelism in optical computing has been widely done by applying the technology of wavelength division multiplexing (WDM) in the linear transformation part of neural networks. However, inter-channel crosstalk has obstructed WDM technologies to be deployed in nonlinear activation in ONNs. Here, we propose a universal WDM structure called multiplexed neuron sets (MNS) which apply WDM technologies to optical neurons and enable ONNs to be further compressed. A corresponding back-propagation (BP) training algorithm is proposed to alleviate or even cancel the influence of inter-channel crosstalk on MNS-based WDM-ONNs. For simplicity, semiconductor optical amplifiers (SOAs) are employed as an example of MNS to construct a WDM-ONN trained with the new algorithm. The result shows that the combination of MNS and the corresponding BP training algorithm significantly downsize the system and improve the energy efficiency to tens of times while giving similar performance to traditional ONNs.
Influenced mixed moving average fields are a versatile modeling class for spatio-temporal data. However, their predictive distribution is not generally known. Under this modeling assumption, we define a novel spatio-temporal embedding and a theory-guided machine learning approach that employs a generalized Bayesian algorithm to make ensemble forecasts. We employ Lipschitz predictors and determine fixed-time and any-time PAC Bayesian bounds in the batch learning setting. Performing causal forecast is a highlight of our methodology as its potential application to data with spatial and temporal short and long-range dependence. We then test the performance of our learning methodology by using linear predictors and data sets simulated from a spatio-temporal Ornstein-Uhlenbeck process.
Stochastic differential equation (SDE in short) solvers find numerous applications across various fields. However, in practical simulations, we usually resort to using Ito-Taylor series-based methods like the Euler-Maruyama method. These methods often suffer from the limitation of fixed time scales and recalculations for different Brownian motions, which lead to computational inefficiency, especially in generative and sampling models. To address these issues, we propose a novel approach: learning a mapping between the solution of SDE and corresponding Brownian motion. This mapping exhibits versatility across different scales and requires minimal paths for training. Specifically, we employ the DeepONet method to learn a nonlinear mapping. And we also assess the efficiency of this method through simulations conducted at varying time scales. Additionally, we evaluate its generalization performance to verify its good versatility in different scenarios.
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.
We derive information-theoretic generalization bounds for supervised learning algorithms based on the information contained in predictions rather than in the output of the training algorithm. These bounds improve over the existing information-theoretic bounds, are applicable to a wider range of algorithms, and solve two key challenges: (a) they give meaningful results for deterministic algorithms and (b) they are significantly easier to estimate. We show experimentally that the proposed bounds closely follow the generalization gap in practical scenarios for deep learning.
When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.