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    Bharath Ramsundar
    @rbharath
    the tox21_graphcnn.py is using one the PetroskiSuchModel which is a variant graph convolution, not the best tested one
    rfhari
    @rfhari
    Thanks! @rbharath
    test-user-18
    @test-user-18
    @rbharath Thank you for your quick response! I appreciate your help. You are awesome!
    Bharath Ramsundar
    @rbharath
    Glad to be helpful :)
    macca1996-bit
    @macca1996-bit
    deepchem/deepchem#1788 made an issue thread regarding a problem i'm having with RFC
    Bharath Ramsundar
    @rbharath
    @macca1996-bit Just responded!
    Vishesh Mangla
    @XtremeGood
    Hey is deep chem participating in gsoc?
    Bharath Ramsundar
    @rbharath
    Vishesh Mangla
    @XtremeGood
    is there still time to submit a proposal?
    Bharath Ramsundar
    @rbharath
    Is cutting a little close to the deadline (March 31st), but it might still be possible if you have relevant experience in the field! If you ping me on here, I'm glad to help review any proposals
    Vishesh Mangla
    @XtremeGood
    yep. I 'm a Msc Chemistry student and know tensorflow 2.0 and data Structures and Algorithm.
    This is the last semester of my MSc Chem degree.
    Bharath Ramsundar
    @rbharath
    https://wiki.openchemistry.org/GSoC_Ideas_2020
    ^ Cool, I'd recommend taking a look at the ideas page
    Vishesh Mangla
    @XtremeGood
    thanks!
    Bharath Ramsundar
    @rbharath
    Our two project (suggested) for the year are exploring the use of Jax for molecular machine learning and improved transfer learning support.
    I'd encourage checking out the forums too for ideas https://forum.deepchem.io/
    Vishesh Mangla
    @XtremeGood
    Hi @rbharath . I checked the following project :"Develop a validation and standardization filter". Can I get more info on this?
    Does this project requires to like read a molecule as a string and count and label the stereocenters? Then it rather seems to require to check whether the string is palindromic or not rather than Data Science. Is the objective something else ?
    Vishesh Mangla
    @XtremeGood
    Checking whether string is palindromic or not is a part of Design and Analysis of Algorithms which is known as Manacher's algorithm.
    Vishesh Mangla
    @XtremeGood
    And the two projects which you are suggesting are already being done by other guys.
    mukeshb23
    @mukeshb23
    Dear sir, I have 76 cardiovascular drugs data with experimental solubility value which are made by himself . when I load this data set in deep chem modeling solubility tutorial then i found only 8 valid data set after validation after that i also geting negative r^2 value for this . is it possible with 77 datasets to get positive r^2 value and good results. help me regarding this please
    Bharath Ramsundar
    @rbharath
    @XtremeGood This sounds like a project from a different OpenChemistry team. The ones I'm personally mentoring are the DeepChem project track (the Jax and transfer learning project). The application process is competitive, so it's normal to have multiple applications for the same project. If you'd like feedback on your ideas for the DeepChem project track, feel free to ping me anytime (you can DM me on here)
    @mukeshb23 76 datapoints is a very small dataset. The machine learning tools we have will likely struggle with a dataset this small. I'd recommend trying to build a simple random forest model to start and going from there, but it might be hard. Maybe see if there's a way to get more datapoints to improve learning
    mukeshb23
    @mukeshb23
    @rbharath Dear sir thank you so much for clarifying . Sir I have one more doubt regarding this. When I mixed this 77 cardiovascular drugs data sets with other large data set and then reperformed on modelling solubility tutorial I got positive r *2 value and also get more valid data after validation. Sir what I am thinking is it possible can I do this?
    Bharath Ramsundar
    @rbharath
    It's not unreasonable at all, but main thing to do is to make sure your validation R^2 is measured on compounds from your original dataset (it's not useful if your numbers are for molecules you don't care about)
    Vishesh Mangla
    @XtremeGood
    @rbharath I 'm not sure why you are using Jax. I think the new tensorflow 2.0 is complete in itself with even more support for if we have any errors. It is a totally different architecture from 1.0 which the tensorflow community too believes was a problem.
    Pytorch and tensorflow both are good.
    mukeshb23
    @mukeshb23
    @rbharath Dear sir I am getting approx 110 molecules after validation this data sets. then how to do only for target drugs any specific code required for separate this terget drugs for measuring r*2 value.
    macca1996-bit
    @macca1996-bit
    macca1996-bit
    @macca1996-bit
    Would love to hear peoples thoughts on this paper if anyone gets time to read it
    macca1996-bit
    @macca1996-bit
    Also I've today started getting a new error when trying to use DeepChem in colab, will make a forum post:----> 3 import deepchem as dc
    macca1996-bit
    @macca1996-bit
    Bharath Ramsundar
    @rbharath
    @macca1996-bit This is due to Colab updating to TF2.X as default. You need to add a fix as in this post: https://forum.deepchem.io/t/getting-deepchem-running-in-colab/81/3
    @XtremeGood Check out the discussion in https://forum.deepchem.io/t/gsoc-project-dynamic-deepchem/103 for more details about Jax/TF2.0
    @mukeshb23 You will need to write a script that separates your original dataset into train/valid/test. If you have an additional dataset, merge that dataset with your train test. Then train a model, and evaluate on your original valid dataset
    Bharath Ramsundar
    @rbharath
    Thanks to @nd-02110114 for a timely fix on colab! deepchem/deepchem#1789
    The tutorials should now run correctly with this update in place, CC @macca1996-bit
    Vishesh Mangla
    @XtremeGood
    hi @rbharath
    For the project Dynamic DeepChem do you require some existing code to be rewritten in Jax?
    Is that the project's goal?
    Vishesh Mangla
    @XtremeGood
    In that's the thing can you tell me which models are to be reworked upon so that I can prepare the timeline for proposal?
    macca1996-bit
    @macca1996-bit
    @rbharath that fixed the problem, thanks a lot for your help :)
    macca1996-bit
    @macca1996-bit
    quick question: Is it better to transform my data before or after the train, test, valid split? In my case I'm using a balancing transformer
    Based on my own research i get the impression that I should be doing it after data splitting
    Bharath Ramsundar
    @rbharath
    @XtremeGood The basic goal would be to implement graph convolutions in Jax. And perhaps another model or two if time permits
    Vishesh Mangla
    @XtremeGood
    Do you mean like in convolutional neural networks?
    move a filter across the image?
    Bharath Ramsundar
    @rbharath
    @macca1996-bit Glad to be of help :). You want to transform after the split. The reason for this is to prevent information leakage from the validation/test set into the training set
    @XtremeGood Yes, graph convolutions are the generalization of 2D convolutions to arbitrary graphs rather than grids. I'd recommend working through DeepChem tutorial #4 as an intro.
    Vishesh Mangla
    @XtremeGood
    ya I got it