APR 12 2022
-
Dmytro:
- updates on qnet application
- IPF doc complete?
- ASD results?
-
David
- print cognet state
- testtrain split
- PTSD example
- NN estimate of neighbor coordinates
-
Nic
- network represention
- discussion with literature
- python script fro searching pubmed for associations
-
Drew
- write why patternly is important
- plot
- Marian' meeting Thursday
- update paper
-
Kevin
- why is the axis zero in panel 1 (befor emergence).. how doe sit look with log
- look at diffusion diameter
- strat a notebook for diffusion analysis
- qnet uncertainty analysis
- make clusters and look more closely at teh geometry
-
Mei wei
- classification and categorization of complex diseases from the perspective of screening and diagnostic tools
- importance of prevalence, false neg cost, false pos cost, ethics of early diagnosis
- Can we identify the optimal operating point given these considerations
- classification and categorization of complex diseases from the perspective of screening and diagnostic tools
-
Nicole Li
- meeting with David
- PTSD notebook annotation
APR 6 2022
-
Dmytro:
- updates on pscore
- updates on asd
- ucm on ADRD deleting amnesia, already ran it --> 0.794 .788 (without)
- truven? runs.
- IPF NN results?
- ASD results?
-
David
- NN results? update
- saving of models
-
Nic
- network represention
- discussion with lietaryure
-
Drew
- write why patternly is important
- plot
- Marian' meeting Thursday
- update paper
-
Kevin
- why is the axis zero in panel 1 (befor emergence).. how doe sit look with log
- look at diffusion diameter
- strat a notebook for diffusion analysis
- qnet uncertainty analysis
- make clusters and look more closely at teh geometry
Mar 30 2022
-
Dmytro:
- updates on pscore
- updates on asd
- ucm on ADRD deleting amnesia, already ran it --> 0.794 .788 (without)
- truven? runs.
- IPF NN results?
- ASD results?
-
David
- NN results? update
- saving of models
-
Nic
- how the biomes actually interact *
- plot the network structure of the top biomes * remove iterfeeding arcs
- closure with the top biomes
- look in thelitrature which interactions are knowm
- link me to Fig 1 fig 2 csvs
-
Drew
- update
- plot
- discuss Marian' comments
- Need a complete descriptoion of the tools so far
-
Kevin
- why is the axis zero in panel 1 (befor emergence).. how doe sit look with log
- look at diffusion diameter
- strat a notebook for diffusion analysis
- qnet uncertainty analysis
- make clusters and look more closely at teh geometry
Mar 23
-
Dmytro:
- updates on pscore
- updates on asd
- ucm on ADRD deleting amnesia, already ran it --> 0.794 .788 (without)
- truven? runs.
-
David
- NN results? update
- saving of models
-
Nic
- feeding control
- what are the poinst of simialrities/differences with K's paper
- finalize vingettes for figures
- how the biomes actually interact
- plot the network structure of the top biomes
-
Drew
- update
- plot
- discuss Marian' comments
- Need a complete descriptoion of the tools so far
-
Kevin
- why is the axis zero in panel 1 (befor emergence).. how doe sit look with log
- look at diffusion diameter
- strat a notebook for diffusion analysis
- qnet uncertainty analysis
Mar 2
Feb 16
-
nic
- lfs push the big file
- fig 1 i will do
- fig 2 regress on head center growth
dmytro
- drew
- david
- kevin
- nicole
Feb 9
- nic
Feb 2
- dmytro
- frailty paper explanation of downsampling
- add table
- generate ADRD results
-
Nic
- figure 1. feeding variable included qnets for dataset 1
- individual results
- feeding variable: what does the feeding impact the ecosystem
- confidence variables
-
David
- find a measure of neighborhood density for each sample
-
drew
- agitation results (how many are correct?)
- Add library
- Monday 330
-
kevin
- Results: match?
- Share : put them in the dataframe?
- compare the variant distance
Jan 26
- dmytro
- frailty paper explanation of downsampling
- add table
- generate ADRD results
-
Nic
- friday 430
- figure 1. feeding variable included qnets for dataset 1
-
David
- find a measure of neighborhood density for each sample
-
drew
- agitation results (how many are correct?)
- Add library
- Monday 330
-
kevin
- Influenza analysis (data is miising?)
- dominant strain per flu season
- 202021 Sep 2021
Jan 19
- dmytro
- frailty paper explanation of downsampling
- add table
- generate ADRD results
-
Nic
- paper update
- DFI hypotheses
-
David
- find a measure of neighborhood density for each sample
- drew
- finish agitation PAI
- Add library
Jan 12
- dmytro
- frailty paper sub
- adrd paper sub
-
Nic
- figures for DFI
- paper prop
-
David
- small samples completed
- 1785 samples?
- drew
- finish agitation PAI
- Add library
Jan 3, 2022
-
david
- random vs qnet disssonance
- incorporate into cognet
Nicholas
- dmytro ifx
dec 13 2021
-
drew
- meeting this week (?)... Friday
- new dataset
-
Dmytro
- IPF results
- NN writeup
-
Nick
- Thursday(?)
Dec 6, 2021
- Nick
- paper
- narrative
- qbiome upadted code
- dmytro
- cell writeup
- david
- docuemntation for cognet
Nov 15, 2021
-
drew
- pattern of patterns (performance eval)
- ALex next steps
-
david
- status of 4 steps
- qnet construction error fixed
- # 4------) the example on cognet repo is not complete. Make it so that it is.. it computes qnet, adds polar features, computes distance matrix on a sample # and can update poles and recompute # 5-----) check trees to make sure no "nan" in qnet (eg. after taking qsamples) # 6-----) embedding
-
dmytro
- ADRD/ASD performance
- erik meeting
-
nic
- lets start draft
- datframe comparison (resolve conlict)
- alpha vs time
-
lucas
- hypothesis class for cognet
Nov 8, 2021
-
drew
- pattern of patterns (performance eval)
-
david
- check for ther nan bug.
- Please organize where current results are: dmat,embed,pca,clusters, figures, csvs
-
dmytro
- IPF (done for Dmytro)
- CKD Arleen (done)
- Alex cancers (ongoing)
- EDA for ASD
- EDA for "pneumococcal pneumonia" Pnenomia codes
-
nic
- looking at the hypothesis datframes
- simulate the cycle model
- doing the qbiome analysis for class
-
lucas
- hypothesis class for cognet
Nov 1, 2021
-
drew
- pattern of patterns (performance eval)
-
david
- check for ther nan bug.
- Please organize where current results are: dmat,embed,pca,clusters, figures, csvs
-
dmytro
- IPF (done for Dmytro)
- CKD Arleen (done)
- Alex cancers (ongoing)
- EDA for ASD
- EDA for "pneumococcal pneumonia" Pnenomia codes
-
nic
- looking at the hypothesis datframes
- simulate the cycle model
- doing the qbiome analysis for class
-
lucas
- hypothesis class for cognet
Oct 25, 2021
-
drew
-
david
- add polar vectors
- see movement of cluster of cluster vectors on qsampling
- Notes: wher are dmat, embed files?
- Please organize where current results are: dmat,embed,pca,clusters, figures, csvs
-
dmytro
- IPF (done for Dmytro)
- CKD Arleen (done)
- Alex cancers (ongoing)
- EDA for ASD
- EDA for "pneumococcal pneumonia" Pnenomia codes
-
nic
- looking at the hypothesis datframes
- doing the qbiome analysis for class
-
lucas
- hypothesis class for cognet
Oct 20, 2021
-
drew
- fixed PFSA segfaults
- lets meet Friday 430PM
-
david
- do teh PCA for 2016 for polar vectors
- perturb the opinion centers for steps =20, 120
-
dmytro
- IPF (done for Dmytro)
- CKD Arleen (done)
- Alex cancers (ongoing)
- EDA for ASD
- EDA for "pneumococcal pneumonia" Pnenomia codes
-
nic
- looking at the hypothesis datframes
- doing the qbiome analysis for class
lucas
oct 13, 2021
-
drew
- anomaly within 2 hrs (83/ 530 ~15%%s)
- seg faults |
-
david
- get clusters /cluster center opinion vectors
- collect the opinion vectors into a polar csv
- cluster the polar csv
-
dmytro
- plots AED for autism
-
nic
- question of alpha parameter (subtle)
- can we have instability with alpha < 0?
- friday 430.
Sep 29, 2021
-
drew
- interictal period
-
dmytro
- autism infection POS vs NEG pscores (look at negative or RR < 1, dont do square)
- manic trajectory:
-
david
- add notebook to repo, make clean directory
- generate distance matrices and embeddings for all years
-
nic
- add notebook to scratch2
- sign of network
- qualitative stability
- Monday 330.. discuss alpha(p,q)
- https://github.com/zeroknowledgediscovery/scratch_2/blob/master/sample_networks.ipynb
- qualitative stability
- color test
Sep22,2021
- drew
- patternly | seizures (time period upto before seizure. lets train on preictal period)
- dmytro
- manic | patient movement through clusters
- david
- cognet mpi 1-off error: should be fixed now
- documentation---
- GSS notebook update--- 1
- POlar vector distance notebook
- set_nsamples arguments
- nic
- qbiome run (isuues: label matrix has nans)
- hypothesis and graphtool setup
- network signature goes down
- victor
- ?