Osteoporosis is a prevalent bone disease that causes fractures in fragile bones, leading to a decline in daily living activities. Dual-energy X-ray absorptiometry (DXA) and quantitative computed tomography (QCT) are highly accurate for diagnosing osteoporosis; however, these modalities require special equipment and scan protocols. To frequently monitor bone health, low-cost, low-dose, and ubiquitously available diagnostic methods are highly anticipated. In this study, we aim to perform bone mineral density (BMD) estimation from a plain X-ray image for opportunistic screening, which is potentially useful for early diagnosis. Existing methods have used multi-stage approaches consisting of extraction of the region of interest and simple regression to estimate BMD, which require a large amount of training data. Therefore, we propose an efficient method that learns decomposition into projections of bone-segmented QCT for BMD estimation under limited datasets. The proposed method achieved high accuracy in BMD estimation, where Pearson correlation coefficients of 0.880 and 0.920 were observed for DXA-measured BMD and QCT-measured BMD estimation tasks, respectively, and the root mean square of the coefficient of variation values were 3.27 to 3.79% for four measurements with different poses. Furthermore, we conducted extensive validation experiments, including multi-pose, uncalibrated-CT, and compression experiments toward actual application in routine clinical practice.
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The attention towards food products characteristics, such as nutritional properties and traceability, has risen substantially in the recent years. Consequently, we are witnessing an increased demand for the development of modern tools to monitor, analyse and assess food quality and authenticity. Within this framework, an essential set of data collection techniques is provided by vibrational spectroscopy. In fact, methods such as Fourier near infrared and mid infrared spectroscopy have been often exploited to analyze different foodstuffs. Nonetheless, existing statistical methods often struggle to deal with the challenges presented by spectral data, such as their high dimensionality, paired with strong relationships among the wavelengths. Therefore, the definition of proper statistical procedures accounting for the peculiarities of spectroscopy data is paramount. In this work, motivated by two dairy science applications, we propose an adaptive functional regression framework for spectroscopy data. The method stems from the trend filtering literature, allowing the definition of a highly flexible and adaptive estimator able to handle different degrees of smoothness. We provide a fast optimization procedure that is suitable for both Gaussian and non Gaussian scalar responses, and allows for the inclusion of scalar covariates. Moreover, we develop inferential procedures for both the functional and the scalar component thus enhancing not only the interpretability of the results, but also their usability in real world scenarios. The method is applied to two sets of MIR spectroscopy data, providing excellent results when predicting milk chemical composition and cows' dietary treatments. Moreover, the developed inferential routine provides relevant insights, potentially paving the way for a richer interpretation and a better understanding of the impact of specific wavelengths on milk features.
While several previous studies have devised methods for segmentation of polyps, most of these methods are not rigorously assessed on multi-center datasets. Variability due to appearance of polyps from one center to another, difference in endoscopic instrument grades, and acquisition quality result in methods with good performance on in-distribution test data, and poor performance on out-of-distribution or underrepresented samples. Unfair models have serious implications and pose a critical challenge to clinical applications. We adapt an implicit bias mitigation method which leverages Bayesian epistemic uncertainties during training to encourage the model to focus on underrepresented sample regions. We demonstrate the potential of this approach to improve generalisability without sacrificing state-of-the-art performance on a challenging multi-center polyp segmentation dataset (PolypGen) with different centers and image modalities.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
The self-supervised learning (SSL) paradigm is an essential exploration area, which tries to eliminate the need for expensive data labeling. Despite the great success of SSL methods in computer vision and natural language processing, most of them employ contrastive learning objectives that require negative samples, which are hard to define. This becomes even more challenging in the case of graphs and is a bottleneck for achieving robust representations. To overcome such limitations, we propose a framework for self-supervised graph representation learning - Graph Barlow Twins, which utilizes a cross-correlation-based loss function instead of negative samples. Moreover, it does not rely on non-symmetric neural network architectures - in contrast to state-of-the-art self-supervised graph representation learning method BGRL. We show that our method achieves as competitive results as the best self-supervised methods and fully supervised ones while requiring fewer hyperparameters and substantially shorter computation time (ca. 30 times faster than BGRL).
Confounder selection, namely choosing a set of covariates to control for confounding between a treatment and an outcome, is arguably the most important step in the design of observational studies. Previous methods, such as Pearl's celebrated back-door criterion, typically require pre-specifying a causal graph, which can often be difficult in practice. We propose an interactive procedure for confounder selection that does not require pre-specifying the graph or the set of observed variables. This procedure iteratively expands the causal graph by finding what we call "primary adjustment sets" for a pair of possibly confounded variables. This can be viewed as inverting a sequence of latent projections of the underlying causal graph. Structural information in the form of primary adjustment sets is elicited from the user, bit by bit, until either a set of covariates are found to control for confounding or it can be determined that no such set exists. We show that if the user correctly specifies the primary adjustment sets in every step, our procedure is both sound and complete.
The age and stroke-associated decline in musculoskeletal strength degrades the ability to perform daily human tasks using the upper extremities. Although there are a few examples of exoskeletons, they need manual operations due to the absence of sensor feedback and no intention prediction of movements. Here, we introduce an intelligent upper-limb exoskeleton system that uses cloud-based deep learning to predict human intention for strength augmentation. The embedded soft wearable sensors provide sensory feedback by collecting real-time muscle signals, which are simultaneously computed to determine the user's intended movement. The cloud-based deep-learning predicts four upper-limb joint motions with an average accuracy of 96.2% at a 200-250 millisecond response rate, suggesting that the exoskeleton operates just by human intention. In addition, an array of soft pneumatics assists the intended movements by providing 897 newton of force and 78.7 millimeter of displacement at maximum. Collectively, the intent-driven exoskeleton can augment human strength by 5.15 times on average compared to the unassisted exoskeleton. This report demonstrates an exoskeleton robot that augments the upper-limb joint movements by human intention based on a machine-learning cloud computing and sensory feedback.
Social insects such as ants communicate via pheromones which allows them to coordinate their activity and solve complex tasks as a swarm, e.g. foraging for food. This behavior was shaped through evolutionary processes. In computational models, self-coordination in swarms has been implemented using probabilistic or simple action rules to shape the decision of each agent and the collective behavior. However, manual tuned decision rules may limit the behavior of the swarm. In this work we investigate the emergence of self-coordination and communication in evolved swarms without defining any explicit rule. We evolve a swarm of agents representing an ant colony. We use an evolutionary algorithm to optimize a spiking neural network (SNN) which serves as an artificial brain to control the behavior of each agent. The goal of the evolved colony is to find optimal ways to forage for food and return it to the nest in the shortest amount of time. In the evolutionary phase, the ants are able to learn to collaborate by depositing pheromone near food piles and near the nest to guide other ants. The pheromone usage is not manually encoded into the network; instead, this behavior is established through the optimization procedure. We observe that pheromone-based communication enables the ants to perform better in comparison to colonies where communication via pheromone did not emerge. We assess the foraging performance by comparing the SNN based model to a rule based system. Our results show that the SNN based model can efficiently complete the foraging task in a short amount of time. Our approach illustrates self coordination via pheromone emerges as a result of the network optimization. This work serves as a proof of concept for the possibility of creating complex applications utilizing SNNs as underlying architectures for multi-agent interactions where communication and self-coordination is desired.
The inherent nature of patient data poses several challenges. Prevalent cases amass substantial longitudinal data owing to their patient volume and consistent follow-ups, however, longitudinal laboratory data are renowned for their irregularity, temporality, absenteeism, and sparsity; In contrast, recruitment for rare or specific cases is often constrained due to their limited patient size and episodic observations. This study employed self-supervised learning (SSL) to pretrain a generalized laboratory progress (GLP) model that captures the overall progression of six common laboratory markers in prevalent cardiovascular cases, with the intention of transferring this knowledge to aid in the detection of specific cardiovascular event. GLP implemented a two-stage training approach, leveraging the information embedded within interpolated data and amplify the performance of SSL. After GLP pretraining, it is transferred for TVR detection. The proposed two-stage training improved the performance of pure SSL, and the transferability of GLP exhibited distinctiveness. After GLP processing, the classification exhibited a notable enhancement, with averaged accuracy rising from 0.63 to 0.90. All evaluated metrics demonstrated substantial superiority (p < 0.01) compared to prior GLP processing. Our study effectively engages in translational engineering by transferring patient progression of cardiovascular laboratory parameters from one patient group to another, transcending the limitations of data availability. The transferability of disease progression optimized the strategies of examinations and treatments, and improves patient prognosis while using commonly available laboratory parameters. The potential for expanding this approach to encompass other diseases holds great promise.
Linearization of the dynamics of recurrent neural networks (RNNs) is often used to study their properties. The same RNN dynamics can be written in terms of the ``activations" (the net inputs to each unit, before its pointwise nonlinearity) or in terms of the ``activities" (the output of each unit, after its pointwise nonlinearity); the two corresponding linearizations are different from each other. This brief and informal technical note describes the relationship between the two linearizations, between the left and right eigenvectors of their dynamics matrices, and shows that some context-dependent effects are readily apparent under linearization of activity dynamics but not linearization of activation dynamics.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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