arXiv subjects

Matthew B. Blaschko

Publications and source records attributed to Matthew B. Blaschko.

At least 55 records · Page 3Linked to original sources

arXiv2023

Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at \url{https://github.com/Oulu-IMEDS/CLIMATv2}.

eess.IV↗

arXiv2023

Dense Transformer based Enhanced Coding Network for Unsupervised Metal Artifact Reduction

CT images corrupted by metal artifacts have serious negative effects on clinical diagnosis. Considering the difficulty of collecting paired data with ground truth in clinical settings, unsupervised methods for metal artifact reduction are of high interest. However, it is difficult for previous unsupervised methods to retain structural information from CT images while handling the non-local characteristics of metal artifacts. To address these challenges, we proposed a novel Dense Transformer based Enhanced Coding Network (DTEC-Net) for unsupervised metal artifact reduction. Specifically, we introduce a Hierarchical Disentangling Encoder, supported by the high-order dense process, and transformer to obtain densely encoded sequences with long-range correspondence. Then, we present a second-order disentanglement method to improve the dense sequence's decoding process. Extensive experiments and model discussions illustrate DTEC-Net's effectiveness, which outperforms the previous state-of-the-art methods on a benchmark dataset, and greatly reduces metal artifacts while restoring richer texture details.

cs.CV↗

arXiv2023

Improving Differentially Private SGD via Randomly Sparsified Gradients

Differentially private stochastic gradient descent (DP-SGD) has been widely adopted in deep learning to provide rigorously defined privacy, which requires gradient clipping to bound the maximum norm of individual gradients and additive isotropic Gaussian noise. With analysis of the convergence rate of DP-SGD in a non-convex setting, we identify that randomly sparsifying gradients before clipping and noisification adjusts a trade-off between internal components of the convergence bound and leads to a smaller upper bound when the noise is dominant. Additionally, our theoretical analysis and empirical evaluations show that the trade-off is not trivial but possibly a unique property of DP-SGD, as either canceling noisification or gradient clipping eliminates the trade-off in the bound. This observation is indicative, as it implies DP-SGD has special inherent room for (even simply random) gradient compression. To verify the observation and utilize it, we propose an efficient and lightweight extension using random sparsification (RS) to strengthen DP-SGD. Experiments with various DP-SGD frameworks show that RS can improve performance. Additionally, the produced sparse gradients of RS exhibit advantages in reducing communication cost and strengthening privacy against reconstruction attacks, which are also key problems in private machine learning.

cs.LG↗

arXiv2023

Surrogate Model Extension (SME): A Fast and Accurate Weight Update Attack on Federated Learning

In Federated Learning (FL) and many other distributed training frameworks, collaborators can hold their private data locally and only share the network weights trained with the local data after multiple iterations. Gradient inversion is a family of privacy attacks that recovers data from its generated gradients. Seemingly, FL can provide a degree of protection against gradient inversion attacks on weight updates, since the gradient of a single step is concealed by the accumulation of gradients over multiple local iterations. In this work, we propose a principled way to extend gradient inversion attacks to weight updates in FL, thereby better exposing weaknesses in the presumed privacy protection inherent in FL. In particular, we propose a surrogate model method based on the characteristic of two-dimensional gradient flow and low-rank property of local updates. Our method largely boosts the ability of gradient inversion attacks on weight updates containing many iterations and achieves state-of-the-art (SOTA) performance. Additionally, our method runs up to $100\times$ faster than the SOTA baseline in the common FL scenario. Our work re-evaluates and highlights the privacy risk of sharing network weights. Our code is available at https://github.com/JunyiZhu-AI/surrogate_model_extension.

cs.LG↗

arXiv2023

Confidence-aware Personalized Federated Learning via Variational Expectation Maximization

Federated Learning (FL) is a distributed learning scheme to train a shared model across clients. One common and fundamental challenge in FL is that the sets of data across clients could be non-identically distributed and have different sizes. Personalized Federated Learning (PFL) attempts to solve this challenge via locally adapted models. In this work, we present a novel framework for PFL based on hierarchical Bayesian modeling and variational inference. A global model is introduced as a latent variable to augment the joint distribution of clients' parameters and capture the common trends of different clients, optimization is derived based on the principle of maximizing the marginal likelihood and conducted using variational expectation maximization. Our algorithm gives rise to a closed-form estimation of a confidence value which comprises the uncertainty of clients' parameters and local model deviations from the global model. The confidence value is used to weigh clients' parameters in the aggregation stage and adjust the regularization effect of the global model. We evaluate our method through extensive empirical studies on multiple datasets. Experimental results show that our approach obtains competitive results under mild heterogeneous circumstances while significantly outperforming state-of-the-art PFL frameworks in highly heterogeneous settings. Our code is available at https://github.com/JunyiZhu-AI/confidence_aware_PFL.

cs.LG↗

arXiv2022

A Consistent and Differentiable Lp Canonical Calibration Error Estimator

Calibrated probabilistic classifiers are models whose predicted probabilities can directly be interpreted as uncertainty estimates. It has been shown recently that deep neural networks are poorly calibrated and tend to output overconfident predictions. As a remedy, we propose a low-bias, trainable calibration error estimator based on Dirichlet kernel density estimates, which asymptotically converges to the true $L_p$ calibration error. This novel estimator enables us to tackle the strongest notion of multiclass calibration, called canonical (or distribution) calibration, while other common calibration methods are tractable only for top-label and marginal calibration. The computational complexity of our estimator is $\mathcal{O}(n^2)$, the convergence rate is $\mathcal{O}(n^{-1/2})$, and it is unbiased up to $\mathcal{O}(n^{-2})$, achieved by a geometric series debiasing scheme. In practice, this means that the estimator can be applied to small subsets of data, enabling efficient estimation and mini-batch updates. The proposed method has a natural choice of kernel, and can be used to generate consistent estimates of other quantities based on conditional expectation, such as the sharpness of a probabilistic classifier. Empirical results validate the correctness of our estimator, and demonstrate its utility in canonical calibration error estimation and calibration error regularized risk minimization.

stat.ML↗

arXiv2022

On confidence intervals for precision matrices and the eigendecomposition of covariance matrices

The eigendecomposition of a matrix is the central procedure in probabilistic models based on matrix factorization, for instance principal component analysis and topic models. Quantifying the uncertainty of such a decomposition based on a finite sample estimate is essential to reasoning under uncertainty when employing such models. This paper tackles the challenge of computing confidence bounds on the individual entries of eigenvectors of a covariance matrix of fixed dimension. Moreover, we derive a method to bound the entries of the inverse covariance matrix, the so-called precision matrix. The assumptions behind our method are minimal and require that the covariance matrix exists, and its empirical estimator converges to the true covariance. We make use of the theory of U-statistics to bound the $L_2$ perturbation of the empirical covariance matrix. From this result, we obtain bounds on the eigenvectors using Weyl's theorem and the eigenvalue-eigenvector identity and we derive confidence intervals on the entries of the precision matrix using matrix inversion perturbation bounds. As an application of these results, we demonstrate a new statistical test, which allows us to test for non-zero values of the precision matrix. We compare this test to the well-known Fisher-z test for partial correlations, and demonstrate the soundness and scalability of the proposed statistical test, as well as its application to real-world data from medical and physics domains.

math.ST↗

arXiv2022

MRF-UNets: Searching UNet with Markov Random Fields

UNet [27] is widely used in semantic segmentation due to its simplicity and effectiveness. However, its manually-designed architecture is applied to a large number of problem settings, either with no architecture optimizations, or with manual tuning, which is time consuming and can be sub-optimal. In this work, firstly, we propose Markov Random Field Neural Architecture Search (MRF-NAS) that extends and improves the recent Adaptive and Optimal Network Width Search (AOWS) method [4] with (i) a more general MRF framework (ii) diverse M-best loopy inference (iii) differentiable parameter learning. This provides the necessary NAS framework to efficiently explore network architectures that induce loopy inference graphs, including loops that arise from skip connections. With UNet as the backbone, we find an architecture, MRF-UNet, that shows several interesting characteristics. Secondly, through the lens of these characteristics, we identify the sub-optimality of the original UNet architecture and further improve our results with MRF-UNetV2. Experiments show that our MRF-UNets significantly outperform several benchmarks on three aerial image datasets and two medical image datasets while maintaining low computational costs. The code is available at: https://github.com/zifuwanggg/MRF-UNets.

cs.LG↗

arXiv2022

Greedy Bayesian Posterior Approximation with Deep Ensembles

Ensembles of independently trained neural networks are a state-of-the-art approach to estimate predictive uncertainty in Deep Learning, and can be interpreted as an approximation of the posterior distribution via a mixture of delta functions. The training of ensembles relies on non-convexity of the loss landscape and random initialization of their individual members, making the resulting posterior approximation uncontrolled. This paper proposes a novel and principled method to tackle this limitation, minimizing an $f$-divergence between the true posterior and a kernel density estimator (KDE) in a function space. We analyze this objective from a combinatorial point of view, and show that it is submodular with respect to mixture components for any $f$. Subsequently, we consider the problem of greedy ensemble construction. From the marginal gain on the negative $f$-divergence, which quantifies an improvement in posterior approximation yielded by adding a new component into the KDE, we derive a novel diversity term for ensemble methods. The performance of our approach is demonstrated on computer vision out-of-distribution detection benchmarks in a range of architectures trained on multiple datasets. The source code of our method is made publicly available at https://github.com/Oulu-IMEDS/greedy_ensembles_training.

cs.LG↗

arXiv2022

Designing MacPherson Suspension Architectures using Bayesian Optimization

Engineering design is traditionally performed by hand: an expert makes design proposals based on past experience, and these proposals are then tested for compliance with certain target specifications. Testing for compliance is performed first by computer simulation using what is called a discipline model. Such a model can be implemented by a finite element analysis, multibody systems approach, etc. Designs passing this simulation are then considered for physical prototyping. The overall process may take months, and is a significant cost in practice. We have developed a Bayesian optimization system for partially automating this process by directly optimizing compliance with the target specification with respect to the design parameters. The proposed method is a general framework for computing a generalized inverse of a high-dimensional non-linear function that does not require e.g. gradient information, which is often unavailable from discipline models. We furthermore develop a two-tier convergence criterion based on (i) convergence to a solution optimally satisfying all specified design criteria, or (ii) convergence to a minimum-norm solution. We demonstrate the proposed approach on a vehicle chassis design problem motivated by an industry setting using a state-of-the-art commercial discipline model. We show that the proposed approach is general, scalable, and efficient, and that the novel convergence criteria can be implemented straightforwardly based on existing concepts and subroutines in popular Bayesian optimization software packages.

cs.LG↗

arXiv2022

Combinatorial optimization for low bit-width neural networks

Low-bit width neural networks have been extensively explored for deployment on edge devices to reduce computational resources. Existing approaches have focused on gradient-based optimization in a two-stage train-and-compress setting or as a combined optimization where gradients are quantized during training. Such schemes require high-performance hardware during the training phase and usually store an equivalent number of full-precision weights apart from the quantized weights. In this paper, we explore methods of direct combinatorial optimization in the problem of risk minimization with binary weights, which can be made equivalent to a non-monotone submodular maximization under certain conditions. We employ an approximation algorithm for the cases with single and multilayer neural networks. For linear models, it has $\mathcal{O}(nd)$ time complexity where $n$ is the sample size and $d$ is the data dimension. We show that a combination of greedy coordinate descent and this novel approach can attain competitive accuracy on binary classification tasks.

cs.LG↗

arXiv2021

On the relationship between calibrated predictors and unbiased volume estimation

Machine learning driven medical image segmentation has become standard in medical image analysis. However, deep learning models are prone to overconfident predictions. This has led to a renewed focus on calibrated predictions in the medical imaging and broader machine learning communities. Calibrated predictions are estimates of the probability of a label that correspond to the true expected value of the label conditioned on the confidence. Such calibrated predictions have utility in a range of medical imaging applications, including surgical planning under uncertainty and active learning systems. At the same time it is often an accurate volume measurement that is of real importance for many medical applications. This work investigates the relationship between model calibration and volume estimation. We demonstrate both mathematically and empirically that if the predictor is calibrated per image, we can obtain the correct volume by taking an expectation of the probability scores per pixel/voxel of the image. Furthermore, we show that convex combinations of calibrated classifiers preserve volume estimation, but do not preserve calibration. Therefore, we conclude that having a calibrated predictor is a sufficient, but not necessary condition for obtaining an unbiased estimate of the volume. We validate our theoretical findings empirically on a collection of 18 different (calibrated) training strategies on the tasks of glioma volume estimation on BraTS 2018, and ischemic stroke lesion volume estimation on ISLES 2018 datasets.

eess.IV↗

arXiv2021

CLIMAT: Clinically-Inspired Multi-Agent Transformers for Knee Osteoarthritis Trajectory Forecasting

In medical applications, deep learning methods are built to automate diagnostic tasks. However, a clinically relevant question that practitioners usually face, is how to predict the future trajectory of a disease (prognosis). Current methods for such a problem often require domain knowledge, and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many forecasting problem from multimodal data. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner, we model a prognosis prediction problem with two transformer-based components that share information between each other. The first block in this model aims to analyze the imaging data, and the second block leverages the internal representations of the first one as inputs, also fusing them with auxiliary patient data. We show the effectiveness of our method in predicting the development of structural knee osteoarthritis changes over time. Our results show that the proposed method outperforms the state-of-the-art baselines in terms of various performance metrics. In addition, we empirically show that the existence of the multi-agent transformers with depths of 2 is sufficient to achieve good performances. Our code is publicly available at \url{https://github.com/MIPT-Oulu/CLIMAT}.

cs.LG↗

arXiv2021

Deep learning on fundus images detects glaucoma beyond the optic disc

Although unprecedented sensitivity and specificity values are reported, recent glaucoma detection deep learning models lack in decision transparency. Here, we propose a methodology that advances explainable deep learning in the field of glaucoma detection and vertical cup-disc ratio (VCDR), an important risk factor. We trained and evaluated deep learning models using fundus images that underwent a certain cropping policy. We defined the crop radius as a percentage of image size, centered on the optic nerve head (ONH), with an equidistant spaced range from 10%-60% (ONH crop policy). The inverse of the cropping mask was also applied (periphery crop policy). Trained models using original images resulted in an area under the curve (AUC) of 0.94 [95% CI: 0.92-0.96] for glaucoma detection, and a coefficient of determination (R^2) equal to 77% [95% CI: 0.77-0.79] for VCDR estimation. Models that were trained on images with absence of the ONH are still able to obtain significant performance (0.88 [95% CI: 0.85-0.90] AUC for glaucoma detection and 37% [95% CI: 0.35-0.40] R^2 score for VCDR estimation in the most extreme setup of 60% ONH crop). Our findings provide the first irrefutable evidence that deep learning can detect glaucoma from fundus image regions outside the ONH.

eess.IV↗

arXiv2021

Meta-Cal: Well-controlled Post-hoc Calibration by Ranking

In many applications, it is desirable that a classifier not only makes accurate predictions, but also outputs calibrated posterior probabilities. However, many existing classifiers, especially deep neural network classifiers, tend to be uncalibrated. Post-hoc calibration is a technique to recalibrate a model by learning a calibration map. Existing approaches mostly focus on constructing calibration maps with low calibration errors, however, this quality is inadequate for a calibrator being useful. In this paper, we introduce two constraints that are worth consideration in designing a calibration map for post-hoc calibration. Then we present Meta-Cal, which is built from a base calibrator and a ranking model. Under some mild assumptions, two high-probability bounds are given with respect to these constraints. Empirical results on CIFAR-10, CIFAR-100 and ImageNet and a range of popular network architectures show our proposed method significantly outperforms the current state of the art for post-hoc multi-class classification calibration.

stat.ML↗

arXiv2020

Post Training Uncertainty Calibration of Deep Networks For Medical Image Segmentation

Neural networks for automated image segmentation are typically trained to achieve maximum accuracy, while less attention has been given to the calibration of their confidence scores. However, well-calibrated confidence scores provide valuable information towards the user. We investigate several post hoc calibration methods that are straightforward to implement, some of which are novel. They are compared to Monte Carlo (MC) dropout. They are applied to neural networks trained with cross-entropy (CE) and soft Dice (SD) losses on BraTS 2018 and ISLES 2018. Surprisingly, models trained on SD loss are not necessarily less calibrated than those trained on CE loss. In all cases, at least one post hoc method improves the calibration. There is limited consistency across the results, so we can't conclude on one method being superior. In all cases, post hoc calibration is competitive with MC dropout. Although average calibration improves compared to the base model, subject-level variance of the calibration remains similar.

eess.IV↗

arXiv2020

Optimization for Medical Image Segmentation: Theory and Practice when evaluating with Dice Score or Jaccard Index

In many medical imaging and classical computer vision tasks, the Dice score and Jaccard index are used to evaluate the segmentation performance. Despite the existence and great empirical success of metric-sensitive losses, i.e. relaxations of these metrics such as soft Dice, soft Jaccard and Lovasz-Softmax, many researchers still use per-pixel losses, such as (weighted) cross-entropy to train CNNs for segmentation. Therefore, the target metric is in many cases not directly optimized. We investigate from a theoretical perspective, the relation within the group of metric-sensitive loss functions and question the existence of an optimal weighting scheme for weighted cross-entropy to optimize the Dice score and Jaccard index at test time. We find that the Dice score and Jaccard index approximate each other relatively and absolutely, but we find no such approximation for a weighted Hamming similarity. For the Tversky loss, the approximation gets monotonically worse when deviating from the trivial weight setting where soft Tversky equals soft Dice. We verify these results empirically in an extensive validation on six medical segmentation tasks and can confirm that metric-sensitive losses are superior to cross-entropy based loss functions in case of evaluation with Dice Score or Jaccard Index. This further holds in a multi-class setting, and across different object sizes and foreground/background ratios. These results encourage a wider adoption of metric-sensitive loss functions for medical segmentation tasks where the performance measure of interest is the Dice score or Jaccard index.

eess.IV↗

arXiv2020

Additive Tree-Structured Conditional Parameter Spaces in Bayesian Optimization: A Novel Covariance Function and a Fast Implementation

Bayesian optimization (BO) is a sample-efficient global optimization algorithm for black-box functions which are expensive to evaluate. Existing literature on model based optimization in conditional parameter spaces are usually built on trees. In this work, we generalize the additive assumption to tree-structured functions and propose an additive tree-structured covariance function, showing improved sample-efficiency, wider applicability and greater flexibility. Furthermore, by incorporating the structure information of parameter spaces and the additive assumption in the BO loop, we develop a parallel algorithm to optimize the acquisition function and this optimization can be performed in a low dimensional space. We demonstrate our method on an optimization benchmark function, on a neural network compression problem, on pruning pre-trained VGG16 and ResNet50 models as well as on searching activation functions of ResNet20. Experimental results show our approach significantly outperforms the current state of the art for conditional parameter optimization including SMAC, TPE and Jenatton et al. (2017).

stat.ML↗