Artificial intelligence (AI) models are increasingly used in the medical domain. However, as medical data is highly sensitive, special precautions to ensure its protection are required. The gold standard for privacy preservation is the introduction of differential privacy (DP) to model training. Prior work indicates that DP has negative implications on model accuracy and fairness, which are unacceptable in medicine and represent a main barrier to the widespread use of privacy-preserving techniques. In this work, we evaluated the effect of privacy-preserving training of AI models regarding accuracy and fairness compared to non-private training. For this, we used two datasets: (1) A large dataset (N=193,311) of high quality clinical chest radiographs, and (2) a dataset (N=1,625) of 3D abdominal computed tomography (CT) images, with the task of classifying the presence of pancreatic ductal adenocarcinoma (PDAC). Both were retrospectively collected and manually labeled by experienced radiologists. We then compared non-private deep convolutional neural networks (CNNs) and privacy-preserving (DP) models with respect to privacy-utility trade-offs measured as area under the receiver-operator-characteristic curve (AUROC), and privacy-fairness trade-offs, measured as Pearson's r or Statistical Parity Difference. We found that, while the privacy-preserving trainings yielded lower accuracy, they did largely not amplify discrimination against age, sex or co-morbidity. Our study shows that -- under the challenging realistic circumstances of a real-life clinical dataset -- the privacy-preserving training of diagnostic deep learning models is possible with excellent diagnostic accuracy and fairness.
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Collaborative problem-solving (CPS) is a vital skill used both in the workplace and in educational environments. CPS is useful in tackling increasingly complex global, economic, and political issues and is considered a central 21st century skill. The increasingly connected global community presents a fruitful opportunity for creative and collaborative problem-solving interactions and solutions that involve diverse perspectives. Unfortunately, women and underrepresented minorities (URMs) often face obstacles during collaborative interactions that hinder their key participation in these problem-solving conversations. Here, we explored the communication patterns of minority and non-minority individuals working together in a CPS task. Group Communication Analysis (GCA), a temporally-sensitive computational linguistic tool, was used to examine how URM status impacts individuals' sociocognitive linguistic patterns. Results show differences across racial/ethnic groups in key sociocognitive features that indicate fruitful collaborative interactions. We also investigated how the groups' racial/ethnic composition impacts both individual and group communication patterns. In general, individuals in more demographically diverse groups displayed more productive communication behaviors than individuals who were in majority-dominated groups. We discuss the implications of individual and group diversity on communication patterns that emerge during CPS and how these patterns can impact collaborative outcomes.
With the widespread application of convolutional neural networks (CNNs), the traditional model based denoising algorithms are now outperformed. However, CNNs face two problems. First, they are computationally demanding, which makes their deployment especially difficult for mobile terminals. Second, experimental evidence shows that CNNs often over-smooth regular textures present in images, in contrast to traditional non-local models. In this letter, we propose a solution to both issues by combining a nonlocal algorithm with a lightweight residual CNN. This solution gives full latitude to the advantages of both models. We apply this framework to two GPU implementations of classic nonlocal algorithms (NLM and BM3D) and observe a substantial gain in both cases, performing better than the state-of-the-art with low computational requirements. Our solution is between 10 and 20 times faster than CNNs with equivalent performance and attains higher PSNR. In addition the final method shows a notable gain on images containing complex textures like the ones of the MIT Moire dataset.
The use of deep learning models in computational biology has increased massively in recent years, and is expected to do so further with the current advances in fields like Natural Language Processing. These models, although able to draw complex relations between input and target, are also largely inclined to learn noisy deviations from the pool of data used during their development. In order to assess their performance on unseen data (their capacity to generalize), it is common to randomly split the available data in development (train/validation) and test sets. This procedure, although standard, has lately been shown to produce dubious assessments of generalization due to the existing similarity between samples in the databases used. In this work, we present SpanSeq, a database partition method for machine learning that can scale to most biological sequences (genes, proteins and genomes) in order to avoid data leakage between sets. We also explore the effect of not restraining similarity between sets by reproducing the development of the state-of-the-art model DeepLoc, not only confirming the consequences of randomly splitting databases on the model assessment, but expanding those repercussions to the model development. SpanSeq is available for downloading and installing at //github.com/genomicepidemiology/SpanSeq.
Current deep neural networks (DNNs) are overparameterized and use most of their neuronal connections during inference for each task. The human brain, however, developed specialized regions for different tasks and performs inference with a small fraction of its neuronal connections. We propose an iterative pruning strategy introducing a simple importance-score metric that deactivates unimportant connections, tackling overparameterization in DNNs and modulating the firing patterns. The aim is to find the smallest number of connections that is still capable of solving a given task with comparable accuracy, i.e. a simpler subnetwork. We achieve comparable performance for LeNet architectures on MNIST, and significantly higher parameter compression than state-of-the-art algorithms for VGG and ResNet architectures on CIFAR-10/100 and Tiny-ImageNet. Our approach also performs well for the two different optimizers considered -- Adam and SGD. The algorithm is not designed to minimize FLOPs when considering current hardware and software implementations, although it performs reasonably when compared to the state of the art.
We study a new technique for understanding convergence of learning agents under small modifications of data. We show that such convergence can be understood via an analogue of Fatou's lemma which yields gamma-convergence. We show it's relevance and applications in general machine learning tasks and domain adaptation transfer learning.
Regression methods are fundamental for scientific and technological applications. However, fitted models can be highly unreliable outside of their training domain, and hence the quantification of their uncertainty is crucial in many of their applications. Based on the solution of a constrained optimization problem, we propose "prediction rigidities" as a method to obtain uncertainties of arbitrary pre-trained regressors. We establish a strong connection between our framework and Bayesian inference, and we develop a last-layer approximation that allows the new method to be applied to neural networks. This extension affords cheap uncertainties without any modification to the neural network itself or its training procedure. We show the effectiveness of our method on a wide range of regression tasks, ranging from simple toy models to applications in chemistry and meteorology.
Randomized controlled trials (RCTs) are the accepted standard for treatment effect estimation but they can be infeasible due to ethical reasons and prohibitive costs. Single-arm trials, where all patients belong to the treatment group, can be a viable alternative but require access to an external control group. We propose an identifiable deep latent-variable model for this scenario that can also account for missing covariate observations by modeling their structured missingness patterns. Our method uses amortized variational inference to learn both group-specific and identifiable shared latent representations, which can subsequently be used for {\em (i)} patient matching if treatment outcomes are not available for the treatment group, or for {\em (ii)} direct treatment effect estimation assuming outcomes are available for both groups. We evaluate the model on a public benchmark as well as on a data set consisting of a published RCT study and real-world electronic health records. Compared to previous methods, our results show improved performance both for direct treatment effect estimation as well as for effect estimation via patient matching.
As data from monitored structures become increasingly available, the demand grows for it to be used efficiently to add value to structural operation and management. One way in which this can be achieved is to use structural response measurements to assess the usefulness of models employed to describe deterioration processes acting on a structure, as well the mechanical behavior of the latter. This is what this work aims to achieve by first, framing Structural Health Monitoring as a Bayesian model updating problem, in which the quantities of inferential interest characterize the deterioration process and/or structural state. Then, using the posterior estimates of these quantities, a decision-theoretic definition is proposed to assess the structural and/or deterioration models based on (a) their ability to explain the data and (b) their performance on downstream decision support-based tasks. The proposed framework is demonstrated on strain response data obtained from a test specimen which was subjected to three-point bending while simultaneously exposed to accelerated corrosion leading to thickness loss. Results indicate that the level of \textit{a priori} domain knowledge on the deterioration form is critical.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
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.
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