A simple method for detecting chaos in nature

Chaos, or exponential sensitivity to small perturbations, appears everywhere in nature. Moreover, chaos is predicted to play diverse functional roles in living systems. A method for detecting chaos from empirical measurements should therefore be a key component of the biologist's toolkit. But, classic chaos-detection tools are highly sensitive to measurement noise and break down for common edge cases, making it difficult to detect chaos in domains, like biology, where measurements are noisy. However, newer tools promise to overcome these limitations. Here, we combine several such tools into an automated processing pipeline, and show that our pipeline can detect the presence (or absence) of chaos in noisy recordings, even for difficult edge cases. As a first-pass application of our pipeline, we show that heart rate variability is not chaotic as some have proposed, and instead reflects a stochastic process in both health and disease. Our tool is easy-to-use and freely available

Generative Adversarial Networks Selection Approach for Extremely Imbalanced Fault Diagnosis of Reciprocating Machinery

At present, countless approaches to fault diagnosis in reciprocating machines have been proposed, all considering that the available machinery dataset is in equal proportions for all conditions. However, when the application is closer to reality, the problem of data imbalance is increasingly evident. In this paper, we propose a method for the creation of diagnoses that consider an extreme imbalance in the available data. Our approach first processes the vibration signals of the machine using a wavelet packet transform-based feature-extraction stage. Then, improved generative models are obtained with a dissimilarity-based model selection to artificially balance the dataset. Finally, a Random Forest classifier is created to address the diagnostic task. This methodology provides a considerable improvement with 99% of data imbalance over other approaches reported in the literature, showing performance similar to that obtained with a balanced set of data.National Natural Science Foundation of China, under Grant 51605406National Natural Science Foundation of China under Grant 7180104

BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes

Machine learning is helping the interpretation of biological complexity by enabling the inference and classification of cellular, organismal and ecological phenotypes based on large datasets, e.g. from genomic, transcriptomic and metagenomic analyses. A number of available algorithms can help search these datasets to uncover patterns associated with specific traits, including disease-related attributes. While, in many instances, treating an algorithm as a black box is sufficient, it is interesting to pursue an enhanced understanding of how system variables end up contributing to a specific output, as an avenue towards new mechanistic insight. Here we address this challenge through a suite of algorithms, named BowSaw, which takes advantage of the structure of a trained random forest algorithm to identify combinations of variables (“rules”) frequently used for classification. We first apply BowSaw to a simulated dataset, and show that the algorithm can accurately recover the sets of variables used to generate the phenotypes through complex Boolean rules, even under challenging noise levels. We next apply our method to data from the integrative Human Microbiome Project and find previously unreported high-order combinations of microbial taxa putatively associated with Crohn’s disease. By leveraging the structure of trees within a random forest, BowSaw provides a new way of using decision trees to generate testable biological hypotheses.Accepted manuscrip

Computer analysis and mapping of gypsy moth levels in Pennsylvania using LANDSAT-1 digital data

The effectiveness of using LANDSAT-1 multispectral digital data and imagery, supplemented by ground truth and aerial photography, was investigated as a new method of surveying gypsy moth (Porthetria dispar (L.)) (Lepidoptera; Lymantriidae) defoliation, which has greatly increased in Pennsylvania in recent years. Since the acreage and severity of gypsy moth defoliation reaches a peak from mid-June through the first few days of July, the July 8, 1973, LANDSAT-1 scene was chosen for analysis. Results indicate that LANDSAT-1 data can be used to discriminate between defoliated and healthy vegetation in Pennsylvania and that digital processing methods can be used to map the extent and degree of defoliation

Remote sensing applications to forest vegetation classification and conifer vigor loss due to dwarf mistletoe

Criteria was established for practical remote sensing of vegetation stress and mortality caused by dwarf mistletoe infections in black spruce subboreal forest stands. The project was accomplished in two stages: (1) A fixed tower-tramway site in an infected black spruce stand was used for periodic multispectral photo coverage to establish basic film/filter/scale/season/weather parameters; (2) The photographic combinations suggested by the tower-tramway tests were used in low, medium, and high altitude aerial photography