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Development #108

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merged 15 commits into from
Jun 20, 2024
Merged

Development #108

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7da3880
results(kiba): aflow only model #h4h
jyaacoub Jun 14, 2024
67c86eb
docs(model_stats): removed untuned duplicate models (PDBbind_aflow, a…
jyaacoub Jun 14, 2024
0e7521c
fix(ESM_branch): edge_weight_opt Keyword error
jyaacoub Jun 14, 2024
d932190
feat(tuned): + PDBbind_aflow params
jyaacoub Jun 14, 2024
a67aeb3
docs(init): tuned pdbbind_gvpl h-params
jyaacoub Jun 14, 2024
b5f6e3a
results(pdbbind): retrained GVPL with correct h-params
jyaacoub Jun 17, 2024
8151254
results(pdbbind): GVPL and GVPL_aflow #90
jyaacoub Jun 17, 2024
387688b
refactor: increased patience for early stopping
jyaacoub Jun 17, 2024
59836dd
fix(tuned_config): updated hparams for pdbbind_GVPL_aflow
jyaacoub Jun 17, 2024
5ed093d
refactor(ray): for kiba_GVPL_aflow run from ESM on cedar
jyaacoub Jun 19, 2024
e195864
fix(split): ensuring consistent test set #99
jyaacoub Jun 19, 2024
63f9406
refactor(tuned): GVPL_aflow hparams for davis and kiba #90
jyaacoub Jun 20, 2024
91311df
revert(raytune)): explicit definition for batch size for ESM when usi…
jyaacoub Jun 20, 2024
d939e46
fix(gnn_dropout): mask error due to not dropping out ew as well
jyaacoub Jun 20, 2024
11876db
feat(init_dataset): test_prots_csv for test set consistency
jyaacoub Jun 20, 2024
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8 changes: 6 additions & 2 deletions rayTrain_Tune.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ def train_func(config):

## hyperparameters to tune:
"lr": ray.tune.loguniform(1e-5, 1e-3),
"batch_size": ray.tune.choice([4, 8, 10, 12]), # local batch size
"batch_size": ray.tune.choice([16, 32, 64, 128]), # local batch size

# model architecture hyperparams
"architecture_kwargs":{
Expand All @@ -124,6 +124,10 @@ def train_func(config):
arch_kwargs["pro_extra_fc_lyr"] = ray.tune.choice([True, False])
arch_kwargs["pro_emb_dim"] = ray.tune.choice([128, 256, 320])

if 'esm' in search_space['model'].lower():
search_space['batch_size'] = ray.tune.choice([4,8,12,16])


# each worker is a node from the ray cluster.
# WARNING: SBATCH GPU directive should match num_workers*GPU_per_worker
# same for cpu-per-task directive
Expand All @@ -133,7 +137,7 @@ def train_func(config):
# trainer_resources={"CPU": 2, "GPU": 1},
# placement_strategy="PACK", # place workers on same node
)

print('init Tuner')
tuner = ray.tune.Tuner(
TorchTrainer(train_func),
Expand Down
32 changes: 21 additions & 11 deletions results/model_media/model_stats.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,6 @@ DGM_kibaD_nomsaF_af2E_128B_0.0001LR_0.4D_2000E,0.7421544771099204,0.732030831449
DGM_davisD_nomsaF_af2E_64B_0.0001LR_0.4D_2000E,0.8371815910480507,0.7268638307639713,0.6356548295003425,0.4133190204335282,0.3667126292760789,0.642898919297216
EDIM_PDBbindD_nomsaF_anmE_32B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6929249918113332,0.5373233573074141,0.5551808770122657,2.6186518594530783,1.258185145017263,1.6182249100335462
EDIM_PDBbindD_nomsaF_anmE_64B_0.0001LR_0.4D_2000E_originalLF_binaryLE,0.6904623260666497,0.5184772560303198,0.5502737601079014,2.8358724195646863,1.322164628956769,1.6840048751606054
DGM_davis4D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8372000580825498,0.7097254405448715,0.6167136172064404,0.4038543732328936,0.3597778618417262,0.6354953762482412
DGM_davis1D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8259045903365158,0.6727098716351115,0.5969862332191551,0.4777166877928197,0.3703959785636244,0.6911705200547978
DGM_davis3D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E,0.842545467746034,0.7168413490003224,0.623085263864242,0.4159492493391408,0.3558861870119901,0.6449412758842008
DGM_davis2D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8219248012487749,0.6776357016678246,0.5900163003204868,0.4347317921133404,0.368497045519577,0.6593419386883717
DGM_davis0D_nomsaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8118490670490435,0.681294197609124,0.5718484991508404,0.4293578322249251,0.3500587517846625,0.6552540211436517
DGM_davis0D_msaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8293327722196834,0.7023779705235912,0.6229347721106537,0.4493630702908394,0.3565351886078822,0.6703454857689723
DGM_davis1D_msaF_binaryE_64B_0.0001LR_0.4D_2000E,0.8212757240173636,0.6902984939419878,0.6084680827736445,0.4717995428983164,0.3579402144362287,0.6868766577037805
DGM_davis2D_msaF_binaryE_64B_0.0001LR_0.4D_2000E,0.826504184715153,0.6936343607518232,0.6220887747340503,0.4539645759565525,0.3707979739652987,0.6737689336534837
Expand Down Expand Up @@ -142,11 +137,6 @@ RNGM_PDBbind0D_nomsaF_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0
RNGM_PDBbind3D_nomsaF_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.6845608518246677,0.5357292380549965,0.5262643639158158,2.8033910565957822,1.3118297254568652,1.674333018427273
RNGM_PDBbind1D_nomsaF_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.6750296545462767,0.5185901583683697,0.5034912454720577,2.8088523469193527,1.2984564747465284,1.6759631102501489
RNGM_PDBbind4D_nomsaF_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.6763045391457404,0.5057256652457955,0.5047101950511758,2.618698229612088,1.2698856009464514,1.6182392374467034
DGM_PDBbind0D_nomsaF_aflowE_128B_0.00012LR_0.24D_2000E_originalLF_binaryLE,0.7138386406186538,0.632161676666746,0.5969379768993622,2.305938375785052,1.20129866702216,1.5185316512292564
DGM_PDBbind1D_nomsaF_aflowE_128B_0.00012LR_0.24D_2000E_originalLF_binaryLE,0.7071928697529236,0.6119312740868981,0.5825821216776425,2.227630691345381,1.1882162758282253,1.492524938265817
DGM_PDBbind2D_nomsaF_aflowE_128B_0.00012LR_0.24D_2000E_originalLF_binaryLE,0.7131792416345327,0.6300842144746225,0.5973837933267879,2.1487191174387785,1.156409247072916,1.4658509874604508
DGM_PDBbind3D_nomsaF_aflowE_128B_0.00012LR_0.24D_2000E_originalLF_binaryLE,0.660154663447613,0.477928410118703,0.4613848634220896,2.752867466543676,1.3047904886139765,1.6591767436122278
DGM_PDBbind4D_nomsaF_aflowE_128B_0.00012LR_0.24D_2000E_originalLF_binaryLE,0.6849966099610509,0.5521829232190218,0.528410191518849,2.6060140340268965,1.2870582908675785,1.614315345286322
RNGM_PDBbind0D_nomsaF_aflow_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.705837663251816,0.5925769047757962,0.5819610003983905,2.305359361226593,1.1903962990215846,1.518340989773573
RNGM_PDBbind1D_nomsaF_aflow_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.6960348680473861,0.5877518727647189,0.5567275097196549,2.3528305312600524,1.195004482080066,1.5338939113446055
RNGM_PDBbind2D_nomsaF_aflow_ring3E_48B_0.0001071LR_0.3383D_2000E_originalLF_binaryLE,0.7174010132899236,0.6351541961659758,0.6076186024009358,2.095580516039397,1.1347450122757563,1.447612004661262
Expand Down Expand Up @@ -190,7 +180,7 @@ GVPLM_davis2D_nomsaF_binaryE_128B_0.00020535607176845963LR_0.08845592454543601D_
DGM_davis1D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7618267865956071,0.4923371930328827,0.4613806752914631,0.4662829663578006,0.411145990216076,0.6828491534429846
DGM_davis0D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7636053478309109,0.4921759568376547,0.4648783804454143,0.4664726196058547,0.4114446927293202,0.6829880083909634
DGM_davis2D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7627598258454263,0.4909617783259909,0.4629240453488026,0.4675438018075736,0.4069470615043133,0.6837717468626308
DGM_davis3D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7586087337447441,0.48792801067181446,0.45565623472699257,0.4699824575652958,0.406830881759383,0.6855526657852742
DGM_davis3D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7586087337447441,0.4879280106718144,0.4556562347269925,0.4699824575652958,0.406830881759383,0.6855526657852742
DGM_davis4D_nomsaF_aflowE_128B_0.0008279387625584954LR_0.3480347297724069D_2000E_originalLF_binaryLE,0.7627751294107745,0.4910000034597989,0.463033422941668,0.4667885899388577,0.4158912707098973,0.6832192839336854
GVPLM_kiba0D_nomsaF_aflowE_32B_5.480618584919115e-05LR_0.0808130125360696D_2000E_gvpLF_binaryLE,0.6990933443140916,0.6227583767207777,0.5124656886492125,0.3874969197099424,0.4424602830299733,0.6224925057460069
GVPLM_kiba1D_nomsaF_aflowE_32B_5.480618584919115e-05LR_0.0808130125360696D_2000E_gvpLF_binaryLE,0.70978923821572,0.6245931929660367,0.5489066995277002,0.4011673269900183,0.407424328365187,0.6333777127354722
Expand All @@ -202,3 +192,23 @@ GVPLM_kiba2D_nomsaF_binaryE_32B_3.372637625954074e-05LR_0.09399264336737133D_200
GVPLM_kiba4D_nomsaF_aflowE_32B_5.480618584919115e-05LR_0.0808130125360696D_2000E_gvpLF_binaryLE,0.7013528905401658,0.6250248722716073,0.5171373465290922,0.3808855093784095,0.4271708875630601,0.6171592253044667
GVPLM_kiba3D_nomsaF_binaryE_32B_3.372637625954074e-05LR_0.09399264336737133D_2000E_gvpLF_binaryLE,0.6975845475921519,0.6064399311172254,0.5135792108542759,0.39910064830136,0.4353593608266028,0.63174413198807
GVPLM_kiba4D_nomsaF_binaryE_32B_3.372637625954074e-05LR_0.09399264336737133D_2000E_gvpLF_binaryLE,0.6935772666692046,0.6022132230956811,0.5044512666096735,0.4025857463348725,0.4328029182107182,0.6344964510025825
DGM_kiba0D_nomsaF_aflowE_64B_0.0001139464546302261LR_0.4321620419748407D_2000E_originalLF_binaryLE,0.6833072849286168,0.6179585946798826,0.4727062867906341,0.4652485169636371,0.4847738638760487,0.6820912819877095
DGM_kiba1D_nomsaF_aflowE_64B_0.0001139464546302261LR_0.4321620419748407D_2000E_originalLF_binaryLE,0.6319399207854125,0.5827772702783164,0.3484199826852496,0.4922941579440291,0.5148003016031965,0.7016367706613081
DGM_kiba2D_nomsaF_aflowE_64B_0.0001139464546302261LR_0.4321620419748407D_2000E_originalLF_binaryLE,0.6957607612858523,0.6214073872153388,0.4986083842961703,0.452748185796174,0.4765085403346378,0.6728656521150221
DGM_kiba3D_nomsaF_aflowE_64B_0.0001139464546302261LR_0.4321620419748407D_2000E_originalLF_binaryLE,0.6974294222044406,0.6012218059551159,0.5013974025588194,0.491169945360959,0.4609703423233422,0.7008351770287783
DGM_kiba4D_nomsaF_aflowE_64B_0.0001139464546302261LR_0.4321620419748407D_2000E_originalLF_binaryLE,0.7244322791516395,0.6458432916136384,0.5594966433719704,0.4308429350512986,0.4458192640807841,0.6563862697004704
GVPLM_PDBbind0D_nomsaF_binaryE_128B_0.0001LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6678798890840328,0.4896741551372414,0.4891211256936132,2.904874286920722,1.3519085603519854,1.7043691756543595
GVPLM_PDBbind2D_nomsaF_binaryE_128B_0.0001LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6709156636560543,0.4988289093016924,0.4953432777076078,2.864293386602017,1.339912495673216,1.69242234285713
GVPLM_PDBbind3D_nomsaF_binaryE_128B_0.0001LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6885412122614492,0.546594227557393,0.5441389649076723,2.7604737400170225,1.2944456345114177,1.661467345456125
GVPLM_PDBbind1D_nomsaF_binaryE_128B_0.0001LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6933219028688695,0.5538827419859854,0.5553824976404049,2.705459027185816,1.2695058672557165,1.6448279627930138
GVPLM_PDBbind4D_nomsaF_binaryE_128B_0.0001LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.676430736316634,0.5174490877105464,0.5106368202466385,2.7894814673104245,1.3190480916775753,1.6701740829357952
GVPLM_PDBbind2D_nomsaF_binaryE_128B_0.00020066831190641135LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6574373252713155,0.4637746181496499,0.4607019256521232,2.989336503081218,1.3696321064622343,1.728969780846738
GVPLM_PDBbind4D_nomsaF_binaryE_128B_0.00020066831190641135LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6679713075111049,0.4962407370372961,0.4900979111492484,2.8746986390390545,1.3413662884434798,1.6954936269532406
GVPLM_PDBbind3D_nomsaF_binaryE_128B_0.00020066831190641135LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6815000967290411,0.5208901839051482,0.5303883169579683,2.8010927687600886,1.3162882675910494,1.6736465483369207
GVPLM_PDBbind1D_nomsaF_binaryE_128B_0.00020066831190641135LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6861127443356612,0.5310529816224904,0.5380334435709785,2.759075340929806,1.297114357627186,1.661046459594013
GVPLM_PDBbind0D_nomsaF_aflowE_128B_0.00020048122460779208LR_0.042268679447260635D_2000E_gvpLF_binaryLE,0.7015701786607161,0.5634102832749822,0.5691773211791266,2.442901347407971,1.2002801681321764,1.5629783579461267
GVPLM_PDBbind0D_nomsaF_binaryE_128B_0.00020066831190641135LR_0.4661593536060576D_2000E_gvpLF_binaryLE,0.6850555528159531,0.5311038215844754,0.5335067223135304,2.820819380481298,1.315100869166162,1.6795295116434537
GVPLM_PDBbind3D_nomsaF_aflowE_128B_0.00020048122460779208LR_0.042268679447260635D_2000E_gvpLF_binaryLE,0.70023803089709,0.5589897695780572,0.5660036088465252,2.415406919150389,1.1958711257435026,1.5541579453679697
GVPLM_PDBbind4D_nomsaF_aflowE_128B_0.00020048122460779208LR_0.042268679447260635D_2000E_gvpLF_binaryLE,0.7127039080110099,0.5976033645560985,0.6006064125516688,2.282110245197861,1.156606004465194,1.5106654974539735
GVPLM_PDBbind1D_nomsaF_aflowE_128B_0.00020048122460779208LR_0.042268679447260635D_2000E_gvpLF_binaryLE,0.7104874374380044,0.594977799338086,0.5945328584235519,2.270213382939843,1.165092654266055,1.5067227292836074
GVPLM_PDBbind2D_nomsaF_aflowE_128B_0.00020048122460779208LR_0.042268679447260635D_2000E_gvpLF_binaryLE,0.7082159495264464,0.5882531427551811,0.5879428169952992,2.321420004071001,1.1716289097543746,1.5236206890400907
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