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jbloomlab
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polyclonal
Model mutational escape from polyclonal antibodies.
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gradient of site spread regularization
#35
jbloom
closed
2 years ago
4
Extract atom locations
#34
caelanradford
closed
2 years ago
1
Refactor core calculations as free functions
#33
matsen
closed
2 years ago
1
Use JAX for automatic differentiation
#32
matsen
closed
1 year ago
2
Use JAX for automatic differentiation
#31
matsen
closed
1 year ago
9
Black formatting everything
#30
matsen
closed
2 years ago
2
3D coordinates for SARS-CoV-2 RBD
#29
jbloom
closed
2 years ago
5
Handle label overlap
#28
timcyu
closed
2 years ago
0
Overlapping labels in site bar zoom
#27
timcyu
closed
2 years ago
0
somehow automating pickling of models
#26
jbloom
closed
2 years ago
1
Specifying epitopes
#25
timcyu
closed
2 years ago
3
regularizing 3D spread of epitopes
#24
jbloom
closed
1 year ago
32
organize exptl design section in docs
#23
jbloom
closed
2 years ago
1
Library size notebook
#22
timcyu
closed
2 years ago
1
Mutation rate notebook
#21
timcyu
closed
2 years ago
1
some little fixes to the docs
#20
matsen
closed
2 years ago
0
Setting page width to 1300px
#19
matsen
closed
2 years ago
0
group lasso per site?
#18
jbloom
closed
1 year ago
15
sharing information across sites
#17
jbloom
opened
2 years ago
0
is the underlying statistical model correct (what about competing antibodies)
#16
jbloom
closed
2 years ago
11
estimating "error" on `beta` values and/or predictions
#15
jbloom
closed
2 years ago
37
Concentration notebook [new]
#14
timcyu
closed
2 years ago
4
Concentration Notebook [new]
#13
timcyu
closed
2 years ago
0
Concentration notebook
#12
timcyu
closed
2 years ago
4
modify icXX function to exclude variants with mutations not seen by the model
#11
timcyu
closed
2 years ago
3
compute ICXX values and add to simulation
#10
jbloom
closed
2 years ago
0
how to handle incorrect numbers of epitopes?
#9
jbloom
closed
2 years ago
1
compute the IC50 as a metric
#8
jbloom
closed
2 years ago
1
how does fitting accuracy scale with number of variants
#7
jbloom
closed
2 years ago
0
how many concentrations
#6
jbloom
closed
2 years ago
0
figure out what average mutation rate we want
#5
jbloom
closed
2 years ago
0
compare fitting of `polyclonal` and `torchdms`
#4
jbloom
closed
2 years ago
4
add gradient-based fitting and test on simulated data
#3
jbloom
closed
2 years ago
0
improve simulations, set up to fit internally with `scipy`
#2
jbloom
closed
2 years ago
0
merge a variety of re-factoring changes
#1
jbloom
closed
2 years ago
0
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