mitosis 0.4.0

Reproduce Machine Learning experiments easily

mitosis

Reproduce Machine Learning experiments easily

A package designed to manage and visualize experiments, tracking changes across different commits, parameterizations, and random seed.

Trivial Example

sine_experiment.py

import numpy as np

name = "sine-exp"
lookup_dict = {"frequency": {"fast": 10, "slow": 1}}

def run(seed, amplitude, frequency):
    """Deterimne if the maximum value of the sine function equals ``amplitude``"""
    x = np.arange(0, 10, .05)
    y = amplitude * np.sin(frequency * x)
    err = np.abs(max(y) - amplitude)
    return {"main": err}

Commit these changes to a repository. After installing sine_experiment as a python package, in CLI, run:

mitosis sine_experiment --param frequency=slow --eval-param amplitude=4

Mitosis will run sin_experiment.run(), saving all output as an html file in the current directory. It will also track the parameters and results. If you later change the variant named "slow" to set frequency=2, mitosis will raise a RuntimeError, preventing you from running a trial. If you want to run sine_experiment with a different parameter value, you need to name that variant something new. Eval parameters, like "amplitude" in the example, behave differently. Rather than being specified by lookup_dict, they are evaluated directly.

How it Works

Behind the scenes:

The first time mitosis.run() is passed a new experiment, it takes several actions:

1. Create a database for your experiment in trials_folder
2. Add a table to track all of the experiment trials
3. Add tables to track all of the different variants of your experiment.
4. Create a folder for the trial to store metadata.
5. Create and run a jupyter notebook in memory, saving the result as an HTML file
6. Updating the database of all trials with the results of the experiment.
7. Save experiment config of parameters actually created by jupyter notebook (in metadata folder)
8. Save a freezefile of python packages installed (in metadata folder)
9. Save the experiments results (in metadata folder)

In step 3, mitosis attempts to create a unique and reproduceable string from each parameter value. This is tricky, since most python objects are mutable and/or have their id() stored in their string representation. So lists must be sorted, dicts must be ordered, and function and method arguments must be wrapped in a class with and a custom __str__() attribute. This is imperfectly done, see the **Reproduceability ** section for comments on the edge cases where mitosis will either treat the same parameter as a new variant, or treat two different parameters as having the same value.

In step 5, mitosis needs to start the jupyter notebook with the appropriate variables. Instead of sending the variables to the notebook, the notebook re-evaluates eval parameters and re-looks up lookup parameters. Previously, parameters were sent to the notebook via pickle; that proved fragile.

The next time mitosis.run() is given the same experiment, it will

1. Determine whether parameter names and values match parameters in a previously established variant. If they do not, it will either:
   1. Reject the trial if the passed variant names match existing variants but with different values.
   2. Create a new variant for the parameter.
2. do steps 4 to 9 above.

Abstractions

Experiment: the definition of a procedure that will test a hypothesis. As a python object, an experiment must have a Callable attribute named "run" that takes any number of arguments and returns a dict with at least a key named "main". It also requires a name and lookup_dict attribute.

In its current form, mitosis does not require a hypothesis, but it does require experiments to define the "main" metric worth evaluating (though a user can always define an experiment that sets the main metric to a constant).

Parameter: An argument to an experiment. These are the axes by which an experiment may vary, e.g. sim_params, data_params, solver_params... etc. When this argument is a Collection, sometimes the singular (parameter) and plural (parameters) are used interchangeably. Parameters can either be lookup parameters (which require the experiment to have an attribute lookup_dict) or eval parameters (which are typically simple evaluations, e.g. setting the random seed to a given integer). Eval parameters which are strings need quotes.

Variant: An experimental parameter assigned to specific values and given a name.

Trial: a single run of an experiment with all variants specified. Within mitosis, the name of a trial is the experiment name, concatenated with variant names for each argument, and suffixed by the number of times that particular trial has been run. E.g. If an experiment has three arguments, the first trial run could be called "trial_sine-arg1a-arg2test-arg3foo-1" If a bugfix is committed to the experiment and the trial re-run with the same parameters, the new trial would be named "trial_sine-arg1a-arg2test-arg3foo-2".

Within mitosis, the trial is used to name the resulting html file and is stored in the "variant" and "iteration" columns in the experiment's sqlite database.

CLI

See an example.

Untracked parameters

If there are certain parameters that are not worth tracking, e.g. plotting flags that do not change the mathematical results, prepend the argument name with "+". An example:

mitosis project_pkg.exp1 -e +plot=True -p +plot_axes=dense

Fast iterations: Debug

Debug is straightforwards: mitosis project_pkg.exp1 -d ... runs in debug mode. This arg allows you to run experiments in a dirty git repository (or no repository) and will neither save results in the experimental database, nor increment the trials counter, nor verify/lock in the definitions of any variants. It will, however, create the output notebook.

Early experiment prototyping involves quickly iterating on parameter lists and complexity. mitosis will still lock in definitions of variants, which means that you will likely go through variant names quickly. This disambiguation is somewhat intentional, but you can free up names by deleting or renaming the experiment database or deleting records in the variant_param_name table.

Mitosis also sets the log level of the experiment module to INFO and gives it a FileHandler to the metadata directory. In Debug mode, mitosis sets the log level of the experiment to DEBUG.

Sharing code between experiments: Group

If your experimental code is intended to be used for multiple dissimilar experiments and want to track results separately, assign a group at the command line. The string is passed as an argument "group" to the experiment's run() function. It is treated as a special eval parameter, so if passed, there must be no other params named group

Group is more complex, but a simple example will help:

mitosis project_pkg.pdes -g heat -p initial_condition=origin-bump
mitosis project_pkg.pdes -g heat2d -p initial_condition=origin-bump2d
mitosis project_pkg.gridsearch -g pdes-heat -p initial_condition=origin-bump

Some more advanced usage.

It should be noted that mitosis only works on installed packages - modules that you can run using python -m pkgname.

When you want two modules share the same, long lookup_dict, I have found creating a module with multiple dictionaries works well, e.g.

project_pkg/
    |-- __init__.py     # Should look like
    |                   param_1 = {"var1": 1, "var2": 2}
    |                   param_2 = {"foo": "hello", "bar": "world"}
    |
    |                   # Each experiment gets same lookup dict
    |-- exp1.py         lookup_dict = vars(project_pkg)
    |-- exp2.py         lookup_dict = vars(project_pkg)

This way, the same variants can be used for different experiemnts:

mitosis project_pkg.exp1 -e seed=2 -p param_1=var_1 -p param_2=foo
mitosis project_pkg.exp2 -e seed=2 -p param_1=var_1 -p param_2=foo

It is also common to have one experiment wrap another, e.g. if exp2 is a gridsearch around exp1.

I typically run experiments on servers, so nohup ... &> exp.log & frees up the terminal and lets me disconnect ssh, returning later and reading exp.log to see that the experiment worked or what errors occurred (if error occurs inside the experiment and not inside mitosis, they will also be visible in the generated html notebook). If I have a variety of experiments that I want to run, I can copy and paste a lot of experiments all at once into the terminal, and they will all execute in parallel.

Reproduceability Thoughts

The goal of the package, experimental reproduceability, poses a few fun challenges. Here are my thoughts on reproduceable desiderata.

Raison d'être

I designed mitosis for the primary purpose of stopping my confusion when I tried to reproduce plots for my advisor after a small code change. Without an automatic record of the parameters in each run, I could not be sure whether the difference was due to the code change (committed or not), a mistake in setting parameters, or the effect of a new random seed. mitosis prevents this confusion and many other faux-pas.

There's also a broader reason for more rigor around reproduceability. While papers are published about parameterless methods or methods where the user only needs to specify a single parameter, that data that proves the method's efficacy comes from a heavily parametrized distribution (e.g. number of timesteps, noise level, type of noise, initial conditions, etc). Building the method requires even more (e.g. network width, iteration and convergence controls). Setting up the experiment requires more (e.g. number of trials, n_folds). While most of these are reported in a paper, I have found it critical and difficult to keep track of these details when developing a method and convincing with collaborators.

Desiderata

Not all we could wish for is possible. mitosis aspires to items four to nine in the list below, making compromises along the way:

1. No neutrinos or gamma rays messing with bits
2. Same implementation of floating point arithmetic
3. Using the same versions of binary libraries
4. Using the same versions of python packages and python executable
5. Same git commit of all experimental code
6. Only run experiments with hashable parameters
7. Ability to freeze/reproduce mutable arguments
8. Ability to recreate arguments from either their __repr__ string or their serialization
9. Don't run experiments without specifying a hypothesis first
10. For experiments that require randomness, only use a single, reproduceable generator.