Artificial intelligence (AI), machine learning, and deep learning (DL) methods are becoming increasingly important in the field of biomedical image analysis. However, to exploit the full potential of such methods, a representative number of experimentally acquired images containing a significant number of manually annotated objects is needed as training data. Here we introduce SYNTA (synthetic data) as a novel approach for the generation of synthetic, photo-realistic, and highly complex biomedical images as training data for DL systems. We show the versatility of our approach in the context of muscle fiber and connective tissue analysis in histological sections. We demonstrate that it is possible to perform robust and expert-level segmentation tasks on previously unseen real-world data, without the need for manual annotations using synthetic training data alone. Being a fully parametric technique, our approach poses an interpretable and controllable alternative to Generative Adversarial Networks (GANs) and has the potential to significantly accelerate quantitative image analysis in a variety of biomedical applications in microscopy and beyond.
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Diffusion probabilistic models (DPMs) have rapidly evolved to be one of the predominant generative models for the simulation of synthetic data, for instance, for computer vision, audio, natural language processing, or biomolecule generation. Here, we propose using DPMs for the generation of synthetic individual location trajectories (ILTs) which are sequences of variables representing physical locations visited by individuals. ILTs are of major importance in mobility research to understand the mobility behavior of populations and to ultimately inform political decision-making. We represent ILTs as multi-dimensional categorical random variables and propose to model their joint distribution using a continuous DPM by first applying the diffusion process in a continuous unconstrained space and then mapping the continuous variables into a discrete space. We demonstrate that our model can synthesize realistic ILPs by comparing conditionally and unconditionally generated sequences to real-world ILPs from a GNSS tracking data set which suggests the potential use of our model for synthetic data generation, for example, for benchmarking models used in mobility research.
A major challenge in computed tomography is reconstructing objects from incomplete data. An increasingly popular solution for these problems is to incorporate deep learning models into reconstruction algorithms. This study introduces a novel approach by integrating a Fourier neural operator (FNO) into the Filtered Backprojection (FBP) reconstruction method, yielding the FNO back projection (FNO-BP) network. We employ moment conditions for sinogram extrapolation to assist the model in mitigating artefacts from limited data. Notably, our deep learning architecture maintains a runtime comparable to classical filtered back projection (FBP) reconstructions, ensuring swift performance during both inference and training. We assess our reconstruction method in the context of the Helsinki Tomography Challenge 2022 and also compare it against regular FBP methods.
Continual learning algorithms strive to acquire new knowledge while preserving prior information. Often, these algorithms emphasise stability and restrict network updates upon learning new tasks. In many cases, such restrictions come at a cost to the model's plasticity, i.e. the model's ability to adapt to the requirements of a new task. But is all change detrimental? Here, we approach this question by proposing that activation spaces in neural networks can be decomposed into two subspaces: a readout range in which change affects prior tasks and a null space in which change does not alter prior performance. Based on experiments with this novel technique, we show that, indeed, not all activation change is associated with forgetting. Instead, the only change in the subspace visible to the readout of a task can lead to decreased stability, while restricting change outside of this subspace is associated only with a loss of plasticity. Analysing various commonly used algorithms, we show that regularisation-based techniques do not fully disentangle the two spaces and, as a result, restrict plasticity more than need be. We expand our results by investigating a linear model in which we can manipulate learning in the two subspaces directly and thus causally link activation changes to stability and plasticity. For hierarchical, nonlinear cases, we present an approximation that enables us to estimate functionally relevant subspaces at every layer of a deep nonlinear network, corroborating our previous insights. Together, this work provides novel means to derive insights into the mechanisms behind stability and plasticity in continual learning and may serve as a diagnostic tool to guide developments of future continual learning algorithms that stabilise inference while allowing maximal space for learning.
Federated Learning is a machine learning approach that enables the training of a deep learning model among several participants with sensitive data that wish to share their own knowledge without compromising the privacy of their data. In this research, the authors employ a secured Federated Learning method with an additional layer of privacy and proposes a method for addressing the non-IID challenge. Moreover, differential privacy is compared with chaotic-based encryption as layer of privacy. The experimental approach assesses the performance of the federated deep learning model with differential privacy using both IID and non-IID data. In each experiment, the Federated Learning process improves the average performance metrics of the deep neural network, even in the case of non-IID data.
In recent years, Scientific Machine Learning (SciML) methods for solving partial differential equations (PDEs) have gained increasing popularity. Within such a paradigm, Physics-Informed Neural Networks (PINNs) are novel deep learning frameworks for solving initial-boundary value problems involving nonlinear PDEs. Recently, PINNs have shown promising results in several application fields. Motivated by applications to gas filtration problems, here we present and evaluate a PINN-based approach to predict solutions to strongly degenerate parabolic problems with asymptotic structure of Laplacian type. To the best of our knowledge, this is one of the first papers demonstrating the efficacy of the PINN framework for solving such kind of problems. In particular, we estimate an appropriate approximation error for some test problems whose analytical solutions are fortunately known. The numerical experiments discussed include two and three-dimensional spatial domains, emphasizing the effectiveness of this approach in predicting accurate solutions.
The singular value decomposition (SVD) is a crucial tool in machine learning and statistical data analysis. However, it is highly susceptible to outliers in the data matrix. Existing robust SVD algorithms often sacrifice speed for robustness or fail in the presence of only a few outliers. This study introduces an efficient algorithm, called Spherically Normalized SVD, for robust SVD approximation that is highly insensitive to outliers, computationally scalable, and provides accurate approximations of singular vectors. The proposed algorithm achieves remarkable speed by utilizing only two applications of a standard reduced-rank SVD algorithm to appropriately scaled data, significantly outperforming competing algorithms in computation times. To assess the robustness of the approximated singular vectors and their subspaces against data contamination, we introduce new notions of breakdown points for matrix-valued input, including row-wise, column-wise, and block-wise breakdown points. Theoretical and empirical analyses demonstrate that our algorithm exhibits higher breakdown points compared to standard SVD and its modifications. We empirically validate the effectiveness of our approach in applications such as robust low-rank approximation and robust principal component analysis of high-dimensional microarray datasets. Overall, our study presents a highly efficient and robust solution for SVD approximation that overcomes the limitations of existing algorithms in the presence of outliers.
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.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
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.
Machine-learning models have demonstrated great success in learning complex patterns that enable them to make predictions about unobserved data. In addition to using models for prediction, the ability to interpret what a model has learned is receiving an increasing amount of attention. However, this increased focus has led to considerable confusion about the notion of interpretability. In particular, it is unclear how the wide array of proposed interpretation methods are related, and what common concepts can be used to evaluate them. We aim to address these concerns by defining interpretability in the context of machine learning and introducing the Predictive, Descriptive, Relevant (PDR) framework for discussing interpretations. The PDR framework provides three overarching desiderata for evaluation: predictive accuracy, descriptive accuracy and relevancy, with relevancy judged relative to a human audience. Moreover, to help manage the deluge of interpretation methods, we introduce a categorization of existing techniques into model-based and post-hoc categories, with sub-groups including sparsity, modularity and simulatability. To demonstrate how practitioners can use the PDR framework to evaluate and understand interpretations, we provide numerous real-world examples. These examples highlight the often under-appreciated role played by human audiences in discussions of interpretability. Finally, based on our framework, we discuss limitations of existing methods and directions for future work. We hope that this work will provide a common vocabulary that will make it easier for both practitioners and researchers to discuss and choose from the full range of interpretation methods.
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