From 0a33784c4b32764adce4ad10419ad737e9055977 Mon Sep 17 00:00:00 2001 From: xingzhongyu Date: Sun, 12 Jan 2025 16:38:31 +0800 Subject: [PATCH] update ans --- examples/atlas/get_result_web.py | 20 +++-- examples/atlas/sweep_results/Blood_ans.csv | 26 +++--- .../atlas/sweep_results/Intestine_ans.csv | 6 +- examples/atlas/sweep_results/Pancreas_ans.csv | 83 +++++++++++++------ 4 files changed, 87 insertions(+), 48 deletions(-) diff --git a/examples/atlas/get_result_web.py b/examples/atlas/get_result_web.py index 0b76b625..000a9186 100644 --- a/examples/atlas/get_result_web.py +++ b/examples/atlas/get_result_web.py @@ -12,7 +12,7 @@ from tqdm import tqdm from dance import logger -from dance.settings import METADIR +from dance.settings import DANCEDIR, METADIR from dance.utils import try_import # get yaml of best method @@ -73,8 +73,18 @@ def get_sweep_url(step_csv: pd.DataFrame, single=True): """ ids = step_csv["id"] sweep_urls = [] - for run_id in tqdm(reversed(ids), - leave=False): #The reversal of order is related to additional_sweep_ids.append(sweep_id) + test_accs_exists = False + if "test_acc" in step_csv.columns: + test_accs = reversed(step_csv["test_acc"]) + test_accs_exists = True + else: + test_accs = [np.nan] * len(ids) + + for run_id, test_acc in tqdm( + zip(reversed(ids), + test_accs), leave=False): #The reversal of order is related to additional_sweep_ids.append(sweep_id) + if test_accs_exists and pd.isna(test_acc): + continue api = wandb.Api(timeout=1000) run = api.run(f"/{entity}/{project}/runs/{run_id}") sweep_urls.append(run.sweep.url) @@ -291,9 +301,9 @@ def get_new_ans(tissue): for method_folder in tqdm(methods): for dataset_id in collect_datasets: - if dataset_id == "f72958f5-7f42-4ebb-98da-445b0c6de516": #f72958f5-7f42-4ebb-98da-445b0c6de516 + if dataset_id == "0b4a15a7-4e9e-4555-9733-2423e5c66469": #f72958f5-7f42-4ebb-98da-445b0c6de516 pass - file_path = f"../tuning/{method_folder}/{dataset_id}" + file_path = DANCEDIR / 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type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -187,7 +187,7 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4136029481887817,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpjhyj9q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wyv5vmis,https://wandb.ai/xzy11632/dance-dev/sweeps/8qobi3e5,https://wandb.ai/xzy11632/dance-dev/sweeps/jkwnilze","- type: filter.gene +",0.41360294818878174,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpjhyj9q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wyv5vmis,https://wandb.ai/xzy11632/dance-dev/sweeps/8qobi3e5,https://wandb.ai/xzy11632/dance-dev/sweeps/jkwnilze","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -613,7 +613,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.449999988079071,all_total_runs:510|all_finished_runs:408|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.00%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mvhlvdxl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0zk0bilm,https://wandb.ai/xzy11632/dance-dev/sweeps/z9xnldun,https://wandb.ai/xzy11632/dance-dev/sweeps/xctbkm4s","- type: filter.gene 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+",0.4670000076293946,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:341|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:71.18%,False,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3ch2l5s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pgj5t8lc,https://wandb.ai/xzy11632/dance-dev/sweeps/tmjfipc9,https://wandb.ai/xzy11632/dance-dev/sweeps/zudbm7ur","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: ScaleFeature @@ -627,12 +627,12 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: Log1P params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -648,7 +648,7 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.37721022963523865,all_total_runs:196|all_finished_runs:105|step2_total_runs:150|step2_finished_runs:66|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:53.57%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p87lac44|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lfrx75bu,https://wandb.ai/xzy11632/dance-dev/sweeps/9dafryxc,https://wandb.ai/xzy11632/dance-dev/sweeps/yh7p9cq3","- type: filter.gene 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+",0.3791748583316803,all_total_runs:493|all_finished_runs:344|step2_total_runs:450|step2_finished_runs:307|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:69.78%,False,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0tpkjxr3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dxjir4oa,https://wandb.ai/xzy11632/dance-dev/sweeps/ozctmfyc,https://wandb.ai/xzy11632/dance-dev/sweeps/ie0fgnbo","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1256,24 +1256,15 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ feature_channel: feature.cell label_channel: cell_type ",0.2585000097751617,all_total_runs:196|all_finished_runs:151|step2_total_runs:136|step2_finished_runs:91|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.04%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ghnlphpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qmwfsxt6,https://wandb.ai/xzy11632/dance-dev/sweeps/0bv97iz8,https://wandb.ai/xzy11632/dance-dev/sweeps/fhv7qkjx","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + target: FilterGenesPercentile + params: {} - type: normalize - target: ScaleFeature + target: NormalizePlaceHolder params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1289,7 +1280,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.273499995470047,all_total_runs:210|all_finished_runs:114|step2_total_runs:150|step2_finished_runs:87|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:54.29%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tnlms8f7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/37b6ag4h,https://wandb.ai/xzy11632/dance-dev/sweeps/drrj9j62,https://wandb.ai/xzy11632/dance-dev/sweeps/yrm085kp","- type: filter.gene 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feature.cell + log_level: INFO + n_components: 264 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.24699999392032623,all_total_runs:178|all_finished_runs:172|step2_total_runs:118|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:96.63%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zcjk9kzu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xa1zrlvf,https://wandb.ai/xzy11632/dance-dev/sweeps/svep9r0f,https://wandb.ai/xzy11632/dance-dev/sweeps/earmglny","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1510,7 +1539,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type 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