Visualization of incrementally learned projection trajectories for longitudinal data.

Longitudinal studies that continuously generate data enable the capture of temporal variations in experimentally observed parameters, facilitating the interpretation of results in a time-aware manner. We propose IL-VIS (incrementally learned visualizer), a new machine learning pipeline that incrementally learns and visualizes a progression trajectory representing the longitudinal changes in longitudinal studies. At each sampling time point in an experiment, IL-VIS generates a snapshot of the longitudinal process on the data observed thus far, a new feature that is beyond the reach of classical static models. We first verify the utility and correctness of IL-VIS using simulated data, for which the true progression trajectories are known. We find that it accurately captures and visualizes the trends and (dis)similarities between high-dimensional progression trajectories. We then apply IL-VIS to longitudinal multi-electrode array data from brain cortical organoids when exposed to different levels of quinolinic acid, a metabolite contributing to many neuroinflammatory diseases including Alzheimer's disease, and its blocking antibody. We uncover valuable insights into the organoids' electrophysiological maturation and response patterns over time under these conditions.

Classification of Fracture Risk in Fallers Using Dual-Energy X-Ray Absorptiometry (DXA) Images and Deep Learning-Based Feature Extraction.

Dual-energy X-ray absorptiometry (DXA) scans are one of the most frequently used imaging techniques for calculating bone mineral density, yet calculating fracture risk using DXA image features is rarely performed. The objective of this study was to combine deep neural networks, together with DXA images and patient clinical information, to evaluate fracture risk in a cohort of adults with at least one known fall and age-matched healthy controls. DXA images of the entire body as, well as isolated images of the hip, forearm, and spine (1488 total), were obtained from 478 fallers and 48 non-faller controls. A modeling pipeline was developed for fracture risk prediction using the DXA images and clinical data. First, self-supervised pretraining of feature extractors was performed using a small vision transformer (ViT-S) and a convolutional neural network model (VGG-16 and Resnet-50). After pretraining, the feature extractors were then paired with a multilayer perceptron model, which was used for fracture risk classification. Classification was achieved with an average area under the receiver-operating characteristic curve (AUROC) score of 74.3%. This study demonstrates ViT-S as a promising neural network technique for fracture risk classification using DXA scans. The findings have future application as a fracture risk screening tool for older adults at risk of falls. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

Conversion of Upper-Limb Inertial Measurement Unit Data to Joint Angles: A Systematic Review.

Inertial measurement units (IMUs) have become the mainstay in human motion evaluation outside of the laboratory; however, quantification of 3-dimensional upper limb motion using IMUs remains challenging. The objective of this systematic review is twofold. Firstly, to evaluate computational methods used to convert IMU data to joint angles in the upper limb, including for the scapulothoracic, humerothoracic, glenohumeral, and elbow joints; and secondly, to quantify the accuracy of these approaches when compared to optoelectronic motion analysis. Fifty-two studies were included. Maximum joint motion measurement accuracy from IMUs was achieved using Euler angle decomposition and Kalman-based filters. This resulted in differences between IMU and optoelectronic motion analysis of 4° across all degrees of freedom of humerothoracic movement. Higher accuracy has been achieved at the elbow joint with functional joint axis calibration tasks and the use of kinematic constraints on gyroscope data, resulting in RMS errors between IMU and optoelectronic motion for flexion-extension as low as 2°. For the glenohumeral joint, 3D joint motion has been described with RMS errors of 6° and higher. In contrast, scapulothoracic joint motion tracking yielded RMS errors in excess of 10° in the protraction-retraction and anterior-posterior tilt direction. The findings of this study demonstrate high-quality 3D humerothoracic and elbow joint motion measurement capability using IMUs and underscore the challenges of skin motion artifacts in scapulothoracic and glenohumeral joint motion analysis. Future studies ought to implement functional joint axis calibrations, and IMU-based scapula locators to address skin motion artifacts at the scapula, and explore the use of artificial neural networks and data-driven approaches to directly convert IMU data to joint angles.

Dimensionality reduction for visualizing high-dimensional biological data.

High throughput technologies used in experimental biological sciences produce data with a vast number of variables at a rapid pace, making large volumes of high-dimensional data available. The exploratory analysis of such high-dimensional data can be aided by human interpretable low-dimensional visualizations. This work investigates how both discrete and continuous structures in biological data can be captured using the recently proposed dimensionality reduction method SONG, and compares the results with commonly used methods UMAP and PHATE. Using simulated and real-world datasets, we observe that SONG produces insightful visualizations by preserving various patterns, including discrete clusters, continuums, and branching structures in all considered datasets. More importantly, for datasets containing both discrete and continuous structures, SONG performs better at preserving both the structures compared to UMAP and PHATE. Furthermore, our quantitative evaluation of the three methods using downstream analysis validates the on par quality of the SONG's low-dimensional embeddings compared to the other methods.

Real-time conversion of inertial measurement unit data to ankle joint angles using deep neural networks.

Joint angle quantification from inertial measurement units (IMUs) is commonly performed using kinematic modelling, which depends on anatomical sensor placement and/or functional joint calibration; however, accurate three-dimensional joint motion measurement remains challenging to achieve. The aims of this study were firstly to employ deep neural networks to convert IMU data to ankle joint angles that are indistinguishable from those derived from motion capture-based inverse kinematics (IK) - the reference standard; and secondly, to validate the robustness of this approach across contrasting walking speeds in healthy individuals. Kinematics data were simultaneously calculated using IMUs and IK from 9 subjects during walking on a treadmill at 0.5 m/s, 1.0 m/s and 1.5 m/s. A generative adversarial network was trained using gait data at two of the walking speeds to predict ankle kinematics from IMU data alone for the third walking speed. There were significant differences between IK and IMU joint angle predictions for ankle eversion and internal rotation during walking at 0.5 m/s and 1.0 m/s (p < 0.001); however, no significant differences in joint angles were observed between the generative adversarial network prediction and IK at any speed or plane of joint motion (p < 0.05). The RMS difference in ankle joint kinematics between the generative adversarial network and IK for walking at 1.0 m/s was 3.8°, 2.1° and 3.5° for dorsiflexion, inversion and axial rotation, respectively. The modeling approach presented for real-time IMU to ankle joint angle conversion, which can be readily expanded to other joints, may provide enhanced IMU capability in applications such as telemedicine, remote monitoring and rehabilitation.

Self-Organizing Nebulous Growths for Robust and Incremental Data Visualization.

Nonparametric dimensionality reduction techniques, such as t-distributed Stochastic Neighbor Embedding (t-SNE) and uniform manifold approximation and projection (UMAP), are proficient in providing visualizations for data sets of fixed sizes. However, they cannot incrementally map and insert new data points into an already provided data visualization. We present self-organizing nebulous growths (SONG), a parametric nonlinear dimensionality reduction technique that supports incremental data visualization, i.e., incremental addition of new data while preserving the structure of the existing visualization. In addition, SONG is capable of handling new data increments, no matter whether they are similar or heterogeneous to the already observed data distribution. We test SONG on a variety of real and simulated data sets. The results show that SONG is superior to Parametric t-SNE, t-SNE, and UMAP in incremental data visualization. Especially, for heterogeneous increments, SONG improves over Parametric t-SNE by 14.98% on the Fashion MNIST data set and 49.73% on the MNIST data set regarding the cluster quality measured by the adjusted mutual information scores. On similar or homogeneous increments, the improvements are 8.36% and 42.26%, respectively. Furthermore, even when the abovementioned data sets are presented all at once, SONG performs better or comparable to UMAP and superior to t-SNE. We also demonstrate that the algorithmic foundations of SONG render it more tolerant to noise compared with UMAP and t-SNE, thus providing greater utility for data with high variance, high mixing of clusters, or noise.

ENVirT: inference of ecological characteristics of viruses from metagenomic data.

BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases. RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses. CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.