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We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing. While typical multimodal studies need to use multiple independent processing pipelines, with diverse options and hyperparameters, we propose a single and structured framework to jointly process different image modalities. The use of state-of-the-art learning-based techniques enables fast inferences, which makes the presented method suitable for large-scale and/or multi-cohort datasets with a diverse number of modalities per session. The pipeline currently works with structural MRI, resting state fMRI and amyloid PET images. We show the predictive power of the derived biomarkers using in a case-control study and study the cross-modal relationship between different image modalities. The code can be found in https: //github.com/acasamitjana/JUMP.

We propose a two-step Newton's method for refining an approximation of a singular zero whose deflation process terminates after one step, also known as a deflation-one singularity. Given an isolated singular zero of a square analytic system, our algorithm exploits an invertible linear operator obtained by combining the Jacobian and a projection of the Hessian in the direction of the kernel of the Jacobian. We prove the quadratic convergence of the two-step Newton method when it is applied to an approximation of a deflation-one singular zero. Also, the algorithm requires a smaller size of matrices than the existing methods, making it more efficient. We demonstrate examples and experiments to show the efficiency of the method.

The utility of a learned neural representation depends on how well its geometry supports performance in downstream tasks. This geometry depends on the structure of the inputs, the structure of the target outputs, and the architecture of the network. By studying the learning dynamics of networks with one hidden layer, we discovered that the network's activation function has an unexpectedly strong impact on the representational geometry: Tanh networks tend to learn representations that reflect the structure of the target outputs, while ReLU networks retain more information about the structure of the raw inputs. This difference is consistently observed across a broad class of parameterized tasks in which we modulated the degree of alignment between the geometry of the task inputs and that of the task labels. We analyzed the learning dynamics in weight space and show how the differences between the networks with Tanh and ReLU nonlinearities arise from the asymmetric asymptotic behavior of ReLU, which leads feature neurons to specialize for different regions of input space. By contrast, feature neurons in Tanh networks tend to inherit the task label structure. Consequently, when the target outputs are low dimensional, Tanh networks generate neural representations that are more disentangled than those obtained with a ReLU nonlinearity. Our findings shed light on the interplay between input-output geometry, nonlinearity, and learned representations in neural networks.

A generalization of Passing-Bablok regression is proposed for comparing multiple measurement methods simultaneously. Possible applications include assay migration studies or interlaboratory trials. When comparing only two methods, the method reduces to the usual Passing-Bablok estimator. It is close in spirit to reduced major axis regression, which is, however, not robust. To obtain a robust estimator, the major axis is replaced by the (hyper-)spherical median axis. The method is shown to reduce to the usual Passing-Bablok estimator if only two methods are compared. This technique has been applied to compare SARS-CoV-2 serological tests, bilirubin in neonates, and an in vitro diagnostic test using different instruments, sample preparations, and reagent lots. In addition, plots similar to the well-known Bland-Altman plots have been developed to represent the variance structure.

Accurate segmentation of the heart is essential for personalized blood flow simulations and surgical intervention planning. Segmentations need to be accurate in every spatial dimension, which is not ensured by segmenting data slice by slice. Two cardiac computed tomography (CT) datasets consisting of 760 volumes across the whole cardiac cycle from 39 patients, and of 60 volumes from 60 patients respectively were used to train networks to simultaneously segment multiple regions representing the whole heart in 3D. The segmented regions included the left and right atrium and ventricle, left ventricular myocardium, ascending aorta, pulmonary arteries, pulmonary veins, and left atrial appendage. The widely used 3D U-Net and the UNETR architecture were compared to our proposed method optimized for large volumetric inputs. The proposed network architecture, termed Transformer Residual U-Net (TRUNet), maintains the cascade downsampling encoder, cascade upsampling decoder and skip connections from U-Net, while incorporating a Vision Transformer (ViT) block in the encoder alongside a modified ResNet50 block. TRUNet reached higher segmentation performance for all structures within approximately half the training time needed for 3D U-Net and UNETR. The proposed method achieved more precise vessel boundary segmentations and better captured the heart's overall anatomical structure compared to the other methods. The fast training time and accurate delineation of adjacent structures makes TRUNet a promising candidate for medical image segmentation tasks. The code for TRUNet is available at github.com/ljollans/TRUNet.

Depth perception in volumetric visualization plays a crucial role in the understanding and interpretation of volumetric data. Numerous visualization techniques, many of which rely on physically based optical effects, promise to improve depth perception but often do so without considering camera movement or the content of the volume. As a result, the findings from previous studies may not be directly applicable to crowded volumes, where a large number of contained structures disrupts spatial perception. Crowded volumes therefore require special analysis and visualization tools with sparsification capabilities. Interactivity is an integral part of visualizing and exploring crowded spaces, but has received little attention in previous studies. To address this gap, we conducted a study to assess the impact of different rendering techniques on depth perception in crowded volumes, with a particular focus on the effects of camera movement. The results show that depth perception considering camera motion depends much more on the content of the volume than on the chosen visualization technique. Furthermore, we found that traditional rendering techniques, which have often performed poorly in previous studies, showed comparable performance to physically based methods in our study.

Skew normal model suffers from inferential drawbacks, namely singular Fisher information in the vicinity of symmetry and diverging of maximum likelihood estimation. To address the above drawbacks, Azzalini and Arellano-Valle (2013) introduced maximum penalised likelihood estimation (MPLE) by subtracting a penalty function from the log-likelihood function with a pre-specified penalty coefficient. Here, we propose a cross-validated MPLE to improve its performance when the underlying model is close to symmetry. We develop a theory for MPLE, where an asymptotic rate for the cross-validated penalty coefficient is derived. We further show that the proposed cross-validated MPLE is asymptotically efficient under certain conditions. In simulation studies and a real data application, we demonstrate that the proposed estimator can outperform the conventional MPLE when the model is close to symmetry.

Ordinal pattern dependence has been introduced in order to capture co-monotonic behavior between two time series. This concept has several features one would intuitively demand from a dependence measure. It was believed that ordinal pattern dependence satisfies the axioms which Grothe et al. [8] proclaimed for a multivariate measure of dependence. In the present article we show that this is not true and that there is a mistake in the article Betken et al. [5]. Furthermore we show that ordinal pattern dependence satisfies a slightly modified set of axioms.

Languages have long been described according to their perceived rhythmic attributes. The associated typologies are of interest in psycholinguistics as they partly predict newborns' abilities to discriminate between languages and provide insights into how adult listeners process non-native languages. Despite the relative success of rhythm metrics in supporting the existence of linguistic rhythmic classes, quantitative studies have yet to capture the full complexity of temporal regularities associated with speech rhythm. We argue that deep learning offers a powerful pattern-recognition approach to advance the characterization of the acoustic bases of speech rhythm. To explore this hypothesis, we trained a medium-sized recurrent neural network on a language identification task over a large database of speech recordings in 21 languages. The network had access to the amplitude envelopes and a variable identifying the voiced segments, assuming that this signal would poorly convey phonetic information but preserve prosodic features. The network was able to identify the language of 10-second recordings in 40% of the cases, and the language was in the top-3 guesses in two-thirds of the cases. Visualization methods show that representations built from the network activations are consistent with speech rhythm typologies, although the resulting maps are more complex than two separated clusters between stress and syllable-timed languages. We further analyzed the model by identifying correlations between network activations and known speech rhythm metrics. The findings illustrate the potential of deep learning tools to advance our understanding of speech rhythm through the identification and exploration of linguistically relevant acoustic feature spaces.

The goal of explainable Artificial Intelligence (XAI) is to generate human-interpretable explanations, but there are no computationally precise theories of how humans interpret AI generated explanations. The lack of theory means that validation of XAI must be done empirically, on a case-by-case basis, which prevents systematic theory-building in XAI. We propose a psychological theory of how humans draw conclusions from saliency maps, the most common form of XAI explanation, which for the first time allows for precise prediction of explainee inference conditioned on explanation. Our theory posits that absent explanation humans expect the AI to make similar decisions to themselves, and that they interpret an explanation by comparison to the explanations they themselves would give. Comparison is formalized via Shepard's universal law of generalization in a similarity space, a classic theory from cognitive science. A pre-registered user study on AI image classifications with saliency map explanations demonstrate that our theory quantitatively matches participants' predictions of the AI.