scholarly journals FARCI: Fast and Robust Connectome Inference

2021 ◽  
Vol 11 (12) ◽  
pp. 1556
Author(s):  
Saber Meamardoost ◽  
Mahasweta Bhattacharya ◽  
Eun Jung Hwang ◽  
Takaki Komiyama ◽  
Claudia Mewes ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Neuron ◽  
Computationally Efficient ◽  
Noise Levels ◽  
Two Photon ◽  
Computational Speed ◽  
Partial Correlations ◽  
Analysis Package ◽  
Matlab Package ◽  
Neural Anatomy

The inference of neuronal connectome from large-scale neuronal activity recordings, such as two-photon Calcium imaging, represents an active area of research in computational neuroscience. In this work, we developed FARCI (Fast and Robust Connectome Inference), a MATLAB package for neuronal connectome inference from high-dimensional two-photon Calcium fluorescence data. We employed partial correlations as a measure of the functional association strength between pairs of neurons to reconstruct a neuronal connectome. We demonstrated using in silico datasets from the Neural Connectomics Challenge (NCC) and those generated using the state-of-the-art simulator of Neural Anatomy and Optimal Microscopy (NAOMi) that FARCI provides an accurate connectome and its performance is robust to network sizes, missing neurons, and noise levels. Moreover, FARCI is computationally efficient and highly scalable to large networks. In comparison with the best performing connectome inference algorithm in the NCC, Generalized Transfer Entropy (GTE), and Fluorescence Single Neuron and Network Analysis Package (FluoroSNNAP), FARCI produces more accurate networks over different network sizes, while providing significantly better computational speed and scaling.

scholarly journals FARCI: Fast and Robust Connectome Inference

2020 ◽  
Author(s):  
Saber Meamardoost ◽  
Mahasweta Bhattacharya ◽  
EunJung Hwang ◽  
Takaki Komiyama ◽  
Claudia Mewes ◽  
...  
Keyword(s):  
Computational Neuroscience ◽  
Calcium Imaging ◽  
Large Scale ◽  
High Dimensional ◽  
Computationally Efficient ◽  
Noise Levels ◽  
Two Photon ◽  
Computational Speed ◽  
Partial Correlations ◽  
Matlab Package

AbstractThe inference of neuronal connectome from large-scale neuronal activity recordings, such as two-photon Calcium imaging, represents an active area of research in computational neuroscience. In this work, we developed FARCI (Fast and Robust Connectome Inference), a MATLAB package for neuronal connectome inference from high-dimensional two-photon Calcium fluorescence data. We employed partial correlations as a measure of the functional association strength between pairs of neurons to reconstruct a neuronal connectome. We demonstrated using gold standard datasets from the Neural Connectomics Challenge (NCC) that FARCI provides an accurate connectome and its performance is robust to network sizes, missing neurons, and noise levels. Moreover, FARCI is computationally efficient and highly scalable to large networks. In comparison to the best performing algorithm in the NCC, FARCI produces more accurate networks over different network sizes and subsampling, while providing over two orders of magnitude faster computational speed.

scholarly journals Anatomical Modeling of Brain Vasculature in Two-Photon Microscopy by Generalizable Deep Learning

BME Frontiers ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Waleed Tahir ◽  
Sreekanth Kura ◽  
Jiabei Zhu ◽  
Xiaojun Cheng ◽  
Rafat Damseh ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Imaging Systems ◽  
Total Variation Regularization ◽  
Computationally Efficient ◽  
Two Photon Microscopy ◽  
Two Photon ◽  
Brain Vasculature ◽  
Vascular Segmentation ◽  
Anatomical Modeling

Objective and Impact Statement. Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here, we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. Introduction. Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems and is able to segment large-scale angiograms. Methods. We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in vivo angiograms from mouse brains of dimensions up to 808×808×702 μm. Results. To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art. Conclusion. Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning-based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

scholarly journals Anatomical modeling of brain vasculature in two-photon microscopy by generalizable deep learning

2020 ◽  
Author(s):  
Waleed Tahir ◽  
Sreekanth Kura ◽  
Jiabei Zhu ◽  
Xiaojun Cheng ◽  
Rafat Damseh ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Imaging Systems ◽  
Total Variation Regularization ◽  
Computationally Efficient ◽  
Two Photon Microscopy ◽  
Two Photon ◽  
Brain Vasculature ◽  
Vascular Segmentation ◽  
Anatomical Modeling

AbstractObjective and Impact StatementSegmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis.IntroductionVascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems, or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems, and is able to segment large-scale angiograms.MethodsWe employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and a total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in-vivo angiograms from mouse brains of dimensions up to 808×808×702 μm.ResultsTo demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope, and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art.ConclusionOur work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

scholarly journals Anatomical Modeling of Brain Vasculature in Two-Photon Microscopy by Generalizable Deep Learning

BME Frontiers ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Waleed Tahir ◽  
Sreekanth Kura ◽  
Jiabei Zhu ◽  
Xiaojun Cheng ◽  
Rafat Damseh ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Imaging Systems ◽  
Total Variation Regularization ◽  
Computationally Efficient ◽  
Two Photon Microscopy ◽  
Two Photon ◽  
Brain Vasculature ◽  
Vascular Segmentation ◽  
Anatomical Modeling

Objective and Impact Statement. Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here, we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. Introduction. Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems and is able to segment large-scale angiograms. Methods. We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in vivo angiograms from mouse brains of dimensions up to 808×808×702 μm. Results. To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art. Conclusion. Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning-based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

Cloud-Based Multimedia Content Protection System

2020 ◽  
pp. 164-169
Author(s):  
B. Aparna ◽  
S. Madhavi ◽  
G. Mounika ◽  
P. Avinash ◽  
S. Chakravarthi
Keyword(s):  
Large Scale ◽  
Protection System ◽  
Multimedia Content ◽  
Computationally Efficient ◽  
Content Protection ◽  
Protection Systems ◽  
Multimedia Content Protection ◽  
High Scalability ◽  
Cloud Infrastructures ◽  
Rapid Deployment

We propose a new design for large-scale multimedia content protection systems. Our design leverages cloud infrastructures to provide cost efficiency, rapid deployment, scalability, and elasticity to accommodate varying workloads. The proposed system can be used to protect different multimedia content types, including videos, images, audio clips, songs, and music clips. The system can be deployed on private and/or public clouds. Our system has two novel components: (i) method to create signatures of videos, and (ii) distributed matching engine for multimedia objects. The signature method creates robust and representative signatures of videos that capture the depth signals in these videos and it is computationally efficient to compute and compare as well as it requires small storage. The distributed matching engine achieves high scalability and it is designed to support different multimedia objects. We implemented the proposed system and deployed it on two clouds: Amazon cloud and our private cloud. Our experiments with more than 11,000 videos and 1 million images show the high accuracy and scalability of the proposed system. In addition, we compared our system to the protection system used by YouTube and our results show that the YouTube protection system fails to detect most copies of videos, while our system detects more than 98% of them.

scholarly journals GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hongyi Zhang ◽  
Xiaowei Zhan ◽  
Bo Li
Keyword(s):  
T Cell ◽  
T Cell Receptor ◽  
Large Scale ◽  
Cell Receptor ◽  
Alignment Algorithm ◽  
Computationally Efficient ◽  
Antigen Specificity ◽  
Non Invasive ◽  
Isometric Transformation ◽  
Specific Receptors

AbstractSimilarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform.

An Efficient Preconditioner for Linear System Solution in Multi-Domain Modeling of the Circulatory System

2013 ◽  
Author(s):  
Mahdi Esmaily Moghadam ◽  
Yuri Bazilevs ◽  
Tain-Yen Hsia ◽  
Alison Marsden
Keyword(s):  
Strong Coupling ◽  
Large Scale ◽  
Computational Cost ◽  
Circulatory System ◽  
Flow Simulation ◽  
Global Dynamics ◽  
Domain Modeling ◽  
Computationally Efficient ◽  
Lumped Parameter ◽  
System Solution

A closed-loop lumped parameter network (LPN) coupled to a 3D domain is a powerful tool that can be used to model the global dynamics of the circulatory system. Coupling a 0D LPN to a 3D CFD domain is a numerically challenging problem, often associated with instabilities, extra computational cost, and loss of modularity. A computationally efficient finite element framework has been recently proposed that achieves numerical stability without sacrificing modularity [1]. This type of coupling introduces new challenges in the linear algebraic equation solver (LS), producing an strong coupling between flow and pressure that leads to an ill-conditioned tangent matrix. In this paper we exploit this strong coupling to obtain a novel and efficient algorithm for the linear solver (LS). We illustrate the efficiency of this method on several large-scale cardiovascular blood flow simulation problems.

ON THE LOCATION AND CONTINUATION OF HOPF BIFURCATIONS IN LARGE-SCALE PROBLEMS

2008 ◽  
Vol 18 (05) ◽  
pp. 1589-1597 ◽  
Author(s):  
M. FRIEDMAN ◽  
W. QIU
Keyword(s):  
Dynamical Systems ◽  
Large Scale ◽  
Orthonormal Basis ◽  
Invariant Subspaces ◽  
Hopf Bifurcations ◽  
Augmented System ◽  
Large Scale Problems ◽  
System Technique ◽  
Matlab Package ◽  
Parameter Dependent

CL_MATCONT is a MATLAB package for the study of dynamical systems and their bifurcations. It uses a minimally augmented system for continuation of the Hopf curve. The Continuation of Invariant Subspaces (CIS) algorithm produces a smooth orthonormal basis for an invariant subspace [Formula: see text] of a parameter-dependent matrix A(s). We extend a minimally augmented system technique for location and continuation of Hopf bifurcations to large-scale problems using the CIS algorithm, which has been incorporated into CL_MATCONT. We compare this approach with using a standard augmented system and show that a minimally augmented system technique is more suitable for large-scale problems. We also suggest an improvement of a minimally augmented system technique for the case of the torus continuation.

A Low-Fidelity Stochastic Model of Viral Spread in Aircraft to Assess Risk Mitigation Strategies

2021 ◽  
Author(s):  
Leigh McCue
Keyword(s):  
Large Scale ◽  
Risk Mitigation ◽  
Mitigation Strategies ◽  
Traffic Network ◽  
Computationally Efficient ◽  
Passenger Compartment ◽  
Stochastic Effects ◽  
Viral Spread ◽  
Risk Mitigation Strategies ◽  
Baseline Health

Abstract The purpose of this work is to develop a computationally efficient model of viral spread that can be utilized to better understand influences of stochastic factors on a large-scale system - such as the air traffic network. A particle-based model of passengers and seats aboard a single-cabin 737-800 is developed for use as a demonstration of concept on tracking the propagation of a virus through the aircraft's passenger compartment over multiple flights. The model is sufficiently computationally efficient so as to be viable for Monte Carlo simulation to capture various stochastic effects, such as number of passengers, number of initially sick passengers, seating locations of passengers, and baseline health of each passenger. The computational tool is then exercised in demonstration for assessing risk mitigation of intervention strategies, such as passenger-driven cleaning of seating environments and elimination of middle seating.

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