Pre-exposure cognitive performance variability is associated with severity of respiratory infection.

Using data from a longitudinal viral challenge study, we find that the post-exposure viral shedding and symptom severity are associated with a novel measure of pre-exposure cognitive performance variability (CPV), defined before viral exposure occurs. Each individual's CPV score is computed from data collected from a repeated NeuroCognitive Performance Test (NCPT) over a 3 day pre-exposure period. Of the 18 NCPT measures reported by the tests, 6 contribute materially to the CPV score, prospectively differentiating the high from the low shedders.

Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions.

Background: Development of new methods for analysis of protein-protein interactions (PPIs) at molecular and nanometer scales gives insights into intracellular signaling pathways and will improve understanding of protein functions, as well as other nanoscale structures of biological and abiological origins. Recent advances in computational tools, particularly the ones involving modern deep learning algorithms, have been shown to complement experimental approaches for describing and rationalizing PPIs. However, most of the existing works on PPI predictions use protein-sequence information, and thus have difficulties in accounting for the three-dimensional organization of the protein chains.

A Pattern Dictionary Method for Anomaly Detection.

In this paper, we propose a compression-based anomaly detection method for time series and sequence data using a pattern dictionary. The proposed method is capable of learning complex patterns in a training data sequence, using these learned patterns to detect potentially anomalous patterns in a test data sequence. The proposed pattern dictionary method uses a measure of complexity of the test sequence as an anomaly score that can be used to perform stand-alone anomaly detection.

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.

Predicting the dynamics and functions of microbiomes constructed from the bottom-up is a key challenge in exploiting them to our benefit. Current models based on ecological theory fail to capture complex community behaviors due to higher order interactions, do not scale well with increasing complexity and in considering multiple functions. We develop and apply a long short-term memory (LSTM) framework to advance our understanding of community assembly and health-relevant metabolite production using a synthetic human gut community.

Penalized ensemble Kalman filters for high dimensional non-linear systems.

The ensemble Kalman filter (EnKF) is a data assimilation technique that uses an ensemble of models, updated with data, to track the time evolution of a usually non-linear system. It does so by using an empirical approximation to the well-known Kalman filter. However, its performance can suffer when the ensemble size is smaller than the state space, as is often necessary for computationally burdensome models.

Adaptive Multi-Channel Event Segmentation and Feature Extraction for Monitoring Health Outcomes.

Objective: To develop a multi-channel device event segmentation and feature extraction algorithm that is robust to changes in data distribution.

Methods: We introduce an adaptive transfer learning algorithm to classify and segment events from non-stationary multi-channel temporal data. Using a multivariate hidden Markov model (HMM) and Fisher's linear discriminant analysis (FLDA) the algorithm adaptively adjusts to shifts in distribution over time.

Expectation-propagation for weak radionuclide identification at radiation portal monitors.

We propose a sparsity-promoting Bayesian algorithm capable of identifying radionuclide signatures from weak sources in the presence of a high radiation background. The proposed method is relevant to radiation identification for security applications. In such scenarios, the background typically consists of terrestrial, cosmic, and cosmogenic radiation that may cause false positive responses.

A deep learning architecture for metabolic pathway prediction.

Motivation: Understanding the mechanisms and structural mappings between molecules and pathway classes are critical for design of reaction predictors for synthesizing new molecules. This article studies the problem of prediction of classes of metabolic pathways (series of chemical reactions occurring within a cell) in which a given biochemical compound participates. We apply a hybrid machine learning approach consisting of graph convolutional networks used to extract molecular shape features as input to a random forest classifier.

Geometric Estimation of Multivariate Dependency.

This paper proposes a geometric estimator of dependency between a pair of multivariate random variables. The proposed estimator of dependency is based on a randomly permuted geometric graph (the minimal spanning tree) over the two multivariate samples. This estimator converges to a quantity that we call the geometric mutual information (GMI), which is equivalent to the Henze-Penrose divergence.

Quantum-inspired computational imaging.

Computational imaging combines measurement and computational methods with the aim of forming images even when the measurement conditions are weak, few in number, or highly indirect. The recent surge in quantum-inspired imaging sensors, together with a new wave of algorithms allowing on-chip, scalable and robust data processing, has induced an increase of activity with notable results in the domain of low-light flux imaging and sensing. We provide an overview of the major challenges encountered in low-illumination (e.

Ensemble Estimation of Information Divergence .

Recent work has focused on the problem of nonparametric estimation of information divergence functionals between two continuous random variables. Many existing approaches require either restrictive assumptions about the density support set or difficult calculations at the support set boundary which must be known a priori. The mean squared error (MSE) convergence rate of a leave-one-out kernel density plug-in divergence functional estimator for general bounded density support sets is derived where knowledge of the support boundary, and therefore, the boundary correction is not required.

Multi-Functional Sensing for Swarm Robots Using Time Sequence Classification: HoverBot, an Example.

Scaling up robot swarms to collectives of hundreds or even thousands without sacrificing sensing, processing, and locomotion capabilities is a challenging problem. Low-cost robots are potentially scalable, but the majority of existing systems have limited capabilities, and these limitations substantially constrain the type of experiments that could be performed by robotics researchers. Instead of adding functionality by adding more components and therefore increasing the cost, we demonstrate how low-cost hardware can be used beyond its standard functionality.

Joint camera blur and pose estimation from aliased data.

A joint-estimation algorithm is presented that enables simultaneous camera blur and pose estimation from a known calibration target in the presence of aliasing. Specifically, a parametric maximum-likelihood (ML) point-spread function estimate is derived for characterizing a camera's optical imperfections through the use of a calibration target in an otherwise loosely controlled environment. The imaging perspective, ambient-light levels, target reflectance, detector gain and offset, quantum efficiency, and read-noise levels are all treated as nuisance parameters.

Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection.

Infection of respiratory mucosa with viral pathogens triggers complex immunologic events in the affected host. We sought to characterize this response through proteomic analysis of nasopharyngeal lavage in human subjects experimentally challenged with influenza A/H3N2 or human rhinovirus, and to develop targeted assays measuring peptides involved in this host response allowing classification of acute respiratory virus infection. Unbiased proteomic discovery analysis identified 3285 peptides corresponding to 438 unique proteins, and revealed that infection with H3N2 induces significant alterations in protein expression.

THE INTRINSIC VALUE OF HFO FEATURES AS A BIOMARKER OF EPILEPTIC ACTIVITY.

High frequency oscillations (HFOs) are a promising biomarker of epileptic brain tissue and activity. HFOs additionally serve as a prototypical example of challenges in the analysis of discrete events in high-temporal resolution, intracranial EEG data. Two primary challenges are 1) dimensionality reduction, and 2) assessing feasibility of classification.

Spectral identification of topological domains.

Motivation: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription.

Foundational Principles for Large-Scale Inference: Illustrations Through Correlation Mining.

When can reliable inference be drawn in fue "Big Data" context? This paper presents a framework for answering this fundamental question in the context of correlation mining, wifu implications for general large scale inference. In large scale data applications like genomics, connectomics, and eco-informatics fue dataset is often variable-rich but sample-starved: a regime where the number of acquired samples (statistical replicates) is far fewer than fue number of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for "Big Data".

A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses.

Early, presymptomatic intervention with oseltamivir (corresponding to the onset of a published host-based genomic signature of influenza infection) resulted in decreased overall influenza symptoms (aggregate symptom scores of 23.5 vs 46.3), more rapid resolution of clinical disease (20 hours earlier), reduced viral shedding (total median tissue culture infectious dose [TCID50] 7.

Empirically Estimable Classification Bounds Based on a Nonparametric Divergence Measure.

Information divergence functions play a critical role in statistics and information theory. In this paper we show that a non-parametric -divergence measure can be used to provide improved bounds on the minimum binary classification probability of error for the case when the training and test data are drawn from the same distribution for the case where there exists some mismatch between training and test distributions. We confirm the theoretical results by designing feature selection algorithms using the criteria from these bounds and by evaluating the algorithms on a series of pathological speech classification tasks.

An individualized predictor of health and disease using paired reference and target samples.

Background: Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy.

Multicriteria Similarity-Based Anomaly Detection Using Pareto Depth Analysis.

We consider the problem of identifying patterns in a data set that exhibits anomalous behavior, often referred to as anomaly detection. Similarity-based anomaly detection algorithms detect abnormally large amounts of similarity or dissimilarity, e.g.

Single- and dual-site pace mapping of idiopathic septal intramural ventricular arrhythmias.

Background: Pace mapping (PM) is used to identify the origin of ventricular arrhythmias (VAs). For intramural VAs, the site of origin often cannot be reached and therefore PM is less accurate.

Objective: The purpose of this study was to assess the value of single- and dual-site pace maps to differentiate intramural from nonintramural VAs.

A Dictionary Approach to Electron Backscatter Diffraction Indexing.

We propose a framework for indexing of grain and subgrain structures in electron backscatter diffraction patterns of polycrystalline materials. We discretize the domain of a dynamical forward model onto a dense grid of orientations, producing a dictionary of patterns. For each measured pattern, we identify the most similar patterns in the dictionary, and identify boundaries, detect anomalies, and index crystal orientations.

Universal phase transition in community detectability under a stochastic block model.

We prove the existence of an asymptotic phase-transition threshold on community detectability for the spectral modularity method [M. E. J.

Pareto-depth for multiple-query image retrieval.

Most content-based image retrieval systems consider either one single query, or multiple queries that include the same object or represent the same semantic information. In this paper, we consider the content-based image retrieval problem for multiple query images corresponding to different image semantics. We propose a novel multiple-query information retrieval algorithm that combines the Pareto front method with efficient manifold ranking.