Skip to content

Commit

Permalink
sync with manuscript (#89)
Browse files Browse the repository at this point in the history 
* sync with manuscript

* upgrade python

* update dependencies
  • Loading branch information
@armaan-abraham
armaan-abraham authored May 16, 2024
1 parent ef070d1 commit 4747ef5
Show file tree
Hide file tree
Showing 36 changed files with 25,180 additions and 12,102 deletions.
13 changes: 4 additions & 9 deletions maserol/core.py
View file
Original file line number Diff line number Diff line change
@@ -1,25 +1,20 @@
# Base Python
from copy import deepcopy
from typing import Collection, Dict, Tuple

# Extended Python
import numpy as np
import xarray as xr
from scipy.optimize import least_squares, newton


# Current Package
from .util import (
assemble_Ka,
HIgGs,
DEFAULT_RCPS,
HIgGs,
assemble_Ka,
logistic_ligand_map,
n_logistic_ligands,
)


"""
This implementation relies on the multivalent binding model paper:
This is an implementation of the binding model from
https://www.sciencedirect.com/science/article/pii/S002555642100122X.
"""

Expand Down Expand Up @@ -70,7 +65,7 @@ def model_loss(
np.where(
residual_mask,
np.nan_to_num(
(np.log(Lbound) - np.log(data.values)),
(np.log(Lbound + 1) - np.log(data.values + 1)),
neginf=0,
posinf=0,
),
Expand Down
Binary file added maserol/data/cache/2f_perturbations.nc
View file
Binary file not shown.
Binary file added maserol/data/cache/2f_perturbations_backup.nc
View file
Binary file not shown.
194 changes: 133 additions & 61 deletions maserol/data/cache/3e.csv
View file
Original file line number Diff line number Diff line change
@@ -1,61 +1,133 @@
,r2,r,Ligand,Missingness
0,-0.21695427653073018,0.6039906264543344,IgG1,0.1
1,0.7186801420257153,0.8510340726188023,IgG3,0.1
2,0.4371867811704755,0.9150668376882705,FcR2A,0.1
3,0.33702274861383097,0.9447478999698466,FcR2B,0.1
4,0.6188473361693961,0.8832007340440785,FcR3A,0.1
5,0.584092556745825,0.9851544896778108,FcR3B,0.1
6,-0.5102327315046409,0.5058805542954073,IgG1,0.2
7,0.6247769763040301,0.8256309531587698,IgG3,0.2
8,0.4252004457391121,0.9540751667868318,FcR2A,0.2
9,0.23954272307826274,0.9219179257443371,FcR2B,0.2
10,0.5467353976192728,0.9695377891031652,FcR3A,0.2
11,0.5797838137648523,0.9682765949178817,FcR3B,0.2
12,-0.8871985554078814,0.48757760718437276,IgG1,0.30000000000000004
13,0.6882520196867776,0.8345912987489575,IgG3,0.30000000000000004
14,0.4037886738404426,0.9227305930583487,FcR2A,0.30000000000000004
15,0.21726524323258334,0.933808466866401,FcR2B,0.30000000000000004
16,0.613376836186367,0.9419339841973344,FcR3A,0.30000000000000004
17,0.589238419870306,0.9755748698379315,FcR3B,0.30000000000000004
18,-0.9985188725462029,0.5570903127193426,IgG1,0.4
19,0.7470870054395163,0.8643691560433703,IgG3,0.4
20,0.3762218180026976,0.9176276793329619,FcR2A,0.4
21,0.29805181870796327,0.941962254999225,FcR2B,0.4
22,0.5733943437318313,0.9696937596307974,FcR3A,0.4
23,0.5299992146655057,0.9549219754320034,FcR3B,0.4
24,-0.43889681234100286,0.5092615329762512,IgG1,0.5
25,0.7336461381153705,0.8575453734999564,IgG3,0.5
26,0.27222695973165334,0.9263990112171687,FcR2A,0.5
27,0.2667921560881119,0.9374449390357162,FcR2B,0.5
28,0.5325554094295974,0.9233741393227257,FcR3A,0.5
29,0.5460668476192967,0.9594225774901053,FcR3B,0.5
30,0.052101043224273225,0.5465141155977477,IgG1,0.6
31,0.7265269722859555,0.8529090102644896,IgG3,0.6
32,0.37786288387337963,0.9313727731630872,FcR2A,0.6
33,0.20318679375311943,0.930223041127242,FcR2B,0.6
34,0.5705386149528655,0.9458385515655682,FcR3A,0.6
35,0.5476408606112422,0.9522507859686172,FcR3B,0.6
36,-0.5378165949972296,0.5099591721558229,IgG1,0.7000000000000001
37,0.7560651071185123,0.8700899760128892,IgG3,0.7000000000000001
38,0.2923974360675079,0.9301296187578534,FcR2A,0.7000000000000001
39,0.2837437081837325,0.9398040705998016,FcR2B,0.7000000000000001
40,0.563779706490511,0.9395855411545319,FcR3A,0.7000000000000001
41,0.5434515204772774,0.9559286294205357,FcR3B,0.7000000000000001
42,-0.07522405975628565,0.5121432269456115,IgG1,0.8
43,0.7443617276417598,0.8634304561829617,IgG3,0.8
44,0.3298756665902536,0.9325432255008816,FcR2A,0.8
45,0.19710363340464276,0.9355654557449135,FcR2B,0.8
46,0.574620432421859,0.936768005948502,FcR3A,0.8
47,0.544149735723736,0.9528034881917121,FcR3B,0.8
48,-0.2806121669589319,0.5000245868859936,IgG1,0.9
49,0.7354860611591527,0.8656175195109441,IgG3,0.9
50,0.3054919004776464,0.9334648163534771,FcR2A,0.9
51,0.23278104099766173,0.9398752867205066,FcR2B,0.9
52,0.5637153143036678,0.9458612883196194,FcR3A,0.9
53,0.5407350418161683,0.9567864152497865,FcR3B,0.9
54,-1.3606597428207357,0.19545219805677422,IgG1,1.0
55,0.3247162679692184,0.8645595533924803,IgG3,1.0
56,0.26879581659644447,0.9353130721423616,FcR2A,1.0
57,0.1624630880080996,0.9393873734782942,FcR2B,1.0
58,0.5592195395965712,0.9356437717324119,FcR3A,1.0
59,0.5514558095036499,0.9563708132677856,FcR3B,1.0
,Method,r2,r,Ligand,Missingness
0,impute_missing_ms,-0.49326344693254764,0.5295087515974022,IgG1,0.01
1,impute_missing_ms,-0.04650527193783649,0.5090640982362357,IgG1,0.01
2,impute_missing_ms,0.7893225368993573,0.893508285253054,IgG3,0.01
3,impute_missing_ms,0.7282405097514464,0.8558304554528063,IgG3,0.01
4,impute_missing_ms,0.5170717494586734,0.8936493238876885,FcR2A,0.01
5,impute_missing_ms,0.8007653149213101,0.9828544279114975,FcR2A,0.01
6,impute_missing_ms,0.6630698180575599,0.9426676190811135,FcR2B,0.01
7,impute_missing_ms,0.5895722250084412,0.9373976735228428,FcR2B,0.01
8,impute_missing_ms,0.7468820589267138,0.9779006707240225,FcR3A,0.01
9,impute_missing_ms,0.7240706898705168,0.9475229988753022,FcR3A,0.01
10,impute_missing_ms,0.732185933816969,0.9436083746187978,FcR3B,0.01
11,impute_missing_ms,0.7527778132981829,0.9623800324992053,FcR3B,0.01
12,impute_missing_ms,-0.5567314511858636,0.5321592175896679,IgG1,0.1
13,impute_missing_ms,-0.3783507712988996,0.5878072349717249,IgG1,0.1
14,impute_missing_ms,0.7191419621273398,0.8485057751821583,IgG3,0.1
15,impute_missing_ms,0.7335478337707344,0.8566872859240816,IgG3,0.1
16,impute_missing_ms,0.6395829978578698,0.9317476161475087,FcR2A,0.1
17,impute_missing_ms,0.6688771154915529,0.9485520917647052,FcR2A,0.1
18,impute_missing_ms,0.5661739084830297,0.9376938561182955,FcR2B,0.1
19,impute_missing_ms,0.5851037384031998,0.92513240456098,FcR2B,0.1
20,impute_missing_ms,0.6267422398431423,0.8796586663419453,FcR3A,0.1
21,impute_missing_ms,0.672969882448143,0.8889838982447008,FcR3A,0.1
22,impute_missing_ms,0.7244071282915344,0.9411890282577667,FcR3B,0.1
23,impute_missing_ms,0.7226486267352015,0.9566609161384588,FcR3B,0.1
24,impute_missing_ms,-0.4251525489317196,0.5253248082503128,IgG1,0.2
25,impute_missing_ms,-0.1744276999367571,0.5649973980814967,IgG1,0.2
26,impute_missing_ms,0.7257063936110774,0.8526840106847726,IgG3,0.2
27,impute_missing_ms,0.7492682218470861,0.8680280133676923,IgG3,0.2
28,impute_missing_ms,0.594821055460361,0.9216831046478539,FcR2A,0.2
29,impute_missing_ms,0.5921796332472682,0.9231540858535435,FcR2A,0.2
30,impute_missing_ms,0.5511682024981803,0.928143546640281,FcR2B,0.2
31,impute_missing_ms,0.5168444276882292,0.9205494525787147,FcR2B,0.2
32,impute_missing_ms,0.6519203965090914,0.875219499138687,FcR3A,0.2
33,impute_missing_ms,0.6668030286853674,0.8944390900441211,FcR3A,0.2
34,impute_missing_ms,0.722222471148807,0.9477998644769451,FcR3B,0.2
35,impute_missing_ms,0.7529935967435948,0.9529015398595116,FcR3B,0.2
36,impute_missing_ms,-0.528260946055066,0.5069055215898821,IgG1,0.3
37,impute_missing_ms,-0.30643916844967567,0.512734747826155,IgG1,0.3
38,impute_missing_ms,0.7409812748301392,0.8618579258260448,IgG3,0.3
39,impute_missing_ms,0.7351307670974431,0.8586203834029493,IgG3,0.3
40,impute_missing_ms,0.5481086526909237,0.9176353668354972,FcR2A,0.3
41,impute_missing_ms,0.5823584030009348,0.9213064868536824,FcR2A,0.3
42,impute_missing_ms,0.5536541187531252,0.921984319175841,FcR2B,0.3
43,impute_missing_ms,0.5346420103862191,0.9247889027904919,FcR2B,0.3
44,impute_missing_ms,0.6706407442212798,0.8935804544193925,FcR3A,0.3
45,impute_missing_ms,0.6776052755027627,0.9020308254834423,FcR3A,0.3
46,impute_missing_ms,0.7039633780536974,0.9382762797908981,FcR3B,0.3
47,impute_missing_ms,0.7025055887219593,0.9443451640093481,FcR3B,0.3
48,impute_missing_ms,-0.046007402457706625,0.4825186269191987,IgG1,0.4
49,impute_missing_ms,-0.3794356078776484,0.5317437872540538,IgG1,0.4
50,impute_missing_ms,0.7352888766822976,0.8582461093804465,IgG3,0.4
51,impute_missing_ms,0.7393822246716379,0.8600165553664609,IgG3,0.4
52,impute_missing_ms,0.590093142453846,0.9243524547613298,FcR2A,0.4
53,impute_missing_ms,0.5528229793497355,0.9151763136588517,FcR2A,0.4
54,impute_missing_ms,0.548154035009936,0.9313020873634275,FcR2B,0.4
55,impute_missing_ms,0.541078618818883,0.929061477071566,FcR2B,0.4
56,impute_missing_ms,0.661808117844696,0.8851456147370642,FcR3A,0.4
57,impute_missing_ms,0.6571226304814888,0.8797031713125192,FcR3A,0.4
58,impute_missing_ms,0.7141439849805893,0.9436027342969766,FcR3B,0.4
59,impute_missing_ms,0.7325991208306046,0.9488315502193011,FcR3B,0.4
60,impute_missing_ms,-0.6078745264831364,0.5593055040614737,IgG1,0.5
61,impute_missing_ms,-0.44600489824582734,0.5115665902289798,IgG1,0.5
62,impute_missing_ms,0.7112190200781001,0.8436092180547032,IgG3,0.5
63,impute_missing_ms,0.7264222230329991,0.8530076582919475,IgG3,0.5
64,impute_missing_ms,0.5615991677556923,0.9235558807596896,FcR2A,0.5
65,impute_missing_ms,0.5668081891278396,0.9215701447293669,FcR2A,0.5
66,impute_missing_ms,0.5194137573633335,0.9248568170567678,FcR2B,0.5
67,impute_missing_ms,0.5443276760335396,0.9342906686120896,FcR2B,0.5
68,impute_missing_ms,0.6514506088777081,0.8793160008446984,FcR3A,0.5
69,impute_missing_ms,0.6793356141606747,0.9003255214344412,FcR3A,0.5
70,impute_missing_ms,0.7219633547316562,0.9432422887197872,FcR3B,0.5
71,impute_missing_ms,0.7185302816423912,0.9405493138523041,FcR3B,0.5
72,impute_missing_ms,-0.3567556999358543,0.535111593784207,IgG1,0.6
73,impute_missing_ms,-0.20631527628619994,0.48171013329340623,IgG1,0.6
74,impute_missing_ms,0.7290496358360001,0.8542829062828728,IgG3,0.6
75,impute_missing_ms,0.7121415777683764,0.8446045743154731,IgG3,0.6
76,impute_missing_ms,0.5502943222809246,0.9182987472401393,FcR2A,0.6
77,impute_missing_ms,0.549866367291202,0.9196059224499579,FcR2A,0.6
78,impute_missing_ms,0.5162876121542543,0.9282735187878999,FcR2B,0.6
79,impute_missing_ms,0.5121097548744484,0.9293127735792308,FcR2B,0.6
80,impute_missing_ms,0.6807510412044897,0.9017917987530608,FcR3A,0.6
81,impute_missing_ms,0.6563417393296509,0.8790861097769002,FcR3A,0.6
82,impute_missing_ms,0.7142614584082208,0.9414669384787354,FcR3B,0.6
83,impute_missing_ms,0.7289698232487889,0.9485440772019189,FcR3B,0.6
84,impute_missing_ms,-0.26242394250302237,0.505447999692826,IgG1,0.7
85,impute_missing_ms,-0.2863263859544838,0.5027419811650234,IgG1,0.7
86,impute_missing_ms,0.733644106962225,0.8573378030393761,IgG3,0.7
87,impute_missing_ms,0.7331738392678073,0.8577438475134259,IgG3,0.7
88,impute_missing_ms,0.53842748591814,0.9190465319670817,FcR2A,0.7
89,impute_missing_ms,0.5468330660146226,0.9212752456432693,FcR2A,0.7
90,impute_missing_ms,0.5127037404657688,0.9302266271726021,FcR2B,0.7
91,impute_missing_ms,0.4988475795660736,0.9312405517624468,FcR2B,0.7
92,impute_missing_ms,0.6660399384952658,0.886742291676764,FcR3A,0.7
93,impute_missing_ms,0.6615663094998607,0.8858885458768446,FcR3A,0.7
94,impute_missing_ms,0.713772674860399,0.9436754170764747,FcR3B,0.7
95,impute_missing_ms,0.7078290553886057,0.9448933034922985,FcR3B,0.7
96,impute_missing_ms,-0.2154777114237718,0.5372520570657995,IgG1,0.8
97,impute_missing_ms,-0.5411926964619498,0.5122278335518845,IgG1,0.8
98,impute_missing_ms,0.7140706768539037,0.8455154779767894,IgG3,0.8
99,impute_missing_ms,0.7226239202477693,0.8527178327720052,IgG3,0.8
100,impute_missing_ms,0.5206748773696831,0.9164004612868667,FcR2A,0.8
101,impute_missing_ms,0.5358111808862382,0.9222228378412336,FcR2A,0.8
102,impute_missing_ms,0.48065049844517727,0.9262436881175288,FcR2B,0.8
103,impute_missing_ms,0.4794401401270548,0.9287570722244233,FcR2B,0.8
104,impute_missing_ms,0.6700499444343561,0.8932388583501527,FcR3A,0.8
105,impute_missing_ms,0.6737478390138811,0.8966577018052209,FcR3A,0.8
106,impute_missing_ms,0.7173017101689104,0.9479709653884463,FcR3B,0.8
107,impute_missing_ms,0.7119995888502353,0.9451150358964767,FcR3B,0.8
108,impute_missing_ms,-0.027343644501037545,0.47441878831875384,IgG1,0.9
109,impute_missing_ms,-0.16560321728291671,0.46562057944940727,IgG1,0.9
110,impute_missing_ms,0.7247605578605582,0.8528494751886375,IgG3,0.9
111,impute_missing_ms,0.7239266223819139,0.852505076405865,IgG3,0.9
112,impute_missing_ms,0.5261301521267601,0.9211280136793889,FcR2A,0.9
113,impute_missing_ms,0.49755525399448075,0.916461754333368,FcR2A,0.9
114,impute_missing_ms,0.46253432500487535,0.9280352719305157,FcR2B,0.9
115,impute_missing_ms,0.46439710033299286,0.9288423150079919,FcR2B,0.9
116,impute_missing_ms,0.6672259392095443,0.8897939164747972,FcR3A,0.9
117,impute_missing_ms,0.6699486594618422,0.8922573505661184,FcR3A,0.9
118,impute_missing_ms,0.7182812463252428,0.94623273776363,FcR3B,0.9
119,impute_missing_ms,0.7129562902697751,0.9457359682454659,FcR3B,0.9
120,impute_missing_ms,-0.6205128620795772,0.44514156260159066,IgG1,1.0
121,impute_missing_ms,-1.9933435531632333,0.4575195471279924,IgG1,1.0
122,impute_missing_ms,-1.2813126966123511,0.8496432446993977,IgG3,1.0
123,impute_missing_ms,0.04942384232119146,0.8509627841585272,IgG3,1.0
124,impute_missing_ms,0.4120526914819648,0.905804170407806,FcR2A,1.0
125,impute_missing_ms,0.3663295508586403,0.9090973342281977,FcR2A,1.0
126,impute_missing_ms,0.4376749670985953,0.9293649519825266,FcR2B,1.0
127,impute_missing_ms,0.4211090988266004,0.9286403098114981,FcR2B,1.0
128,impute_missing_ms,0.6735449824977864,0.893519423031422,FcR3A,1.0
129,impute_missing_ms,0.6718263098497408,0.8931050058037502,FcR3A,1.0
130,impute_missing_ms,0.7156592836756079,0.9456277362735903,FcR3B,1.0
131,impute_missing_ms,0.7146192248455839,0.9452648756726253,FcR3B,1.0
Loading

0 comments on commit 4747ef5

Please sign in to comment.