Synthetic Datasets for Machine Learning on Spatio-Temporal Graphs using PDEs

Many physical processes can be expressed through partial differential equations (PDEs). Real-world measurements of such processes are often collected at irregularly distributed points in space, which can be effectively represented as graphs; however, there are currently only a few existing datasets. Our work aims to make advancements in the field of PDE-modeling accessible to the temporal graph machine learning community, while addressing the data scarcity problem, by creating and utilizing datasets based on PDEs. In this work, we create and use synthetic datasets based on PDEs to support spatio-temporal graph modeling in machine learning for different applications. More precisely, we showcase three equations to model different types of disasters and hazards in the fields of epidemiology, atmospheric particles, and tsunami waves. Further, we show how such created datasets can be used by benchmarking several machine learning models on the epidemiological dataset. Additionally, we show how pre-training on this dataset can improve model performance on real-world epidemiological data. The presented methods enable others to create datasets and benchmarks customized to individual requirements. The source code for our methodology and the three created datasets can be found on https://github.com/github-usr-ano/Temporal_Graph_Data_PDEs.

Spatial Shortcuts in Graph Neural Controlled Differential Equations

We incorporate prior graph topology information into a Neural Controlled Differential Equation (NCDE) to predict the future states of a dynamical system defined on a graph. The informed NCDE infers the future dynamics at the vertices of simulated advection data on graph edges with a known causal graph, observed only at vertices during training. We investigate different positions in the model architecture to inform the NCDE with graph information and identify an outer position between hidden state and control as theoretically and empirically favorable. Our such informed NCDE requires fewer parameters to reach a lower Mean Absolute Error (MAE) compared to previous methods that do not incorporate additional graph topology information.

Synthetic Generation of Dermatoscopic Images with GAN and Closed-Form Factorization

In the realm of dermatological diagnoses, where the analysis of dermatoscopic and microscopic skin lesion images is pivotal for the accurate and early detection of various medical conditions, the costs associated with creating diverse and high-quality annotated datasets have hampered the accuracy and generalizability of machine learning models. We propose an innovative unsupervised augmentation solution that harnesses Generative Adversarial Network (GAN) based models and associated techniques over their latent space to generate controlled semiautomatically-discovered semantic variations in dermatoscopic images. We created synthetic images to incorporate the semantic variations and augmented the training data with these images. With this approach, we were able to increase the performance of machine learning models and set a new benchmark amongst non-ensemble based models in skin lesion classification on the HAM10000 dataset; and used the observed analytics and generated models for detailed studies on model explainability, affirming the effectiveness of our solution.

From CNNs to Vision Transformers -- A Comprehensive Evaluation of Deep Learning Models for Histopathology

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we conducted an extensive evaluation by benchmarking a wide range of classification models, including recent vision transformers, convolutional neural networks and hybrid models comprising transformer and convolutional models. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classification strategies that allow for plausibility checks and systematic comparisons. The study resulted in specific model recommendations for practitioners as well as putting forward a general methodology to quantify a model's quality according to complementary requirements that can be transferred to future model architectures.

On the Robustness of Pretraining and Self-Supervision for a Deep Learning-based Analysis of Diabetic Retinopathy

There is an increasing number of medical use-cases where classification algorithms based on deep neural networks reach performance levels that are competitive with human medical experts. To alleviate the challenges of small dataset sizes, these systems often rely on pretraining. In this work, we aim to assess the broader implications of these approaches. For diabetic retinopathy grading as exemplary use case, we compare the impact of different training procedures including recently established self-supervised pretraining methods based on contrastive learning. To this end, we investigate different aspects such as quantitative performance, statistics of the learned feature representations, interpretability and robustness to image distortions. Our results indicate that models initialized from ImageNet pretraining report a significant increase in performance, generalization and robustness to image distortions. In particular, self-supervised models show further benefits to supervised models. Self-supervised models with initialization from ImageNet pretraining not only report higher performance, they also reduce overfitting to large lesions along with improvements in taking into account minute lesions indicative of the progression of the disease. Understanding the effects of pretraining in a broader sense that goes beyond simple performance comparisons is of crucial importance for the broader medical imaging community beyond the use-case considered in this work.

Risk Estimation of SARS-CoV-2 Transmission from Bluetooth Low Energy Measurements

Digital contact tracing approaches based on Bluetooth low energy (BLE) have the potential to efficiently contain and delay outbreaks of infectious diseases such as the ongoing SARS-CoV-2 pandemic. In this work we propose a novel machine learning based approach to reliably detect subjects that have spent enough time in close proximity to be at risk of being infected. Our study is an important proof of concept that will aid the battery of epidemiological policies aiming to slow down the rapid spread of COVID-19.

Shearlet-based compressed sensing for fast 3D cardiac MR imaging using iterative reweighting

High-resolution three-dimensional (3D) cardiovascular magnetic resonance (CMR) is a valuable medical imaging technique, but its widespread application in clinical practice is hampered by long acquisition times. Here we present a novel compressed sensing (CS) reconstruction approach using shearlets as a sparsifying transform allowing for fast 3D CMR (3DShearCS). Shearlets are mathematically optimal for a simplified model of natural images and have been proven to be more efficient than classical systems such as wavelets. Data is acquired with a 3D Radial Phase Encoding (RPE) trajectory and an iterative reweighting scheme is used during image reconstruction to ensure fast convergence and high image quality. In our in-vivo cardiac MRI experiments we show that the proposed method 3DShearCS has lower relative errors and higher structural similarity compared to the other reconstruction techniques especially for high undersampling factors, i.e. short scan times. In this paper, we further show that 3DShearCS provides improved depiction of cardiac anatomy (measured by assessing the sharpness of coronary arteries) and two clinical experts qualitatively analyzed the image quality.