https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4998301/
Predicting the risk for lymphoma development in Sjogren syndrome
An easy tool for clinical use
Sofia Fragkioudaki, MD,a Clio P. Mavragani, MD,a,b,c,∗ and Haralampos M. Moutsopoulos, MD, FACP, FRCP, MACRb,c
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Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
Recording file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
Probe file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
Recording Duration: 1200.0s
Data Type: int16
#Channels in file: 64
#Sites: 64
#Shanks: 1
Pre-processing
Filter type: bandpass
Filter range (Hz): [300.0, 8000.0]
Common ref: trimmean
Whiten: 0
FFT threshold: 8
blank threshold: 0
Events
#Spikes: 510735
Feature extracted: gpca
#Sites/event: 18
maxDist_site_um: 50
maxDist_site_spk_um: 100
spkLim_ms: [-0.250, 0.750]
#Features/event: 45
#PC/chan: 2.500000e+00
Cluster
#Clusters: 88
#Unique events: 508992
min. spk/clu: 30
Cluster method: drift-knn
knn: 30
step_sec_drift: 20.0s
batch_sec_drift: 300.0s
Auto-merge
delta_cut: 1.000
maxWavCor: 0.990
Runtime (s)
Detect + feature (s): 156.2s
Cluster runtime (s): 36.5s
merge runtime (s): 12.4s
Total runtime (s): 205.0s
Runtime speed: x5.9 realtime
Processing speed: 2491.4 spikes/s
memory usage (GiB): -0.018
detect: -0.048
sort: -0.018
auto-merge: -0.018
Execution
irc2 version: v5.5.4
fGpu (GPU use): 0
fParfor (parfor use): 0
fLargeRecording: 0
Parameter file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
Recording file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
Probe file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
Recording Duration: 1200.0s
Data Type: int16
#Channels in file: 64
#Sites: 64
#Shanks: 1
Pre-processing
Filter type: bandpass
Filter range (Hz): [300.0, 8000.0]
Common ref: trimmean
Whiten: 0
FFT threshold: 8
blank threshold: 0
Events
#Spikes: 510737
Feature extracted: gpca
#Sites/event: 18
maxDist_site_um: 50
maxDist_site_spk_um: 100
spkLim_ms: [-0.250, 0.750]
#Features/event: 45
#PC/chan: 2.500000e+00
Cluster
#Clusters: 84
#Unique events: 502857
min. spk/clu: 30
Cluster method: drift-knn
knn: 30
step_sec_drift: 20.0s
batch_sec_drift: 300.0s
Auto-merge
delta_cut: 1.000
maxWavCor: 0.990
Runtime (s)
Detect + feature (s): 92.5s
Cluster runtime (s): 20.3s
merge runtime (s): 12.7s
Total runtime (s): 125.4s
Runtime speed: x9.6 realtime
Processing speed: 4072.3 spikes/s
memory usage (GiB): 0.049
detect: 0.049
sort: 0.049
auto-merge: 0.049
Execution
irc2 version: v5.5.4
fGpu (GPU use): 1
fParfor (parfor use): 0
fLargeRecording: 0
Parameter file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
Recording file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
Probe file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
Recording Duration: 1200.0s
Data Type: int16
#Channels in file: 64
#Sites: 64
#Shanks: 1
Pre-processing
Filter type: bandpass
Filter range (Hz): [300.0, 8000.0]
Common ref: trimmean
Whiten: 0
FFT threshold: 8
blank threshold: 0
Events
#Spikes: 510735
Feature extracted: gpca
#Sites/event: 18
maxDist_site_um: 50
maxDist_site_spk_um: 100
spkLim_ms: [-0.250, 0.750]
#Features/event: 45
#PC/chan: 2.500000e+00
Cluster
#Clusters: 88
#Unique events: 508992
min. spk/clu: 30
Cluster method: drift-knn
knn: 30
step_sec_drift: 20.0s
batch_sec_drift: 300.0s
Auto-merge
delta_cut: 1.000
maxWavCor: 0.990
Runtime (s)
Detect + feature (s): 58.3s
Cluster runtime (s): 24.8s
merge runtime (s): 9.4s
Total runtime (s): 92.5s
Runtime speed: x13.0 realtime
Processing speed: 5522.3 spikes/s
memory usage (GiB): 0.065
detect: 0.065
sort: 0.018
auto-merge: 0.018
Execution
irc2 version: v5.5.4
fGpu (GPU use): 0
fParfor (parfor use): 1
fLargeRecording: 0
Parameter file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
------------------------------
Summary of ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------
Recording format
Recording file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/raw.mda
Probe file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/geom.csv
Recording Duration: 1200.0s
Data Type: int16
#Channels in file: 64
#Sites: 64
#Shanks: 1
Pre-processing
Filter type: bandpass
Filter range (Hz): [300.0, 8000.0]
Common ref: trimmean
Whiten: 0
FFT threshold: 8
blank threshold: 0
Events
#Spikes: 510737
Feature extracted: gpca
#Sites/event: 18
maxDist_site_um: 50
maxDist_site_spk_um: 100
spkLim_ms: [-0.250, 0.750]
#Features/event: 45
#PC/chan: 2.500000e+00
Cluster
#Clusters: 84
#Unique events: 502857
min. spk/clu: 30
Cluster method: drift-knn
knn: 30
step_sec_drift: 20.0s
batch_sec_drift: 300.0s
Auto-merge
delta_cut: 1.000
maxWavCor: 0.990
Runtime (s)
Detect + feature (s): 38.1s
Cluster runtime (s): 15.2s
merge runtime (s): 9.3s
Total runtime (s): 62.6s
Runtime speed: x19.2 realtime
Processing speed: 8152.4 spikes/s
memory usage (GiB): 0.018
detect: 0.018
sort: -0.029
auto-merge: -0.029
Execution
irc2 version: v5.5.4
fGpu (GPU use): 1
fParfor (parfor use): 1
fLargeRecording: 0
Parameter file: ~/ceph/groundtruth/hybrid_synth/static_siprobe/rec_64c_1200s_11/irc2/raw_geom.prm
------------------------------OS: CentOS Linux 7
Memory: 251.7 GiB
Processor: Intel® Xeon(R) CPU E5-2643 v4 @ 3.40GHz × 24
Graphics: Quadro P4000/PCIe/SSE2
after filling the missing values with the median value per dimension do a low-rank approximation (svd) and re-project the matrix and repeat until the missing value vector values converge. It was tested to about ~70% missing matrix.
also, he runs a fast-tsne (Mannas’ implementation) followed by K-means to cluster the genetic data. Better discrimination when you apply missing-value filling procedure using the low-rank matrix method.
https://www.dell.com/community/Inspiron/Suspend-resume-problems-on-Ubuntu-18-04/td-p/6072410
1. I already had the Nvidia drivers installed and was already using them
2. sudo systemctl disable nvidia-fallback.service
3. Edited /etc/default/grub and added the line :
GRUB_CMDLINE_LINUX=”nouveau.blacklist=1″
4. sudo update-grub
5. Restarted the laptop
wget http://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_418.87.00_linux.run
sudo sh cuda_10.1.243_418.87.00_linux.runQT is required for yakuake
sudo apt-get install build-essential
sudo apt-get install qtcreator
sudo apt-get install qt5-default
sudo apt-get install qt5-doc
sudo apt-get install qt5-doc-html qtbase5-doc-html
sudo apt-get install qtbase5-examples[installing yakuake (pull-down terimnal)]sudo apt-get install yakuake
install docker
run sudo service docker start
share docker daemon on windows and wsl
Export and import WSL environment:
wsl –export Ubuntu-18.04 ubuntu.tar
