scholarly journals Towards a Computational Framework for Automated Discovery and Modeling of Biological Rhythms from Wearable Data Streams

2021 ◽  
pp. 643-661
Author(s):  
Runze Yan ◽  
Afsaneh Doryab
2020 ◽  
Author(s):  
Zhenqin Wu ◽  
Bryant B. Chhun ◽  
Galina Schmunk ◽  
Chang N. Kim ◽  
Li-Hao Yeh ◽  
...  

Morphological states of human cells are widely imaged and analyzed to diagnose diseases and to discover biological mechanisms. Morphodynamics of cells capture their functions more fully than their morphology. Discovery of morphodynamic states of human cells is challenging, because genetic labeling or manual annotation may not be feasible. We propose a computational framework, DynaMorph, that combines quantitative label-free imaging and deep learning for automated discovery of morphodynamic states. As a case study, we apply DynaMorph to study the morphodynamic states of live primary human microglia, which are mobile immune cells of the brain that exhibit complex functional states. DynaMorph identifies two distinct morphodynamic states of microglia under perturbation by cytokines and glioblastoma supernatant. We find that microglia actively transition between the two states. Moreover, single-cell RNA-sequencing of the perturbed microglia shows that the morphodynamic states correspond to distinct transcriptomic clusters of the cells, revealing how perturbations alter gene expression and phenotype. DynaMorph can broadly enable automated discovery of functional states of cellular systems.


2014 ◽  
Vol 11 (101) ◽  
pp. 20140826 ◽  
Author(s):  
Ishanu Chattopadhyay ◽  
Hod Lipson

From automatic speech recognition to discovering unusual stars, underlying almost all automated discovery tasks is the ability to compare and contrast data streams with each other, to identify connections and spot outliers. Despite the prevalence of data, however, automated methods are not keeping pace. A key bottleneck is that most data comparison algorithms today rely on a human expert to specify what ‘features' of the data are relevant for comparison. Here, we propose a new principle for estimating the similarity between the sources of arbitrary data streams, using neither domain knowledge nor learning. We demonstrate the application of this principle to the analysis of data from a number of real-world challenging problems, including the disambiguation of electro-encephalograph patterns pertaining to epileptic seizures, detection of anomalous cardiac activity from heart sound recordings and classification of astronomical objects from raw photometry. In all these cases and without access to any domain knowledge, we demonstrate performance on a par with the accuracy achieved by specialized algorithms and heuristics devised by domain experts. We suggest that data smashing principles may open the door to understanding increasingly complex observations, especially when experts do not know what to look for.


2017 ◽  
Vol 76 ◽  
pp. 561-581 ◽  
Author(s):  
Feng Gao ◽  
Muhammad Intizar Ali ◽  
Edward Curry ◽  
Alessandra Mileo

2020 ◽  
Author(s):  
Runze Yan ◽  
Xinwen Liu ◽  
Janine M Dutcher ◽  
Michael J Tumminia ◽  
Daniella Villalba ◽  
...  

AbstractThis paper presents CoRhythMo, the first computational framework for modeling biobehavioral rhythms - the repeating cycles of physiological, psychological, social, and environmental events - from mobile and wearable data streams. The framework incorporates four main components: mobile data processing, rhythm discovery, rhythm modeling, and machine learning. We use a dataset of smartphone and Fitbit data collected from 138 college students over a semester to evaluate the framework’s ability to 1) model biobehavioral rhythms of students, 2) measure the stability of their rhythms over the course of the semester, 3) model differences between rhythms of students with different health status, and 4) predict the mental health status in students using the model of their biobehavioral rhythms. Our evaluation provides evidence for the feasibility of using CoRhythMo for modeling and discovering human rhythms and using them to assess and predict different life and health outcomes.


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