KoslickiLab / DiversityOptimization

Minimizing biological diversity to improve microbial taxonomic reconstruction
MIT License
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Benchmark speed #2

Closed dkoslicki closed 4 years ago

dkoslicki commented 4 years ago

Goal: determine performance of MinDivLp.py as a function of:

Approach: using the data (or modifications thereof, or randomly generated "similar looking" sensing matrices), in pseudo-code:

for num_rows in <some range>:
    for num_columns in <some range>:
        form the sensing matrix A
        for support sizes in <some range>:
            for N random x vectors:
                form y
                time MinDivLP.py
                store timing results
average over N
report performance (plot or tabular form): min, max, median, mean, std dev of time
cmcolbert commented 4 years ago

Results from benchmarking speed: results_N=20.xlsx Log-log graphs of results (support size vs. mean time over varying column counts and large_k values): logSvslogt-k4 logSvslogt-k6 logSvslogt-k8 logSvslogt-k10 logSvslogt-k12 logSvslogt-k13

dkoslicki commented 4 years ago

@cmcolbert is this log base 10 or log base e, or...?

cmcolbert commented 4 years ago

@dkoslicki This is log base e.