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emi_pareto_opt_ml's Introduction

1. Download the anaconda distribution of python from: https://www.anaconda.com/

2. Open the anaconda command prompt, navigate to where the code for this paper is stored on your computer using:

cd PATH\TO\CODE

and use the following commands to activate the environment:

conda env create -f environment.yml
conda activate emi_env

3. The attached folder includes scripts to import data, fit LDA models to binary labeled data, and correlated those models to continuous measurements of sequences. 
Each model type (onehot, physchem, or unirep) is included as its own script. The physchem and unirep models scripts additionally correlate LDA models with out-of-library sequences. 

Scripts can be run using any development environment (ex: Spyder, included with anaconda) or by typing

python SCRIPTNAME.py

into the anaconda command prompt. For example:

python onehot_models.py

emi_pareto_opt_ml's People

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emilymak avatar pkinn avatar

Stargazers

avatar Natasha Seelam avatar Taeyoon Kim avatar avatar Roberto Alejandro Calzadilla avatar sci1729usr avatar avatar Yingfei(Jeremy) Xiang avatar avatar Marshall Case avatar Amman Safeer avatar avatar Isao Sugawara avatar avatar Rongqing Yuan avatar avatar Qingyang Ding avatar avatar

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xiaogou159 biocoder007 superxiang ancientor

emi_pareto_opt_ml's Issues

humanness of antibodies - other species?

Dear all, while reading the paper associated to this software, I wondered if the tool would also work for non-human Antibody design? E.g. if we design antibodies for dogs or cats, would the tool turn them more human than dog-like or cat-like? Would the software need retraining? And if so, how many dog-specific mAbs would it need to successfully retrain? Thx in advance.

Environment creation fails

I wish to implement and test this project. As you have mentioned in the Readme.md I have tried creating the environment with the command,

conda env create -f environment.yml

But it fails to create an environment, by throwing the following error:

Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound: 
  - libspatialindex==1.9.3=h33f27b4_0
  - win_unicode_console==0.5=py38_0
  - blosc==1.20.1=h7bd577a_0
  - libtiff==4.1.0=h56a325e_1
  - pandocfilters==1.4.3=py38haa95532_1
  - zeromq==4.3.2=ha925a31_3
  - win_inet_pton==1.1.0=py38_0
  - liblief==0.10.1=ha925a31_0
  - pycurl==7.43.0.6=py38h7a1dbc1_0
  - astropy==4.0.2=py38he774522_0
  - libcurl==7.71.1=h2a8f88b_1
  - llvmlite==0.34.0=py38h1a82afc_4
  - lzo==2.10=he774522_2
  - pyodbc==4.0.30=py38ha925a31_0
  - scikit-image==0.17.2=py38h1e1f486_0
  - pywin32-ctypes==0.2.0=py38_1000
  - ujson==4.0.1=py38ha925a31_0
  - numpy-base==1.19.2=py38ha3acd2a_0
  - pip==20.2.4=py38haa95532_0
  - distributed==2.30.1=py38haa95532_0
  - matplotlib-base==3.3.2=py38hba9282a_0
  - pyqt==5.9.2=py38ha925a31_4
  - tornado==6.0.4=py38he774522_1
  - msys2-conda-epoch==20160418=1
  - hdf5==1.10.4=h7ebc959_0
  - msgpack-python==1.0.0=py38h74a9793_1
  - pywinpty==0.5.7=py38_0
  - m2w64-gcc-libs-core==5.3.0=7
  - ipython==7.19.0=py38hd4e2768_0
  - krb5==1.18.2=hc04afaa_0
  - powershell_shortcut==0.0.1=3
  - python==3.8.5=h5fd99cc_1
  - sqlalchemy==1.3.20=py38h2bbff1b_0
  - numba==0.51.2=py38hf9181ef_1
  - cytoolz==0.11.0=py38he774522_0
  - pytables==3.6.1=py38ha5be198_0
  - icu==58.2=ha925a31_3
  - sqlite==3.33.0=h2a8f88b_0
  - pillow==8.0.1=py38h4fa10fc_0
  - sympy==1.6.2=py38haa95532_1
  - gevent==20.9.0=py38he774522_0
  - vs2015_runtime==14.16.27012=hf0eaf9b_3
  - setuptools==50.3.1=py38haa95532_1
  - zope.interface==5.1.2=py38he774522_0
  - argon2-cffi==20.1.0=py38he774522_1
  - conda-package-handling==1.7.2=py38h76e460a_0
  - m2w64-gcc-libs==5.3.0=7
  - pandas==1.1.3=py38ha925a31_0
  - pynacl==1.4.0=py38h62dcd97_1
  - scipy==1.5.2=py38h14eb087_0
  - brotlipy==0.7.0=py38he774522_1000
  - numexpr==2.7.1=py38h25d0782_0
  - libxml2==2.9.10=hb89e7f3_3
  - m2w64-gcc-libgfortran==5.3.0=6
  - xz==5.2.5=h62dcd97_0
  - kiwisolver==1.3.0=py38hd77b12b_0
  - bottleneck==1.3.2=py38h2a96729_1
  - pywavelets==1.1.1=py38he774522_2
  - py-lief==0.10.1=py38ha925a31_0
  - pywin32==227=py38he774522_1
  - six==1.15.0=py38haa95532_0
  - get_terminal_size==1.0.0=h38e98db_0
  - qt==5.9.7=vc14h73c81de_0
  - psutil==5.7.2=py38he774522_0
  - pyyaml==5.3.1=py38he774522_1
  - m2w64-libwinpthread-git==5.0.0.4634.697f757=2
  - conda==4.10.1=py38haa244fe_0
  - ruamel_yaml==0.15.87=py38he774522_1
  - libssh2==1.9.0=h7a1dbc1_1
  - winpty==0.4.3=4
  - xlwings==0.20.8=py38_0
  - wincertstore==0.2=py38_0
  - vc==14.1=h0510ff6_4
  - freetype==2.10.4=hd328e21_0
  - mkl_fft==1.2.0=py38h45dec08_0
  - fastcache==1.1.0=py38he774522_0
  - mkl_random==1.1.1=py38h47e9c7a_0
  - yaml==0.2.5=he774522_0
  - numpy==1.19.2=py38hadc3359_0
  - bitarray==1.6.1=py38h2bbff1b_0
  - menuinst==1.4.16=py38he774522_1
  - libpng==1.6.37=h2a8f88b_0
  - markupsafe==1.1.1=py38he774522_0
  - comtypes==1.1.7=py38_1001
  - mistune==0.8.4=py38he774522_1000
  - pandoc==2.11=h9490d1a_0
  - scikit-learn==0.23.2=py38h47e9c7a_0
  - zlib==1.2.11=h62dcd97_4
  - rtree==0.9.4=py38h21ff451_1
  - pyzmq==19.0.2=py38ha925a31_1
  - jpeg==9b=hb83a4c4_2
  - zstd==1.4.5=h04227a9_0
  - lazy-object-proxy==1.4.3=py38he774522_0
  - openssl==1.1.1h=he774522_0
  - lxml==4.6.1=py38h1350720_0
  - lz4-c==1.9.2=hf4a77e7_3
  - cffi==1.14.3=py38h7a1dbc1_0
  - greenlet==0.4.17=py38he774522_0
  - pycosat==0.6.3=py38he774522_0
  - libxslt==1.1.34=he774522_0
  - mkl-service==2.3.0=py38hb782905_0
  - libiconv==1.15=h1df5818_7
  - curl==7.71.1=h2a8f88b_1
  - pyrsistent==0.17.3=py38he774522_0
  - icc_rt==2019.0.0=h0cc432a_1
  - bcrypt==3.2.0=py38he774522_0
  - console_shortcut==0.1.1=4
  - tk==8.6.10=he774522_0
  - regex==2020.10.15=py38he774522_0
  - m2w64-gmp==6.1.0=2
  - cryptography==3.1.1=py38h7a1dbc1_0
  - sip==4.19.13=py38ha925a31_0
  - libsodium==1.0.18=h62dcd97_0
  - statsmodels==0.12.0=py38he774522_0
  - pyreadline==2.1=py38_1
  - pkginfo==1.6.1=py38haa95532_0
  - tifffile==2020.10.1=py38h8c2d366_2
  - biopython==1.78=py38h294d835_2
  - cython==0.29.21=py38ha925a31_0
  - bzip2==1.0.8=he774522_0
  - libarchive==3.4.2=h5e25573_0

I went and looked into the content of the environment.yml file. It had a line

....
....
....
    - umap-learn==0.5.1
    - wrapt==1.12.1
    - xgboost==1.5.0
prefix: C:\Users\makow\anaconda3

I commented on the last line and tried again. But still throws the same error.

I request the creators to provide the correct YAML file, with only necessary packages.

Thankyou.

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