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README.md

scimod-agency

What can science funding agencies do to improve the quality of the scientific work they fund? They can change how much they give to award recipients, or the policy of whom to give awards to. We show that the proper choice of how much and to whom depends on cultural factors of a scientific field: how often negative results are published and how good is peer review.

run the model

build the code

To run the model first you must get and build the code. To do that you need to get the D compiler installed, called dmd. On macOS, type brew install dmd into the terminal and press enter. We use dub to build our compiled executable, so get dub installed by following the instructions at the link.

When all this is done, fetch the code by cloning this repository, then cd scimod-agency and build the code by running dub build. Run the unit tests using dub test.

run executable ./scimod-agency

The scimod-agency executable prints its help like so

./scimod-agency -h

SCIMOD
./scimod-agency WRITE_DIR <OPTIONS>
Options:
                      --nTrials Number of trials to run (default 10)
                     --baseRate Base rate of true hypotheses (default 0.1)
                  --awardAmount Amount given to grant-winning lab in a timestep (default 50)
     --initialFalsePositiveRate False positive rate of all PIs at t=0 (default 0.05)
              --fprMutationRate How often the false positive rate mutates (default 0.25)
    --publishNegativeResultRate Rate that negative results are published (default 0.0)
         --fprMutationMagnitude Std. dev. of the false positive mutations (default 0.01)
   --falsePositiveDetectionRate Std. dev. of the false positive mutations (default 0.01)
                       --policy One of: RANDOM, PUBLICATIONS, FPR (default PUBLICATIONS)
-h                       --help This help information.

Build the parameters files

There is a command line option to pass a comma-separated tuple of the four parameters we varied in our experiments. The four in order are policy, award amount, negative results publishing rate, and false positive detection rate. This option is meant to be used in conjunction with the script to make files with one parameter tuple on each line, experiment_makeparams.sh:

./experiment_makeparams.sh | cat > finaldraft-params.txt

1452 parameter combinations are contained in finaldraft-params.txt. Because the MERCED cluster limits the number of jobs allowed in a job array to 1000, we split the finaldraft-params.txt in two:

tail -n452 finaldraft-params.txt > finaldraft-params-2.txt

Deploy job arrays to queue

Job arrays make submitting many parameter combinations easy. With the parameter files set up using the above instructions, we submit the jobs to the cluster in two steps:

sbatch --array=1-1000 experiment.sh finaldraft-params.txt
sbatch --array=1-452 experiment.sh finaldraft-params-2.txt

It is somewhat sloppy, but for other parameter sensitivity analysis, we just commented out a block of code in experiment.sh

Data pipeline

Currently there is a process that must be done to convert the directory of JSONs created by the distributed model runs into a single HDF. It should be changed to be submitted to the scheduler asap; it can be multithreaded. See sandbox/multiprocessing_example.py.

To run,

python json_to_hdf.py path/to/jsons/dir new.hdf

Doing this on the cluster, you need to submit it as a job to the queue, like so

sbatch json_to_hdf_slurm.sh ~/scr/scimod-baseRate0.5/ ~/scr/scimod-baseRate0.5.hdf

for example.

The HDF can be read as an ExperimentData instance

from experiment_data import ExperimentData
ed = ExperimentData('new.hdf')

This object takes advantage of Python indexing ordered as policy, award_amount, pubneg_rate, and fpdr. For example,

policy = 'FPR'; award_amount = 10; pubneg_rate = '0.10'; fpdr = '0.10'
measures = ed[policy, award_amount, pubneg_rate, fpdr]
assert list(measures.keys()) == [
    'falseDiscoveryRate', 'falsePositiveRate', 'meanFunds', 'meanPublications', 
    'medianFunds', 'medianPublications', 'sumFunds', 'sumPublications'
]

Subtler funding strategies

In our first round of experiments, we tested only very simple strategies the funding agency would use for deciding which PI received a grant: totally random, given to PI with best methodological integrity in a random sample of ten as evidenced by lowest false positive rate, and given to the PI with the most publications in a random sample of ten. In addition to these, we considered the modified random and mixed funding strategies. In the modified random strategy, a PI is only qualified for receiving a grant if its false positive rate is not greater than some threshold value we call A in the paper. In that strategy the grant is awarded at random to one qualified PI. In the mixed strategy, the grant is awarded to the PI with the best methodological integrity a fraction $X$ of the time, with the grant awarded randomly the other $1-X$ of the time. As a reminder, best methodological integrity means the PI with the minimum false positive rate among all PIs.

These experiments required us to add an additional parameter, --policyParam, set to zero by default. It is only used if one of the two new policies are specified, indicated by strings MODIFIED_RANDOM and MIXED. We also enabled the policyParam to be passed as a fifth comma-separated value in the paramsList option, e.g. --paramsList=MIXED,85,0.3,0.3,0.8 says use the mixed funding strategy, funding per grant of 85, peer review efficacy and publication rate of negative results of 0.3, and the policyParam, $X$, of 0.8.

In our experiments with these we generate .txt lists of comma-separated parameters used in submitting an array job to the Slurm cluster. Generate the .txt files and submit the jobs using the following lines of code. Check that the length of the .txt files is 484. Make an appropriately-named directory in scratch, follow the examples in experiment.sh and put that directory name in the appropriate place. There is certainly a better way to streamline all this; we or others will do that later if it makes sense to.

# Build parameter lists, one for each funding strategy.
./experiment_makeparams_suppPolicies_modran.sh > modran-final-params.txt
./experiment_makeparams_suppPolicies_mixed.sh > mixed-final-params.txt

# Submit jobs to the cluster.
sbatch --array=1-484 experiment.sh modran-final-params.txt
sbatch --array=1-484 experiment.sh mixed-final-params.txt

Then when it's time to analyze the results, there is not yet a converter to HDF. Nonetheless, the process is zippy. scp the two directories with 484 JSONs. Let's say you do that and now the two directories are modran-dir and mixed-dir. Here's how to load the JSONs from each of these directories into one single JSON, then pass with the right auxiliary arguments to the heatmap plotting routine. I just executed this in an IPython shell. Loading each JSON takes well over a minute on my MacBook Pro.

from vis import all_supplemental_policy_heatmaps, _make_json_dict

# Pre-process 2x484 JSON: calculate avg final FPR and final FDR across dims.
jd_modran = _make_json_dict('modran-dir')
jd_mixed = _make_json_dict('mixed-dir')

# Peer review efficacy and negative publishing rates, equal in this experiment.
fpdr_npr_rates = np.arange(0.0, 1.01, 0.1)

# Can specify different scales for each strategy. We use the same scale here.
policy_params_dict = {
    'MODIFIED_RANDOM': fpdr_npr_rates, 
    'MIXED': fpdr_npr_rates
}


# Could have also created JSONs using this method, so it returns them back
# unchanged. This will create 16 heatmap figures saved to 
# os.path.expanduser('~/workspace/papers/sciencefunding/Figures/') -- not 
# useful to most. You might have to make some changes to change this behavior
# more easily. 16 = 4 funding per grant values x 2 funding strategies x 2
# measures of research quality (ave FPR and FDR).

jd_modran, jd_mixed = all_supplemental_policy_heatmaps(
    json_dict_modran=jd_modran, json_dict_mixed=jd_mixed,
    fpdr_npr_rates=fpdr_npr_rates, policy_params_dict=policy_params_dict
)

Other supplemental analyses, figures, etc.

We have generated a supplement that demonstrates model convergence and that our choice of base rate and selection process do not influence our results. Below I briefly explain these checks further as I show you how the checks were done and visualized using the software in this repository.

One colleague who graciously reviewed a preliminary version of the paper claimed his base rate was 0.5. On our view, a base rate of 0.1 may be inflated for most fields/researchers. In any case, we thought since 0.5 is on the extreme end of reasonable, we'll use that. For testing this parameter setting, we clumsily copy/pasted the single-line block of a bash command in experiment.sh, commented out the original, and added the option --baseRate=0.5 to the command block. See experiment.sh for this command, which itself is now commented out.

Another colleague helpfully suggested we use an alternative selection method. Our original selection method was to select ten PIs at random, then the one with the most publications of the ten reproduced. This alternative selection method our colleague called "Wright-Fisher", so we did too. Here we see the beauty of D in the implementation of Wright-Fisher selection in source/app.d:

reproducingIdx = dice(pis.map!"a.publications");

So, the PI is selected at random with probability equal to the number of its publications divided by the sum of publications over all PIs. A short aside on what's going on to help with D: map is not a method of pis, which is just an array of PI instances, i.e. PI[]. No, instead this is D's universal function call syntax (UFCS), where pis is actually the first (and in this case only) argument to map, which can be found in the standard library's std.algorithm module. Since pis is the only argument, no parentheses are needed at the end of this function call in D. If there were more arguments, they would go in parentheses after the second quote. The bang, !, indicates the start of a template argument, which can be a string that defines a function, in this case "a.publications". Making alternative choices for both UFCS and string definition of the anonymous function template argument, we get,

reproducingIdx = dice(map!(anonFuncVar => anonFuncVar.publications)(pis));

where anonFuncVar is arbitrary. In the string version, one must use a as the first function argument.

Back to the experiment in the paper, we tested Wright-Fisher selection with a base rate of 0.1 and 0.5. These commented-out calls to ./scimod-agency (the old name of the repo/program) can be found in experiment.sh. To use the Wright-Fisher selection instead of the best of random ten, add the option --selectionMethod=WRIGHT_FISHER to your ./scimod-agency call.

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