Bo Yuan DesmondYuan
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| # Adapted from `configs/cross_evaluate_DNPR-RPDR_11.json` | |
| { | |
| "search_space": { | |
| "model_name": ["transformer"], | |
| "resume_experiment": [ | |
| "snapshot/ac3f725f4cdefda0a4a4f0db6a3bf838.results", | |
| "snapshot/7ea4cee1897bde30bebaf5a5a22acd39.results", | |
| "snapshot/ddbe06c97363f29de426febb2f07546e.results" | |
| ], | |
| "map_to_icd_system": ["usa"], |
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| data # 91 zeros + 8 ones | |
| weight = (data*8+1).flatten() | |
| # Type I: no balancing | |
| loader = torch.utils.data.DataLoader(data, batch_size=20) | |
| for i in loader: | |
| print(i.sum().numpy(),len(i)) | |
| ''' | |
| 1 20 | |
| 1 20 |
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| # Step 0: Load your virtual environment | |
| # {conda/virtualenv} | |
| # Step 1: Install the latest version of lisa2 | |
| pip install lisa2>=2.2 | |
| # Step 2: See the tutorial to add genome file manually | |
| # https://github.com/liulab-dfci/lisa2/blob/master/docs/troubleshooting.md | |
| # This step would take some time to finish. | |
| wget http://cistrome.org/~alynch/data/lisa_data/hg38_1000_2.0.h5 |
DesmondYuan
/ single condition ntotal=1
Last active
February 4, 2021 01:24
Benchmarking_CellBoxJulia
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| >>>>>>> ntotal = 1 | |
| julia> @benchmark Zygote.gradient(x -> loss_neuralode(x), p) | |
| @benchmark ForwardDiff.gradient(x -> loss_neuralode(x), p) | |
| BenchmarkTools.Trial: | |
| memory estimate: 137.73 MiB | |
| allocs estimate: 2610308 | |
| -------------- | |
| minimum time: 71.966 ms (26.55% GC) | |
| median time: 78.912 ms (26.48% GC) | |
| mean time: 82.457 ms (28.71% GC) |
DesmondYuan
/ GENT2_loc.tsv
Created
September 7, 2020 02:09
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
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| http://www.appex.kr/web_download/GENT2/GENT2_dump.sql.gz |
DesmondYuan
/ log.log
Last active
June 21, 2020 23:49
[Comparison] Training with 100 times larger regularization and short/long n_iter_patience
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| () by40@login04.o2.rc.hms.harvard.edu: /n/data1/hms/cellbio/sander/bo/CellBox/CellBox/results $ cat ENet_Jun10_0_2_447032c3be95cf3ac39f37d0eeb2667c/b11_000/record_eval.csv |grep "None,None" | |
| -1,None,None,0.8225287199020386,None,0.12510168552398682,None,0.960000000000008, | |
| -1,None,None,None,None,None,0.11767731606960297,0.9799999999999898, | |
| -1,None,None,0.1939428746700287,None,0.08495153486728668,None,0.060000000000002274, | |
| -1,None,None,None,None,None,0.08560443669557571,0.12999999999999545, | |
| -1,None,None,0.07230990380048752,None,0.057170797139406204,None,0.06999999999999318, | |
| -1,None,None,None,None,None,0.056659966707229614,0.12000000000000455, | |
| -1,None,None,0.06658506393432617,None,0.051017481833696365,None,0.06999999999999318, | |
| -1,None,None,None,None,None,0.051169801503419876,0.12999999999999545, | |
| -1,None,None,0.06918351352214813,None,0.053757112473249435,None,2.17999999999995, |
DesmondYuan
/ grid_1_0.json
Last active
June 9, 2020 17:46
results/ENet_1_0_8e2770390be348087fdc07f762b74a2a/b11_001/record_eval.csv
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| { | |
| "n_x": 99, | |
| "batchsize": 4, | |
| "l2lambda": 0, | |
| "node_index_file": "data/node_Index.csv", | |
| "export_verbose": 3, | |
| "n_activity_nodes": 87, | |
| "validset_ratio": 0.8, | |
| "n_epoch": 10000, | |
| "polynomial_k": 3, |
DesmondYuan
/ A piece of codes
Created
January 17, 2018 19:52
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| conf = new NeuralNetConfiguration.Builder() | |
| .seed(123) | |
| .iterations(5) | |
| .optimizationAlgo(OptimizationAlgorithm.STOCHASTIC_GRADIENT_DESCENT) | |
| .updater(Updater.NESTEROVS) | |
| .momentum(0.1) | |
| .weightInit(WeightInit.XAVIER) | |
| .learningRate(0.3) | |
| .regularization(true).l2(1e-4).l1(1e-4) | |
| .gradientNormalization(GradientNormalization.ClipElementWiseAbsoluteValue) |
DesmondYuan
/ 1 with batchSize=1000
Last active
October 18, 2016 17:27
Deep autoencoder pretrained with RBM
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| package onRuddle0924; | |
| import onRuddle.ModelSerializer; | |
| import org.datavec.api.records.reader.RecordReader; | |
| import org.datavec.api.records.reader.impl.csv.CSVRecordReader; | |
| import org.datavec.api.split.FileSplit; | |
| import org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator; | |
| import org.deeplearning4j.datasets.iterator.*; | |
| import org.deeplearning4j.datasets.iterator.MultipleEpochsIterator; | |
| import org.deeplearning4j.nn.api.OptimizationAlgorithm; |
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| package onRuddle; | |
| import org.datavec.api.records.reader.RecordReader; | |
| import org.datavec.api.records.reader.impl.csv.CSVRecordReader; | |
| import org.datavec.api.split.FileSplit; | |
| import org.deeplearning4j.datasets.datavec.RecordReaderDataSetIterator; | |
| import org.nd4j.linalg.dataset.DataSet; | |
| import org.nd4j.linalg.dataset.api.iterator.DataSetIterator; | |
| import org.slf4j.Logger; | |
| import org.slf4j.LoggerFactory; |
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