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View Code? Open in Web Editor NEWExperiments applying FIDDLE on MIMIC-III and eICU. https://doi.org/10.1093/jamia/ocaa139
Experiments applying FIDDLE on MIMIC-III and eICU. https://doi.org/10.1093/jamia/ocaa139
I tried to reproduce the FIDDLE experiments, however, the output X.npz is not a sparse matrix (and thus won't load using spicy.sparse.load_npz(), so I used lumpy.load()). X.npz contains:
X['data']: a long vector of only 1's
X['shape']: a vector describing the correct dimensions of the expected output tensor
X['fill_value']: a vector with just a single zero in it
X['coords']: a vector with 3 rows and the same number of columns as the length of X['data']
Is this an error or do I need to process this output first in order to get the sparse N x L x D tensor? I did not see anything in the documentation or paper regarding this. Cheers.
Hi Shengpu,
I have summarized some bugs in the mimic3_experiments directory. You may check them while available.
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Suggestion: I think it's better to include FIDDLE module in this directory. After that, there are some other bugs.
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You should set the output_dir for each run, since it's required in run.py
Since the dir features/outcome=mortality,T=48.0,dt=1.0 is replaced by features/benckmark,outcome=mortality,T=48.0,dt=1.0 in 1_data_extraction/run_prepare_all.sh, this script is not able to run:
OUTCOME=mortality
T=48.0
dt=1.0
python run.py \
--data_fname="$DATAPATH/features/outcome=$OUTCOME,T=$T,dt=$dt/input_data.p" \
Since the file pop.mortality_benchmark.csv is not exist, this script is not able to run:
python run.py \
--data_fname="$DATAPATH/features/benchmark,outcome=mortality,T=48.0,dt=1.0/input_data.p" \
--population="$DATAPATH/population/pop.mortality_benchmark.csv" \
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Hi,
Thanks for open-sourcing the code. However, it seems that the code snippets hosted in https://github.com/MLD3/FIDDLE-experiments/tree/jamia-replication/eicu_experiments/1_data_extraction only preprocess a subset of tables mentioned in the paper, namely "medication", "nurseCharting", 'patient', 'lab', 'respiratoryCare', 'intakeOutput' tables.
Am I missing something?
Thanks,
YD
I am trying to reproduce your results using these instructions: https://github.com/MLD3/FIDDLE-experiments/tree/master/mimic3_experiments.
However, when running the IHM_Benchmark notebook, I get an error [Errno 2] No such file or directory 'train_listfile.csv'
I am not sure at which step the csv was supposed to be created since the other steps do not appear to generate it anywhere. Any help would be greatly appreciated.
Hi!
I tried to replicate the eICU experiments with the descretize option turned off, but got an error in the FIDDLE code saying "TypeError: bad operand type for unary ~: 'float' ". I adjusted the FIDDLE code and eventually it worked, but then I got a dimension error in the process of training the CNN, where it said that matrix 1 could not multiply with matrix 2 because they were not the right shape.
Do you have any idea in what direction I could go to fix this problem? Thank you so much!
I want to run an experiment to assess whether a model trained on MIMIC is able to generalize on eICU. Are the FIDDLE features comparable as it is? If not, is it possible to carve out a subset that is comparable across the datasets?
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