Git Product home page Git Product logo

gimlet's Introduction

gimlet

Graph Inference on MoLEcular Topology. A package for modelling, learning, and inference on molecular topological space written in Python and TensorFlow.

Dependencies

gimlet doesn't depend on any packages except TensorFlow 2.0 , and pandas and pytest, if you must.

Examples

https://github.com/choderalab/gimlet/blob/master/lime/scripts/notebooks/190728_yuanqing_gn_with_gru_on_sereina_riniker_dataset.ipynb

Authors

  • yuanqing wang <[email protected]><[email protected]> (while at Chodera Lab at Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, and the City College of the City University of New York.)

Manifest

  • gin/ the core (and fun) part of the package.
    • i_o/ reading and writing popular molecule embedding/representing structures.
    • deterministic/ property predictions, conformer and charge generations.
    • probabilistic/ molecular machine learning through graph networks.
  • lime/ auxiliary scripts.
    • for_biologists/ ready-to-use modules and scripts.
    • architectures/ off-the-shelf model architectures developed elsewhere.
    • scripts/ fun scripts we used to generate data and hypothesis.
    • trained_models/ Nomen est omen.

gimlet's People

Contributors

chayast avatar klllllll avatar maxentile avatar yuanqing-wang avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

gimlet's Issues

Saving the model

Hello Sir/Madam,
I am student of mathematical modelling and simulation and referring the Graph Net work for my project. I am facing issue saving the model.(Unable to save it.)
Can you help me how can I save the model?

This will be of great help to my project.

Performance issue in lime/scripts/lipo_gru/ht_lipo_gru.py

Hello! Our static bug checker has found a performance issue in lime/scripts/lipo_gru/ht_lipo_gru.py: init is repeatedly called in a for loop, but there are several tf.function decorated functions call, call and call defined and called in init.

In that case, when init is called in a loop, the function call will create a new graph every time, and that can trigger tf.function retracing warning.

Similar issues in:
lime/scripts/lipo_gru/ht_lipo_ind_gru.py, lime/scripts/elf_with_wbo/ht_elf_with_wbo.py, lime/scripts/partial_charge/ht_charge.py and lime/scripts/partial_charge/ht_charge_fast.py.

Here is the tensorflow document to support it.

Briefly, for better efficiency, it's better to use:

@tf.function
def inner():
    pass

def outer():
    inner()  

than:

def outer():
    @tf.function
    def inner():
        pass
    inner()

Looking forward to your reply.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.