a machine learning dashboard that displays hyperparameter settings alongside visualizations, and logs the scientist's thoughts throughout the training process
bbli, updated
🕥
2022-12-27 15:34:26
ml_board
Why ml_board/Limitations of Tensorboard
I decided to create this machine learning dashboard after using tensorboardX for a couple months in training regular neural networks for deep reinforcement learning. As great as tensorboardX was in helping me debug and understand neural networks(it certainly beats printing out statistics to the terminal), I found myself using only a subset of its features, and also discover certain limitations about tensorboard
- Text is buggy: The text tab will sometimes take a long time to load, or it will load the text from another run. When training a machine learning model, I often go through many settings and test various hypotheses. Having a reliable log is a must, so that I can know which thoughts goes with which runs.
- Disconnect between visualization and settings: My hypotheses often involve varying a hyperparameter and seeing its effect on quantities such as the loss, percentage of activations, etc. But the graphs don't have a legend that tells me which the setting each run used. As a result, I am forced to go back and forth between the Scalars and Text tab, interrupting my train of thought. As an example, if I were to log a bunch of experiments from random search, I would have put in a non-trivial amount of effort to remember which experiment used which setting(since the number won't monotonically increase/decrease as in grid search)
- Inadequate search: Suppose I wanted to view all the runs that achieved a certain accuracy, or were run on a particular hyperparameter setting. As far as I know, this is not possible in tensorboard. So in some senses, past runs are only useful if I can remember them.
Although tensorboard has great visualization capabilities(embeddings,computational graphs,etc), it is not the best tool for tracking, presenting, and organizing the knowledge one obtains as they run through many machine learning experiments. So the focus of this project will not be on visualization tensorboard, or experiment control and reproducibility sacred, but on creating a better interface for the scientist to view the relationship between model parameters and its output characteristics.
Features
- Interactive Table -> Filters Visualizations: Allows individual selection of runs, and numerical filtering based on equality/inequality. Once these choices are made, the Plots, Histograms, and Image Tabs are updated accordingly, allowing you to choose which run's visualizations you see. Also, because the plots are plotly Graph objects, one can click on the individual items in the plot legend to remove the corresponding plot from view
* Legend Dropdown -> Hyperparameter Display: Allows you to choose the hyperparameter setting(well technically any statistic you wish) to be displayed as the title(or legend) for each run in the Plots/Histogram/Image Tabs. I limited the title to one item because I did not want the figures to be cluttered with words, which I believe is worth the tradeoff of the occasional lack of uniqueness.
* Figure/AutoUpdate Toggle: As in tensorboard, you can click on the figure's title to minimize it. Also, every 10 seconds, the app will reread the data from the database, unless the autoupdate toggle is turned off.
- Log of Thoughts: As explained later, the user specifies a mongodb database name and mongodb collection(I call them folder) name where the run's statistics will be stored. The intended usage for this is that the user will specify a different folder for every "hypotheses" they want to test. Examples include "debug_binary_loss" or "lr_hyper_tune". The dashboard will only display all the runs in one folder at a time, since visual information takes up a substantial amount of space -> inevitably will lead to scrolling, a flow state killer. The limitations with this is that the user is unable to view the entire progression of their ideas. To preserve this folder-independent, sequential flow of thoughts, the Thoughts Tab aggregates logged thoughts across all folders within the given database and displays them in order by time, and furthermore is labeled by the folder name to give the comments context.
- Extensibility: The Dash library comes with awesome interactive components, such as the Table and Tabs components that were used in my project. Because I did not need to write these primitives myself, I could focus my attention on the domain problem/vision at hand, something that Peter Norvig talks about in As We May Program (see 17:50-19:00). Though this is a project geared towards my own personal usage, it can be easily extended(b/c it is written in a language data scientists are intimately familiar with+official tutorial is excellent+great community) by end-users as they see fit. After all, I created this with no prior web app experience!
Installation
Until the tabs feature is integrated into the master branch of dash, and I do more testing, and write up the documentation, you will have to manually install the package with the following commands: ``` git clone https://github.com/bbli/ml_board.git cd ml_board
Activate/create conda environment you want to install in
pip3 install . ``` After this, install MongoDB(and make sure it is enabled and started) and you are good to go!
If something goes wrong during usage, and you can't debug it, you can try installing the exact versions this package was tested on:
1. Commenting out the install_requires field in setup.py
2. run pip install -r requirements.txt && pip install .
Usage
Logging
Usage is very similar to tensorboard. Difference are:
* No need to specify a count, as ml_board will append the result to a MongoDB list. The other is that ml_board has an additional add_experiment_parameter which is intended to log hyperparameters to a table
```
from ml_board import SummaryWriter
w= SummaryWriter('name_of_mongodb_database','name_of_mongo_db_collection')
These two append to a list
w.add_scalar("example_loss_name",example_loss_value) w.add_histogram("example_histogram_name",example_loss_value)
w.add_image("example_picture_name",2d_numpy_matrix_in_range_0_to_1) w.add_thought("example_thoughts")
the current time is automatically logged as an experiment parameter when you create a SummaryWriter object
w.add_experiment_parameter("example_hyperparameter_name",example_hyperparamter_value)
w.close()
``
For more details, look at theLogger.py` file in the ml_board folder
Visualizing
From the command line, enter ``` ml_board --database_name name_of_mongodb_database --folder_name name_of_mongo_db_collection
shorthand notation
ml_board -db name_of_mongodb_database -f name_of_mongo_db_collection
specific port. Default 8000
ml_board -db name_of_mongodb_database -f name_of_mongo_db_collection -p 8050 ```
Comments
- If autoUpdate is on, do not filter rows as it will be overwritten
- Don't click on the filter rows button twice, or it will filter permemantly. If this does happen, refresh the webpage to reset the app's state.
- FYI, the Histogram Tab generally takes the longest time to update(b/c multiple plotly Figure objects are created for each histogram name).
TODO
- allow user to change folders from within the dashboard
- put priority on the callbacks(basically if I am on the Plots Tab, its callbacks should finish first)
- testing/documentation
Issues
Bump setuptools from 39.2.0 to 65.5.1
opened on 2022-12-27 15:34:26 by dependabot[bot]Bumps setuptools from 39.2.0 to 65.5.1.
Release notes
Sourced from setuptools's releases.
v65.5.1
No release notes provided.
v65.5.0
No release notes provided.
v65.4.1
No release notes provided.
v65.4.0
No release notes provided.
v65.3.0
No release notes provided.
v65.2.0
No release notes provided.
v65.1.1
No release notes provided.
v65.1.0
No release notes provided.
v65.0.2
No release notes provided.
v65.0.1
No release notes provided.
v65.0.0
No release notes provided.
v64.0.3
No release notes provided.
v64.0.2
No release notes provided.
v64.0.1
No release notes provided.
v64.0.0
No release notes provided.
v63.4.3
No release notes provided.
v63.4.2
No release notes provided.
... (truncated)
Changelog
Sourced from setuptools's changelog.
v65.5.1
Misc ^^^^
- #3638: Drop a test dependency on the
mockpackage, always use :external+python:py:mod:unittest.mock-- by :user:hroncok- #3659: Fixed REDoS vector in package_index.
v65.5.0
Changes ^^^^^^^
- #3624: Fixed editable install for multi-module/no-package
src-layout projects.- #3626: Minor refactorings to support distutils using stdlib logging module.
Documentation changes ^^^^^^^^^^^^^^^^^^^^^
- #3419: Updated the example version numbers to be compliant with PEP-440 on the "Specifying Your Project’s Version" page of the user guide.
Misc ^^^^
- #3569: Improved information about conflicting entries in the current working directory and editable install (in documentation and as an informational warning).
- #3576: Updated version of
validate_pyproject.v65.4.1
Misc ^^^^
- #3613: Fixed encoding errors in
expand.StaticModulewhen system default encoding doesn't match expectations for source files.- #3617: Merge with pypa/[email protected] including fix for pypa/distutils#181.
v65.4.0
Changes ^^^^^^^
- #3609: Merge with pypa/[email protected] including support for DIST_EXTRA_CONFIG in pypa/distutils#177.
v65.3.0
... (truncated)
Commits
a462cb5Bump version: 65.5.0 → 65.5.1de35d8bMerge pull request #3656 from bmorris3/typos58e23deUpdate changelog. Ref #3659.43a9c9bLimit the amount of whitespace to search/backtrack. Fixes #3659.5791343Add test capturing failed expectation. Ref #3659.1f97905⚫ Fade to black.6254567Remove workaround for emacs.729b180⚫ Fade to black.c068081Typo correctionsf777a40Suppress deprecation warning in --rsyncdir. Workaround for #3655.- Additional commits viewable in compare view
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Bump certifi from 2018.4.16 to 2022.12.7
opened on 2022-12-08 02:19:26 by dependabot[bot]Bumps certifi from 2018.4.16 to 2022.12.7.
Commits
9e9e8402022.12.07b81bdb22022.09.24939a28f2022.09.14aca828a2022.06.15.2de0eae1Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ...b8eb5e92022.06.15.147fb7abFix deprecation warning on Python 3.11 (#199)b0b48e0fixes #198 -- update link in license9d514b42022.06.154151e88Add py.typed to MANIFEST.in to package in sdist (#196)- Additional commits viewable in compare view
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Bump pillow from 5.2.0 to 9.3.0
opened on 2022-11-22 02:48:31 by dependabot[bot]Bumps pillow from 5.2.0 to 9.3.0.
Release notes
Sourced from pillow's releases.
9.3.0
https://pillow.readthedocs.io/en/stable/releasenotes/9.3.0.html
Changes
- Initialize libtiff buffer when saving #6699 [
@radarhere]- Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [
@wiredfool]- Inline fname2char to fix memory leak #6329 [
@nulano]- Fix memory leaks related to text features #6330 [
@nulano]- Use double quotes for version check on old CPython on Windows #6695 [
@hugovk]- GHA: replace deprecated set-output command with GITHUB_OUTPUT file #6697 [
@nulano]- Remove backup implementation of Round for Windows platforms #6693 [
@cgohlke]- Upload fribidi.dll to GitHub Actions #6532 [
@nulano]- Fixed set_variation_by_name offset #6445 [
@radarhere]- Windows build improvements #6562 [
@nulano]- Fix malloc in _imagingft.c:font_setvaraxes #6690 [
@cgohlke]- Only use ASCII characters in C source file #6691 [
@cgohlke]- Release Python GIL when converting images using matrix operations #6418 [
@hmaarrfk]- Added ExifTags enums #6630 [
@radarhere]- Do not modify previous frame when calculating delta in PNG #6683 [
@radarhere]- Added support for reading BMP images with RLE4 compression #6674 [
@npjg]- Decode JPEG compressed BLP1 data in original mode #6678 [
@radarhere]- pylint warnings #6659 [
@marksmayo]- Added GPS TIFF tag info #6661 [
@radarhere]- Added conversion between RGB/RGBA/RGBX and LAB #6647 [
@radarhere]- Do not attempt normalization if mode is already normal #6644 [
@radarhere]- Fixed seeking to an L frame in a GIF #6576 [
@radarhere]- Consider all frames when selecting mode for PNG save_all #6610 [
@radarhere]- Don't reassign crc on ChunkStream close #6627 [
@radarhere]- Raise a warning if NumPy failed to raise an error during conversion #6594 [
@radarhere]- Only read a maximum of 100 bytes at a time in IMT header #6623 [
@radarhere]- Show all frames in ImageShow #6611 [
@radarhere]- Allow FLI palette chunk to not be first #6626 [
@radarhere]- If first GIF frame has transparency for RGB_ALWAYS loading strategy, use RGBA mode #6592 [
@radarhere]- Round box position to integer when pasting embedded color #6517 [
@radarhere]- Removed EXIF prefix when saving WebP #6582 [
@radarhere]- Pad IM palette to 768 bytes when saving #6579 [
@radarhere]- Added DDS BC6H reading #6449 [
@ShadelessFox]- Added support for opening WhiteIsZero 16-bit integer TIFF images #6642 [
@JayWiz]- Raise an error when allocating translucent color to RGB palette #6654 [
@jsbueno]- Moved mode check outside of loops #6650 [
@radarhere]- Added reading of TIFF child images #6569 [
@radarhere]- Improved ImageOps palette handling #6596 [
@PososikTeam]- Defer parsing of palette into colors #6567 [
@radarhere]- Apply transparency to P images in ImageTk.PhotoImage #6559 [
@radarhere]- Use rounding in ImageOps contain() and pad() #6522 [
@bibinhashley]- Fixed GIF remapping to palette with duplicate entries #6548 [
@radarhere]- Allow remap_palette() to return an image with less than 256 palette entries #6543 [
@radarhere]- Corrected BMP and TGA palette size when saving #6500 [
@radarhere]
... (truncated)
Changelog
Sourced from pillow's changelog.
9.3.0 (2022-10-29)
Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [wiredfool]
Initialize libtiff buffer when saving #6699 [radarhere]
Inline fname2char to fix memory leak #6329 [nulano]
Fix memory leaks related to text features #6330 [nulano]
Use double quotes for version check on old CPython on Windows #6695 [hugovk]
Remove backup implementation of Round for Windows platforms #6693 [cgohlke]
Fixed set_variation_by_name offset #6445 [radarhere]
Fix malloc in _imagingft.c:font_setvaraxes #6690 [cgohlke]
Release Python GIL when converting images using matrix operations #6418 [hmaarrfk]
Added ExifTags enums #6630 [radarhere]
Do not modify previous frame when calculating delta in PNG #6683 [radarhere]
Added support for reading BMP images with RLE4 compression #6674 [npjg, radarhere]
Decode JPEG compressed BLP1 data in original mode #6678 [radarhere]
Added GPS TIFF tag info #6661 [radarhere]
Added conversion between RGB/RGBA/RGBX and LAB #6647 [radarhere]
Do not attempt normalization if mode is already normal #6644 [radarhere]
... (truncated)
Commits
d594f4cUpdate CHANGES.rst [ci skip]909dc649.3.0 version bump1a51ce7Merge pull request #6699 from hugovk/security-libtiff_buffer2444cddMerge pull request #6700 from hugovk/security-samples_per_pixel-sec744f455Added release notes0846bfaAdd to release notes799a6a0Fix linting00b25fdHide UserWarning in logs05b175eTighter test case13f2c5aPrevent DOS with large SAMPLESPERPIXEL in Tiff IFD- Additional commits viewable in compare view
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Bump numpy from 1.14.5 to 1.22.0
opened on 2022-06-21 21:22:48 by dependabot[bot]Bumps numpy from 1.14.5 to 1.22.0.
Release notes
Sourced from numpy's releases.
v1.22.0
NumPy 1.22.0 Release Notes
NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:
- Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
- A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
- NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
- New methods for
quantile,percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.- A new configurable allocator for use by downstream projects.
These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.
The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.
Expired deprecations
Deprecated numeric style dtype strings have been removed
Using the strings
"Bytes0","Datetime64","Str0","Uint32", and"Uint64"as a dtype will now raise aTypeError.(gh-19539)
Expired deprecations for
loads,ndfromtxt, andmafromtxtin npyio
numpy.loadswas deprecated in v1.15, with the recommendation that users usepickle.loadsinstead.ndfromtxtandmafromtxtwere both deprecated in v1.17 - users should usenumpy.genfromtxtinstead with the appropriate value for theusemaskparameter.(gh-19615)
... (truncated)
Commits
4adc87dMerge pull request #20685 from charris/prepare-for-1.22.0-releasefd66547REL: Prepare for the NumPy 1.22.0 release.125304bwipc283859Merge pull request #20682 from charris/backport-204165399c03Merge pull request #20681 from charris/backport-20954f9c45f8Merge pull request #20680 from charris/backport-20663794b36fUpdate armccompiler.pyd93b14eUpdate test_public_api.py7662c07Update init.py311ab52Update armccompiler.py- Additional commits viewable in compare view
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Bump ipython from 6.4.0 to 7.16.3
opened on 2022-01-21 19:25:59 by dependabot[bot]Bumps ipython from 6.4.0 to 7.16.3.
Commits
d43c7c7release 7.16.35fa1e40Merge pull request from GHSA-pq7m-3gw7-gq5x8df8971back to dev9f477b7release 7.16.2138f266bring back release helper from master branch5aa3634Merge pull request #13341 from meeseeksmachine/auto-backport-of-pr-13335-on-7...bcae8e0Backport PR #13335: What's new 7.16.28fcdcd3Pin Jedi to <0.17.2.2486838release 7.16.120bdc6ffix conda build- Additional commits viewable in compare view
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Bump urllib3 from 1.23 to 1.26.5
opened on 2021-06-01 22:28:26 by dependabot[bot]Bumps urllib3 from 1.23 to 1.26.5.
Release notes
Sourced from urllib3's releases.
1.26.5
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Fixed deprecation warnings emitted in Python 3.10.
- Updated vendored
sixlibrary to 1.16.0.- Improved performance of URL parser when splitting the authority component.
If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors
1.26.4
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Changed behavior of the default
SSLContextwhen connecting to HTTPS proxy during HTTPS requests. The defaultSSLContextnow setscheck_hostname=True.If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors
1.26.3
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
Fixed bytes and string comparison issue with headers (Pull #2141)
Changed
ProxySchemeUnknownerror message to be more actionable if the user supplies a proxy URL without a scheme (Pull #2107)If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors
1.26.2
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Fixed an issue where
wrap_socketandCERT_REQUIREDwouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)1.26.1
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
- Fixed an issue where two
User-Agentheaders would be sent if aUser-Agentheader key is passed asbytes(Pull #2047)1.26.0
:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap
Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)
Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning should opt-in explicitly by setting
ssl_version=ssl.PROTOCOL_TLSv1_1(Pull #2002) Starting in urllib3 v2.0: Connections that receive aDeprecationWarningwill failDeprecated
RetryoptionsRetry.DEFAULT_METHOD_WHITELIST,Retry.DEFAULT_REDIRECT_HEADERS_BLACKLISTandRetry(method_whitelist=...)in favor ofRetry.DEFAULT_ALLOWED_METHODS,Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT, andRetry(allowed_methods=...)(Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed
... (truncated)
Changelog
Sourced from urllib3's changelog.
1.26.5 (2021-05-26)
- Fixed deprecation warnings emitted in Python 3.10.
- Updated vendored
sixlibrary to 1.16.0.- Improved performance of URL parser when splitting the authority component.
1.26.4 (2021-03-15)
- Changed behavior of the default
SSLContextwhen connecting to HTTPS proxy during HTTPS requests. The defaultSSLContextnow setscheck_hostname=True.1.26.3 (2021-01-26)
Fixed bytes and string comparison issue with headers (Pull #2141)
Changed
ProxySchemeUnknownerror message to be more actionable if the user supplies a proxy URL without a scheme. (Pull #2107)1.26.2 (2020-11-12)
- Fixed an issue where
wrap_socketandCERT_REQUIREDwouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)1.26.1 (2020-11-11)
- Fixed an issue where two
User-Agentheaders would be sent if aUser-Agentheader key is passed asbytes(Pull #2047)1.26.0 (2020-11-10)
NOTE: urllib3 v2.0 will drop support for Python 2.
Read more in the v2.0 Roadmap <https://urllib3.readthedocs.io/en/latest/v2-roadmap.html>_.Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)
Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning
... (truncated)
Commits
d161647Release 1.26.52d4a3feImprove performance of sub-authority splitting in URL2698537Update vendored six to 1.16.007bed79Fix deprecation warnings for Python 3.10 ssl moduled725a9bAdd Python 3.10 to GitHub Actions339ad34Use pytest==6.2.4 on Python 3.10+f271c9cApply latest Black formatting1884878[1.26] Properly proxy EOF on the SSLTransport test suitea891304Release 1.26.48d65ea1Merge pull request from GHSA-5phf-pp7p-vc2r- Additional commits viewable in compare view
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