Thresholding Step Research Articles

A Statistical Approach for Functional Reach-to-Grasp Segmentation Using a Single Inertial Measurement Unit.

The aim of this contribution is to present a segmentation method for the identification of voluntary movements from inertial data acquired through a single inertial measurement unit placed on the subject's wrist. Inertial data were recorded from 25 healthy subjects while performing 75 consecutive reach-to-grasp movements. The approach herein presented, called DynAMoS, is based on an adaptive thresholding step on the angular velocity norm, followed by a statistics-based post-processing on the movement duration distribution. Post-processing aims at reducing the number of erroneous transitions in the movement segmentation. We assessed the segmentation quality of this method using a stereophotogrammetric system as the gold standard. Two popular methods already presented in the literature were compared to DynAMoS in terms of the number of movements identified, onset and offset mean absolute errors, and movement duration. Moreover, we analyzed the sub-phase durations of the drinking movement to further characterize the task. The results show that the proposed method performs significantly better than the two state-of-the-art approaches (i.e., percentage of erroneous movements = 3%; onset and offset mean absolute error < 0.08 s), suggesting that DynAMoS could make more effective home monitoring applications for assessing the motion improvements of patients following domicile rehabilitation protocols.

A new robust covariance matrix estimation for high‐dimensional microbiome data

SummaryMicrobiome data typically lie in a high‐dimensional simplex. One of the key questions in metagenomic analysis is to exploit the covariance structure for this kind of data. In this paper, a framework called approximate‐estimate‐threshold (AET) is developed for the robust basis covariance estimation for high‐dimensional microbiome data. To be specific, we first construct a proxy matrix , which is almost indistinguishable from the real basis covariance matrix . Then, any estimator satisfying some conditions can be used to estimate . Finally, we impose a thresholding step on to obtain the final estimator . In particular, this paper applies a Huber‐type estimator , and achieves robustness by only requiring the boundedness of 2+ moments for some . We derive the convergence rate of under the spectral norm, and provide theoretical guarantees on support recovery. Extensive simulations and a real example are used to illustrate the empirical performance of our method.

SAMGAT: structure-aware multilevel graph attention networks for automatic rumor detection.

The rapid dissemination of unverified information through social platforms like Twitter poses considerable dangers to societal stability. Identifying real versus fake claims is challenging, and previous work on rumor detection methods often fails to effectively capture propagation structure features. These methods also often overlook the presence of comments irrelevant to the discussion topic of the source post. To address this, we introduce a novel approach: the Structure-Aware Multilevel Graph Attention Network (SAMGAT) for rumor classification. SAMGAT employs a dynamic attention mechanism that blends GATv2 and dot-product attention to capture the contextual relationships between posts, allowing for varying attention scores based on the stance of the central node. The model incorporates a structure-aware attention mechanism that learns attention weights that can indicate the existence of edges, effectively reflecting the propagation structure of rumors. Moreover, SAMGAT incorporates a top-k attention filtering mechanism to select the most relevant neighboring nodes, enhancing its ability to focus on the key structural features of rumor propagation. Furthermore, SAMGAT includes a claim-guided attention pooling mechanism with a thresholding step to focus on the most informative posts when constructing the event representation. Experimental results on benchmark datasets demonstrate that SAMGAT outperforms state-of-the-art methods in identifying rumors and improves the effectiveness of early rumor detection.

The Innovative Development Path of Intelligent Sports Training in Colleges and Universities under the Perspective of National Fitness

Abstract Information technology, as the driving force of a new round of technological and industrial changes, brings new opportunities to sports training. In this paper, a dynamic threshold step monitoring strategy based on sinusoidal waveform curve of acceleration change is designed, and blood oxygen saturation content is monitored by near-infrared spectroscopy. By mining the high-frequency exercise load monitoring information, the intelligent sports training model is discussed in depth. In the application effect study at X University of S Province, the model successfully measured the average heart rate of students to be 160.91 beats/minute and the average energy consumption to be 137.27 Kcal, which provided a critical decision-making basis for physical education teaching. This finding offers a scientific implementation program for reforming physical education in colleges and universities, ensuring that physical training is accomplished efficiently and highly.

Fast Frequency-Diverse Radar Imaging Based on Adaptive Sampling Iterative Soft-Thresholding Deep Unfolding Network

Frequency-diverse radar imaging is an emerging field that combines computational imaging with frequency-diverse techniques to interrogate the high-quality images of objects. Despite the success of deep reconstruction networks in improving scene image reconstruction from noisy or under-sampled frequency-diverse measurements, their reliance on large amounts of high-quality training data and the inherent uninterpretable features pose significant challenges in the design and optimization of imaging networks, particularly in the face of dynamic variations in radar operating frequency bands. Here, aiming at reducing the latency and processing burden involved in scene image reconstruction, we propose an adaptive sampling iterative soft-thresholding deep unfolding network (ASISTA-Net). Specifically, we embed an adaptively sampling module into the iterative soft-thresholding (ISTA) unfolding network, which contains multiple measurement matrices with different compressed sampling ratios. The outputs of the convolutional layers are then passed through a series of ISTA layers that perform a sparse coding step followed by a thresholding step. The proposed method requires no need for heavy matrix operations and massive amount of training scene targets and measurements datasets. Unlike recent work using matrix-inversion-based and data-driven deep reconstruction networks, our generic approach is directly adapted to multi-compressed sampling ratios and multi-scene target image reconstruction, and no restrictions on the types of imageable scenes are imposed. Multiple measurement matrices with different scene compressed sampling ratios are trained in parallel, which enables the frequency-diverse radar to select operation frequency bands flexibly. In general, the application of the proposed approach paves the way for the widespread deployment of computational microwave and millimeter wave frequency-diverse radar imagers to achieve real-time imaging. Extensive imaging simulations demonstrate the effectiveness of our proposed method.

A New Region-Based Minimal Path Selection Algorithm for Crack Detection and Ground Truth Labeling Exploiting Gabor Filters

Cracks are fractures or breaks that occur in materials such as concrete, metals, rocks, and other solids. Various methods are used to detect and monitor cracks; among many of them, image-based methodologies allow fast identification of the distress and easy quantification of the percentage of cracks in the scene. Two main categories can be identified: classical and deep learning approaches. In the last decade, the tendency has moved towards the use of the latter. Even though they have proven their outstanding predicting performance, they suffer some drawbacks: a “black-box” nature leaves the user blind and without the possibility of modifying any parameters, a huge amount of labeled data is generally needed, a process that requires expert judgment is always required, and, finally, they tend to be time-consuming. Accordingly, the present study details the methodology for a new algorithm for crack segmentation based on the theory of minimal path selection combined with a region-based approach obtained through the segmentation of texture features extracted using Gabor filters. A pre-processing step is described, enabling the equalization of brightness and shadows, which results in better detection of local minima. These local minimal are constrained by a minimum distance between adjacent points, enabling a better coverage of the cracks. Afterward, a region-based segmentation technique is introduced to determine two areas that are used to determine threshold values used for rejection. This step is critical to generalize the algorithm to images presenting close-up scenes or wide cracks. Finally, a geometrical thresholding step is presented, allowing the exclusion of rounded areas and small isolated cracks. The results showed a very competitive F1-score (0.839), close to state-of-the-art values achieved with deep learning techniques. The main advantage of this approach is the transparency of the workflow, contrary to what happens with deep learning frameworks. In the proposed approach, no prior information is required; however, the statistical parameters may have to be adjusted to the particular case and requirements of the situation. The proposed algorithm results in a useful tool for researchers and practitioners needing to validate their results against some reference or needing labeled data for their models. Moreover, the current study could establish the grounds to standardize the procedure for crack segmentation with a lower human bias and faster results. The direct application of the methodology to images obtained with any low-cost sensor makes the proposed algorithm an operational support tool for authorities needing crack detection systems in order to monitor and evaluate the current state of the infrastructures, such as roads, tunnels, or bridges.

Homeostasis at different backgrounds: The roles of overlayed feedback structures in vertebrate photoadaptation.

We have studied the resetting behavior of eight basic integral controller motifs with respect to different but constant backgrounds. We found that the controllers split symmetrically into two classes: one class, based on derepression of the compensatory flux, leads to more rapid resetting kinetics as backgrounds increase. The other class, which directly activates the compensatory flux, shows a slowing down in the resetting at increased backgrounds. We found a striking analogy between the resetting kinetics of vertebrate photoreceptors and controllers based on derepression, i.e. vertebrate rod or cone cells show decreased sensitivities and accelerated response kinetics as background illuminations increase. The central molecular model of vertebrate photoadaptation consists of an overlay of three negative feedback loops with cytosolic calcium ([Formula: see text]), cyclic guanosine monophosphate (cGMP) and cyclic nucleotide-gated (CNG) channels as components. While in one of the feedback loops the extrusion of [Formula: see text] by potassium-dependent sodium-calcium exchangers (NCKX) can lead to integral control with cGMP as the controlled variable, the expected robust perfect adaptation of cGMP is lost, because of the two other feedback loops. They avoid that [Formula: see text] levels become too high and toxic. Looking at psychophysical laws, we found that in all of the above mentioned basic controllers Weber's law is followed when a "just noticeable difference" (threshold) of 1% of the controlled variable's set-point was considered. Applying comparable threshold pulses or steps to the photoadaptation model we find, in agreement with experimental results, that Weber's law is followed for relatively high backgrounds, while Stephens' power law gives a better description when backgrounds are low. Limitations of our photoadaption model, in particular with respect to potassium/sodium homeostasis, are discussed. Finally, we discuss possible implication of background perturbations in biological controllers when compensatory fluxes are based on activation.

Saliency and superpixel improved detection and segmentation of concealed objects for passive terahertz images

Application of passive terahertz imaging in concealed weapon detection has been looked at, such that the final result is the segmentation of the foreground concealed weapons from the rest of the background. For the same, a fully automatic and completely generic technique, without any learning, has been proposed. It was observed that a simple thresholding step, exploiting varied intensity bands of the tetrahertz images is not enough. Thus, an innovative method to isolate humans and thus improve the region of interest (ROI) has been proposed. Thereafter, saliency has been used to further improve ROI, as these images are quite noisy and the central focusing aspect of saliency could handle the noise around the concealed weapons. It was observed that this step could handle the noise around the concealed weapons but degraded the boundaries of the concealed weapons. To further improve boundary adherence, superpixels are used. Finally, results are evaluated both quantitatively and qualitatively and outperformed the traditional approach.

Combined segmentation and classification-based approach to automated analysis of biomedical signals obtained from calcium imaging.

Automated screening systems in conjunction with machine learning-based methods are becoming an essential part of the healthcare systems for assisting in disease diagnosis. Moreover, manually annotating data and hand-crafting features for training purposes are impractical and time-consuming. We propose a segmentation and classification-based approach for assembling an automated screening system for the analysis of calcium imaging. The method was developed and verified using the effects of disease IgGs (from Amyotrophic Lateral Sclerosis patients) on calcium (Ca2+) homeostasis. From 33 imaging videos we analyzed, 21 belonged to the disease and 12 to the control experimental groups. The method consists of three main steps: projection, segmentation, and classification. The entire Ca2+ time-lapse image recordings (videos) were projected into a single image using different projection methods. Segmentation was performed by using a multi-level thresholding (MLT) step and the Regions of Interest (ROIs) that encompassed cell somas were detected. A mean value of the pixels within these boundaries was collected at each time point to obtain the Ca2+ traces (time-series). Finally, a new matrix called feature image was generated from those traces and used for assessing the classification accuracy of various classifiers (control vs. disease). The mean value of the segmentation F-score for all the data was above 0.80 throughout the tested threshold levels for all projection methods, namely maximum intensity, standard deviation, and standard deviation with linear scaling projection. Although the classification accuracy reached up to 90.14%, interestingly, we observed that achieving better scores in segmentation results did not necessarily correspond to an increase in classification performance. Our method takes the advantage of the multi-level thresholding and of a classification procedure based on the feature images, thus it does not have to rely on hand-crafted training parameters of each event. It thus provides a semi-autonomous tool for assessing segmentation parameters which allows for the best classification accuracy.

White Blood Cells Detection Using Spectral Tresholding

The study of the morphology of White Blood Cells (WBCs) further contributes to the clinical diagnosis of blood diseases. In this research paper, we come up with an image segmentation enhancement by combining Fourier Fast Transform on smear blood capture and classical thresholding. The Fast Fourier Transform (FFT) is a very powerful tool in image processing and it was used to segment and extract the WBCs. Our image processing method uses a Fast Fourier Transform combined with filtering and an Inverse Fast Fourier Transform for the extraction and visualization of the high frequency region of the image. In order to remove residual Red Blood Cells acting as noise in the expected result, a final thresholding step is added at the end of the processing. The results presented in this article report the tests performed using our mathematical implementation. Moreover, we were able to detect and differentiate the sub-families of WBCs.

Nearly minimax-optimal rates for noisy sparse phase retrieval via early-stopped mirror descent

AbstractThis paper studies early-stopped mirror descent applied to noisy sparse phase retrieval, which is the problem of recovering a $k$-sparse signal $\textbf{x}^\star \in{\mathbb{R}}^n$ from a set of quadratic Gaussian measurements corrupted by sub-exponential noise. We consider the (non-convex) unregularized empirical risk minimization problem and show that early-stopped mirror descent, when equipped with the hypentropy mirror map and proper initialization, achieves a nearly minimax-optimal rate of convergence, provided the sample size is at least of order $k^2$ (modulo logarithmic term) and the minimum (in modulus) non-zero entry of the signal is on the order of $\|\textbf{x}^\star \|_2/\sqrt{k}$. Our theory leads to a simple algorithm that does not rely on explicit regularization or thresholding steps to promote sparsity. More generally, our results establish a connection between mirror descent and sparsity in the non-convex problem of noisy sparse phase retrieval, adding to the literature on early stopping that has mostly focused on non-sparse, Euclidean and convex settings via gradient descent. Our proof combines a potential-based analysis of mirror descent with a quantitative control on a variational coherence property that we establish along the path of mirror descent, up to a prescribed stopping time.

A study on the relationship between odor hedonic ratings and individual odor detection threshold

Odor hedonic perception (pleasant/unpleasant character) is considered as the first and one of the most prominent dimensions in olfaction and is known to depend on several parameters. Among them, the relation between the odorant concentration and the hedonic estimation has been widely studied. However, few studies have considered odor hedonic ratings (OHR) in relation to individual detection thresholds (IDT). Thus, the aim of this study was to determine olfactory detection thresholds and to describe hedonic rating variations from individual thresholds to higher concentrations. IDT were performed for two pleasant (apple and jasmine) and two unpleasant (durian and trimethylamine) odorant stimuli. The experimenter presented one by one in a randomized order, the different odorant concentrations above IDT. Participants rated odor hedonic valence of these stimuli on a visual analog scale. Results showed, except for trimethylamine, the same relationship between hedonic ratings and stimulus concentration, i.e., an increase of pleasantness (apple and jasmine)/unpleasantness (durian) ratings at low and middle concentrations followed by a plateau at high concentrations. Correlations between OHR and concentrations as well as between OHR and threshold steps were always significant. Moreover, comparisons between both conditions showed that the correlation coefficient was significantly higher for trimethylamine (and a trend for apple) when IDTs were considered, while no difference was found for jasmine and durian. Overall, results suggested that the relationship between OHR and IDT is odor specific. These findings contribute to explain the large variability of the hedonic tone (i.e., weakly vs. very pleasant, weakly vs. very unpleasant) at specific concentration in the general population and could serve future research in this field (e.g., olfactory preferences in nutrition studies, anhedonia in psychiatric disorders…).

A semiparametric Bayesian method with birth-death Markov Chain Monte Carlo algorithm for extreme mooring tension analysis

A series of 1: 50 model tests have been conducted to study the dynamics of a taut mooring system and two hybrid mooring systems attached to a deep-water semi-submersible in the 100-year wave condition of the South China Sea. Three typical environmental conditions were tested, including head sea, beam sea and quartering sea. The mixture Gamma- Generalized Pareto distribution (GPD) model is applied to study short term extreme dynamic mooring tensions based on the measured data, the results are compared with the estimations from mixture Gamma and two-parameter Weibull models. A birth-death Markov chain Monte Carlo (MCMC) sampling procedure is developed to fit the parameters of a mixture Gamma- GPD via Bayesian inference, and an extensive discussion of the de-clustering procedure, parameters of the prior distribution for threshold and MCMC iteration steps on Bayesian inference are carried out. It is found that the Weibull model underestimates the most probable largest dynamic mooring tensions. On the contrary, the mixture Gamma model overestimates the extreme dynamic mooring tension significantly. The mixture Gamma- GPD can present good estimations of extreme dynamic mooring tension, and its performance is robust to the sample definition, MCMC iteration steps and parameters of threshold prior distribution.

482-P: Do Varied Off-Loading Modalities Have Differing Impacts Upon Users' Fall Risk?

Aim: Adherence to offloading devices for diabetic foot ulcers (DFU) is poor and postural instability influences adherence. Prior research suggests an ankle-high removable cast walker (RCW) in tandem with a contralateral shoe lift might increase users’ balance relative to a traditional knee-high RCW without a lift. This study compared compensatory responses to perturbations under both conditions. Methods: Twenty-five individuals (48% male; age: 68±8 years) with diabetic peripheral neuropathy participated. Participants completed trials under three conditions: bilateral standardized shoes, knee-high RCW, and ankle-high RCW with contralateral shoe lift. Stepping thresholds (ST) were assessed for two types of perturbations:1) From a stopped position, a treadmill rapidly accelerated at 3.5m/s² to reach a set peak-velocity and then decelerated and stopped. The smallest peak-velocity to elicit a step was identified as the ST. Participants were separately oriented on the treadmill to elicit anterior and lateral ST; 2) A waist mounted spring scale was pulled until a target load was reached, then the spring was rapidly released. ST was the lowest load necessary to force a step upon release. Anterior and posterior waist-pull perturbations were done.Participants also rated their stability in each footwear condition via a 10cm visual analog scale. Data analyses focused upon the primary comparison of the two offloading conditions. Results: The knee-high RCW resulted in significantly decreased ST for two of the four tests (treadmill anterior: mean difference .037m/s2, p=.048 and anterior waist-pull: mean difference 2.2lbs, p&amp;lt;.001) relative to the ankle-high RCW with a contralateral lift. Participants reported a large and statistically significant reduction in perceived stability with the knee-high RCW (mean difference= 0.93cm, p=0.030) . Conclusions: Future prospective studies should assesses whether the differences noted in this study translate into differences in RCW adherence by patients with DFU. Disclosure R.T.Crews: None. N.J.Rosenblatt: None. Funding National Institute of Diabetes and Digestive and Kidney Disease

An Efficient Threshold Dynamics Method for Topology Optimization for Fluids

We propose an efficient threshold dynamics method for topology optimization for fluids modeled with the Stokes equation. The proposed algorithm is based on minimization of an objective energy function that consists of the dissipation power in the fluid and the perimeter approximated by nonlocal energy, subject to a fluid volume constraint and the incompressibility condition. We show that the minimization problem can be solved with an iterative scheme in which the Stokes equation is approximated by a Brinkman equation. The indicator functions of the fluid-solid regions are then updated according to simple convolutions followed by a thresholding step. We demonstrate mathematically that the iterative algorithm has the total energy decaying property. The proposed algorithm is simple and easy to implement. A simple adaptive time strategy is also used to accelerate the convergence of the iteration. Extensive numerical experiments in both two and three dimensions show that the proposed iteration algorithm converges in much fewer iterations and is more efficient than many existing methods. In addition, the numerical results show that the algorithm is very robust and insensitive to the initial guess and the parameters in the model.

Improved Regional Frequency Analysis of rainfall data

Rainfall are subject to local orography features and their intensities can be highly variable. In this context, identifying climatically coherent regions can greatly help interpreting rainfall patterns and improve the inference of return levels. In practice, partitioning a region of interest into homogeneous sub-regions is a delicate statistical task, especially in regards to modeling heavy rainfall features.In this work, our main goal is to propose and study a fast and efficient clustering algorithm. Compared to classical regional frequency analysis techniques, a key aspect is that our algorithm does not rely on the a priori choice of covariates. The proposed numerical scheme is only based on the precipitation dataset at hand, including low, moderate and heavy rainfall. In terms of inference, our approach builds on the easy-to-compute and reliable probability weighted moments commonly used in hydrology. While being in compliance with extreme value theory, we do not impose a parametric form on rainfall distributions and, neither thresholding nor block maxima steps are required in our proposed approach. By construction, our clustering method preserves the scale invariance principle of any classical regional frequency analysis.The performance of our clustering algorithm is assessed on a detailed experimental design based on the extended Generalized Pareto distribution.Sensitivity to the number of clusters is carefully analyzed.We apply our clustering algorithm on Switzerland daily precipitation measured at 191 sites. The found homogeneous regions are consistent with local orography and our approach outperforms the classical regional frequency analysis based on normalized elevation and coordinates as covariates. To complete our analysis of Swiss rainfall, we propose three models based on our clustering outputs. A comparison between our local, semi-regional and regional models indicates that a relatively simple model with two clusters and a spatially varying scale parameter can compete very well against complex models.

Vulnerability assessment of freeway network considering the probabilities and consequences from a perspective based on network cascade failure.

Freeway networks are vulnerable to natural disasters and man-made disruptions. The closure of one or more toll stations of the network often causes a sharp decrease in freeway performance. Therefore, measuring the probability and consequences of vulnerability to identify critical parts in the network is crucial for road emergency management. Most existing techniques only measure the consequences of node closure and rarely consider the probability of node closure owing to the lack of an extensive historical database; moreover, they ignore highways outside the study area, which can lead to errors in topological analysis and traffic distribution. Furthermore, the negative effects produced by the operation of freeway tunnels in vulnerability assessment have been neglected. In this study, a framework for freeway vulnerability assessment that considers both the probability and consequences of vulnerability is proposed, based on the perspective of network cascade failure analysis. The cascade failure analysis is conducted using an improved coupled map lattice model, developed by considering the negative effects of tunnels and optimizing the rules of local traffic redistribution. The perturbation threshold and propagation time step of network cascade failure are captured to reflect the probabilities and consequences of vulnerability. A nodal vulnerability index is established based on risk assessment, and a hierarchical clustering method is used to identify the vulnerability classification of critical nodes. The freeway network of Fuzhou in China is utilized to demonstrate the effectiveness of the proposed approach. Specifically, the toll stations in the study area are classified into five clusters of vulnerability: extremely high, high, medium, low, and extremely low. Approximately 31% of the toll stations were classified as the high or extremely high cluster, and three extremely vulnerable freeway sections requiring different precautions were identified. The proposed network vulnerability analysis method provides a new perspective to examine the vulnerability of freeway networks.

Sources of Information Waste in Neuroimaging: Mishandling Structures, Thinking Dichotomously, and Over-Reducing Data

Neuroimaging relies on separate statistical inferences at tens of thousands of spatial locations. Such massively univariate analysis typically requires an adjustment for multiple testing in an attempt to maintain the family-wise error rate at a nominal level of 5%. First, we examine three sources of substantial information loss that are associated with the common practice under the massively univariate framework: (a) the hierarchical data structures (spatial units and trials) are not well maintained in the modeling process; (b) the adjustment for multiple testing leads to an artificial step of strict thresholding; (c) information is excessively reduced during both modeling and result reporting. These sources of information loss have far-reaching impacts on result interpretability as well as reproducibility in neuroimaging. Second, to improve inference efficiency, predictive accuracy, and generalizability, we propose a Bayesian multilevel modeling framework that closely characterizes the data hierarchies across spatial units and experimental trials. Rather than analyzing the data in a way that first creates multiplicity and then resorts to a post hoc solution to address them, we suggest directly incorporating the cross-space information into one single model under the Bayesian framework (so there is no multiplicity issue). Third, regardless of the modeling framework one adopts, we make four actionable suggestions to alleviate information waste and to improve reproducibility: (1) model data hierarchies, (2) quantify effects, (3) abandon strict dichotomization, and (4) report full results. We provide examples for all of these points using both demo and real studies, including the recent Neuroimaging Analysis Replication and Prediction Study (NARPS).

Sources of Information Waste in Neuroimaging: Mishandling Structures, Thinking Dichotomously, and Over-Reducing Data

Neuroimaging relies on separate statistical inferences at tens of thousands of spatial locations. Such massively univariate analysis typically requires an adjustment for multiple testing in an attempt to maintain the family-wise error rate at a nominal level of 5%. First, we examine three sources of substantial information loss that are associated with the common practice under the massively univariate framework: (a) the hierarchical data structures (spatial units and trials) are not well maintained in the modeling process; (b) the adjustment for multiple testing leads to an artificial step of strict thresholding; (c) information is excessively reduced during both modeling and result reporting. These sources of information loss have far-reaching impacts on result interpretability as well as reproducibility in neuroimaging. Second, to improve inference efficiency, predictive accuracy, and generalizability, we propose a Bayesian multilevel modeling framework that closely characterizes the data hierarchies across spatial units and experimental trials. Rather than analyzing the data in a way that first creates multiplicity and then resorts to a post hoc solution to address them, we suggest directly incorporating the cross-space information into one single model under the Bayesian framework (so there is no multiplicity issue). Third, regardless of the modeling framework one adopts, we make four actionable suggestions to alleviate information waste and to improve reproducibility: (1) model data hierarchies, (2) quantify effects, (3) abandon strict dichotomization, and (4) report full results. We provide examples for all of these points using both demo and real studies, including the recent Neuroimaging Analysis Replication and Prediction Study (NARPS).

From complex data to biological insight: \u2018DEKER\u2019 feature selection and network inference

Network inference is a valuable approach for gaining mechanistic insight from high-dimensional biological data. Existing methods for network inference focus on ranking all possible relations (edges) among all measured quantities such as genes, proteins, metabolites (features) observed, which yields a dense network that is challenging to interpret. Identifying a sparse, interpretable network using these methods thus requires an error-prone thresholding step which compromises their performance. In this article we propose a new method, DEKER-NET, that addresses this limitation by directly identifying a sparse, interpretable network without thresholding, improving real-world performance. DEKER-NET uses a novel machine learning method for feature selection in an iterative framework for network inference. DEKER-NET is extremely flexible, handling linear and nonlinear relations while making no assumptions about the underlying distribution of data, and is suitable for categorical or continuous variables. We test our method on the Dialogue for Reverse Engineering Assessments and Methods (DREAM) challenge data, demonstrating that it can directly identify sparse, interpretable networks without thresholding while maintaining performance comparable to the hypothetical best-case thresholded network of other methods.