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163 results for “tensor”
Efficient parallelization of tensor network contractions for simulating quantum computation
<p> In this paper, we demonstrate a classical simulation framework for quantum computation by contracting tensor networks of sizes previously deemed out of reach. The main contribution of this work is a parallelization scheme called <em>index slicing</em> that breaks down an infeasibly large tensor network contraction task into smaller subtasks that can be executed fully in parallel, without interdependencies or intermediate communications. As a benchmarking example, we show that our algorithm can reduce the simulation of the Sycamore random circuit sampling task to less than 20 days, achieving an acceleration of over five orders of magnitude compared to the original proposal. We then showcase the capabilities of the simulation framework via investigations of near-term quantum algorithms and quantum error correction. Given the ubiquity of tensor networks in quantum information science, we believe that our simulation framework will be a valuable tool in the era of quantum information technology.</p>
Grond reports for the seismic moment tensor inversions done for "The January 2022 Hunga Volcano explosive eruption from the multi-technological perspective of CTBT monitoring"
<p>This are the Grond reports of the seismic moment tensor inversion done for the manuscript submitted to GJI titled:</p> <p>"The January 2022 Hunga Volcano explosive eruption from the multi-technological perspective of CTBT monitoring"</p> <p>You can view the summary figures of the inversions in the subfolders for each event manually if you wish.</p> <p>However to view the reports interactively you need to have the pyrocko and grond softwares installed. See here for installation instruction for pyrocko: https://pyrocko.org/ and here for grond https://pyrocko.org/grond/docs/current/</p> <p>After correct installation you can view the reports in any browser by executing the command "grond report --so" in the folder which contains the unpacked "report" folder.</p>
Evidence for microscopic kurtosis in neural tissue revealed by correlation tensor MRI
<p>Three sample double diffusion encoding (DDE) datasets for three female rat brains acquired using a 9.4T Bruker Biospec scanner equipped with an 86 mm quadrature transmission coil and four-element array reception cryocoil (Rat1_invivo_cti_data.nii, Rat2_invivo_cti_data.nii, Rat3_invivo_cti_data.nii).</p> <p>All animal experiments for the collection of these datasets were preapproved by the institutional and national authorities and carried out according to European Directive 2010/63.</p> <p>DDE data were acquired for 636 pairs of DDE b-values (bvals1.bval and bvals2.bval) and gradient directions (bvecs1.bvec and bvecs2.bvec) according to the DDE protocol for Correlation Tensor MRI (CTI) fitting described by Henriques et al. (Magn Reson Med 2021, doi:10.1002/mrm.28938).</p> <p>For each rat brain dataset, thermal noise from each cryocoil channel was suppressed using the threshold-based PCA denoising algorithm (Henriques et al., bioRxiv 2023, doi:10.1101/2023.03.29.534707). The denoised data was subsequently corrected for Gibbs ringing using the sub-voxel shift algorithm (Kellner et al. Magn Reson Med 2016, doi: 10.1002/mrm.26054) which is implemented in DIPY (Garyfallidis et al., Frontiers in Neuroinformatics 2014, doi: 10.3389/fninf.2014.00008). The processed diffusion-weighted signals from the four channels were then combined using sum-of-squares. Combined data for different gradient direction pairs were then aligned along the different b-values and directions using a sub-pixel registration technique (Guizar-Sicairos et al., Opt Lett. 2008, doi: 10.1364/ol.33.000156).</p> <p>Full description of these datasets acquisition and preprocessing can be found in its original manuscript (Henriques et al., Magn Reson Med 2021, doi:10.1002/mrm.28938).</p>
Diffusion Tensor Imaging (DTI) in Infants With Krabbe Disease
ClinicalTrials.gov study NCT00787865. IPD Sharing: NO. Countries: 1. Publications: 2.
Tractography and Diffusion Tensor Imaging of the Human Spinal Cord in Healthy Subjects : Anatomical Atlas
ClinicalTrials.gov study NCT05079945. IPD Sharing: NO. Countries: 1. Publications: 1.
Diffusion Tensor Brain MRI in the Detection of Structural Abnormality of the White Substance in Concussion
ClinicalTrials.gov study NCT06144359. IPD Sharing: NO. Countries: 1. Publications: 8.
Diffusion Tensor Weighted MRI in Alzheimer's Disease Modifying Treatment Effects of Galantamine (Reminyl®)
ClinicalTrials.gov study NCT00523666. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Clinical Experience With a Tensor Fasciae Latae Perforator Flap Based on Septocutaneous Perforators
ClinicalTrials.gov study NCT01136044. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparison of Intramuscular Distribution of Different Injection Volumes Via Diffusion Tensor Imaging (DTI)
ClinicalTrials.gov study NCT01162291. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Furlow Palatoplasty With Tensor Tenopexy
ClinicalTrials.gov study NCT01535131. IPD Sharing: NO. Countries: 1. Publications: 0.
Myofascial Release With and Without METS of Gluteus Maximus and Tensor Fascia Lata in ITB Syndrome
ClinicalTrials.gov study NCT04954703. IPD Sharing: NO. Countries: 1. Publications: 5.
Efficient parallelization of tensor network contractions for simulating quantum computation
Open the record for dataset details and reuse information.
Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI
<p>Repository of an anonymized sample patient dataset for paper "Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI"</p> <p>https://doi.org/10.1002/mrm.28328.</p>
Data from: Delay of gratification is associated with white matter connectivity in the dorsal prefrontal cortex: a diffusion tensor imaging study in chimpanzees (Pan troglodytes)
Individual variability in delay of gratification (DG) is associated with a number of important outcomes in both non-human and human primates. Using diffusion tensor imaging (DTI), this study describes the relationship between probabilistic estimates of white matter tracts projecting from the caudate to the prefrontal cortex (PFC) and DG abilities in a sample of 49 captive chimpanzees (Pan troglodytes). After accounting for time between collection of DTI scans and DG measurement, age and sex, higher white matter connectivity between the caudate and right dorsal PFC was found to be significantly associated with the acquisition (i.e. training phase) but not the maintenance of DG abilities. No other associations were found to be significant. The integrity of white matter connectivity between regions of the striatum and the PFC appear to be associated with inhibitory control in chimpanzees, with perturbations on this circuit potentially leading to a variety of maladaptive outcomes. Additionally, results have potential translational implications for understanding the pathophysiology of a number of psychiatric and clinical outcomes in humans.
Data from: Magnetic resonance imaging and tensor-based morphometry in the MPTP non-human primate model of Parkinson's disease
Parkinson's disease (PD) is the second most common neurodegenerative disorder producing a variety of motor and cognitive deficits with the causes remaining largely unknown. The gradual loss of the nigrostriatal pathway is currently considered the pivotal pathological event. To better understand the progression of PD and improve treatment management, defining the disease on a structural basis and expanding brain analysis to extra-nigral structures is indispensable. The anatomical complexity and the presence of neuromelanin, make the use of non-human primates an essential element in developing putative imaging biomarkers of PD. To this end, ex vivo T2-weighted magnetic resonance images were acquired from control and 1-methyl-4 phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated marmosets. Volume measurements of the caudate, putamen, and substantia nigra indicated significant atrophy and cortical thinning. Tensor-based morphometry provided a more extensive and hypothesis free assessment of widespread changes caused by the toxin insult to the brain, especially highlighting regional cortical atrophy. The results highlight the importance of developing imaging biomarkers of PD in non-human primate models considering their distinct neuroanatomy. It is essential to further develop these biomarkers in vivo to provide non-invasive tools to detect pre-symptomatic PD and to monitor potential disease altering therapeutics.
Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.
Non-human primate white matter development during the first year of life as assessed by diffusion tensor imaging and quantitative relaxometry
<p>In this project, we use diffusion tensor imaging (DTI) and quantitative relaxometry (QR) metrics to assess longitudinal changes in white matter (WM) throughout the postnatal rhesus macaque brain across the first year of life. DTI and QR metrics are measured at 3, 7, 13, 25, and 53 weeks of age in each of 35 non-human primates (NHPs) in this sample, for a total 175 datapoints (i.e., scans). Leveraging a previously published NHP WM atlas (Adluru et al., 2012; Zakszewski et al., 2014), we assess WM microstructure in 76 WM regions across the brain. DTI metrics include fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD); the QR metric assessed is the longitudinal relaxation rate (qR<sub>1</sub>). These longitudinal data enable the direct comparison of DTI and QR metrics in very early life on a within-subject level, as well as robust, multimodal modeling of WM growth in infancy, providing insights into early postnatal neurodevelopment that may have important implications neuropsychiatric and neurodevelopmental disorders in childhood.</p>
Fig. 3 in Microstructural Impact of Ischemia and Bone Marrow-Derived Cell Therapy Revealed With Diffusion Tensor Magnetic Resonance Imaging Tractography of the Heart In Vivo
Fig. 3. Amblyomma variegatum female before engorgement
Data from: Validation of diffusion tensor imaging measures of nigrostriatal neurons in macaques
Objective: Interpretation of diffusion MRI in the living brain requires validation against gold standard histological measures. We compared diffusion values of the nigrostriatal tract to PET and histological results in non-human primates (NHPs) with varying degrees of unilateral nigrostriatal injury induced by MPTP, a toxin selective for dopaminergic neurons. Methods: Sixteen NHPs had MRI and PET scans of three different presynaptic radioligands and blinded video-based motor ratings before and after unilateral carotid artery infusion of variable doses of MPTP. Diffusion measures of connections between midbrain and striatum were calculated. Then animals were euthanized to quantify striatal dopamine concentration, stereologic measures of striatal tyrosine hydroxylase (TH) immunostained fiber density and unbiased stereologic counts of TH stained nigral cells. Results: Diffusion measures correlated with MPTP dose, nigral TH-positive cell bodies and striatal TH-positive fiber density but did not correlate with in vitro nigrostriatal terminal field measures or in vivo PET measures of striatal uptake of presynaptic markers. Once nigral TH cell count loss exceeded 50% the stereologic terminal field measures reached a near zero floor effect but the diffusion measures continued to correlate with nigral cell counts. Conclusion: Diffusion measures in the nigrostriatal tract correlate with nigral dopamine neurons and striatal fiber density, but have the same relationship to terminal field measures as a previous report of striatal PET measures of presynaptic neurons. These diffusion measures have the potential to act as non-invasive index of the severity of nigrostriatal injury. Diffusion imaging of the nigrostriatal tract could potentially have diagnostic value in humans with Parkinson disease or related disorders.
ICML Supplement Absolute Times for Uber Tensor
<p>Absolute times for 40 iterations, Uber Tensor</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.