David Meyer

Subin Erattakulangara, Karthika Kelat, Katie Burnham et al.

Accurate segmentation of the vocal tract from magnetic resonance imaging (MRI) data is essential for various voice and speech applications. Manual segmentation is time intensive and susceptible to errors. This study aimed to evaluate the efficacy of deep learning algorithms for automatic vocal tract segmentation from 3D MRI.

David Meyer, Sue Grimmond, Peter Dueben et al.

Can we improve the modeling of urban land surface processes with machine learning (ML)? A prior comparison of urban land surface models (ULSMs) found that no single model is 'best' at predicting all common surface fluxes. Here, we develop an urban neural network (UNN) trained on the mean predicted fluxes from 22 ULSMs at one site. The UNN emulates the mean output of ULSMs accurately. When compared to a reference ULSM (Town Energy Balance; TEB), the UNN has greater accuracy relative to flux observations, less computational cost, and requires fewer input parameters. When coupled to the Weather Research Forecasting (WRF) model using TensorFlow bindings, WRF-UNN is stable and more accurate than the reference WRF-TEB. Although the application is currently constrained by the training data (1 site), we show a novel approach to improve the modeling of surface fluxes by combining the strengths of several ULSMs into one using ML.

David Meyer, Robin J. Hogan, Peter D. Dueben et al.

The treatment of cloud structure in numerical weather and climate models is often greatly simplified to make them computationally affordable. Here we propose to correct the European Centre for Medium-Range Weather Forecasts 1D radiation scheme ecRad for 3D cloud effects using computationally cheap neural networks. 3D cloud effects are learned as the difference between ecRad's fast 1D Tripleclouds solver that neglects them and its 3D SPARTACUS (SPeedy Algorithm for Radiative TrAnsfer through CloUd Sides) solver that includes them but is about five times more computationally expensive. With typical errors between 20 % and 30 % of the 3D signal, neural networks improve Tripleclouds' accuracy for about 1 % increase in runtime. Thus, rather than emulating the whole of SPARTACUS, we keep Tripleclouds unchanged for cloud-free parts of the atmosphere and 3D-correct it elsewhere. The focus on the comparably small 3D correction instead of the entire signal allows us to improve predictions significantly if we assume a similar signal-to-noise ratio for both.

David Meyer, Thomas Nagler, Robin J. Hogan

Can we improve machine-learning (ML) emulators with synthetic data? If data are scarce or expensive to source and a physical model is available, statistically generated data may be useful for augmenting training sets cheaply. Here we explore the use of copula-based models for generating synthetically augmented datasets in weather and climate by testing the method on a toy physical model of downwelling longwave radiation and corresponding neural network emulator. Results show that for copula-augmented datasets, predictions are improved by up to 62 % for the mean absolute error (from 1.17 to 0.44 W m$^{-2}$).

Jacek Cyranka, Alexander Georges, David Meyer

Topological data analysis aims to extract topological quantities from data, which tend to focus on the broader global structure of the data rather than local information. The Mapper method, specifically, generalizes clustering methods to identify significant global mathematical structures, which are out of reach of many other approaches. We propose a classifier based on applying the Mapper algorithm to data projected onto a latent space. We obtain the latent space by using PCA or autoencoders. Notably, a classifier based on the Mapper method is immune to any gradient based attack, and improves robustness over traditional CNNs (convolutional neural networks). We report theoretical justification and some numerical experiments that confirm our claims.

Nils Gessert, Torben Priegnitz, Thore Saathoff et al.

Purpose. Precise placement of needles is a challenge in a number of clinical applications such as brachytherapy or biopsy. Forces acting at the needle cause tissue deformation and needle deflection which in turn may lead to misplacement or injury. Hence, a number of approaches to estimate the forces at the needle have been proposed. Yet, integrating sensors into the needle tip is challenging and a careful calibration is required to obtain good force estimates. Methods. We describe a fiber-optical needle tip force sensor design using a single OCT fiber for measurement. The fiber images the deformation of an epoxy layer placed below the needle tip which results in a stream of 1D depth profiles. We study different deep learning approaches to facilitate calibration between this spatio-temporal image data and the related forces. In particular, we propose a novel convGRU-CNN architecture for simultaneous spatial and temporal data processing. Results. The needle can be adapted to different operating ranges by changing the stiffness of the epoxy layer. Likewise, calibration can be adapted by training the deep learning models. Our novel convGRU-CNN architecture results in the lowest mean absolute error of 1.59 +- 1.3 mN and a cross-correlation coefficient of 0.9997, and clearly outperforms the other methods. Ex vivo experiments in human prostate tissue demonstrate the needle's application. Conclusions. Our OCT-based fiber-optical sensor presents a viable alternative for needle tip force estimation. The results indicate that the rich spatio-temporal information included in the stream of images showing the deformation throughout the epoxy layer can be effectively used by deep learning models. Particularly, we demonstrate that the convGRU-CNN architecture performs favorably, making it a promising approach for other spatio-temporal learning problems.

Nils Gessert, Torben Priegnitz, Thore Saathoff et al.

Needle insertion is common during minimally invasive interventions such as biopsy or brachytherapy. During soft tissue needle insertion, forces acting at the needle tip cause tissue deformation and needle deflection. Accurate needle tip force measurement provides information on needle-tissue interaction and helps detecting and compensating potential misplacement. For this purpose we introduce an image-based needle tip force estimation method using an optical fiber imaging the deformation of an epoxy layer below the needle tip over time. For calibration and force estimation, we introduce a novel deep learning-based fused convolutional GRU-CNN model which effectively exploits the spatio-temporal data structure. The needle is easy to manufacture and our model achieves a mean absolute error of 1.76 +- 1.5 mN with a cross-correlation coefficient of 0.9996, clearly outperforming other methods. We test needles with different materials to demonstrate that the approach can be adapted for different sensitivities and force ranges. Furthermore, we validate our approach in an ex-vivo prostate needle insertion scenario.